final results and comments d6-2013...

15
FINAL RESULTS AND COMMENTS D6-2013 BACTERIOLOGY PROGRAM MYCOLOGY MYCOBACTERIOLOGY AUTHORISED BY CHAIR CHAIR: DR ARTHUR MORRIS PROGRAM MANAGER: ELIZABETH HAREMZA Report prepared by D.Walker and M.Bullivant No information related to any of the participants will be divulged to a third party, unless required by legislation, without the prior written consent of the participant. General information may be discussed at meetings or presented as papers to journals. COPYRIGHT The written material produced by the RCPAQAP is copyright and may not be used in any form for advertising, sales promotion or publicity. The material may not be reproduced in whole or in part for any purpose whatsoever (including presentations at meetings and conferences), without the prior written permission of the RCPA Quality Assurance Programs Pty Limited. Permission must be sought in writing from the Program Chair or Discipline Manager, but will not be unreasonably refused. NATA Accredited Proficiency Testing Scheme Provider Number: 14863 This Facility is accredited by the National Association of Testing Authorities, Australia and complies with the Requirements of ISO/IEC 17043:2010 Amended Date: 28th February 2014 Suite 201, Level 2 8 Herbert Street, St Leonards NSW 2065 Australia PH: +61 2 9045 6060 Fax: 1300 78 29 21 (Australia) +61 2 9356 2003 (International) [email protected] www.rcpaqap.com.au/ microbiology

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Page 1: FINAL RESULTS AND COMMENTS D6-2013 …dataentry.rcpaqap.com.au/micro/reports/uploadedfiles/fnl2013-6.pdf · FINAL RESULTS AND COMMENTS D6/2013 ... This item contained a pure growth

FINAL RESULTS AND COMMENTS

D6-2013

BACTERIOLOGY PROGRAM

MYCOLOGY

MYCOBACTERIOLOGY

AUTHORISED BY CHAIR CHAIR DR ARTHUR MORRIS PROGRAM MANAGER ELIZABETH HAREMZA Report prepared by DWalker and MBullivant

No information related to any of the participants will be divulged to a third party unless required by legislation without the

prior written consent of the participant General information may be discussed at meetings or presented as papers to journals

COPYRIGHT The written material produced by the RCPAQAP is copyright and may not be used in any form for advertising sales promotion

or publicity The material may not be reproduced in whole or in part for any purpose whatsoever (including presentations at

meetings and conferences) without the prior written permission of the RCPA Quality Assurance Programs Pty

Limited Permission must be sought in writing from the Program Chair or Discipline Manager but will not be unreasonably

refused

NATA Accredited Proficiency Testing Scheme Provider Number 14863 This Facility is accredited by the National Association of Testing Authorities Australia and complies with the Requirements of ISOIEC 170432010

Amended Date 28th February 2014

Suite 201 Level 2 8 Herbert Street St Leonards NSW 2065 Australia PH +61 2 9045 6060 Fax 1300 78 29 21 (Australia) +61 2 9356 2003 (International) microbiologyrcpaqapcomau wwwrcpaqapcomaumicrobiology

copy2013 RCPA Quality Assurance Programs Pty Limited 2 Date of issue 13th November 2013

FINAL RESULTS AND COMMENTS D62013

ITEM 201361AB URINE FOR MICROSCOPY CULTURE AND SUSCEPTIBILITY TESTING

ITEM 201361A

Quality Control This item contained a pure growth of Proteus mirabilis and passed homogeneity and stability testing with the total counts remaining above 10 x 1010 CFUL throughout the survey period

Microscopy Homogeneity testing indicated that the white cell count was 10-100 x 106L or gt100 x 106L Both counts have been scored correct The red cell count was 10-100 x 106L There were no epithelial cells added to the sample so lt10 x 106L was the expected result for epithelial cells Ninety six percent reported 10-100 or gt100 x 106L WBC 82 reported 10-100 X 106 RBCL and 98 reported lt10 x 106 epithelial cellsL Comparisons of cell count method versus counts reported are outlined in Table 1

Table 1 Cell counts reported 1A

Bacterial counts Two hundred and sixty five participants submitted culture results for this item Where reported 92 reported growth of gt108 CFUL and 99 a pure growth Three participants transposed results

Identification and susceptibility testing IdentificationmdashProteus mirabilis Excluding the three transposed results 99 of participants correctly identified this isolate to genus level Commercial kitssystems were utilised by 229 (86) The participant reporting Pvulgaris did not use a kit only identifying that the colony was cream on their in-house chromogenic medium Mmorganii in the hands of the user was incorrectly identified by using Microbact 24E The other three users of this kit reported the correct identification The two reporting Proteus species did not use a kitcommercial system with one using chromogenic agar (clearyellow- brown) and the other did not identify any further reporting that catheter colonisation was the likely cause Forty eight

White1A Red1A Epi1A IQ 200 Manual Omitted U(F) 2000 UF-1

UF-1000(i)

Urisys 2400 UX-2000

10-100 10-100 lt10 14 136 15 - 1 2 1 -

gt100 10-100 lt10 1 26 1 1 - 1 - 1

10-100 10-100 Not Tested - 3 - - - - - -

10-100 Not Tested Not Tested 1 1 - - - - - -

gt100 10-100 Not Tested - 1 - - - - - -

10-100 lt10 lt10 - 16 3 - - - - -

gt100 gt100 lt10 - 7 4 - - - - -

10-100 gt100 lt10 - 5 - - - - - -

lt10 lt10 lt10 - 8 - - - - - -

10-100 10-100 10-100 - 2 - - - 1 - -

lt10 lt10 Not Tested - - 1 - - - - -

lt10 Not Tested lt10 - - 1 - - - - -

lt10 Not Tested Not Tested - 1 - - - - - -

gt100 gt100 10-100 - 1 - - - - - -

gt100 10-100 10-100 - 1 - - - - - -

10-100 lt10 10-100 - - - - - 1 - -

Not Tested lt10 Not Tested - 1 - - - - - -

1A Proteus mirabilis

256 966

1 04

2 08

1 04

3 11

1 04

1 04 1

1

3

1

2

1

256

0 50 100 150 200 250 300

Sent to Reference Lab

Mixed growth-probable contamination

Escherichia coli

Morganella morganii

Proteus species

Proteus vulgaris

Proteus mirabilis

copy2013 RCPA Quality Assurance Programs Pty Limited 3 Date of issue 13th November 2013

participants successfully used MALDI-TOF MS to correctly identify this isolate Susceptibility Testing Proteus mirabilis This strain of Pmirabilis expresses a plasmid mediated AmpC (PM AmpC) type of β-lactamase This was a clinical isolate sourced from a hospital laboratory south of Sydney The isolate was grown from both the patientrsquos blood cultures and catheter urine The isolate was resistant to ampicillin cephalexin and ceftriaxone but susceptible to cefepime and aztreonam ESBL and MBL phenotypic tests (CDS) were negative When referred to the CDS laboratory for further testing phenotypic tests (showing synergy between boronic acid disc and ceftazidime) suggested high activity plasmid-mediated AmpC cephalosporinase1 Figure 1A illustrates the method used but please note the isolate in image is Ecoli not Pmirabilis The CDS laboratory commented that ldquoDue to its characteristic swarming back into the zone of inhibition around imipenem disc this organism may appear resistant to imipenem with a double zone The testing on MacConkey agar confirms that the organism is susceptible to imipenem with a clear zone of 7 mm It is also clearly susceptible to all other carbapenems ie meropenem ertapenem and doripenemrdquo Nine participants reported imipenem resistance Five were users of the CDS method three used the CLSI standard disk method and one used Vitek2

Forty five participants incorrectly reported the presence of ESBL Thirty nine confirmed or suspected AmpC A further 15 referred to another laboratory for ESBL testing We thank Dr Peter Newton Medical Microbiologist Wollongong Hospital Wollongong NSW for providing this isolate

Pmirabilis

Item 1A

Susceptibilities

(all methods)

Antibiotic S IRS R

Amikacin 76 1 -

AmpicillinAmoxycillin 1 - 230

Augmentin 1 - 234

Cefaclor - - 16

Cefazolin - - 36

Cefepime 23 - 1

Cefotaxime 1 7 62

Cefoxitin 1 - 27

Ceftazidime 20 11 46

Ceftriaxone 18 11 63

Cefuroxime 9 18 37

Cephalexin 1 - 82

Cephalothin 1 - 54

Ciprofloxacin 1 - 113

Cotrimoxazole 26 - 72

Ertapenem 17 - -

Fosfomycin 8 - -

Gentamicin 166 16 35

Imipenem 67 1 9

Levofloxacin - - 13

Meropenem 126 - 2

Nitrofurantoin 5 4 194

Norfloxacin - - 149

Piperacillin - - 7

Piperacillintazobactam 56 2 3

Tetracycline - - 6

Timentin 20 - 12

Tobramycin 1 1 29

Trimethoprim 2 - 182

Table 2 Proteus mirabilis susceptibilities (all methods)

Figure 1A Phenotypic detection using boronic acid discs in an E coli producing a plamid mediated AmpC Synergy between boronic acid discs (blank) and adjacent discs cefotaxime (CTX 5) Augmentin (AMC 60) cephalexin (CL 100) ceftazidime (CAZ 10) Blank disc = 250 microg boronic acid disc2

Reference Item 1A

1 ASM 2013 mdash PowerPoint Presentation Proceedings of the CDS Workshop -Part 2

httpwebmedunsweduaucdstestGTF_CDS_siteWebPagesArchiveASMconferencehtm

2 ASM 2013 mdash PowerPoint Presentation Proceedings of the CDS Workshop -Part 1 Slide 20

httpwebmedunsweduaucdstestGTF_CDS_siteWebPagesArchiveASMconferencehtm

copy2013 RCPA Quality Assurance Programs Pty Limited 4 Date of issue 13th November 2013

ITEM 201361B

Quality Control This item contained a pure growth of Escherichia coli and passed homogeneity and stability testing with counts remaining above 10 x 1010 CFUL throughout the survey period

Microscopy Homogeneity testing indicated that the white cell count was 10-100 x 106L or gt100 x 106L Both counts have been scored correct The red cell count was 10-100 x 106L There were no epithelial cells added to the sample so lt10 x 106L was the expected result for epithelial cells Ninety five percent reported 10-100 or gt100 x 106L WBC 79 reported 10-100 X 106 RBCL and 98 reported lt10 x 106 epithelial cellsL Comparisons of cell count method versus counts reported are outlined in Table 3

Bacterial counts Two hundred and sixty five participants returned results for this item Where reported 97 reported growth of gt108 CFUL and 99 reported a pure growth

Table 3 Cell counts reported 1B

White1B Red1B Epi1B IQ 200 Manual Omitted U(F) 2000 UF-1 UF-1000(i) Urisys 2400 UX-2000

10-100 10-100 lt10 10 117 8 1 1 4 1 -

gt100 10-100 lt10 4 38 8 - - - - -

10-100 10-100 Not Tested - 2 1 - - - - -

10-100 Not Tested Not Tested 1 1 - - - - - -

gt100 10-100 Not Tested - 1 - - - - - -

10-100 lt10 lt10 - 15 3 - - - - -

10-100 lt10 lt10 - 15 3 - - - - -

gt100 gt100 lt10 - 11 2 - - - - 1

10-100 gt100 lt10 1 8 - - - - -

lt10 lt10 lt10 - 7 1 - - - - -

lt10 10-100 lt10 - 1 1 - - - - -

10-100 10-100 10-100 - 1 - - 1 - -

lt10 10-100 Not Tested - 1 - - - - - -

lt10 Not Tested lt10 - 1 - - - - -

lt10 Not Tested Not Tested - 1 - - - - - -

gt100 lt10 lt10 - 1 - - - - - -

gt100 lt10 10-100 - 1 - - - - - -

gt100 gt100 Not Tested - 1 - - - - - -

gt100 10-100 10-100 - 1 - - - - - -

10-100 lt10 10-100 - 1 - - - - - -

copy2013 RCPA Quality Assurance Programs Pty Limited 5 Date of issue 13th November 2013

IdentificationmdashEscherichia coli

Ninety eight percent of participants correctly reported Escherichia coli for this item The two results of Pmirabilis and the ldquoUnable to identify-referrdquo were transposed results The participant reporting Kpneumoniae used ldquoRapid Onerdquo kit Two other participants used this same kit and reported correctly Eighty five participants reported the use of chromogenic agar Commercial kitssystems were used by 182 participants All kits performed well Thirty five participants used MALDI-TOF with all reporting Ecoli

Ecoli Item 1B Susceptibilities

(all methods)

Antibiotic S IRS R

Amikacin 40 - -

AmpicillinAmoxycillin 233 - 5

Augmentin 217 2 2

Cefaclor 16 - -

Cefazolin 37 - -

Cefepime 12 - -

CefoperzoneSulbactum 1 - -

Cefotaxime 49 - -

Cefoxitin 20 - -

Ceftazidime 54 - -

Ceftriaxone 53 - -

Cefuroxime 56 - -

Cephalexin 93 - 1

Cephalothin 53 3 -

Chloramphenicol 5 - -

Ciprofloxacin 80 - -

Cotrimoxazole 91 - 1

Ertapenem 12 - -

Gentamicin 180 1 -

Imipenem 50 - -

Levofloxacin 13 - -

Meropenem 57 - -

Nalidixic acid 6 - -

Nitrofurantoin 209 - 2

Norfloxacin 133 - 1

Piperacillintazobactam 37 1 -

Polymyxin B 2 - -

Tetracycline 6 - -

Timentin 10 - -

Tobramycin 8 - -

Trimethoprim 191 - 1

Table 4 Escherichia coli susceptibilities (all methods)

1B Escherichia coli

260 981

1 04

2 04

1 04

1 04

1

1

2

1

260

0 50 100 150 200 250 300

Sent to Reference Lab

Unable to Identify - Refer

Proteus mirabilis

Klebsiella pneumoniae

Escherichia coli

Susceptibility testingndash Escherichia coli Susceptibility testing was performed well with the majority of participants reporting susceptible to the commonly reported antibiotics for gram-negative urine isolates

copy2013 RCPA Quality Assurance Programs Pty Limited 6 Date of issue 13th November 2013

ITEM 201362 NOSE SWAB

includes presumptive identifications

ITEM 201362 Nose swab Quality Control This item represented an infection control nose swab containing Methicillin resistant Staphylococcus aureus (MRSA) and Staphylococcus epidermidis Counts for MRSA remained above 10 x 1010 CFUL throughout the survey Homogeneity and stability testing were satisfactory Culture and identification results Two hundred and forty seven participants returned results with 242 (98) reporting MRSA This isolate was a non multi-resistant MRSA (NMRSA) with a susceptibility pattern as follows Resistant to ampicillin Augmentin cefotaxime cefoxitin cephalothin oxacillin and penicillin susceptible to ciprofloxacin clindamycin erythromycin fusidic acid gentamicin rifampicin and tetracycline Many laboratories screened using chromogenic agars Follow up tests included Gram stain (gram-positive cocci) catalase (positive) DNAase (positive) slidetube coagulase (positive) and conventional susceptibility testing or other method to confirm MRSA Staphylococcus aureus agglutination kits used are shown in Table 5 below Identification kitssystems employed are also shown below in Table 6 Most kitssystems accurately identified S aureus Three laboratories reporting S aureus mentioned that it was MRSA in the comments box One of the four laboratories reporting S aureus (only) reported it oxacillin susceptible in the comments box The other three gave no indication of it being or possibly being MRSA

239 968

3 12

4 16

1 04 1

4

3

239

0 50 100 150 200 250 300

Staphylococcus coag negative

Staphylococcus aureus

Staphylococcus aureus (MRSA in comments)

MRSA or Staphylococcus aureus (MRSA)

Most common kits used

Number of users

Biomerieux Slidex Staph 5

Bio-Rad 6

Omega Avipath 2

Oxoid Staphylase 4

Oxoid Staphytect Plus 7

Pastorex Staph Plus 25

Phadebact 9

Prolex Staph 8

Remel BactiStaph 7

Remel Staphaurex (Plus) 20

Table 5 Staphylococcus aureus agglutination kits Table 6 Identification kitssystems

Most common kits used Number of users

API StaphmdashBiomerieux 2

BBL Crystal-BD Gram Positive ID Kit 2

MALDI-TOF Bruker 25

MALDI-TOF VITEK MS 9

Microbact 12S 2

Microscan 1

Phadebact 1

Phoenix 7

RapID Staph Plus 1

SAM-PCR 1

VITEK2 GPmdashBiomerieux 23

copy2013 RCPA Quality Assurance Programs Pty Limited 7 Date of issue 13th November 2013

ITEM 201363 SKIN SWAB

36 146

109 441

29 117

3 12

24 97

1 04

30 121

8 32

5 20

1 04

1 04

Aeromonas veronii biovar sobria (formally A sobria)

ITEM 201363

Quality Control This item contained the pure isolate Aeromonas veronii bv sobria Homogeneity and stability testing were satisfactory with the bacterial count for the A veronii bv sobria remaining above 41 X 109 CFUL during the 3 week survey period Identification

Two hundred and forty seven participants submitted results with 246 (996) reporting an Aeromonas species The most frequently isolated Aeromonas species of clinical significance in humans are A veronii bv sobria A hydrophila and A caviae1 2 A sobria reported by the majority of participants now refers to the organism originally described by Popoff and Veacuteron in 1976 and is primarily a fish pathogen Aldquosobriardquo that are negative for aesculin hydrolysis salicin KCN L-arabinose and ornithine decarboxylase (ODC) and positive for arginine dihydrolase (ADH) should be designated A veronii bv sobria 2 3 A ichthiosmia reported by one laboratory is identical to A veronii bv sobria using gene sequencing2 A liquefaciens (one laboratory) is exclusively a fish pathogen4 Laboratories identified using Gram stain (gram-negative rods) oxidase reaction (positive) and a variety of identification kitssystems the most commonly used being API 20E (n=49) API 20NE (n=52) MALDI-TOFBruker (n=36) MALDI-TOFVITEK MS (n=10) and VITEK2 GN (n=68)

Susceptibility testing Aeromonas veronii bv sobria

Most discrepancies occurred in the reporting of Augmentin and the carbapenems for this isolate The CDS susceptibility method acknowledges the presence of chromosomally-linked β-lactamases (A1 and A2) in Aeromonas species5678 A1 is an inducible cephalosporinase which is inhibited by aztreonam but not by clavulanic acid and which hydrolyses cephalosporins and cephamycins but not carbapenems (AmpCBush group 1) It is detected by adjacent disc testing in the CDS method (Figure 3a) A2 is a carbapenemase which hydrolyses carbapenems but not cephalosporins or cephamycins It may show heterogeneous expression of resistance and so resistance to imipenem and meropenem may not be detectable by conventional methods unless a heavy inoculum is used 6789 and inaccurate reporting of sensitivity to carbapenems may ensue(Figure 3b) CDS users should report A veronii bv sobria as resistant to both Augmentin and carbapenems and are directed to Table 104a of the current CDS guidelines For CLSI users standard M45-A2 states that ldquointerpretive breakpoints for cefazolin and for ertapenem imipenem and meropenem for the Enterobacteriaceae were voted to be changed by the Subcommittee on Antimicrobial Susceptibility Testing subsequent to final approval of this edition of M45 It is anticipated that these modified breakpoints will be adopted for use with Aeromonas spp and Vibrio spp in the next edition of M45 or possibly in a future supplementrdquo10 The CLSI standard inoculum equivalent of 05 McFarland would likely fail to detect carbapenem resistance in Aeromonas species

Antibiotic

Aeromonas veronii bv sobria susceptibilities (all methods)

Susc IntRS Res

Amikacin 42 - 1

AmpicillinAmoxycillin - - 146

Augmentin 28 17 98

Cefazolin 9 - 18

Cefepime 21 - 1

Cefotaxime 51 - 2

Cefoxitin 11 - 1

Ceftazidime 82 - 3

Ceftriaxone 75 - 10

Cefuroxime 43 - -

Cephalexin 6 - 7

Cephalothin 9 - 5

Chloramphenicol 15 - -

Ciprofloxacin 213 - 1

Cotrimoxazole 153 2 3

Gentamicin 198 - 1

Imipenem 25 5 26

Levofloxacin 13 - -

Meropenem 40 2 43

Piperacillin 6 - -

Piperacillintazobactam 44 - 15

Sulphafurazole 8 - -

Tetracycline 29 - -

Timentin 5 - 19

Tobramycin 12 - -

Trimethoprim 19 - 1

Table 7 Aeromonas veronii bv sobria

1

1

5

8

30

1

24

3

29

109

36

0 20 40 60 80 100 120

Citrobacter freundii

Aeromonas liquefaciens

Aeromonas hydrophilacaviae

Aeromonas hydrophila group

Aeromonas hydrophila

Aeromonas ichthiosmia

Aeromonas species

Aeromonas veronii

Aeromonas veronii complex

Aeromonas sobria

Aeromonas veronii bv sobria

copy2013 RCPA Quality Assurance Programs Pty Limited 8 Date of issue 13th November 2013

Figure 3a A hydrophilia with cephalosporinase A1 amp carbapenemase A2 copy South Eastern Area Laboratory Services httpwebmedunsweduaucdstest

Figure 3b A sobria with carbapenemase A2 but lacking cephalosporinase A1 copy South Eastern Area Laboratory Services httpwebmedunsweduaucdstest

References Item 3 1 Parker JL and Shaw JG Aeromonas spp clinical microbiology and disease Journal of infection 201162 109-118 httpwwwsciencedirectcomsciencearticlepiiS0163445310003543bbib10 2 Janda JM and Abbott SL The genus Aeromonas taxonomy pathogenicity and infection Clin Microbiol Rev 201023 35ndash73 httpwwwncbinlmnihgovpmcarticlesPMC2806660 3 Horneman AJ and Afsar A Aeromonas Ch 38 In Versalovic J Carroll KC Funke G Jorgensen JH Landry ML WarnockDW(ed) Manual of clinical

microbiology 10th ed ASM Press Washington DC 4 Bullock GL The identification and separation of Aeromonas liquefaciens from Pseudomonas fluorescens and related organisms occurring in dis-

eased fish Appl Microbiol 19619 587ndash590 httpwwwncbinlmnihgovpmcarticlesPMC1057793 5 Antibiotic susceptibility testing by the CDS method httpwebmedunsweduaucdstest 6 Walsh TR et al Distribution and expression of β-lactamase genes among Aeromonas spp Journal of Antimicrobial Chemotherapy 199740 171ndash

178 httpjacoxfordjournalsorgcontent402171fullpdf 7 Wu C-J et al Distribution and phenotypic and genotypic detection of a metallo-b-lactamase CphA among bacteraemic Aeromonas isolates Jour-

nal of Medical Microbiology 201261 712ndash719 httpwwwncbinlmnihgovpubmed22322339 8 Aravena-Romaacuten M et al Antimicrobial susceptibilities of Aeromonas strains isolated from clinical and environmental sources to 26 antimicrobial

agents J Med Microbiol 201261 712-9 httpaacasmorgcontent5621110 9 Rossolini GM et al The Aeromonas metallo-β-lactamases genetics enzymology and contribution to drug resistance Microb Drug Resist 1996 2

245-252 httponlineliebertpubcomdoiabs101089mdr19962245

10 CLSI standard A45-A2 Methods for antimicrobial dilution and disk susceptibility testing for infrequently isolated or fastidious bacteria approved guidelinemdashsecond edition August 2010

copy2013 RCPA Quality Assurance Programs Pty Limited 9 Date of issue 13th November 2013

ITEM 201364ABCD CULTURE AND MICROSCOPY FOR AFB

Reference laboratory report

Culture results C D

Mycobacterium species isolated 59 0

Mycobacterium species not isolated 10 70

Not result reported 2 1

Participant smear results A B

Negative 17 178

1 - 9100 HPF 115 3

10 - 99100 HPF 47 2

1 - 10HPF 4 -

Table 11 Results for mediamethods used for specimen 4C

Table 9 Participant smear results

Table 10 Participant culture results

Table 12 Molecular Diagnostics

Molecular Diagnostics

C D

Mycobacterium TB Complex DNA amplification Positive

13 0

Mycobacterium TB Complex DNA amplification Negative

1 12

No result reported 1 3

Media Total no inoculated

Number positive

BacTALERT amp 3D 9 6

BD BACTEC MGIT 960 System 43 38

BD BBL MGIT 5 3

Brown amp Buckle 3 1

LJ 32 21

LJ Glycerol 6 5

LJ Pyruvate 15 8

LJ Pyruvate Glycerol 4 3

Ogawa 6 2

Other 10 7

Test A B

AFB stain Ziehl Neelsen

Positive 1-9100 HPF

No AFB seen

C D

Culture Bactec MGIT 960 (BD)L-J

Mycobacterium tuberculosis

present

Mycobacterium species absent

Microscopy Results Slides were prepared in this survey using sputum seeded with Mycobacterium tuberculosis H37Ra The sputum used was examined before inoculation with the M tuberculosis strain using a Ziehl-Neelsen stain and tested for M tuberculosis and MAC by molecular methods and found to be negative Smear 4A Slide 4A contained scanty (1-9100HPF) numbers of AFB It was examined by a reference laboratory and a RCPAQAP scientist The three smears examined by the reference laboratory were confirmed positive and contained 4 1 and 3 AFB100HPF Ten randomly selected smears examined by RCPAQAP contained from 4 to 9 AFB100HPF Most laboratories (91 or 92 when transcription errors were included) reported a positive result with the majority (63) reporting 1-9 AFB100 HPF Three transcription errors were apparent among the 17 negative results reported It is recommended these laboratories carefully review their smears Participants are requested to report AFB counts based on acid fast stains rather than on fluorescent stains Smear 4B Smear 4B contained no AFB and this was confirmed by the reference laboratory and 10 smears examined by a RCPAQAP scientist As already mentioned 3 of the 5 laboratories reporting positive results transcribed them in error The other 2 reported positive results in both smears Culture Results Item 4C Sample 4C contained Mycobacterium tuberculosis and organisms representing normal upper respiratory tract flora such as Staphylococcus epidermidis Neisseria subflava and alpha-haemolytic streptococci Of the 69 participants returning a result the majority (86) reported this sample positive Item 4D Sample 4D contained the above upper respiratory organisms only and no Mycobacteria species All participants returning a result reported it negative for Mycobacteria species Molecular Diagnostics Results Fifteen laboratories performed molecular diagnostics for M tuberculosis (14 laboratories returned results on sample 4C and 12 on 4D) Please refer to Table 12 for participant results All methods used are listed below Gene Expert 2 HAIN (MTBDR) 1 HAIN (Mycobacterium CM) 1 Inhouse PCR 3 ProbeTec 2 qPCR 1 Roche Cobas 1 Seegene 1 Taqman 2 Not stated 1

Table 8 4A-D expected results

copy2013 RCPA Quality Assurance Programs Pty Limited 10 Date of issue 13th November 2013

includes presumptive identification(s)

ITEM 201365 ISOLATE FOR IDENTIFICATION

includes presumptive identification(s)

103 475

1 05

72 332

4 18

3 14

2 09

7 32

1 05

1 05

1 05

1 05

1 05

1 05

2 09

1 05

1 05

1 05

14 65

Fig 5b H haemolyticus on HBA copy 2013 RCPA QAP

ITEM 201365 Haemophilus haemolyticus This item contained a pure growth of Haemophilus haemolyticus Homogeneity and stability testing for this organism was satisfactory with bacterial counts for the H haemolyticus remaining above 10 x 1010CFUL throughout the survey

This organism represented an isolate from blood culture collected from a patient with endocarditis H haemolyticus is a human commensal of the nasopharynx in some individuals Some authors find its pathogenicity debatable but it has occasionally been implicated in disease 123 Phenotypically and genotypically it is difficult to distinguish from non-typeable H influenzae except for β-haemolysis on blood agar in the case of H haemolyticus 45678 But even this can be an unreliable characteristic as non-haemolytic strains occur and upon repeated sub-culture this trait may disappear 5910 For this reason it has been suggested that H haemolyticus is more commonly misidentified as H influenzae than is recognised5 Like H influenzae H haemolyticus is a fastidious facultative anaerobe XV-dependent oxidase and catalase positive gram-negative coccobacillus

Fig 5a H haemolyticus on Chocolate Agar copy 2013 RCPA QAP

14

1

1

1

2

1

1

1

1

1

1

7

2

3

4

72

1

103

0 20 40 60 80 100 120

Unable to Identify - Refer

Psychrobacter phenylpyruvicus

Pasteurella species

Other

Kingella kingae

Gram negative rod

Francisella tularensis

Corynebacterium jeikeium

Brucella spp

Bacteroides ureolyticus

Actinobacillus actinomycetemcomitans

Haemophilus species

Haemophilus parainfluenzae

Haemophilus parahaemolyticus

Haemophilus influenzae type B

Haemophilus influenzae

Haemophilus aegyptius

Haemophilus haemolyticus

copy2013 RCPA Quality Assurance Programs Pty Limited 11 Date of issue 13th November 2013

SUMMARY OF PHENOTYPIC AND BIOCHEMICAL RESULTS 811

Phenotypic characteristics

Gram stain Small gram-positive rods and coccobacilli

Motility RT (BHI broth) non-motile

Colonial appearance on Chocolate agar (CA) 24hrs 10mm beige shiny round entire colonies

Colonial appearance on Horse Blood agar (HBA) 24hrs pinpoint translucent shiny round entire colonies

Pigment pale yellow

Haemolysis β (key distinguishing test if apparent) This isolate was haemolytic on HBA

Catalase positive

Oxidase positive

KIA slope NCNC gas negative

Satellitism XV + V - X - Growth conditions

Growth on HBA 35degC in O2 +

Growth on HBA 35degC in CO2 ++

Growth on HBA 35degC in ANO2 +

Growth on CA 35degC 35degC +++

Growth on MacConkey agar no growth Biochemical tests Rapid substrate utilisation

Urease positive

Nitrate positive

Indole negative

Aesculin negative

ADH negative

LDC negative

ODC negative

Glucose positive

Xylose negative

Mannitol negative

Lactose positive (weak) 11

Sucrose negative

Maltose positive (weak) 11 16S rRNA gene analysis by PCR H haemolyticus with a 99 match Although standard genetic testing may be inadequate to distinguish H influenzae and H haemolyticus because of their genetic similarity1012 the demonstration of β-haemolysis on HBA for this isolate supports the PCR findings A few other Haemophilus species are known to display β-haemolysis on blood agar but they are not X and V-dependent 8 Participant results Two hundred and seventeen participants submitted results for this item with 192 (88) correctly identifying to genus level Under half were able to fully speciate The graph on the previous page illustrates participantsrsquo results Some biochemical tests commonly used by participants to identify include catalase (+) oxidase (+) indole (-) urea (+) growth on MacConkey agar (-) and XV-dependency (+) Many participants correctly identifying H haemolyticus observed the β-haemolytic activity of this isolate on blood agar and made note of it in their comments Identification kitssystems used and success rates in the hands of the users are listed below Please note that success rates may have been influenced by the observation (or lack thereof) of β-haemolysis

API NHmdashBiomerieux 1236 (33) correct H influenzae (24)

BBL Crystal-BD NeisseriaHaemophilus ID Kit 22 (100) correct

MALDI-TOF (Bruker ) 423(17) correct Pasteurella species (1) H influenzae (17) gram-negative rod (1)

MALDI-TOF (VITEK MS) 914 (64) correct H influenzae (4) Haemophilus species (1)

Rapid NH 1528 (54) correct Kingella kingae (1) H aegypticus (1) Haemophilus species (2) H influenzae (8) H parainfluenzae (1)

Sequencing 16S rRNA 78 (88) correct H influenzae (1)

VITEK2 GN 56 (83) correct H influenzae (1)

VITEK2 NH 3150 (62) correct Haemophilus species (1) Unable to identify-refer (1) H influenzae (17)

VITEK NHI 45 (80) correct H influenzae (1)

copy2013 RCPA Quality Assurance Programs Pty Limited 12 Date of issue 13th November 2013

References Item 5 1 McCrea KW et al Relationships of nontypeable Haemophilus influenzae strains to hemolytic and nonhemolytic Haemophilus haemolyticus strains J Clin

Microbiol 200846 406ndash416 httpwwwncbinlmnihgovpmcarticlesPMC2238123

2 Jordan IK et al Genome sequences for five strains of the emerging pathogen Haemophilus haemolyticus J Bacteriol 2011193 5879ndash5880

httpwwwncbinlmnihgovpmcarticlesPMC3187195

3 Anderson R et al Haemophilus haemolyticus isolates causing clinical disease J Clin Microbiol 201250 2462-5

httpwwwncbinlmnihgovpubmed22573587

4 Morton DJ et al An invasive Haemophilus haemolyticus isolate J Clin Microbiol 201250 1502ndash1503

httpwwwncbinlmnihgovpmcarticlesPMC3318549

5 Agrawal A Murphy TF Haemophilus influenzae infections in the H influenzae type b conjugate vaccine era J Clin Microbiol 201149 3728ndash3732

httpwwwncbinlmnihgovpmcarticlesPMC3209133

6 Kilian M A taxonomic study of the genus Haemophilus with the proposal of a new species J Gen Microbiol 197693 9ndash62

httpwwwncbinlmnihgovpubmed772168

7 Kilian M 2005 Genus III Haemophilus Winslow Broadhurst Buchanan Krumweide Rogers and Smith 1917 561 p 883ndash904 In Brenner DJ Krieg NR Staley JT (ed) Bergeyrsquos manual of systematic bacteriology 2nd ed vol 2 Springer New York NY

8 Ledeboer NA Doern GV 2012 Haemophilus In Versalovic J Carroll KC Funke G Jorgensen JH Landry ML WarnockDW(ed) Manual of clinical microbiology 10th ed ASM Press Washington DC

9 McCrea KW et al Relationships of nontypeable Haemophilus influenzae strains to hemolytic and nonhemolytic Haemophilus haemolyticus strains J Clin Microbiol 200846 406ndash416 httpwwwncbinlmnihgovpmcarticlesPMC2238123

10 Murphy TF et al Haemophilus haemolyticus a human respiratory tract commensal to be distinguished from Haemophilus influenzae J Infect Dis 2007195 81ndash 89 httpwwwncbinlmnihgovpubmed17152011

11 Identification Reference Laboratory Centre for Infectious Diseases and Microbiology ICPMR Westmead Hospital 12 Binks MJ et al Molecular Surveillance of True Nontypeable Haemophilus influenzae An Evaluation of PCR Screening Assays PLOS

httpwwwplosoneorgarticleinfo3Adoi2F1013712Fjournalpone0034083

13 Duerden B Bennet KW and Faulkner J Isolation of Bacteroides ureolyticus (B corrodens) from clinical infections J Clin Pathol 1982 35 309-312 httpjcpbmjcomcontent353309fullpdf

The most common misidentification by participants was H influenzae (35) because of the phenotypicgenetic similarity of the two species and because of the failure of all kitsidentification systems to differentiate between them Reliance on one type of identification system is discouraged and may lead to incorrect identification of some organisms In this instance β-haemolysis on blood agar facilitated an accurate identification if detected however as already noted it may not always be displayed in this species even in primary cultures H parahaemolyticus reported by three laboratories is also β-haemolytic but unlike H haemolyticus it is V-dependent only (and δ-Aminolevulinic acid (ALA) test negative) as is H parainfluenzae reported by two laboratories which is not β-haemolytic All other false identifications reported do not exhibit X+V dependency or X- or V-dependency The laboratory reporting Corynebacterium jeikeium should note that this is a gram-positive rod B ureolyticus reported by one laboratory is an anaerobic organism with corroding colonies on agar plates 13 Brucella and Francisella tularensis are slow-growing fastidious organisms (also not XV-dependent) that would not be dispatched in this type of QAP

ITEM 201364C CLERICAL ERROR

Clerical Errors reported in Item 201364C Number labs (71)

No error reported 6

Error first name only (correct) in 4C 60(85)

Error first name only in 4D (incorrect) 1

Error first name (correct) + last name (incorrect) 1

Error first name (correct) + unit number (incorrect) 1

Error last name (incorrect) 2

Table 13 Clerical errors reported

Specimen label Karina DANIELS UN 831248 Paperwork Amelia DANIELS UN 831248

The clerical error was placed in item 201364C Mycobacteriology culture As only 95 participants receive 4C and 4D culture vials and only 71 performed testing this clerical error has not been scored

copy2013 RCPA Quality Assurance Programs Pty Limited 13 Date of issue 13th November 2013

ITEM 201367ABC MYCOLOGY

7A This item contained Trichophyton interdigitale [zoophilic] (previously T mentagrophytes) 973 correct to genus level 634 correct to species level (required) The Trichophyton species have undergone extensive reclassification in the last 5 years This is because there exists much phenotypic variation but genetic variation is low Most of the species formerly known as T mentagrophytes are now classified within T interdigitale T mentagrophytes still exists but encompasses only the organism previously known as T quinckeanum (T mentagrophytes var quinckeanum) which is associated with mice T interdigitale is recognised as having two ecological groups the anthropophilic and the zoophilic group with the former T mentagrophytes species falls into the zoophilic group For this item T interdigitale and T mentagrophytes were both marked as correct This newly merged species encompasses a wide range of phenotypes which may or may not be observed for a given specimen Sequencing of the internal transcribed spacer (ITS) region is the gold standard for identification using reference strains that are correctly named according to the revised taxonomy Chen et al have published a useful book chapter with phenotypic descriptions and recommendations for molecular identification of the revised Trichophyton species1

7A Trichophyton interdigitale [zoophilic]

Figures 7A (i-iii) Trichophyton interdigitale [zoophilic group] (previously T mentagrophytes) may have [7A(i)] numerous single-celled microconidia often in dense clusters along with smooth thin-walled cigar-shaped multicelled macroconidia Microconidia are hyaline smooth-walled and are predominantly spherical to subspherical in shape however occasional clavate to pyriform forms may occur [7A(ii)] varying numbers of spherical chlamydoconidia and [7A (iii)] spiral hyphae may also be observed The zoophilic form of the species tends to have powdery-granular colonies on Sabouraudrsquos lactritmel and 1 peptone media while the anthropophilic form has suede-downy textured colonies

1

1

1

1

1

2

2

5

6

7

14

1

31

1

5

20

13

0 5 10 15 20 25 30 35

Chrysosporium tropicum

Microsporum gypseum

Microsporum persicolor

Trichophyton equinum

Trichophyton terrestre

Trichophyton erinacei

Trichophyton verrucosum

Trichophyton species

Trichophyton rubrum [Worldwide population]

Trichophyton tonsurans

Trichophyton rubrum

Trichophyton mentagrophytes complex

Trichophyton mentagrophytes

Trichophyton interdigitale [anthropophilic] and [zoophilic]

Trichophyton interdigitale [anthropophilic]

Trichophyton interdigitale

Trichophyton interdigitale [zoophilic]

13 116

20 179

5 45

1 09

31 277

1 09

14 125

7 63

6 54

5 45

2 18

2 18

1 09

1 09

1 09

1 09

1 09

7A (i)

7A (ii) 7A (iii)

copy2013 RCPA Quality Assurance Programs Pty Limited 14 Date of issue 13th November 2013

7B Cryptococcus neoformans

82 732

8 71

1 09

1 09

5 45

11 98

1 09

1 09

1 09

1 09

7B This item contained Cryptococcus neoformans 964 correct to genus level 812 correct to species level (required) Cryptococcosis is typically caused by either Cryptococcus neoformans or Cryptococcus gattii although occasionally other Cryptococcus species have been implicated C neoformans typically infects the immunocompromised host frequently in the setting of HIV with gt1 million new cases and~600000 deaths per year globally C neoformans is a yeast-like basidiomycete fungus with a distinctive polysaccharide capsule Differentiation from the closely related C gattii is important Presumptive identification is by India Ink stain to highlight the capsule and birdseed agar to observe dark brown colonies

Figure 7B (i-iii) [7B (i)] India Ink stain highlighting the capsule of C neoformansgattii [7B(ii)] Dark brown colonies of C neoformansgattii mixed with white colonies of Candida albicans on birdseed agar [7B(iii)] Canavanine glycine bromothyol blue (CGB) media for distinguishing C neoformans (left) from C gattii (right)

1

1

1

1

11

5

1

1

8

82

0 10 20 30 40 50 60 70 80 90

Unable to identify- refer

Candida (not albicans)

Candida glabrata complex

Candida krusei

Cryptococcus neoformansgattii- unable to speciate

Cryptococcus species

Cryptococcus laurentii

Cryptococcus neoformans var grubii

Cryptococcus neoformans var neoformans

Cryptococcus neoformans

81 of labs correctly reported this isolate as Cryptococcus neoformans While no lab reported C gattii 11 labs were unable to differentiate C neoformans from C gattii Epidemiology risk factors and treatment of infections caused by these species are different and accurate identification is important for effective management All labs should seek to differentiate these species using CGB media a validated molecular method or by referral to a reference laboratory API ID32C and Vitek-2 does not distinguish C neoformans from C gattii These species may be differentiated by a number of DNA-based assays MALDI-ToF and canavanine-glycine-bromothymol blue (CGB) media C neoformans does not grow on CGB media which remains yellow whereas C gattii will grow triggering a blue colour change reaction in the media usually within 3 days It is worth noting that some slow growing C gattii isolates may take as long as 10 days to effect the blue colour change and may initially be mis-identified as C neoformans Nine labs unnecessarily attempted to further identify the C neoformans isolate to variety level either Cn var grubii (serotype A molecular types VNI and VNII) or Cn var neoformans (serotype D molecular type VNIV) It is not clear what methods were used to achieve this varietal identification but 8 of the 9 labs incorrectly reported Cn var neoformans In fact the isolate was confirmed by molecular methods to be Cryptococcus neoformans var grubii molecular type VNI The 8 reports of Cn var neoformans may reflect persistence of the now obsolete classification of Cryptococcus neoformans having two varieties var neoformans and var gattii If it is the normal practice of these labs to report to varietal level it would be worthwhile reviewing methods interpretation and reporting procedures

7B (i) 7B (ii) 7B(iii)

copy2013 RCPA Quality Assurance Programs Pty Limited 15 Date of issue 13th November 2013

Reference item 7

1 Chen SC DH Ellis TC Sorrell and W Meyer Chapter 44 Trichophyton In ldquoMolecular Detection of Human Fungal Pathogensrdquo Dongyou Liu (Ed) CRC Press 2011

All mycology isolates were identified by both conventional and molecular techniques

86 768

9 80

1 09

2 18

3 27

3 27

2 18

1 09

1 09

1 09

1 09

2 18

7C Scedosporium prolificans

This item contained Scedosporium prolificans 875 correct to genus level 768 correct to species level (required) Colonies are rapid growing flat spreading olive-grey to black (the culture may contain a mixture of the colurs depending on the age) and have a suede-like to downy surface texture [7C (i)] Conidia are borne in small groups on distinctive basally swollen flask-shaped annellides which occur singly or in clusters along the vegetative hyphae Conidia are single-celled hyaline to pale-brown ovoid to pyriform 2-5 x 3-13 um (average 34-53 um) in size and have smooth thin walls [7C (ii)] Identification of Scedosporium prolificans to

species level is very important due to its intrinsic resistance to most antifungal drugs It may be distinguished from other members of the genus in particular the human pathogen S apiospermum by its basally swollen (inflated) flask-shaped annellides conidia borne in small groups rather than singly and by not growing on media containing cycloheximide (actidione) DNA sequencing (ITS region) will also definitively identify Scedosporium species Three laboratories reported Sporothrix schenckii which is easily distinguished from Scedosporium spp because it is a dimorphic pathogen with a yeast-like phase when grown at 37degC

2

1

1

1

1

2

3

3

2

1

9

86

0 10 20 30 40 50 60 70 80 90 100

Unable to identify- refer

Chaetomium species

Hortaea werneckii

Ochroconis gallopava

Wangiella species

Exophiala species

Exophiala dermatitidis

Sporothrix schenckii

Scedosporium species

Scedosporium aurantiacum

Scedosporium apiospermum (sensu stricto)

Scedosporium prolificans

7C (i) 7C (ii)

Page 2: FINAL RESULTS AND COMMENTS D6-2013 …dataentry.rcpaqap.com.au/micro/reports/uploadedfiles/fnl2013-6.pdf · FINAL RESULTS AND COMMENTS D6/2013 ... This item contained a pure growth

copy2013 RCPA Quality Assurance Programs Pty Limited 2 Date of issue 13th November 2013

FINAL RESULTS AND COMMENTS D62013

ITEM 201361AB URINE FOR MICROSCOPY CULTURE AND SUSCEPTIBILITY TESTING

ITEM 201361A

Quality Control This item contained a pure growth of Proteus mirabilis and passed homogeneity and stability testing with the total counts remaining above 10 x 1010 CFUL throughout the survey period

Microscopy Homogeneity testing indicated that the white cell count was 10-100 x 106L or gt100 x 106L Both counts have been scored correct The red cell count was 10-100 x 106L There were no epithelial cells added to the sample so lt10 x 106L was the expected result for epithelial cells Ninety six percent reported 10-100 or gt100 x 106L WBC 82 reported 10-100 X 106 RBCL and 98 reported lt10 x 106 epithelial cellsL Comparisons of cell count method versus counts reported are outlined in Table 1

Table 1 Cell counts reported 1A

Bacterial counts Two hundred and sixty five participants submitted culture results for this item Where reported 92 reported growth of gt108 CFUL and 99 a pure growth Three participants transposed results

Identification and susceptibility testing IdentificationmdashProteus mirabilis Excluding the three transposed results 99 of participants correctly identified this isolate to genus level Commercial kitssystems were utilised by 229 (86) The participant reporting Pvulgaris did not use a kit only identifying that the colony was cream on their in-house chromogenic medium Mmorganii in the hands of the user was incorrectly identified by using Microbact 24E The other three users of this kit reported the correct identification The two reporting Proteus species did not use a kitcommercial system with one using chromogenic agar (clearyellow- brown) and the other did not identify any further reporting that catheter colonisation was the likely cause Forty eight

White1A Red1A Epi1A IQ 200 Manual Omitted U(F) 2000 UF-1

UF-1000(i)

Urisys 2400 UX-2000

10-100 10-100 lt10 14 136 15 - 1 2 1 -

gt100 10-100 lt10 1 26 1 1 - 1 - 1

10-100 10-100 Not Tested - 3 - - - - - -

10-100 Not Tested Not Tested 1 1 - - - - - -

gt100 10-100 Not Tested - 1 - - - - - -

10-100 lt10 lt10 - 16 3 - - - - -

gt100 gt100 lt10 - 7 4 - - - - -

10-100 gt100 lt10 - 5 - - - - - -

lt10 lt10 lt10 - 8 - - - - - -

10-100 10-100 10-100 - 2 - - - 1 - -

lt10 lt10 Not Tested - - 1 - - - - -

lt10 Not Tested lt10 - - 1 - - - - -

lt10 Not Tested Not Tested - 1 - - - - - -

gt100 gt100 10-100 - 1 - - - - - -

gt100 10-100 10-100 - 1 - - - - - -

10-100 lt10 10-100 - - - - - 1 - -

Not Tested lt10 Not Tested - 1 - - - - - -

1A Proteus mirabilis

256 966

1 04

2 08

1 04

3 11

1 04

1 04 1

1

3

1

2

1

256

0 50 100 150 200 250 300

Sent to Reference Lab

Mixed growth-probable contamination

Escherichia coli

Morganella morganii

Proteus species

Proteus vulgaris

Proteus mirabilis

copy2013 RCPA Quality Assurance Programs Pty Limited 3 Date of issue 13th November 2013

participants successfully used MALDI-TOF MS to correctly identify this isolate Susceptibility Testing Proteus mirabilis This strain of Pmirabilis expresses a plasmid mediated AmpC (PM AmpC) type of β-lactamase This was a clinical isolate sourced from a hospital laboratory south of Sydney The isolate was grown from both the patientrsquos blood cultures and catheter urine The isolate was resistant to ampicillin cephalexin and ceftriaxone but susceptible to cefepime and aztreonam ESBL and MBL phenotypic tests (CDS) were negative When referred to the CDS laboratory for further testing phenotypic tests (showing synergy between boronic acid disc and ceftazidime) suggested high activity plasmid-mediated AmpC cephalosporinase1 Figure 1A illustrates the method used but please note the isolate in image is Ecoli not Pmirabilis The CDS laboratory commented that ldquoDue to its characteristic swarming back into the zone of inhibition around imipenem disc this organism may appear resistant to imipenem with a double zone The testing on MacConkey agar confirms that the organism is susceptible to imipenem with a clear zone of 7 mm It is also clearly susceptible to all other carbapenems ie meropenem ertapenem and doripenemrdquo Nine participants reported imipenem resistance Five were users of the CDS method three used the CLSI standard disk method and one used Vitek2

Forty five participants incorrectly reported the presence of ESBL Thirty nine confirmed or suspected AmpC A further 15 referred to another laboratory for ESBL testing We thank Dr Peter Newton Medical Microbiologist Wollongong Hospital Wollongong NSW for providing this isolate

Pmirabilis

Item 1A

Susceptibilities

(all methods)

Antibiotic S IRS R

Amikacin 76 1 -

AmpicillinAmoxycillin 1 - 230

Augmentin 1 - 234

Cefaclor - - 16

Cefazolin - - 36

Cefepime 23 - 1

Cefotaxime 1 7 62

Cefoxitin 1 - 27

Ceftazidime 20 11 46

Ceftriaxone 18 11 63

Cefuroxime 9 18 37

Cephalexin 1 - 82

Cephalothin 1 - 54

Ciprofloxacin 1 - 113

Cotrimoxazole 26 - 72

Ertapenem 17 - -

Fosfomycin 8 - -

Gentamicin 166 16 35

Imipenem 67 1 9

Levofloxacin - - 13

Meropenem 126 - 2

Nitrofurantoin 5 4 194

Norfloxacin - - 149

Piperacillin - - 7

Piperacillintazobactam 56 2 3

Tetracycline - - 6

Timentin 20 - 12

Tobramycin 1 1 29

Trimethoprim 2 - 182

Table 2 Proteus mirabilis susceptibilities (all methods)

Figure 1A Phenotypic detection using boronic acid discs in an E coli producing a plamid mediated AmpC Synergy between boronic acid discs (blank) and adjacent discs cefotaxime (CTX 5) Augmentin (AMC 60) cephalexin (CL 100) ceftazidime (CAZ 10) Blank disc = 250 microg boronic acid disc2

Reference Item 1A

1 ASM 2013 mdash PowerPoint Presentation Proceedings of the CDS Workshop -Part 2

httpwebmedunsweduaucdstestGTF_CDS_siteWebPagesArchiveASMconferencehtm

2 ASM 2013 mdash PowerPoint Presentation Proceedings of the CDS Workshop -Part 1 Slide 20

httpwebmedunsweduaucdstestGTF_CDS_siteWebPagesArchiveASMconferencehtm

copy2013 RCPA Quality Assurance Programs Pty Limited 4 Date of issue 13th November 2013

ITEM 201361B

Quality Control This item contained a pure growth of Escherichia coli and passed homogeneity and stability testing with counts remaining above 10 x 1010 CFUL throughout the survey period

Microscopy Homogeneity testing indicated that the white cell count was 10-100 x 106L or gt100 x 106L Both counts have been scored correct The red cell count was 10-100 x 106L There were no epithelial cells added to the sample so lt10 x 106L was the expected result for epithelial cells Ninety five percent reported 10-100 or gt100 x 106L WBC 79 reported 10-100 X 106 RBCL and 98 reported lt10 x 106 epithelial cellsL Comparisons of cell count method versus counts reported are outlined in Table 3

Bacterial counts Two hundred and sixty five participants returned results for this item Where reported 97 reported growth of gt108 CFUL and 99 reported a pure growth

Table 3 Cell counts reported 1B

White1B Red1B Epi1B IQ 200 Manual Omitted U(F) 2000 UF-1 UF-1000(i) Urisys 2400 UX-2000

10-100 10-100 lt10 10 117 8 1 1 4 1 -

gt100 10-100 lt10 4 38 8 - - - - -

10-100 10-100 Not Tested - 2 1 - - - - -

10-100 Not Tested Not Tested 1 1 - - - - - -

gt100 10-100 Not Tested - 1 - - - - - -

10-100 lt10 lt10 - 15 3 - - - - -

10-100 lt10 lt10 - 15 3 - - - - -

gt100 gt100 lt10 - 11 2 - - - - 1

10-100 gt100 lt10 1 8 - - - - -

lt10 lt10 lt10 - 7 1 - - - - -

lt10 10-100 lt10 - 1 1 - - - - -

10-100 10-100 10-100 - 1 - - 1 - -

lt10 10-100 Not Tested - 1 - - - - - -

lt10 Not Tested lt10 - 1 - - - - -

lt10 Not Tested Not Tested - 1 - - - - - -

gt100 lt10 lt10 - 1 - - - - - -

gt100 lt10 10-100 - 1 - - - - - -

gt100 gt100 Not Tested - 1 - - - - - -

gt100 10-100 10-100 - 1 - - - - - -

10-100 lt10 10-100 - 1 - - - - - -

copy2013 RCPA Quality Assurance Programs Pty Limited 5 Date of issue 13th November 2013

IdentificationmdashEscherichia coli

Ninety eight percent of participants correctly reported Escherichia coli for this item The two results of Pmirabilis and the ldquoUnable to identify-referrdquo were transposed results The participant reporting Kpneumoniae used ldquoRapid Onerdquo kit Two other participants used this same kit and reported correctly Eighty five participants reported the use of chromogenic agar Commercial kitssystems were used by 182 participants All kits performed well Thirty five participants used MALDI-TOF with all reporting Ecoli

Ecoli Item 1B Susceptibilities

(all methods)

Antibiotic S IRS R

Amikacin 40 - -

AmpicillinAmoxycillin 233 - 5

Augmentin 217 2 2

Cefaclor 16 - -

Cefazolin 37 - -

Cefepime 12 - -

CefoperzoneSulbactum 1 - -

Cefotaxime 49 - -

Cefoxitin 20 - -

Ceftazidime 54 - -

Ceftriaxone 53 - -

Cefuroxime 56 - -

Cephalexin 93 - 1

Cephalothin 53 3 -

Chloramphenicol 5 - -

Ciprofloxacin 80 - -

Cotrimoxazole 91 - 1

Ertapenem 12 - -

Gentamicin 180 1 -

Imipenem 50 - -

Levofloxacin 13 - -

Meropenem 57 - -

Nalidixic acid 6 - -

Nitrofurantoin 209 - 2

Norfloxacin 133 - 1

Piperacillintazobactam 37 1 -

Polymyxin B 2 - -

Tetracycline 6 - -

Timentin 10 - -

Tobramycin 8 - -

Trimethoprim 191 - 1

Table 4 Escherichia coli susceptibilities (all methods)

1B Escherichia coli

260 981

1 04

2 04

1 04

1 04

1

1

2

1

260

0 50 100 150 200 250 300

Sent to Reference Lab

Unable to Identify - Refer

Proteus mirabilis

Klebsiella pneumoniae

Escherichia coli

Susceptibility testingndash Escherichia coli Susceptibility testing was performed well with the majority of participants reporting susceptible to the commonly reported antibiotics for gram-negative urine isolates

copy2013 RCPA Quality Assurance Programs Pty Limited 6 Date of issue 13th November 2013

ITEM 201362 NOSE SWAB

includes presumptive identifications

ITEM 201362 Nose swab Quality Control This item represented an infection control nose swab containing Methicillin resistant Staphylococcus aureus (MRSA) and Staphylococcus epidermidis Counts for MRSA remained above 10 x 1010 CFUL throughout the survey Homogeneity and stability testing were satisfactory Culture and identification results Two hundred and forty seven participants returned results with 242 (98) reporting MRSA This isolate was a non multi-resistant MRSA (NMRSA) with a susceptibility pattern as follows Resistant to ampicillin Augmentin cefotaxime cefoxitin cephalothin oxacillin and penicillin susceptible to ciprofloxacin clindamycin erythromycin fusidic acid gentamicin rifampicin and tetracycline Many laboratories screened using chromogenic agars Follow up tests included Gram stain (gram-positive cocci) catalase (positive) DNAase (positive) slidetube coagulase (positive) and conventional susceptibility testing or other method to confirm MRSA Staphylococcus aureus agglutination kits used are shown in Table 5 below Identification kitssystems employed are also shown below in Table 6 Most kitssystems accurately identified S aureus Three laboratories reporting S aureus mentioned that it was MRSA in the comments box One of the four laboratories reporting S aureus (only) reported it oxacillin susceptible in the comments box The other three gave no indication of it being or possibly being MRSA

239 968

3 12

4 16

1 04 1

4

3

239

0 50 100 150 200 250 300

Staphylococcus coag negative

Staphylococcus aureus

Staphylococcus aureus (MRSA in comments)

MRSA or Staphylococcus aureus (MRSA)

Most common kits used

Number of users

Biomerieux Slidex Staph 5

Bio-Rad 6

Omega Avipath 2

Oxoid Staphylase 4

Oxoid Staphytect Plus 7

Pastorex Staph Plus 25

Phadebact 9

Prolex Staph 8

Remel BactiStaph 7

Remel Staphaurex (Plus) 20

Table 5 Staphylococcus aureus agglutination kits Table 6 Identification kitssystems

Most common kits used Number of users

API StaphmdashBiomerieux 2

BBL Crystal-BD Gram Positive ID Kit 2

MALDI-TOF Bruker 25

MALDI-TOF VITEK MS 9

Microbact 12S 2

Microscan 1

Phadebact 1

Phoenix 7

RapID Staph Plus 1

SAM-PCR 1

VITEK2 GPmdashBiomerieux 23

copy2013 RCPA Quality Assurance Programs Pty Limited 7 Date of issue 13th November 2013

ITEM 201363 SKIN SWAB

36 146

109 441

29 117

3 12

24 97

1 04

30 121

8 32

5 20

1 04

1 04

Aeromonas veronii biovar sobria (formally A sobria)

ITEM 201363

Quality Control This item contained the pure isolate Aeromonas veronii bv sobria Homogeneity and stability testing were satisfactory with the bacterial count for the A veronii bv sobria remaining above 41 X 109 CFUL during the 3 week survey period Identification

Two hundred and forty seven participants submitted results with 246 (996) reporting an Aeromonas species The most frequently isolated Aeromonas species of clinical significance in humans are A veronii bv sobria A hydrophila and A caviae1 2 A sobria reported by the majority of participants now refers to the organism originally described by Popoff and Veacuteron in 1976 and is primarily a fish pathogen Aldquosobriardquo that are negative for aesculin hydrolysis salicin KCN L-arabinose and ornithine decarboxylase (ODC) and positive for arginine dihydrolase (ADH) should be designated A veronii bv sobria 2 3 A ichthiosmia reported by one laboratory is identical to A veronii bv sobria using gene sequencing2 A liquefaciens (one laboratory) is exclusively a fish pathogen4 Laboratories identified using Gram stain (gram-negative rods) oxidase reaction (positive) and a variety of identification kitssystems the most commonly used being API 20E (n=49) API 20NE (n=52) MALDI-TOFBruker (n=36) MALDI-TOFVITEK MS (n=10) and VITEK2 GN (n=68)

Susceptibility testing Aeromonas veronii bv sobria

Most discrepancies occurred in the reporting of Augmentin and the carbapenems for this isolate The CDS susceptibility method acknowledges the presence of chromosomally-linked β-lactamases (A1 and A2) in Aeromonas species5678 A1 is an inducible cephalosporinase which is inhibited by aztreonam but not by clavulanic acid and which hydrolyses cephalosporins and cephamycins but not carbapenems (AmpCBush group 1) It is detected by adjacent disc testing in the CDS method (Figure 3a) A2 is a carbapenemase which hydrolyses carbapenems but not cephalosporins or cephamycins It may show heterogeneous expression of resistance and so resistance to imipenem and meropenem may not be detectable by conventional methods unless a heavy inoculum is used 6789 and inaccurate reporting of sensitivity to carbapenems may ensue(Figure 3b) CDS users should report A veronii bv sobria as resistant to both Augmentin and carbapenems and are directed to Table 104a of the current CDS guidelines For CLSI users standard M45-A2 states that ldquointerpretive breakpoints for cefazolin and for ertapenem imipenem and meropenem for the Enterobacteriaceae were voted to be changed by the Subcommittee on Antimicrobial Susceptibility Testing subsequent to final approval of this edition of M45 It is anticipated that these modified breakpoints will be adopted for use with Aeromonas spp and Vibrio spp in the next edition of M45 or possibly in a future supplementrdquo10 The CLSI standard inoculum equivalent of 05 McFarland would likely fail to detect carbapenem resistance in Aeromonas species

Antibiotic

Aeromonas veronii bv sobria susceptibilities (all methods)

Susc IntRS Res

Amikacin 42 - 1

AmpicillinAmoxycillin - - 146

Augmentin 28 17 98

Cefazolin 9 - 18

Cefepime 21 - 1

Cefotaxime 51 - 2

Cefoxitin 11 - 1

Ceftazidime 82 - 3

Ceftriaxone 75 - 10

Cefuroxime 43 - -

Cephalexin 6 - 7

Cephalothin 9 - 5

Chloramphenicol 15 - -

Ciprofloxacin 213 - 1

Cotrimoxazole 153 2 3

Gentamicin 198 - 1

Imipenem 25 5 26

Levofloxacin 13 - -

Meropenem 40 2 43

Piperacillin 6 - -

Piperacillintazobactam 44 - 15

Sulphafurazole 8 - -

Tetracycline 29 - -

Timentin 5 - 19

Tobramycin 12 - -

Trimethoprim 19 - 1

Table 7 Aeromonas veronii bv sobria

1

1

5

8

30

1

24

3

29

109

36

0 20 40 60 80 100 120

Citrobacter freundii

Aeromonas liquefaciens

Aeromonas hydrophilacaviae

Aeromonas hydrophila group

Aeromonas hydrophila

Aeromonas ichthiosmia

Aeromonas species

Aeromonas veronii

Aeromonas veronii complex

Aeromonas sobria

Aeromonas veronii bv sobria

copy2013 RCPA Quality Assurance Programs Pty Limited 8 Date of issue 13th November 2013

Figure 3a A hydrophilia with cephalosporinase A1 amp carbapenemase A2 copy South Eastern Area Laboratory Services httpwebmedunsweduaucdstest

Figure 3b A sobria with carbapenemase A2 but lacking cephalosporinase A1 copy South Eastern Area Laboratory Services httpwebmedunsweduaucdstest

References Item 3 1 Parker JL and Shaw JG Aeromonas spp clinical microbiology and disease Journal of infection 201162 109-118 httpwwwsciencedirectcomsciencearticlepiiS0163445310003543bbib10 2 Janda JM and Abbott SL The genus Aeromonas taxonomy pathogenicity and infection Clin Microbiol Rev 201023 35ndash73 httpwwwncbinlmnihgovpmcarticlesPMC2806660 3 Horneman AJ and Afsar A Aeromonas Ch 38 In Versalovic J Carroll KC Funke G Jorgensen JH Landry ML WarnockDW(ed) Manual of clinical

microbiology 10th ed ASM Press Washington DC 4 Bullock GL The identification and separation of Aeromonas liquefaciens from Pseudomonas fluorescens and related organisms occurring in dis-

eased fish Appl Microbiol 19619 587ndash590 httpwwwncbinlmnihgovpmcarticlesPMC1057793 5 Antibiotic susceptibility testing by the CDS method httpwebmedunsweduaucdstest 6 Walsh TR et al Distribution and expression of β-lactamase genes among Aeromonas spp Journal of Antimicrobial Chemotherapy 199740 171ndash

178 httpjacoxfordjournalsorgcontent402171fullpdf 7 Wu C-J et al Distribution and phenotypic and genotypic detection of a metallo-b-lactamase CphA among bacteraemic Aeromonas isolates Jour-

nal of Medical Microbiology 201261 712ndash719 httpwwwncbinlmnihgovpubmed22322339 8 Aravena-Romaacuten M et al Antimicrobial susceptibilities of Aeromonas strains isolated from clinical and environmental sources to 26 antimicrobial

agents J Med Microbiol 201261 712-9 httpaacasmorgcontent5621110 9 Rossolini GM et al The Aeromonas metallo-β-lactamases genetics enzymology and contribution to drug resistance Microb Drug Resist 1996 2

245-252 httponlineliebertpubcomdoiabs101089mdr19962245

10 CLSI standard A45-A2 Methods for antimicrobial dilution and disk susceptibility testing for infrequently isolated or fastidious bacteria approved guidelinemdashsecond edition August 2010

copy2013 RCPA Quality Assurance Programs Pty Limited 9 Date of issue 13th November 2013

ITEM 201364ABCD CULTURE AND MICROSCOPY FOR AFB

Reference laboratory report

Culture results C D

Mycobacterium species isolated 59 0

Mycobacterium species not isolated 10 70

Not result reported 2 1

Participant smear results A B

Negative 17 178

1 - 9100 HPF 115 3

10 - 99100 HPF 47 2

1 - 10HPF 4 -

Table 11 Results for mediamethods used for specimen 4C

Table 9 Participant smear results

Table 10 Participant culture results

Table 12 Molecular Diagnostics

Molecular Diagnostics

C D

Mycobacterium TB Complex DNA amplification Positive

13 0

Mycobacterium TB Complex DNA amplification Negative

1 12

No result reported 1 3

Media Total no inoculated

Number positive

BacTALERT amp 3D 9 6

BD BACTEC MGIT 960 System 43 38

BD BBL MGIT 5 3

Brown amp Buckle 3 1

LJ 32 21

LJ Glycerol 6 5

LJ Pyruvate 15 8

LJ Pyruvate Glycerol 4 3

Ogawa 6 2

Other 10 7

Test A B

AFB stain Ziehl Neelsen

Positive 1-9100 HPF

No AFB seen

C D

Culture Bactec MGIT 960 (BD)L-J

Mycobacterium tuberculosis

present

Mycobacterium species absent

Microscopy Results Slides were prepared in this survey using sputum seeded with Mycobacterium tuberculosis H37Ra The sputum used was examined before inoculation with the M tuberculosis strain using a Ziehl-Neelsen stain and tested for M tuberculosis and MAC by molecular methods and found to be negative Smear 4A Slide 4A contained scanty (1-9100HPF) numbers of AFB It was examined by a reference laboratory and a RCPAQAP scientist The three smears examined by the reference laboratory were confirmed positive and contained 4 1 and 3 AFB100HPF Ten randomly selected smears examined by RCPAQAP contained from 4 to 9 AFB100HPF Most laboratories (91 or 92 when transcription errors were included) reported a positive result with the majority (63) reporting 1-9 AFB100 HPF Three transcription errors were apparent among the 17 negative results reported It is recommended these laboratories carefully review their smears Participants are requested to report AFB counts based on acid fast stains rather than on fluorescent stains Smear 4B Smear 4B contained no AFB and this was confirmed by the reference laboratory and 10 smears examined by a RCPAQAP scientist As already mentioned 3 of the 5 laboratories reporting positive results transcribed them in error The other 2 reported positive results in both smears Culture Results Item 4C Sample 4C contained Mycobacterium tuberculosis and organisms representing normal upper respiratory tract flora such as Staphylococcus epidermidis Neisseria subflava and alpha-haemolytic streptococci Of the 69 participants returning a result the majority (86) reported this sample positive Item 4D Sample 4D contained the above upper respiratory organisms only and no Mycobacteria species All participants returning a result reported it negative for Mycobacteria species Molecular Diagnostics Results Fifteen laboratories performed molecular diagnostics for M tuberculosis (14 laboratories returned results on sample 4C and 12 on 4D) Please refer to Table 12 for participant results All methods used are listed below Gene Expert 2 HAIN (MTBDR) 1 HAIN (Mycobacterium CM) 1 Inhouse PCR 3 ProbeTec 2 qPCR 1 Roche Cobas 1 Seegene 1 Taqman 2 Not stated 1

Table 8 4A-D expected results

copy2013 RCPA Quality Assurance Programs Pty Limited 10 Date of issue 13th November 2013

includes presumptive identification(s)

ITEM 201365 ISOLATE FOR IDENTIFICATION

includes presumptive identification(s)

103 475

1 05

72 332

4 18

3 14

2 09

7 32

1 05

1 05

1 05

1 05

1 05

1 05

2 09

1 05

1 05

1 05

14 65

Fig 5b H haemolyticus on HBA copy 2013 RCPA QAP

ITEM 201365 Haemophilus haemolyticus This item contained a pure growth of Haemophilus haemolyticus Homogeneity and stability testing for this organism was satisfactory with bacterial counts for the H haemolyticus remaining above 10 x 1010CFUL throughout the survey

This organism represented an isolate from blood culture collected from a patient with endocarditis H haemolyticus is a human commensal of the nasopharynx in some individuals Some authors find its pathogenicity debatable but it has occasionally been implicated in disease 123 Phenotypically and genotypically it is difficult to distinguish from non-typeable H influenzae except for β-haemolysis on blood agar in the case of H haemolyticus 45678 But even this can be an unreliable characteristic as non-haemolytic strains occur and upon repeated sub-culture this trait may disappear 5910 For this reason it has been suggested that H haemolyticus is more commonly misidentified as H influenzae than is recognised5 Like H influenzae H haemolyticus is a fastidious facultative anaerobe XV-dependent oxidase and catalase positive gram-negative coccobacillus

Fig 5a H haemolyticus on Chocolate Agar copy 2013 RCPA QAP

14

1

1

1

2

1

1

1

1

1

1

7

2

3

4

72

1

103

0 20 40 60 80 100 120

Unable to Identify - Refer

Psychrobacter phenylpyruvicus

Pasteurella species

Other

Kingella kingae

Gram negative rod

Francisella tularensis

Corynebacterium jeikeium

Brucella spp

Bacteroides ureolyticus

Actinobacillus actinomycetemcomitans

Haemophilus species

Haemophilus parainfluenzae

Haemophilus parahaemolyticus

Haemophilus influenzae type B

Haemophilus influenzae

Haemophilus aegyptius

Haemophilus haemolyticus

copy2013 RCPA Quality Assurance Programs Pty Limited 11 Date of issue 13th November 2013

SUMMARY OF PHENOTYPIC AND BIOCHEMICAL RESULTS 811

Phenotypic characteristics

Gram stain Small gram-positive rods and coccobacilli

Motility RT (BHI broth) non-motile

Colonial appearance on Chocolate agar (CA) 24hrs 10mm beige shiny round entire colonies

Colonial appearance on Horse Blood agar (HBA) 24hrs pinpoint translucent shiny round entire colonies

Pigment pale yellow

Haemolysis β (key distinguishing test if apparent) This isolate was haemolytic on HBA

Catalase positive

Oxidase positive

KIA slope NCNC gas negative

Satellitism XV + V - X - Growth conditions

Growth on HBA 35degC in O2 +

Growth on HBA 35degC in CO2 ++

Growth on HBA 35degC in ANO2 +

Growth on CA 35degC 35degC +++

Growth on MacConkey agar no growth Biochemical tests Rapid substrate utilisation

Urease positive

Nitrate positive

Indole negative

Aesculin negative

ADH negative

LDC negative

ODC negative

Glucose positive

Xylose negative

Mannitol negative

Lactose positive (weak) 11

Sucrose negative

Maltose positive (weak) 11 16S rRNA gene analysis by PCR H haemolyticus with a 99 match Although standard genetic testing may be inadequate to distinguish H influenzae and H haemolyticus because of their genetic similarity1012 the demonstration of β-haemolysis on HBA for this isolate supports the PCR findings A few other Haemophilus species are known to display β-haemolysis on blood agar but they are not X and V-dependent 8 Participant results Two hundred and seventeen participants submitted results for this item with 192 (88) correctly identifying to genus level Under half were able to fully speciate The graph on the previous page illustrates participantsrsquo results Some biochemical tests commonly used by participants to identify include catalase (+) oxidase (+) indole (-) urea (+) growth on MacConkey agar (-) and XV-dependency (+) Many participants correctly identifying H haemolyticus observed the β-haemolytic activity of this isolate on blood agar and made note of it in their comments Identification kitssystems used and success rates in the hands of the users are listed below Please note that success rates may have been influenced by the observation (or lack thereof) of β-haemolysis

API NHmdashBiomerieux 1236 (33) correct H influenzae (24)

BBL Crystal-BD NeisseriaHaemophilus ID Kit 22 (100) correct

MALDI-TOF (Bruker ) 423(17) correct Pasteurella species (1) H influenzae (17) gram-negative rod (1)

MALDI-TOF (VITEK MS) 914 (64) correct H influenzae (4) Haemophilus species (1)

Rapid NH 1528 (54) correct Kingella kingae (1) H aegypticus (1) Haemophilus species (2) H influenzae (8) H parainfluenzae (1)

Sequencing 16S rRNA 78 (88) correct H influenzae (1)

VITEK2 GN 56 (83) correct H influenzae (1)

VITEK2 NH 3150 (62) correct Haemophilus species (1) Unable to identify-refer (1) H influenzae (17)

VITEK NHI 45 (80) correct H influenzae (1)

copy2013 RCPA Quality Assurance Programs Pty Limited 12 Date of issue 13th November 2013

References Item 5 1 McCrea KW et al Relationships of nontypeable Haemophilus influenzae strains to hemolytic and nonhemolytic Haemophilus haemolyticus strains J Clin

Microbiol 200846 406ndash416 httpwwwncbinlmnihgovpmcarticlesPMC2238123

2 Jordan IK et al Genome sequences for five strains of the emerging pathogen Haemophilus haemolyticus J Bacteriol 2011193 5879ndash5880

httpwwwncbinlmnihgovpmcarticlesPMC3187195

3 Anderson R et al Haemophilus haemolyticus isolates causing clinical disease J Clin Microbiol 201250 2462-5

httpwwwncbinlmnihgovpubmed22573587

4 Morton DJ et al An invasive Haemophilus haemolyticus isolate J Clin Microbiol 201250 1502ndash1503

httpwwwncbinlmnihgovpmcarticlesPMC3318549

5 Agrawal A Murphy TF Haemophilus influenzae infections in the H influenzae type b conjugate vaccine era J Clin Microbiol 201149 3728ndash3732

httpwwwncbinlmnihgovpmcarticlesPMC3209133

6 Kilian M A taxonomic study of the genus Haemophilus with the proposal of a new species J Gen Microbiol 197693 9ndash62

httpwwwncbinlmnihgovpubmed772168

7 Kilian M 2005 Genus III Haemophilus Winslow Broadhurst Buchanan Krumweide Rogers and Smith 1917 561 p 883ndash904 In Brenner DJ Krieg NR Staley JT (ed) Bergeyrsquos manual of systematic bacteriology 2nd ed vol 2 Springer New York NY

8 Ledeboer NA Doern GV 2012 Haemophilus In Versalovic J Carroll KC Funke G Jorgensen JH Landry ML WarnockDW(ed) Manual of clinical microbiology 10th ed ASM Press Washington DC

9 McCrea KW et al Relationships of nontypeable Haemophilus influenzae strains to hemolytic and nonhemolytic Haemophilus haemolyticus strains J Clin Microbiol 200846 406ndash416 httpwwwncbinlmnihgovpmcarticlesPMC2238123

10 Murphy TF et al Haemophilus haemolyticus a human respiratory tract commensal to be distinguished from Haemophilus influenzae J Infect Dis 2007195 81ndash 89 httpwwwncbinlmnihgovpubmed17152011

11 Identification Reference Laboratory Centre for Infectious Diseases and Microbiology ICPMR Westmead Hospital 12 Binks MJ et al Molecular Surveillance of True Nontypeable Haemophilus influenzae An Evaluation of PCR Screening Assays PLOS

httpwwwplosoneorgarticleinfo3Adoi2F1013712Fjournalpone0034083

13 Duerden B Bennet KW and Faulkner J Isolation of Bacteroides ureolyticus (B corrodens) from clinical infections J Clin Pathol 1982 35 309-312 httpjcpbmjcomcontent353309fullpdf

The most common misidentification by participants was H influenzae (35) because of the phenotypicgenetic similarity of the two species and because of the failure of all kitsidentification systems to differentiate between them Reliance on one type of identification system is discouraged and may lead to incorrect identification of some organisms In this instance β-haemolysis on blood agar facilitated an accurate identification if detected however as already noted it may not always be displayed in this species even in primary cultures H parahaemolyticus reported by three laboratories is also β-haemolytic but unlike H haemolyticus it is V-dependent only (and δ-Aminolevulinic acid (ALA) test negative) as is H parainfluenzae reported by two laboratories which is not β-haemolytic All other false identifications reported do not exhibit X+V dependency or X- or V-dependency The laboratory reporting Corynebacterium jeikeium should note that this is a gram-positive rod B ureolyticus reported by one laboratory is an anaerobic organism with corroding colonies on agar plates 13 Brucella and Francisella tularensis are slow-growing fastidious organisms (also not XV-dependent) that would not be dispatched in this type of QAP

ITEM 201364C CLERICAL ERROR

Clerical Errors reported in Item 201364C Number labs (71)

No error reported 6

Error first name only (correct) in 4C 60(85)

Error first name only in 4D (incorrect) 1

Error first name (correct) + last name (incorrect) 1

Error first name (correct) + unit number (incorrect) 1

Error last name (incorrect) 2

Table 13 Clerical errors reported

Specimen label Karina DANIELS UN 831248 Paperwork Amelia DANIELS UN 831248

The clerical error was placed in item 201364C Mycobacteriology culture As only 95 participants receive 4C and 4D culture vials and only 71 performed testing this clerical error has not been scored

copy2013 RCPA Quality Assurance Programs Pty Limited 13 Date of issue 13th November 2013

ITEM 201367ABC MYCOLOGY

7A This item contained Trichophyton interdigitale [zoophilic] (previously T mentagrophytes) 973 correct to genus level 634 correct to species level (required) The Trichophyton species have undergone extensive reclassification in the last 5 years This is because there exists much phenotypic variation but genetic variation is low Most of the species formerly known as T mentagrophytes are now classified within T interdigitale T mentagrophytes still exists but encompasses only the organism previously known as T quinckeanum (T mentagrophytes var quinckeanum) which is associated with mice T interdigitale is recognised as having two ecological groups the anthropophilic and the zoophilic group with the former T mentagrophytes species falls into the zoophilic group For this item T interdigitale and T mentagrophytes were both marked as correct This newly merged species encompasses a wide range of phenotypes which may or may not be observed for a given specimen Sequencing of the internal transcribed spacer (ITS) region is the gold standard for identification using reference strains that are correctly named according to the revised taxonomy Chen et al have published a useful book chapter with phenotypic descriptions and recommendations for molecular identification of the revised Trichophyton species1

7A Trichophyton interdigitale [zoophilic]

Figures 7A (i-iii) Trichophyton interdigitale [zoophilic group] (previously T mentagrophytes) may have [7A(i)] numerous single-celled microconidia often in dense clusters along with smooth thin-walled cigar-shaped multicelled macroconidia Microconidia are hyaline smooth-walled and are predominantly spherical to subspherical in shape however occasional clavate to pyriform forms may occur [7A(ii)] varying numbers of spherical chlamydoconidia and [7A (iii)] spiral hyphae may also be observed The zoophilic form of the species tends to have powdery-granular colonies on Sabouraudrsquos lactritmel and 1 peptone media while the anthropophilic form has suede-downy textured colonies

1

1

1

1

1

2

2

5

6

7

14

1

31

1

5

20

13

0 5 10 15 20 25 30 35

Chrysosporium tropicum

Microsporum gypseum

Microsporum persicolor

Trichophyton equinum

Trichophyton terrestre

Trichophyton erinacei

Trichophyton verrucosum

Trichophyton species

Trichophyton rubrum [Worldwide population]

Trichophyton tonsurans

Trichophyton rubrum

Trichophyton mentagrophytes complex

Trichophyton mentagrophytes

Trichophyton interdigitale [anthropophilic] and [zoophilic]

Trichophyton interdigitale [anthropophilic]

Trichophyton interdigitale

Trichophyton interdigitale [zoophilic]

13 116

20 179

5 45

1 09

31 277

1 09

14 125

7 63

6 54

5 45

2 18

2 18

1 09

1 09

1 09

1 09

1 09

7A (i)

7A (ii) 7A (iii)

copy2013 RCPA Quality Assurance Programs Pty Limited 14 Date of issue 13th November 2013

7B Cryptococcus neoformans

82 732

8 71

1 09

1 09

5 45

11 98

1 09

1 09

1 09

1 09

7B This item contained Cryptococcus neoformans 964 correct to genus level 812 correct to species level (required) Cryptococcosis is typically caused by either Cryptococcus neoformans or Cryptococcus gattii although occasionally other Cryptococcus species have been implicated C neoformans typically infects the immunocompromised host frequently in the setting of HIV with gt1 million new cases and~600000 deaths per year globally C neoformans is a yeast-like basidiomycete fungus with a distinctive polysaccharide capsule Differentiation from the closely related C gattii is important Presumptive identification is by India Ink stain to highlight the capsule and birdseed agar to observe dark brown colonies

Figure 7B (i-iii) [7B (i)] India Ink stain highlighting the capsule of C neoformansgattii [7B(ii)] Dark brown colonies of C neoformansgattii mixed with white colonies of Candida albicans on birdseed agar [7B(iii)] Canavanine glycine bromothyol blue (CGB) media for distinguishing C neoformans (left) from C gattii (right)

1

1

1

1

11

5

1

1

8

82

0 10 20 30 40 50 60 70 80 90

Unable to identify- refer

Candida (not albicans)

Candida glabrata complex

Candida krusei

Cryptococcus neoformansgattii- unable to speciate

Cryptococcus species

Cryptococcus laurentii

Cryptococcus neoformans var grubii

Cryptococcus neoformans var neoformans

Cryptococcus neoformans

81 of labs correctly reported this isolate as Cryptococcus neoformans While no lab reported C gattii 11 labs were unable to differentiate C neoformans from C gattii Epidemiology risk factors and treatment of infections caused by these species are different and accurate identification is important for effective management All labs should seek to differentiate these species using CGB media a validated molecular method or by referral to a reference laboratory API ID32C and Vitek-2 does not distinguish C neoformans from C gattii These species may be differentiated by a number of DNA-based assays MALDI-ToF and canavanine-glycine-bromothymol blue (CGB) media C neoformans does not grow on CGB media which remains yellow whereas C gattii will grow triggering a blue colour change reaction in the media usually within 3 days It is worth noting that some slow growing C gattii isolates may take as long as 10 days to effect the blue colour change and may initially be mis-identified as C neoformans Nine labs unnecessarily attempted to further identify the C neoformans isolate to variety level either Cn var grubii (serotype A molecular types VNI and VNII) or Cn var neoformans (serotype D molecular type VNIV) It is not clear what methods were used to achieve this varietal identification but 8 of the 9 labs incorrectly reported Cn var neoformans In fact the isolate was confirmed by molecular methods to be Cryptococcus neoformans var grubii molecular type VNI The 8 reports of Cn var neoformans may reflect persistence of the now obsolete classification of Cryptococcus neoformans having two varieties var neoformans and var gattii If it is the normal practice of these labs to report to varietal level it would be worthwhile reviewing methods interpretation and reporting procedures

7B (i) 7B (ii) 7B(iii)

copy2013 RCPA Quality Assurance Programs Pty Limited 15 Date of issue 13th November 2013

Reference item 7

1 Chen SC DH Ellis TC Sorrell and W Meyer Chapter 44 Trichophyton In ldquoMolecular Detection of Human Fungal Pathogensrdquo Dongyou Liu (Ed) CRC Press 2011

All mycology isolates were identified by both conventional and molecular techniques

86 768

9 80

1 09

2 18

3 27

3 27

2 18

1 09

1 09

1 09

1 09

2 18

7C Scedosporium prolificans

This item contained Scedosporium prolificans 875 correct to genus level 768 correct to species level (required) Colonies are rapid growing flat spreading olive-grey to black (the culture may contain a mixture of the colurs depending on the age) and have a suede-like to downy surface texture [7C (i)] Conidia are borne in small groups on distinctive basally swollen flask-shaped annellides which occur singly or in clusters along the vegetative hyphae Conidia are single-celled hyaline to pale-brown ovoid to pyriform 2-5 x 3-13 um (average 34-53 um) in size and have smooth thin walls [7C (ii)] Identification of Scedosporium prolificans to

species level is very important due to its intrinsic resistance to most antifungal drugs It may be distinguished from other members of the genus in particular the human pathogen S apiospermum by its basally swollen (inflated) flask-shaped annellides conidia borne in small groups rather than singly and by not growing on media containing cycloheximide (actidione) DNA sequencing (ITS region) will also definitively identify Scedosporium species Three laboratories reported Sporothrix schenckii which is easily distinguished from Scedosporium spp because it is a dimorphic pathogen with a yeast-like phase when grown at 37degC

2

1

1

1

1

2

3

3

2

1

9

86

0 10 20 30 40 50 60 70 80 90 100

Unable to identify- refer

Chaetomium species

Hortaea werneckii

Ochroconis gallopava

Wangiella species

Exophiala species

Exophiala dermatitidis

Sporothrix schenckii

Scedosporium species

Scedosporium aurantiacum

Scedosporium apiospermum (sensu stricto)

Scedosporium prolificans

7C (i) 7C (ii)

Page 3: FINAL RESULTS AND COMMENTS D6-2013 …dataentry.rcpaqap.com.au/micro/reports/uploadedfiles/fnl2013-6.pdf · FINAL RESULTS AND COMMENTS D6/2013 ... This item contained a pure growth

copy2013 RCPA Quality Assurance Programs Pty Limited 3 Date of issue 13th November 2013

participants successfully used MALDI-TOF MS to correctly identify this isolate Susceptibility Testing Proteus mirabilis This strain of Pmirabilis expresses a plasmid mediated AmpC (PM AmpC) type of β-lactamase This was a clinical isolate sourced from a hospital laboratory south of Sydney The isolate was grown from both the patientrsquos blood cultures and catheter urine The isolate was resistant to ampicillin cephalexin and ceftriaxone but susceptible to cefepime and aztreonam ESBL and MBL phenotypic tests (CDS) were negative When referred to the CDS laboratory for further testing phenotypic tests (showing synergy between boronic acid disc and ceftazidime) suggested high activity plasmid-mediated AmpC cephalosporinase1 Figure 1A illustrates the method used but please note the isolate in image is Ecoli not Pmirabilis The CDS laboratory commented that ldquoDue to its characteristic swarming back into the zone of inhibition around imipenem disc this organism may appear resistant to imipenem with a double zone The testing on MacConkey agar confirms that the organism is susceptible to imipenem with a clear zone of 7 mm It is also clearly susceptible to all other carbapenems ie meropenem ertapenem and doripenemrdquo Nine participants reported imipenem resistance Five were users of the CDS method three used the CLSI standard disk method and one used Vitek2

Forty five participants incorrectly reported the presence of ESBL Thirty nine confirmed or suspected AmpC A further 15 referred to another laboratory for ESBL testing We thank Dr Peter Newton Medical Microbiologist Wollongong Hospital Wollongong NSW for providing this isolate

Pmirabilis

Item 1A

Susceptibilities

(all methods)

Antibiotic S IRS R

Amikacin 76 1 -

AmpicillinAmoxycillin 1 - 230

Augmentin 1 - 234

Cefaclor - - 16

Cefazolin - - 36

Cefepime 23 - 1

Cefotaxime 1 7 62

Cefoxitin 1 - 27

Ceftazidime 20 11 46

Ceftriaxone 18 11 63

Cefuroxime 9 18 37

Cephalexin 1 - 82

Cephalothin 1 - 54

Ciprofloxacin 1 - 113

Cotrimoxazole 26 - 72

Ertapenem 17 - -

Fosfomycin 8 - -

Gentamicin 166 16 35

Imipenem 67 1 9

Levofloxacin - - 13

Meropenem 126 - 2

Nitrofurantoin 5 4 194

Norfloxacin - - 149

Piperacillin - - 7

Piperacillintazobactam 56 2 3

Tetracycline - - 6

Timentin 20 - 12

Tobramycin 1 1 29

Trimethoprim 2 - 182

Table 2 Proteus mirabilis susceptibilities (all methods)

Figure 1A Phenotypic detection using boronic acid discs in an E coli producing a plamid mediated AmpC Synergy between boronic acid discs (blank) and adjacent discs cefotaxime (CTX 5) Augmentin (AMC 60) cephalexin (CL 100) ceftazidime (CAZ 10) Blank disc = 250 microg boronic acid disc2

Reference Item 1A

1 ASM 2013 mdash PowerPoint Presentation Proceedings of the CDS Workshop -Part 2

httpwebmedunsweduaucdstestGTF_CDS_siteWebPagesArchiveASMconferencehtm

2 ASM 2013 mdash PowerPoint Presentation Proceedings of the CDS Workshop -Part 1 Slide 20

httpwebmedunsweduaucdstestGTF_CDS_siteWebPagesArchiveASMconferencehtm

copy2013 RCPA Quality Assurance Programs Pty Limited 4 Date of issue 13th November 2013

ITEM 201361B

Quality Control This item contained a pure growth of Escherichia coli and passed homogeneity and stability testing with counts remaining above 10 x 1010 CFUL throughout the survey period

Microscopy Homogeneity testing indicated that the white cell count was 10-100 x 106L or gt100 x 106L Both counts have been scored correct The red cell count was 10-100 x 106L There were no epithelial cells added to the sample so lt10 x 106L was the expected result for epithelial cells Ninety five percent reported 10-100 or gt100 x 106L WBC 79 reported 10-100 X 106 RBCL and 98 reported lt10 x 106 epithelial cellsL Comparisons of cell count method versus counts reported are outlined in Table 3

Bacterial counts Two hundred and sixty five participants returned results for this item Where reported 97 reported growth of gt108 CFUL and 99 reported a pure growth

Table 3 Cell counts reported 1B

White1B Red1B Epi1B IQ 200 Manual Omitted U(F) 2000 UF-1 UF-1000(i) Urisys 2400 UX-2000

10-100 10-100 lt10 10 117 8 1 1 4 1 -

gt100 10-100 lt10 4 38 8 - - - - -

10-100 10-100 Not Tested - 2 1 - - - - -

10-100 Not Tested Not Tested 1 1 - - - - - -

gt100 10-100 Not Tested - 1 - - - - - -

10-100 lt10 lt10 - 15 3 - - - - -

10-100 lt10 lt10 - 15 3 - - - - -

gt100 gt100 lt10 - 11 2 - - - - 1

10-100 gt100 lt10 1 8 - - - - -

lt10 lt10 lt10 - 7 1 - - - - -

lt10 10-100 lt10 - 1 1 - - - - -

10-100 10-100 10-100 - 1 - - 1 - -

lt10 10-100 Not Tested - 1 - - - - - -

lt10 Not Tested lt10 - 1 - - - - -

lt10 Not Tested Not Tested - 1 - - - - - -

gt100 lt10 lt10 - 1 - - - - - -

gt100 lt10 10-100 - 1 - - - - - -

gt100 gt100 Not Tested - 1 - - - - - -

gt100 10-100 10-100 - 1 - - - - - -

10-100 lt10 10-100 - 1 - - - - - -

copy2013 RCPA Quality Assurance Programs Pty Limited 5 Date of issue 13th November 2013

IdentificationmdashEscherichia coli

Ninety eight percent of participants correctly reported Escherichia coli for this item The two results of Pmirabilis and the ldquoUnable to identify-referrdquo were transposed results The participant reporting Kpneumoniae used ldquoRapid Onerdquo kit Two other participants used this same kit and reported correctly Eighty five participants reported the use of chromogenic agar Commercial kitssystems were used by 182 participants All kits performed well Thirty five participants used MALDI-TOF with all reporting Ecoli

Ecoli Item 1B Susceptibilities

(all methods)

Antibiotic S IRS R

Amikacin 40 - -

AmpicillinAmoxycillin 233 - 5

Augmentin 217 2 2

Cefaclor 16 - -

Cefazolin 37 - -

Cefepime 12 - -

CefoperzoneSulbactum 1 - -

Cefotaxime 49 - -

Cefoxitin 20 - -

Ceftazidime 54 - -

Ceftriaxone 53 - -

Cefuroxime 56 - -

Cephalexin 93 - 1

Cephalothin 53 3 -

Chloramphenicol 5 - -

Ciprofloxacin 80 - -

Cotrimoxazole 91 - 1

Ertapenem 12 - -

Gentamicin 180 1 -

Imipenem 50 - -

Levofloxacin 13 - -

Meropenem 57 - -

Nalidixic acid 6 - -

Nitrofurantoin 209 - 2

Norfloxacin 133 - 1

Piperacillintazobactam 37 1 -

Polymyxin B 2 - -

Tetracycline 6 - -

Timentin 10 - -

Tobramycin 8 - -

Trimethoprim 191 - 1

Table 4 Escherichia coli susceptibilities (all methods)

1B Escherichia coli

260 981

1 04

2 04

1 04

1 04

1

1

2

1

260

0 50 100 150 200 250 300

Sent to Reference Lab

Unable to Identify - Refer

Proteus mirabilis

Klebsiella pneumoniae

Escherichia coli

Susceptibility testingndash Escherichia coli Susceptibility testing was performed well with the majority of participants reporting susceptible to the commonly reported antibiotics for gram-negative urine isolates

copy2013 RCPA Quality Assurance Programs Pty Limited 6 Date of issue 13th November 2013

ITEM 201362 NOSE SWAB

includes presumptive identifications

ITEM 201362 Nose swab Quality Control This item represented an infection control nose swab containing Methicillin resistant Staphylococcus aureus (MRSA) and Staphylococcus epidermidis Counts for MRSA remained above 10 x 1010 CFUL throughout the survey Homogeneity and stability testing were satisfactory Culture and identification results Two hundred and forty seven participants returned results with 242 (98) reporting MRSA This isolate was a non multi-resistant MRSA (NMRSA) with a susceptibility pattern as follows Resistant to ampicillin Augmentin cefotaxime cefoxitin cephalothin oxacillin and penicillin susceptible to ciprofloxacin clindamycin erythromycin fusidic acid gentamicin rifampicin and tetracycline Many laboratories screened using chromogenic agars Follow up tests included Gram stain (gram-positive cocci) catalase (positive) DNAase (positive) slidetube coagulase (positive) and conventional susceptibility testing or other method to confirm MRSA Staphylococcus aureus agglutination kits used are shown in Table 5 below Identification kitssystems employed are also shown below in Table 6 Most kitssystems accurately identified S aureus Three laboratories reporting S aureus mentioned that it was MRSA in the comments box One of the four laboratories reporting S aureus (only) reported it oxacillin susceptible in the comments box The other three gave no indication of it being or possibly being MRSA

239 968

3 12

4 16

1 04 1

4

3

239

0 50 100 150 200 250 300

Staphylococcus coag negative

Staphylococcus aureus

Staphylococcus aureus (MRSA in comments)

MRSA or Staphylococcus aureus (MRSA)

Most common kits used

Number of users

Biomerieux Slidex Staph 5

Bio-Rad 6

Omega Avipath 2

Oxoid Staphylase 4

Oxoid Staphytect Plus 7

Pastorex Staph Plus 25

Phadebact 9

Prolex Staph 8

Remel BactiStaph 7

Remel Staphaurex (Plus) 20

Table 5 Staphylococcus aureus agglutination kits Table 6 Identification kitssystems

Most common kits used Number of users

API StaphmdashBiomerieux 2

BBL Crystal-BD Gram Positive ID Kit 2

MALDI-TOF Bruker 25

MALDI-TOF VITEK MS 9

Microbact 12S 2

Microscan 1

Phadebact 1

Phoenix 7

RapID Staph Plus 1

SAM-PCR 1

VITEK2 GPmdashBiomerieux 23

copy2013 RCPA Quality Assurance Programs Pty Limited 7 Date of issue 13th November 2013

ITEM 201363 SKIN SWAB

36 146

109 441

29 117

3 12

24 97

1 04

30 121

8 32

5 20

1 04

1 04

Aeromonas veronii biovar sobria (formally A sobria)

ITEM 201363

Quality Control This item contained the pure isolate Aeromonas veronii bv sobria Homogeneity and stability testing were satisfactory with the bacterial count for the A veronii bv sobria remaining above 41 X 109 CFUL during the 3 week survey period Identification

Two hundred and forty seven participants submitted results with 246 (996) reporting an Aeromonas species The most frequently isolated Aeromonas species of clinical significance in humans are A veronii bv sobria A hydrophila and A caviae1 2 A sobria reported by the majority of participants now refers to the organism originally described by Popoff and Veacuteron in 1976 and is primarily a fish pathogen Aldquosobriardquo that are negative for aesculin hydrolysis salicin KCN L-arabinose and ornithine decarboxylase (ODC) and positive for arginine dihydrolase (ADH) should be designated A veronii bv sobria 2 3 A ichthiosmia reported by one laboratory is identical to A veronii bv sobria using gene sequencing2 A liquefaciens (one laboratory) is exclusively a fish pathogen4 Laboratories identified using Gram stain (gram-negative rods) oxidase reaction (positive) and a variety of identification kitssystems the most commonly used being API 20E (n=49) API 20NE (n=52) MALDI-TOFBruker (n=36) MALDI-TOFVITEK MS (n=10) and VITEK2 GN (n=68)

Susceptibility testing Aeromonas veronii bv sobria

Most discrepancies occurred in the reporting of Augmentin and the carbapenems for this isolate The CDS susceptibility method acknowledges the presence of chromosomally-linked β-lactamases (A1 and A2) in Aeromonas species5678 A1 is an inducible cephalosporinase which is inhibited by aztreonam but not by clavulanic acid and which hydrolyses cephalosporins and cephamycins but not carbapenems (AmpCBush group 1) It is detected by adjacent disc testing in the CDS method (Figure 3a) A2 is a carbapenemase which hydrolyses carbapenems but not cephalosporins or cephamycins It may show heterogeneous expression of resistance and so resistance to imipenem and meropenem may not be detectable by conventional methods unless a heavy inoculum is used 6789 and inaccurate reporting of sensitivity to carbapenems may ensue(Figure 3b) CDS users should report A veronii bv sobria as resistant to both Augmentin and carbapenems and are directed to Table 104a of the current CDS guidelines For CLSI users standard M45-A2 states that ldquointerpretive breakpoints for cefazolin and for ertapenem imipenem and meropenem for the Enterobacteriaceae were voted to be changed by the Subcommittee on Antimicrobial Susceptibility Testing subsequent to final approval of this edition of M45 It is anticipated that these modified breakpoints will be adopted for use with Aeromonas spp and Vibrio spp in the next edition of M45 or possibly in a future supplementrdquo10 The CLSI standard inoculum equivalent of 05 McFarland would likely fail to detect carbapenem resistance in Aeromonas species

Antibiotic

Aeromonas veronii bv sobria susceptibilities (all methods)

Susc IntRS Res

Amikacin 42 - 1

AmpicillinAmoxycillin - - 146

Augmentin 28 17 98

Cefazolin 9 - 18

Cefepime 21 - 1

Cefotaxime 51 - 2

Cefoxitin 11 - 1

Ceftazidime 82 - 3

Ceftriaxone 75 - 10

Cefuroxime 43 - -

Cephalexin 6 - 7

Cephalothin 9 - 5

Chloramphenicol 15 - -

Ciprofloxacin 213 - 1

Cotrimoxazole 153 2 3

Gentamicin 198 - 1

Imipenem 25 5 26

Levofloxacin 13 - -

Meropenem 40 2 43

Piperacillin 6 - -

Piperacillintazobactam 44 - 15

Sulphafurazole 8 - -

Tetracycline 29 - -

Timentin 5 - 19

Tobramycin 12 - -

Trimethoprim 19 - 1

Table 7 Aeromonas veronii bv sobria

1

1

5

8

30

1

24

3

29

109

36

0 20 40 60 80 100 120

Citrobacter freundii

Aeromonas liquefaciens

Aeromonas hydrophilacaviae

Aeromonas hydrophila group

Aeromonas hydrophila

Aeromonas ichthiosmia

Aeromonas species

Aeromonas veronii

Aeromonas veronii complex

Aeromonas sobria

Aeromonas veronii bv sobria

copy2013 RCPA Quality Assurance Programs Pty Limited 8 Date of issue 13th November 2013

Figure 3a A hydrophilia with cephalosporinase A1 amp carbapenemase A2 copy South Eastern Area Laboratory Services httpwebmedunsweduaucdstest

Figure 3b A sobria with carbapenemase A2 but lacking cephalosporinase A1 copy South Eastern Area Laboratory Services httpwebmedunsweduaucdstest

References Item 3 1 Parker JL and Shaw JG Aeromonas spp clinical microbiology and disease Journal of infection 201162 109-118 httpwwwsciencedirectcomsciencearticlepiiS0163445310003543bbib10 2 Janda JM and Abbott SL The genus Aeromonas taxonomy pathogenicity and infection Clin Microbiol Rev 201023 35ndash73 httpwwwncbinlmnihgovpmcarticlesPMC2806660 3 Horneman AJ and Afsar A Aeromonas Ch 38 In Versalovic J Carroll KC Funke G Jorgensen JH Landry ML WarnockDW(ed) Manual of clinical

microbiology 10th ed ASM Press Washington DC 4 Bullock GL The identification and separation of Aeromonas liquefaciens from Pseudomonas fluorescens and related organisms occurring in dis-

eased fish Appl Microbiol 19619 587ndash590 httpwwwncbinlmnihgovpmcarticlesPMC1057793 5 Antibiotic susceptibility testing by the CDS method httpwebmedunsweduaucdstest 6 Walsh TR et al Distribution and expression of β-lactamase genes among Aeromonas spp Journal of Antimicrobial Chemotherapy 199740 171ndash

178 httpjacoxfordjournalsorgcontent402171fullpdf 7 Wu C-J et al Distribution and phenotypic and genotypic detection of a metallo-b-lactamase CphA among bacteraemic Aeromonas isolates Jour-

nal of Medical Microbiology 201261 712ndash719 httpwwwncbinlmnihgovpubmed22322339 8 Aravena-Romaacuten M et al Antimicrobial susceptibilities of Aeromonas strains isolated from clinical and environmental sources to 26 antimicrobial

agents J Med Microbiol 201261 712-9 httpaacasmorgcontent5621110 9 Rossolini GM et al The Aeromonas metallo-β-lactamases genetics enzymology and contribution to drug resistance Microb Drug Resist 1996 2

245-252 httponlineliebertpubcomdoiabs101089mdr19962245

10 CLSI standard A45-A2 Methods for antimicrobial dilution and disk susceptibility testing for infrequently isolated or fastidious bacteria approved guidelinemdashsecond edition August 2010

copy2013 RCPA Quality Assurance Programs Pty Limited 9 Date of issue 13th November 2013

ITEM 201364ABCD CULTURE AND MICROSCOPY FOR AFB

Reference laboratory report

Culture results C D

Mycobacterium species isolated 59 0

Mycobacterium species not isolated 10 70

Not result reported 2 1

Participant smear results A B

Negative 17 178

1 - 9100 HPF 115 3

10 - 99100 HPF 47 2

1 - 10HPF 4 -

Table 11 Results for mediamethods used for specimen 4C

Table 9 Participant smear results

Table 10 Participant culture results

Table 12 Molecular Diagnostics

Molecular Diagnostics

C D

Mycobacterium TB Complex DNA amplification Positive

13 0

Mycobacterium TB Complex DNA amplification Negative

1 12

No result reported 1 3

Media Total no inoculated

Number positive

BacTALERT amp 3D 9 6

BD BACTEC MGIT 960 System 43 38

BD BBL MGIT 5 3

Brown amp Buckle 3 1

LJ 32 21

LJ Glycerol 6 5

LJ Pyruvate 15 8

LJ Pyruvate Glycerol 4 3

Ogawa 6 2

Other 10 7

Test A B

AFB stain Ziehl Neelsen

Positive 1-9100 HPF

No AFB seen

C D

Culture Bactec MGIT 960 (BD)L-J

Mycobacterium tuberculosis

present

Mycobacterium species absent

Microscopy Results Slides were prepared in this survey using sputum seeded with Mycobacterium tuberculosis H37Ra The sputum used was examined before inoculation with the M tuberculosis strain using a Ziehl-Neelsen stain and tested for M tuberculosis and MAC by molecular methods and found to be negative Smear 4A Slide 4A contained scanty (1-9100HPF) numbers of AFB It was examined by a reference laboratory and a RCPAQAP scientist The three smears examined by the reference laboratory were confirmed positive and contained 4 1 and 3 AFB100HPF Ten randomly selected smears examined by RCPAQAP contained from 4 to 9 AFB100HPF Most laboratories (91 or 92 when transcription errors were included) reported a positive result with the majority (63) reporting 1-9 AFB100 HPF Three transcription errors were apparent among the 17 negative results reported It is recommended these laboratories carefully review their smears Participants are requested to report AFB counts based on acid fast stains rather than on fluorescent stains Smear 4B Smear 4B contained no AFB and this was confirmed by the reference laboratory and 10 smears examined by a RCPAQAP scientist As already mentioned 3 of the 5 laboratories reporting positive results transcribed them in error The other 2 reported positive results in both smears Culture Results Item 4C Sample 4C contained Mycobacterium tuberculosis and organisms representing normal upper respiratory tract flora such as Staphylococcus epidermidis Neisseria subflava and alpha-haemolytic streptococci Of the 69 participants returning a result the majority (86) reported this sample positive Item 4D Sample 4D contained the above upper respiratory organisms only and no Mycobacteria species All participants returning a result reported it negative for Mycobacteria species Molecular Diagnostics Results Fifteen laboratories performed molecular diagnostics for M tuberculosis (14 laboratories returned results on sample 4C and 12 on 4D) Please refer to Table 12 for participant results All methods used are listed below Gene Expert 2 HAIN (MTBDR) 1 HAIN (Mycobacterium CM) 1 Inhouse PCR 3 ProbeTec 2 qPCR 1 Roche Cobas 1 Seegene 1 Taqman 2 Not stated 1

Table 8 4A-D expected results

copy2013 RCPA Quality Assurance Programs Pty Limited 10 Date of issue 13th November 2013

includes presumptive identification(s)

ITEM 201365 ISOLATE FOR IDENTIFICATION

includes presumptive identification(s)

103 475

1 05

72 332

4 18

3 14

2 09

7 32

1 05

1 05

1 05

1 05

1 05

1 05

2 09

1 05

1 05

1 05

14 65

Fig 5b H haemolyticus on HBA copy 2013 RCPA QAP

ITEM 201365 Haemophilus haemolyticus This item contained a pure growth of Haemophilus haemolyticus Homogeneity and stability testing for this organism was satisfactory with bacterial counts for the H haemolyticus remaining above 10 x 1010CFUL throughout the survey

This organism represented an isolate from blood culture collected from a patient with endocarditis H haemolyticus is a human commensal of the nasopharynx in some individuals Some authors find its pathogenicity debatable but it has occasionally been implicated in disease 123 Phenotypically and genotypically it is difficult to distinguish from non-typeable H influenzae except for β-haemolysis on blood agar in the case of H haemolyticus 45678 But even this can be an unreliable characteristic as non-haemolytic strains occur and upon repeated sub-culture this trait may disappear 5910 For this reason it has been suggested that H haemolyticus is more commonly misidentified as H influenzae than is recognised5 Like H influenzae H haemolyticus is a fastidious facultative anaerobe XV-dependent oxidase and catalase positive gram-negative coccobacillus

Fig 5a H haemolyticus on Chocolate Agar copy 2013 RCPA QAP

14

1

1

1

2

1

1

1

1

1

1

7

2

3

4

72

1

103

0 20 40 60 80 100 120

Unable to Identify - Refer

Psychrobacter phenylpyruvicus

Pasteurella species

Other

Kingella kingae

Gram negative rod

Francisella tularensis

Corynebacterium jeikeium

Brucella spp

Bacteroides ureolyticus

Actinobacillus actinomycetemcomitans

Haemophilus species

Haemophilus parainfluenzae

Haemophilus parahaemolyticus

Haemophilus influenzae type B

Haemophilus influenzae

Haemophilus aegyptius

Haemophilus haemolyticus

copy2013 RCPA Quality Assurance Programs Pty Limited 11 Date of issue 13th November 2013

SUMMARY OF PHENOTYPIC AND BIOCHEMICAL RESULTS 811

Phenotypic characteristics

Gram stain Small gram-positive rods and coccobacilli

Motility RT (BHI broth) non-motile

Colonial appearance on Chocolate agar (CA) 24hrs 10mm beige shiny round entire colonies

Colonial appearance on Horse Blood agar (HBA) 24hrs pinpoint translucent shiny round entire colonies

Pigment pale yellow

Haemolysis β (key distinguishing test if apparent) This isolate was haemolytic on HBA

Catalase positive

Oxidase positive

KIA slope NCNC gas negative

Satellitism XV + V - X - Growth conditions

Growth on HBA 35degC in O2 +

Growth on HBA 35degC in CO2 ++

Growth on HBA 35degC in ANO2 +

Growth on CA 35degC 35degC +++

Growth on MacConkey agar no growth Biochemical tests Rapid substrate utilisation

Urease positive

Nitrate positive

Indole negative

Aesculin negative

ADH negative

LDC negative

ODC negative

Glucose positive

Xylose negative

Mannitol negative

Lactose positive (weak) 11

Sucrose negative

Maltose positive (weak) 11 16S rRNA gene analysis by PCR H haemolyticus with a 99 match Although standard genetic testing may be inadequate to distinguish H influenzae and H haemolyticus because of their genetic similarity1012 the demonstration of β-haemolysis on HBA for this isolate supports the PCR findings A few other Haemophilus species are known to display β-haemolysis on blood agar but they are not X and V-dependent 8 Participant results Two hundred and seventeen participants submitted results for this item with 192 (88) correctly identifying to genus level Under half were able to fully speciate The graph on the previous page illustrates participantsrsquo results Some biochemical tests commonly used by participants to identify include catalase (+) oxidase (+) indole (-) urea (+) growth on MacConkey agar (-) and XV-dependency (+) Many participants correctly identifying H haemolyticus observed the β-haemolytic activity of this isolate on blood agar and made note of it in their comments Identification kitssystems used and success rates in the hands of the users are listed below Please note that success rates may have been influenced by the observation (or lack thereof) of β-haemolysis

API NHmdashBiomerieux 1236 (33) correct H influenzae (24)

BBL Crystal-BD NeisseriaHaemophilus ID Kit 22 (100) correct

MALDI-TOF (Bruker ) 423(17) correct Pasteurella species (1) H influenzae (17) gram-negative rod (1)

MALDI-TOF (VITEK MS) 914 (64) correct H influenzae (4) Haemophilus species (1)

Rapid NH 1528 (54) correct Kingella kingae (1) H aegypticus (1) Haemophilus species (2) H influenzae (8) H parainfluenzae (1)

Sequencing 16S rRNA 78 (88) correct H influenzae (1)

VITEK2 GN 56 (83) correct H influenzae (1)

VITEK2 NH 3150 (62) correct Haemophilus species (1) Unable to identify-refer (1) H influenzae (17)

VITEK NHI 45 (80) correct H influenzae (1)

copy2013 RCPA Quality Assurance Programs Pty Limited 12 Date of issue 13th November 2013

References Item 5 1 McCrea KW et al Relationships of nontypeable Haemophilus influenzae strains to hemolytic and nonhemolytic Haemophilus haemolyticus strains J Clin

Microbiol 200846 406ndash416 httpwwwncbinlmnihgovpmcarticlesPMC2238123

2 Jordan IK et al Genome sequences for five strains of the emerging pathogen Haemophilus haemolyticus J Bacteriol 2011193 5879ndash5880

httpwwwncbinlmnihgovpmcarticlesPMC3187195

3 Anderson R et al Haemophilus haemolyticus isolates causing clinical disease J Clin Microbiol 201250 2462-5

httpwwwncbinlmnihgovpubmed22573587

4 Morton DJ et al An invasive Haemophilus haemolyticus isolate J Clin Microbiol 201250 1502ndash1503

httpwwwncbinlmnihgovpmcarticlesPMC3318549

5 Agrawal A Murphy TF Haemophilus influenzae infections in the H influenzae type b conjugate vaccine era J Clin Microbiol 201149 3728ndash3732

httpwwwncbinlmnihgovpmcarticlesPMC3209133

6 Kilian M A taxonomic study of the genus Haemophilus with the proposal of a new species J Gen Microbiol 197693 9ndash62

httpwwwncbinlmnihgovpubmed772168

7 Kilian M 2005 Genus III Haemophilus Winslow Broadhurst Buchanan Krumweide Rogers and Smith 1917 561 p 883ndash904 In Brenner DJ Krieg NR Staley JT (ed) Bergeyrsquos manual of systematic bacteriology 2nd ed vol 2 Springer New York NY

8 Ledeboer NA Doern GV 2012 Haemophilus In Versalovic J Carroll KC Funke G Jorgensen JH Landry ML WarnockDW(ed) Manual of clinical microbiology 10th ed ASM Press Washington DC

9 McCrea KW et al Relationships of nontypeable Haemophilus influenzae strains to hemolytic and nonhemolytic Haemophilus haemolyticus strains J Clin Microbiol 200846 406ndash416 httpwwwncbinlmnihgovpmcarticlesPMC2238123

10 Murphy TF et al Haemophilus haemolyticus a human respiratory tract commensal to be distinguished from Haemophilus influenzae J Infect Dis 2007195 81ndash 89 httpwwwncbinlmnihgovpubmed17152011

11 Identification Reference Laboratory Centre for Infectious Diseases and Microbiology ICPMR Westmead Hospital 12 Binks MJ et al Molecular Surveillance of True Nontypeable Haemophilus influenzae An Evaluation of PCR Screening Assays PLOS

httpwwwplosoneorgarticleinfo3Adoi2F1013712Fjournalpone0034083

13 Duerden B Bennet KW and Faulkner J Isolation of Bacteroides ureolyticus (B corrodens) from clinical infections J Clin Pathol 1982 35 309-312 httpjcpbmjcomcontent353309fullpdf

The most common misidentification by participants was H influenzae (35) because of the phenotypicgenetic similarity of the two species and because of the failure of all kitsidentification systems to differentiate between them Reliance on one type of identification system is discouraged and may lead to incorrect identification of some organisms In this instance β-haemolysis on blood agar facilitated an accurate identification if detected however as already noted it may not always be displayed in this species even in primary cultures H parahaemolyticus reported by three laboratories is also β-haemolytic but unlike H haemolyticus it is V-dependent only (and δ-Aminolevulinic acid (ALA) test negative) as is H parainfluenzae reported by two laboratories which is not β-haemolytic All other false identifications reported do not exhibit X+V dependency or X- or V-dependency The laboratory reporting Corynebacterium jeikeium should note that this is a gram-positive rod B ureolyticus reported by one laboratory is an anaerobic organism with corroding colonies on agar plates 13 Brucella and Francisella tularensis are slow-growing fastidious organisms (also not XV-dependent) that would not be dispatched in this type of QAP

ITEM 201364C CLERICAL ERROR

Clerical Errors reported in Item 201364C Number labs (71)

No error reported 6

Error first name only (correct) in 4C 60(85)

Error first name only in 4D (incorrect) 1

Error first name (correct) + last name (incorrect) 1

Error first name (correct) + unit number (incorrect) 1

Error last name (incorrect) 2

Table 13 Clerical errors reported

Specimen label Karina DANIELS UN 831248 Paperwork Amelia DANIELS UN 831248

The clerical error was placed in item 201364C Mycobacteriology culture As only 95 participants receive 4C and 4D culture vials and only 71 performed testing this clerical error has not been scored

copy2013 RCPA Quality Assurance Programs Pty Limited 13 Date of issue 13th November 2013

ITEM 201367ABC MYCOLOGY

7A This item contained Trichophyton interdigitale [zoophilic] (previously T mentagrophytes) 973 correct to genus level 634 correct to species level (required) The Trichophyton species have undergone extensive reclassification in the last 5 years This is because there exists much phenotypic variation but genetic variation is low Most of the species formerly known as T mentagrophytes are now classified within T interdigitale T mentagrophytes still exists but encompasses only the organism previously known as T quinckeanum (T mentagrophytes var quinckeanum) which is associated with mice T interdigitale is recognised as having two ecological groups the anthropophilic and the zoophilic group with the former T mentagrophytes species falls into the zoophilic group For this item T interdigitale and T mentagrophytes were both marked as correct This newly merged species encompasses a wide range of phenotypes which may or may not be observed for a given specimen Sequencing of the internal transcribed spacer (ITS) region is the gold standard for identification using reference strains that are correctly named according to the revised taxonomy Chen et al have published a useful book chapter with phenotypic descriptions and recommendations for molecular identification of the revised Trichophyton species1

7A Trichophyton interdigitale [zoophilic]

Figures 7A (i-iii) Trichophyton interdigitale [zoophilic group] (previously T mentagrophytes) may have [7A(i)] numerous single-celled microconidia often in dense clusters along with smooth thin-walled cigar-shaped multicelled macroconidia Microconidia are hyaline smooth-walled and are predominantly spherical to subspherical in shape however occasional clavate to pyriform forms may occur [7A(ii)] varying numbers of spherical chlamydoconidia and [7A (iii)] spiral hyphae may also be observed The zoophilic form of the species tends to have powdery-granular colonies on Sabouraudrsquos lactritmel and 1 peptone media while the anthropophilic form has suede-downy textured colonies

1

1

1

1

1

2

2

5

6

7

14

1

31

1

5

20

13

0 5 10 15 20 25 30 35

Chrysosporium tropicum

Microsporum gypseum

Microsporum persicolor

Trichophyton equinum

Trichophyton terrestre

Trichophyton erinacei

Trichophyton verrucosum

Trichophyton species

Trichophyton rubrum [Worldwide population]

Trichophyton tonsurans

Trichophyton rubrum

Trichophyton mentagrophytes complex

Trichophyton mentagrophytes

Trichophyton interdigitale [anthropophilic] and [zoophilic]

Trichophyton interdigitale [anthropophilic]

Trichophyton interdigitale

Trichophyton interdigitale [zoophilic]

13 116

20 179

5 45

1 09

31 277

1 09

14 125

7 63

6 54

5 45

2 18

2 18

1 09

1 09

1 09

1 09

1 09

7A (i)

7A (ii) 7A (iii)

copy2013 RCPA Quality Assurance Programs Pty Limited 14 Date of issue 13th November 2013

7B Cryptococcus neoformans

82 732

8 71

1 09

1 09

5 45

11 98

1 09

1 09

1 09

1 09

7B This item contained Cryptococcus neoformans 964 correct to genus level 812 correct to species level (required) Cryptococcosis is typically caused by either Cryptococcus neoformans or Cryptococcus gattii although occasionally other Cryptococcus species have been implicated C neoformans typically infects the immunocompromised host frequently in the setting of HIV with gt1 million new cases and~600000 deaths per year globally C neoformans is a yeast-like basidiomycete fungus with a distinctive polysaccharide capsule Differentiation from the closely related C gattii is important Presumptive identification is by India Ink stain to highlight the capsule and birdseed agar to observe dark brown colonies

Figure 7B (i-iii) [7B (i)] India Ink stain highlighting the capsule of C neoformansgattii [7B(ii)] Dark brown colonies of C neoformansgattii mixed with white colonies of Candida albicans on birdseed agar [7B(iii)] Canavanine glycine bromothyol blue (CGB) media for distinguishing C neoformans (left) from C gattii (right)

1

1

1

1

11

5

1

1

8

82

0 10 20 30 40 50 60 70 80 90

Unable to identify- refer

Candida (not albicans)

Candida glabrata complex

Candida krusei

Cryptococcus neoformansgattii- unable to speciate

Cryptococcus species

Cryptococcus laurentii

Cryptococcus neoformans var grubii

Cryptococcus neoformans var neoformans

Cryptococcus neoformans

81 of labs correctly reported this isolate as Cryptococcus neoformans While no lab reported C gattii 11 labs were unable to differentiate C neoformans from C gattii Epidemiology risk factors and treatment of infections caused by these species are different and accurate identification is important for effective management All labs should seek to differentiate these species using CGB media a validated molecular method or by referral to a reference laboratory API ID32C and Vitek-2 does not distinguish C neoformans from C gattii These species may be differentiated by a number of DNA-based assays MALDI-ToF and canavanine-glycine-bromothymol blue (CGB) media C neoformans does not grow on CGB media which remains yellow whereas C gattii will grow triggering a blue colour change reaction in the media usually within 3 days It is worth noting that some slow growing C gattii isolates may take as long as 10 days to effect the blue colour change and may initially be mis-identified as C neoformans Nine labs unnecessarily attempted to further identify the C neoformans isolate to variety level either Cn var grubii (serotype A molecular types VNI and VNII) or Cn var neoformans (serotype D molecular type VNIV) It is not clear what methods were used to achieve this varietal identification but 8 of the 9 labs incorrectly reported Cn var neoformans In fact the isolate was confirmed by molecular methods to be Cryptococcus neoformans var grubii molecular type VNI The 8 reports of Cn var neoformans may reflect persistence of the now obsolete classification of Cryptococcus neoformans having two varieties var neoformans and var gattii If it is the normal practice of these labs to report to varietal level it would be worthwhile reviewing methods interpretation and reporting procedures

7B (i) 7B (ii) 7B(iii)

copy2013 RCPA Quality Assurance Programs Pty Limited 15 Date of issue 13th November 2013

Reference item 7

1 Chen SC DH Ellis TC Sorrell and W Meyer Chapter 44 Trichophyton In ldquoMolecular Detection of Human Fungal Pathogensrdquo Dongyou Liu (Ed) CRC Press 2011

All mycology isolates were identified by both conventional and molecular techniques

86 768

9 80

1 09

2 18

3 27

3 27

2 18

1 09

1 09

1 09

1 09

2 18

7C Scedosporium prolificans

This item contained Scedosporium prolificans 875 correct to genus level 768 correct to species level (required) Colonies are rapid growing flat spreading olive-grey to black (the culture may contain a mixture of the colurs depending on the age) and have a suede-like to downy surface texture [7C (i)] Conidia are borne in small groups on distinctive basally swollen flask-shaped annellides which occur singly or in clusters along the vegetative hyphae Conidia are single-celled hyaline to pale-brown ovoid to pyriform 2-5 x 3-13 um (average 34-53 um) in size and have smooth thin walls [7C (ii)] Identification of Scedosporium prolificans to

species level is very important due to its intrinsic resistance to most antifungal drugs It may be distinguished from other members of the genus in particular the human pathogen S apiospermum by its basally swollen (inflated) flask-shaped annellides conidia borne in small groups rather than singly and by not growing on media containing cycloheximide (actidione) DNA sequencing (ITS region) will also definitively identify Scedosporium species Three laboratories reported Sporothrix schenckii which is easily distinguished from Scedosporium spp because it is a dimorphic pathogen with a yeast-like phase when grown at 37degC

2

1

1

1

1

2

3

3

2

1

9

86

0 10 20 30 40 50 60 70 80 90 100

Unable to identify- refer

Chaetomium species

Hortaea werneckii

Ochroconis gallopava

Wangiella species

Exophiala species

Exophiala dermatitidis

Sporothrix schenckii

Scedosporium species

Scedosporium aurantiacum

Scedosporium apiospermum (sensu stricto)

Scedosporium prolificans

7C (i) 7C (ii)

Page 4: FINAL RESULTS AND COMMENTS D6-2013 …dataentry.rcpaqap.com.au/micro/reports/uploadedfiles/fnl2013-6.pdf · FINAL RESULTS AND COMMENTS D6/2013 ... This item contained a pure growth

copy2013 RCPA Quality Assurance Programs Pty Limited 4 Date of issue 13th November 2013

ITEM 201361B

Quality Control This item contained a pure growth of Escherichia coli and passed homogeneity and stability testing with counts remaining above 10 x 1010 CFUL throughout the survey period

Microscopy Homogeneity testing indicated that the white cell count was 10-100 x 106L or gt100 x 106L Both counts have been scored correct The red cell count was 10-100 x 106L There were no epithelial cells added to the sample so lt10 x 106L was the expected result for epithelial cells Ninety five percent reported 10-100 or gt100 x 106L WBC 79 reported 10-100 X 106 RBCL and 98 reported lt10 x 106 epithelial cellsL Comparisons of cell count method versus counts reported are outlined in Table 3

Bacterial counts Two hundred and sixty five participants returned results for this item Where reported 97 reported growth of gt108 CFUL and 99 reported a pure growth

Table 3 Cell counts reported 1B

White1B Red1B Epi1B IQ 200 Manual Omitted U(F) 2000 UF-1 UF-1000(i) Urisys 2400 UX-2000

10-100 10-100 lt10 10 117 8 1 1 4 1 -

gt100 10-100 lt10 4 38 8 - - - - -

10-100 10-100 Not Tested - 2 1 - - - - -

10-100 Not Tested Not Tested 1 1 - - - - - -

gt100 10-100 Not Tested - 1 - - - - - -

10-100 lt10 lt10 - 15 3 - - - - -

10-100 lt10 lt10 - 15 3 - - - - -

gt100 gt100 lt10 - 11 2 - - - - 1

10-100 gt100 lt10 1 8 - - - - -

lt10 lt10 lt10 - 7 1 - - - - -

lt10 10-100 lt10 - 1 1 - - - - -

10-100 10-100 10-100 - 1 - - 1 - -

lt10 10-100 Not Tested - 1 - - - - - -

lt10 Not Tested lt10 - 1 - - - - -

lt10 Not Tested Not Tested - 1 - - - - - -

gt100 lt10 lt10 - 1 - - - - - -

gt100 lt10 10-100 - 1 - - - - - -

gt100 gt100 Not Tested - 1 - - - - - -

gt100 10-100 10-100 - 1 - - - - - -

10-100 lt10 10-100 - 1 - - - - - -

copy2013 RCPA Quality Assurance Programs Pty Limited 5 Date of issue 13th November 2013

IdentificationmdashEscherichia coli

Ninety eight percent of participants correctly reported Escherichia coli for this item The two results of Pmirabilis and the ldquoUnable to identify-referrdquo were transposed results The participant reporting Kpneumoniae used ldquoRapid Onerdquo kit Two other participants used this same kit and reported correctly Eighty five participants reported the use of chromogenic agar Commercial kitssystems were used by 182 participants All kits performed well Thirty five participants used MALDI-TOF with all reporting Ecoli

Ecoli Item 1B Susceptibilities

(all methods)

Antibiotic S IRS R

Amikacin 40 - -

AmpicillinAmoxycillin 233 - 5

Augmentin 217 2 2

Cefaclor 16 - -

Cefazolin 37 - -

Cefepime 12 - -

CefoperzoneSulbactum 1 - -

Cefotaxime 49 - -

Cefoxitin 20 - -

Ceftazidime 54 - -

Ceftriaxone 53 - -

Cefuroxime 56 - -

Cephalexin 93 - 1

Cephalothin 53 3 -

Chloramphenicol 5 - -

Ciprofloxacin 80 - -

Cotrimoxazole 91 - 1

Ertapenem 12 - -

Gentamicin 180 1 -

Imipenem 50 - -

Levofloxacin 13 - -

Meropenem 57 - -

Nalidixic acid 6 - -

Nitrofurantoin 209 - 2

Norfloxacin 133 - 1

Piperacillintazobactam 37 1 -

Polymyxin B 2 - -

Tetracycline 6 - -

Timentin 10 - -

Tobramycin 8 - -

Trimethoprim 191 - 1

Table 4 Escherichia coli susceptibilities (all methods)

1B Escherichia coli

260 981

1 04

2 04

1 04

1 04

1

1

2

1

260

0 50 100 150 200 250 300

Sent to Reference Lab

Unable to Identify - Refer

Proteus mirabilis

Klebsiella pneumoniae

Escherichia coli

Susceptibility testingndash Escherichia coli Susceptibility testing was performed well with the majority of participants reporting susceptible to the commonly reported antibiotics for gram-negative urine isolates

copy2013 RCPA Quality Assurance Programs Pty Limited 6 Date of issue 13th November 2013

ITEM 201362 NOSE SWAB

includes presumptive identifications

ITEM 201362 Nose swab Quality Control This item represented an infection control nose swab containing Methicillin resistant Staphylococcus aureus (MRSA) and Staphylococcus epidermidis Counts for MRSA remained above 10 x 1010 CFUL throughout the survey Homogeneity and stability testing were satisfactory Culture and identification results Two hundred and forty seven participants returned results with 242 (98) reporting MRSA This isolate was a non multi-resistant MRSA (NMRSA) with a susceptibility pattern as follows Resistant to ampicillin Augmentin cefotaxime cefoxitin cephalothin oxacillin and penicillin susceptible to ciprofloxacin clindamycin erythromycin fusidic acid gentamicin rifampicin and tetracycline Many laboratories screened using chromogenic agars Follow up tests included Gram stain (gram-positive cocci) catalase (positive) DNAase (positive) slidetube coagulase (positive) and conventional susceptibility testing or other method to confirm MRSA Staphylococcus aureus agglutination kits used are shown in Table 5 below Identification kitssystems employed are also shown below in Table 6 Most kitssystems accurately identified S aureus Three laboratories reporting S aureus mentioned that it was MRSA in the comments box One of the four laboratories reporting S aureus (only) reported it oxacillin susceptible in the comments box The other three gave no indication of it being or possibly being MRSA

239 968

3 12

4 16

1 04 1

4

3

239

0 50 100 150 200 250 300

Staphylococcus coag negative

Staphylococcus aureus

Staphylococcus aureus (MRSA in comments)

MRSA or Staphylococcus aureus (MRSA)

Most common kits used

Number of users

Biomerieux Slidex Staph 5

Bio-Rad 6

Omega Avipath 2

Oxoid Staphylase 4

Oxoid Staphytect Plus 7

Pastorex Staph Plus 25

Phadebact 9

Prolex Staph 8

Remel BactiStaph 7

Remel Staphaurex (Plus) 20

Table 5 Staphylococcus aureus agglutination kits Table 6 Identification kitssystems

Most common kits used Number of users

API StaphmdashBiomerieux 2

BBL Crystal-BD Gram Positive ID Kit 2

MALDI-TOF Bruker 25

MALDI-TOF VITEK MS 9

Microbact 12S 2

Microscan 1

Phadebact 1

Phoenix 7

RapID Staph Plus 1

SAM-PCR 1

VITEK2 GPmdashBiomerieux 23

copy2013 RCPA Quality Assurance Programs Pty Limited 7 Date of issue 13th November 2013

ITEM 201363 SKIN SWAB

36 146

109 441

29 117

3 12

24 97

1 04

30 121

8 32

5 20

1 04

1 04

Aeromonas veronii biovar sobria (formally A sobria)

ITEM 201363

Quality Control This item contained the pure isolate Aeromonas veronii bv sobria Homogeneity and stability testing were satisfactory with the bacterial count for the A veronii bv sobria remaining above 41 X 109 CFUL during the 3 week survey period Identification

Two hundred and forty seven participants submitted results with 246 (996) reporting an Aeromonas species The most frequently isolated Aeromonas species of clinical significance in humans are A veronii bv sobria A hydrophila and A caviae1 2 A sobria reported by the majority of participants now refers to the organism originally described by Popoff and Veacuteron in 1976 and is primarily a fish pathogen Aldquosobriardquo that are negative for aesculin hydrolysis salicin KCN L-arabinose and ornithine decarboxylase (ODC) and positive for arginine dihydrolase (ADH) should be designated A veronii bv sobria 2 3 A ichthiosmia reported by one laboratory is identical to A veronii bv sobria using gene sequencing2 A liquefaciens (one laboratory) is exclusively a fish pathogen4 Laboratories identified using Gram stain (gram-negative rods) oxidase reaction (positive) and a variety of identification kitssystems the most commonly used being API 20E (n=49) API 20NE (n=52) MALDI-TOFBruker (n=36) MALDI-TOFVITEK MS (n=10) and VITEK2 GN (n=68)

Susceptibility testing Aeromonas veronii bv sobria

Most discrepancies occurred in the reporting of Augmentin and the carbapenems for this isolate The CDS susceptibility method acknowledges the presence of chromosomally-linked β-lactamases (A1 and A2) in Aeromonas species5678 A1 is an inducible cephalosporinase which is inhibited by aztreonam but not by clavulanic acid and which hydrolyses cephalosporins and cephamycins but not carbapenems (AmpCBush group 1) It is detected by adjacent disc testing in the CDS method (Figure 3a) A2 is a carbapenemase which hydrolyses carbapenems but not cephalosporins or cephamycins It may show heterogeneous expression of resistance and so resistance to imipenem and meropenem may not be detectable by conventional methods unless a heavy inoculum is used 6789 and inaccurate reporting of sensitivity to carbapenems may ensue(Figure 3b) CDS users should report A veronii bv sobria as resistant to both Augmentin and carbapenems and are directed to Table 104a of the current CDS guidelines For CLSI users standard M45-A2 states that ldquointerpretive breakpoints for cefazolin and for ertapenem imipenem and meropenem for the Enterobacteriaceae were voted to be changed by the Subcommittee on Antimicrobial Susceptibility Testing subsequent to final approval of this edition of M45 It is anticipated that these modified breakpoints will be adopted for use with Aeromonas spp and Vibrio spp in the next edition of M45 or possibly in a future supplementrdquo10 The CLSI standard inoculum equivalent of 05 McFarland would likely fail to detect carbapenem resistance in Aeromonas species

Antibiotic

Aeromonas veronii bv sobria susceptibilities (all methods)

Susc IntRS Res

Amikacin 42 - 1

AmpicillinAmoxycillin - - 146

Augmentin 28 17 98

Cefazolin 9 - 18

Cefepime 21 - 1

Cefotaxime 51 - 2

Cefoxitin 11 - 1

Ceftazidime 82 - 3

Ceftriaxone 75 - 10

Cefuroxime 43 - -

Cephalexin 6 - 7

Cephalothin 9 - 5

Chloramphenicol 15 - -

Ciprofloxacin 213 - 1

Cotrimoxazole 153 2 3

Gentamicin 198 - 1

Imipenem 25 5 26

Levofloxacin 13 - -

Meropenem 40 2 43

Piperacillin 6 - -

Piperacillintazobactam 44 - 15

Sulphafurazole 8 - -

Tetracycline 29 - -

Timentin 5 - 19

Tobramycin 12 - -

Trimethoprim 19 - 1

Table 7 Aeromonas veronii bv sobria

1

1

5

8

30

1

24

3

29

109

36

0 20 40 60 80 100 120

Citrobacter freundii

Aeromonas liquefaciens

Aeromonas hydrophilacaviae

Aeromonas hydrophila group

Aeromonas hydrophila

Aeromonas ichthiosmia

Aeromonas species

Aeromonas veronii

Aeromonas veronii complex

Aeromonas sobria

Aeromonas veronii bv sobria

copy2013 RCPA Quality Assurance Programs Pty Limited 8 Date of issue 13th November 2013

Figure 3a A hydrophilia with cephalosporinase A1 amp carbapenemase A2 copy South Eastern Area Laboratory Services httpwebmedunsweduaucdstest

Figure 3b A sobria with carbapenemase A2 but lacking cephalosporinase A1 copy South Eastern Area Laboratory Services httpwebmedunsweduaucdstest

References Item 3 1 Parker JL and Shaw JG Aeromonas spp clinical microbiology and disease Journal of infection 201162 109-118 httpwwwsciencedirectcomsciencearticlepiiS0163445310003543bbib10 2 Janda JM and Abbott SL The genus Aeromonas taxonomy pathogenicity and infection Clin Microbiol Rev 201023 35ndash73 httpwwwncbinlmnihgovpmcarticlesPMC2806660 3 Horneman AJ and Afsar A Aeromonas Ch 38 In Versalovic J Carroll KC Funke G Jorgensen JH Landry ML WarnockDW(ed) Manual of clinical

microbiology 10th ed ASM Press Washington DC 4 Bullock GL The identification and separation of Aeromonas liquefaciens from Pseudomonas fluorescens and related organisms occurring in dis-

eased fish Appl Microbiol 19619 587ndash590 httpwwwncbinlmnihgovpmcarticlesPMC1057793 5 Antibiotic susceptibility testing by the CDS method httpwebmedunsweduaucdstest 6 Walsh TR et al Distribution and expression of β-lactamase genes among Aeromonas spp Journal of Antimicrobial Chemotherapy 199740 171ndash

178 httpjacoxfordjournalsorgcontent402171fullpdf 7 Wu C-J et al Distribution and phenotypic and genotypic detection of a metallo-b-lactamase CphA among bacteraemic Aeromonas isolates Jour-

nal of Medical Microbiology 201261 712ndash719 httpwwwncbinlmnihgovpubmed22322339 8 Aravena-Romaacuten M et al Antimicrobial susceptibilities of Aeromonas strains isolated from clinical and environmental sources to 26 antimicrobial

agents J Med Microbiol 201261 712-9 httpaacasmorgcontent5621110 9 Rossolini GM et al The Aeromonas metallo-β-lactamases genetics enzymology and contribution to drug resistance Microb Drug Resist 1996 2

245-252 httponlineliebertpubcomdoiabs101089mdr19962245

10 CLSI standard A45-A2 Methods for antimicrobial dilution and disk susceptibility testing for infrequently isolated or fastidious bacteria approved guidelinemdashsecond edition August 2010

copy2013 RCPA Quality Assurance Programs Pty Limited 9 Date of issue 13th November 2013

ITEM 201364ABCD CULTURE AND MICROSCOPY FOR AFB

Reference laboratory report

Culture results C D

Mycobacterium species isolated 59 0

Mycobacterium species not isolated 10 70

Not result reported 2 1

Participant smear results A B

Negative 17 178

1 - 9100 HPF 115 3

10 - 99100 HPF 47 2

1 - 10HPF 4 -

Table 11 Results for mediamethods used for specimen 4C

Table 9 Participant smear results

Table 10 Participant culture results

Table 12 Molecular Diagnostics

Molecular Diagnostics

C D

Mycobacterium TB Complex DNA amplification Positive

13 0

Mycobacterium TB Complex DNA amplification Negative

1 12

No result reported 1 3

Media Total no inoculated

Number positive

BacTALERT amp 3D 9 6

BD BACTEC MGIT 960 System 43 38

BD BBL MGIT 5 3

Brown amp Buckle 3 1

LJ 32 21

LJ Glycerol 6 5

LJ Pyruvate 15 8

LJ Pyruvate Glycerol 4 3

Ogawa 6 2

Other 10 7

Test A B

AFB stain Ziehl Neelsen

Positive 1-9100 HPF

No AFB seen

C D

Culture Bactec MGIT 960 (BD)L-J

Mycobacterium tuberculosis

present

Mycobacterium species absent

Microscopy Results Slides were prepared in this survey using sputum seeded with Mycobacterium tuberculosis H37Ra The sputum used was examined before inoculation with the M tuberculosis strain using a Ziehl-Neelsen stain and tested for M tuberculosis and MAC by molecular methods and found to be negative Smear 4A Slide 4A contained scanty (1-9100HPF) numbers of AFB It was examined by a reference laboratory and a RCPAQAP scientist The three smears examined by the reference laboratory were confirmed positive and contained 4 1 and 3 AFB100HPF Ten randomly selected smears examined by RCPAQAP contained from 4 to 9 AFB100HPF Most laboratories (91 or 92 when transcription errors were included) reported a positive result with the majority (63) reporting 1-9 AFB100 HPF Three transcription errors were apparent among the 17 negative results reported It is recommended these laboratories carefully review their smears Participants are requested to report AFB counts based on acid fast stains rather than on fluorescent stains Smear 4B Smear 4B contained no AFB and this was confirmed by the reference laboratory and 10 smears examined by a RCPAQAP scientist As already mentioned 3 of the 5 laboratories reporting positive results transcribed them in error The other 2 reported positive results in both smears Culture Results Item 4C Sample 4C contained Mycobacterium tuberculosis and organisms representing normal upper respiratory tract flora such as Staphylococcus epidermidis Neisseria subflava and alpha-haemolytic streptococci Of the 69 participants returning a result the majority (86) reported this sample positive Item 4D Sample 4D contained the above upper respiratory organisms only and no Mycobacteria species All participants returning a result reported it negative for Mycobacteria species Molecular Diagnostics Results Fifteen laboratories performed molecular diagnostics for M tuberculosis (14 laboratories returned results on sample 4C and 12 on 4D) Please refer to Table 12 for participant results All methods used are listed below Gene Expert 2 HAIN (MTBDR) 1 HAIN (Mycobacterium CM) 1 Inhouse PCR 3 ProbeTec 2 qPCR 1 Roche Cobas 1 Seegene 1 Taqman 2 Not stated 1

Table 8 4A-D expected results

copy2013 RCPA Quality Assurance Programs Pty Limited 10 Date of issue 13th November 2013

includes presumptive identification(s)

ITEM 201365 ISOLATE FOR IDENTIFICATION

includes presumptive identification(s)

103 475

1 05

72 332

4 18

3 14

2 09

7 32

1 05

1 05

1 05

1 05

1 05

1 05

2 09

1 05

1 05

1 05

14 65

Fig 5b H haemolyticus on HBA copy 2013 RCPA QAP

ITEM 201365 Haemophilus haemolyticus This item contained a pure growth of Haemophilus haemolyticus Homogeneity and stability testing for this organism was satisfactory with bacterial counts for the H haemolyticus remaining above 10 x 1010CFUL throughout the survey

This organism represented an isolate from blood culture collected from a patient with endocarditis H haemolyticus is a human commensal of the nasopharynx in some individuals Some authors find its pathogenicity debatable but it has occasionally been implicated in disease 123 Phenotypically and genotypically it is difficult to distinguish from non-typeable H influenzae except for β-haemolysis on blood agar in the case of H haemolyticus 45678 But even this can be an unreliable characteristic as non-haemolytic strains occur and upon repeated sub-culture this trait may disappear 5910 For this reason it has been suggested that H haemolyticus is more commonly misidentified as H influenzae than is recognised5 Like H influenzae H haemolyticus is a fastidious facultative anaerobe XV-dependent oxidase and catalase positive gram-negative coccobacillus

Fig 5a H haemolyticus on Chocolate Agar copy 2013 RCPA QAP

14

1

1

1

2

1

1

1

1

1

1

7

2

3

4

72

1

103

0 20 40 60 80 100 120

Unable to Identify - Refer

Psychrobacter phenylpyruvicus

Pasteurella species

Other

Kingella kingae

Gram negative rod

Francisella tularensis

Corynebacterium jeikeium

Brucella spp

Bacteroides ureolyticus

Actinobacillus actinomycetemcomitans

Haemophilus species

Haemophilus parainfluenzae

Haemophilus parahaemolyticus

Haemophilus influenzae type B

Haemophilus influenzae

Haemophilus aegyptius

Haemophilus haemolyticus

copy2013 RCPA Quality Assurance Programs Pty Limited 11 Date of issue 13th November 2013

SUMMARY OF PHENOTYPIC AND BIOCHEMICAL RESULTS 811

Phenotypic characteristics

Gram stain Small gram-positive rods and coccobacilli

Motility RT (BHI broth) non-motile

Colonial appearance on Chocolate agar (CA) 24hrs 10mm beige shiny round entire colonies

Colonial appearance on Horse Blood agar (HBA) 24hrs pinpoint translucent shiny round entire colonies

Pigment pale yellow

Haemolysis β (key distinguishing test if apparent) This isolate was haemolytic on HBA

Catalase positive

Oxidase positive

KIA slope NCNC gas negative

Satellitism XV + V - X - Growth conditions

Growth on HBA 35degC in O2 +

Growth on HBA 35degC in CO2 ++

Growth on HBA 35degC in ANO2 +

Growth on CA 35degC 35degC +++

Growth on MacConkey agar no growth Biochemical tests Rapid substrate utilisation

Urease positive

Nitrate positive

Indole negative

Aesculin negative

ADH negative

LDC negative

ODC negative

Glucose positive

Xylose negative

Mannitol negative

Lactose positive (weak) 11

Sucrose negative

Maltose positive (weak) 11 16S rRNA gene analysis by PCR H haemolyticus with a 99 match Although standard genetic testing may be inadequate to distinguish H influenzae and H haemolyticus because of their genetic similarity1012 the demonstration of β-haemolysis on HBA for this isolate supports the PCR findings A few other Haemophilus species are known to display β-haemolysis on blood agar but they are not X and V-dependent 8 Participant results Two hundred and seventeen participants submitted results for this item with 192 (88) correctly identifying to genus level Under half were able to fully speciate The graph on the previous page illustrates participantsrsquo results Some biochemical tests commonly used by participants to identify include catalase (+) oxidase (+) indole (-) urea (+) growth on MacConkey agar (-) and XV-dependency (+) Many participants correctly identifying H haemolyticus observed the β-haemolytic activity of this isolate on blood agar and made note of it in their comments Identification kitssystems used and success rates in the hands of the users are listed below Please note that success rates may have been influenced by the observation (or lack thereof) of β-haemolysis

API NHmdashBiomerieux 1236 (33) correct H influenzae (24)

BBL Crystal-BD NeisseriaHaemophilus ID Kit 22 (100) correct

MALDI-TOF (Bruker ) 423(17) correct Pasteurella species (1) H influenzae (17) gram-negative rod (1)

MALDI-TOF (VITEK MS) 914 (64) correct H influenzae (4) Haemophilus species (1)

Rapid NH 1528 (54) correct Kingella kingae (1) H aegypticus (1) Haemophilus species (2) H influenzae (8) H parainfluenzae (1)

Sequencing 16S rRNA 78 (88) correct H influenzae (1)

VITEK2 GN 56 (83) correct H influenzae (1)

VITEK2 NH 3150 (62) correct Haemophilus species (1) Unable to identify-refer (1) H influenzae (17)

VITEK NHI 45 (80) correct H influenzae (1)

copy2013 RCPA Quality Assurance Programs Pty Limited 12 Date of issue 13th November 2013

References Item 5 1 McCrea KW et al Relationships of nontypeable Haemophilus influenzae strains to hemolytic and nonhemolytic Haemophilus haemolyticus strains J Clin

Microbiol 200846 406ndash416 httpwwwncbinlmnihgovpmcarticlesPMC2238123

2 Jordan IK et al Genome sequences for five strains of the emerging pathogen Haemophilus haemolyticus J Bacteriol 2011193 5879ndash5880

httpwwwncbinlmnihgovpmcarticlesPMC3187195

3 Anderson R et al Haemophilus haemolyticus isolates causing clinical disease J Clin Microbiol 201250 2462-5

httpwwwncbinlmnihgovpubmed22573587

4 Morton DJ et al An invasive Haemophilus haemolyticus isolate J Clin Microbiol 201250 1502ndash1503

httpwwwncbinlmnihgovpmcarticlesPMC3318549

5 Agrawal A Murphy TF Haemophilus influenzae infections in the H influenzae type b conjugate vaccine era J Clin Microbiol 201149 3728ndash3732

httpwwwncbinlmnihgovpmcarticlesPMC3209133

6 Kilian M A taxonomic study of the genus Haemophilus with the proposal of a new species J Gen Microbiol 197693 9ndash62

httpwwwncbinlmnihgovpubmed772168

7 Kilian M 2005 Genus III Haemophilus Winslow Broadhurst Buchanan Krumweide Rogers and Smith 1917 561 p 883ndash904 In Brenner DJ Krieg NR Staley JT (ed) Bergeyrsquos manual of systematic bacteriology 2nd ed vol 2 Springer New York NY

8 Ledeboer NA Doern GV 2012 Haemophilus In Versalovic J Carroll KC Funke G Jorgensen JH Landry ML WarnockDW(ed) Manual of clinical microbiology 10th ed ASM Press Washington DC

9 McCrea KW et al Relationships of nontypeable Haemophilus influenzae strains to hemolytic and nonhemolytic Haemophilus haemolyticus strains J Clin Microbiol 200846 406ndash416 httpwwwncbinlmnihgovpmcarticlesPMC2238123

10 Murphy TF et al Haemophilus haemolyticus a human respiratory tract commensal to be distinguished from Haemophilus influenzae J Infect Dis 2007195 81ndash 89 httpwwwncbinlmnihgovpubmed17152011

11 Identification Reference Laboratory Centre for Infectious Diseases and Microbiology ICPMR Westmead Hospital 12 Binks MJ et al Molecular Surveillance of True Nontypeable Haemophilus influenzae An Evaluation of PCR Screening Assays PLOS

httpwwwplosoneorgarticleinfo3Adoi2F1013712Fjournalpone0034083

13 Duerden B Bennet KW and Faulkner J Isolation of Bacteroides ureolyticus (B corrodens) from clinical infections J Clin Pathol 1982 35 309-312 httpjcpbmjcomcontent353309fullpdf

The most common misidentification by participants was H influenzae (35) because of the phenotypicgenetic similarity of the two species and because of the failure of all kitsidentification systems to differentiate between them Reliance on one type of identification system is discouraged and may lead to incorrect identification of some organisms In this instance β-haemolysis on blood agar facilitated an accurate identification if detected however as already noted it may not always be displayed in this species even in primary cultures H parahaemolyticus reported by three laboratories is also β-haemolytic but unlike H haemolyticus it is V-dependent only (and δ-Aminolevulinic acid (ALA) test negative) as is H parainfluenzae reported by two laboratories which is not β-haemolytic All other false identifications reported do not exhibit X+V dependency or X- or V-dependency The laboratory reporting Corynebacterium jeikeium should note that this is a gram-positive rod B ureolyticus reported by one laboratory is an anaerobic organism with corroding colonies on agar plates 13 Brucella and Francisella tularensis are slow-growing fastidious organisms (also not XV-dependent) that would not be dispatched in this type of QAP

ITEM 201364C CLERICAL ERROR

Clerical Errors reported in Item 201364C Number labs (71)

No error reported 6

Error first name only (correct) in 4C 60(85)

Error first name only in 4D (incorrect) 1

Error first name (correct) + last name (incorrect) 1

Error first name (correct) + unit number (incorrect) 1

Error last name (incorrect) 2

Table 13 Clerical errors reported

Specimen label Karina DANIELS UN 831248 Paperwork Amelia DANIELS UN 831248

The clerical error was placed in item 201364C Mycobacteriology culture As only 95 participants receive 4C and 4D culture vials and only 71 performed testing this clerical error has not been scored

copy2013 RCPA Quality Assurance Programs Pty Limited 13 Date of issue 13th November 2013

ITEM 201367ABC MYCOLOGY

7A This item contained Trichophyton interdigitale [zoophilic] (previously T mentagrophytes) 973 correct to genus level 634 correct to species level (required) The Trichophyton species have undergone extensive reclassification in the last 5 years This is because there exists much phenotypic variation but genetic variation is low Most of the species formerly known as T mentagrophytes are now classified within T interdigitale T mentagrophytes still exists but encompasses only the organism previously known as T quinckeanum (T mentagrophytes var quinckeanum) which is associated with mice T interdigitale is recognised as having two ecological groups the anthropophilic and the zoophilic group with the former T mentagrophytes species falls into the zoophilic group For this item T interdigitale and T mentagrophytes were both marked as correct This newly merged species encompasses a wide range of phenotypes which may or may not be observed for a given specimen Sequencing of the internal transcribed spacer (ITS) region is the gold standard for identification using reference strains that are correctly named according to the revised taxonomy Chen et al have published a useful book chapter with phenotypic descriptions and recommendations for molecular identification of the revised Trichophyton species1

7A Trichophyton interdigitale [zoophilic]

Figures 7A (i-iii) Trichophyton interdigitale [zoophilic group] (previously T mentagrophytes) may have [7A(i)] numerous single-celled microconidia often in dense clusters along with smooth thin-walled cigar-shaped multicelled macroconidia Microconidia are hyaline smooth-walled and are predominantly spherical to subspherical in shape however occasional clavate to pyriform forms may occur [7A(ii)] varying numbers of spherical chlamydoconidia and [7A (iii)] spiral hyphae may also be observed The zoophilic form of the species tends to have powdery-granular colonies on Sabouraudrsquos lactritmel and 1 peptone media while the anthropophilic form has suede-downy textured colonies

1

1

1

1

1

2

2

5

6

7

14

1

31

1

5

20

13

0 5 10 15 20 25 30 35

Chrysosporium tropicum

Microsporum gypseum

Microsporum persicolor

Trichophyton equinum

Trichophyton terrestre

Trichophyton erinacei

Trichophyton verrucosum

Trichophyton species

Trichophyton rubrum [Worldwide population]

Trichophyton tonsurans

Trichophyton rubrum

Trichophyton mentagrophytes complex

Trichophyton mentagrophytes

Trichophyton interdigitale [anthropophilic] and [zoophilic]

Trichophyton interdigitale [anthropophilic]

Trichophyton interdigitale

Trichophyton interdigitale [zoophilic]

13 116

20 179

5 45

1 09

31 277

1 09

14 125

7 63

6 54

5 45

2 18

2 18

1 09

1 09

1 09

1 09

1 09

7A (i)

7A (ii) 7A (iii)

copy2013 RCPA Quality Assurance Programs Pty Limited 14 Date of issue 13th November 2013

7B Cryptococcus neoformans

82 732

8 71

1 09

1 09

5 45

11 98

1 09

1 09

1 09

1 09

7B This item contained Cryptococcus neoformans 964 correct to genus level 812 correct to species level (required) Cryptococcosis is typically caused by either Cryptococcus neoformans or Cryptococcus gattii although occasionally other Cryptococcus species have been implicated C neoformans typically infects the immunocompromised host frequently in the setting of HIV with gt1 million new cases and~600000 deaths per year globally C neoformans is a yeast-like basidiomycete fungus with a distinctive polysaccharide capsule Differentiation from the closely related C gattii is important Presumptive identification is by India Ink stain to highlight the capsule and birdseed agar to observe dark brown colonies

Figure 7B (i-iii) [7B (i)] India Ink stain highlighting the capsule of C neoformansgattii [7B(ii)] Dark brown colonies of C neoformansgattii mixed with white colonies of Candida albicans on birdseed agar [7B(iii)] Canavanine glycine bromothyol blue (CGB) media for distinguishing C neoformans (left) from C gattii (right)

1

1

1

1

11

5

1

1

8

82

0 10 20 30 40 50 60 70 80 90

Unable to identify- refer

Candida (not albicans)

Candida glabrata complex

Candida krusei

Cryptococcus neoformansgattii- unable to speciate

Cryptococcus species

Cryptococcus laurentii

Cryptococcus neoformans var grubii

Cryptococcus neoformans var neoformans

Cryptococcus neoformans

81 of labs correctly reported this isolate as Cryptococcus neoformans While no lab reported C gattii 11 labs were unable to differentiate C neoformans from C gattii Epidemiology risk factors and treatment of infections caused by these species are different and accurate identification is important for effective management All labs should seek to differentiate these species using CGB media a validated molecular method or by referral to a reference laboratory API ID32C and Vitek-2 does not distinguish C neoformans from C gattii These species may be differentiated by a number of DNA-based assays MALDI-ToF and canavanine-glycine-bromothymol blue (CGB) media C neoformans does not grow on CGB media which remains yellow whereas C gattii will grow triggering a blue colour change reaction in the media usually within 3 days It is worth noting that some slow growing C gattii isolates may take as long as 10 days to effect the blue colour change and may initially be mis-identified as C neoformans Nine labs unnecessarily attempted to further identify the C neoformans isolate to variety level either Cn var grubii (serotype A molecular types VNI and VNII) or Cn var neoformans (serotype D molecular type VNIV) It is not clear what methods were used to achieve this varietal identification but 8 of the 9 labs incorrectly reported Cn var neoformans In fact the isolate was confirmed by molecular methods to be Cryptococcus neoformans var grubii molecular type VNI The 8 reports of Cn var neoformans may reflect persistence of the now obsolete classification of Cryptococcus neoformans having two varieties var neoformans and var gattii If it is the normal practice of these labs to report to varietal level it would be worthwhile reviewing methods interpretation and reporting procedures

7B (i) 7B (ii) 7B(iii)

copy2013 RCPA Quality Assurance Programs Pty Limited 15 Date of issue 13th November 2013

Reference item 7

1 Chen SC DH Ellis TC Sorrell and W Meyer Chapter 44 Trichophyton In ldquoMolecular Detection of Human Fungal Pathogensrdquo Dongyou Liu (Ed) CRC Press 2011

All mycology isolates were identified by both conventional and molecular techniques

86 768

9 80

1 09

2 18

3 27

3 27

2 18

1 09

1 09

1 09

1 09

2 18

7C Scedosporium prolificans

This item contained Scedosporium prolificans 875 correct to genus level 768 correct to species level (required) Colonies are rapid growing flat spreading olive-grey to black (the culture may contain a mixture of the colurs depending on the age) and have a suede-like to downy surface texture [7C (i)] Conidia are borne in small groups on distinctive basally swollen flask-shaped annellides which occur singly or in clusters along the vegetative hyphae Conidia are single-celled hyaline to pale-brown ovoid to pyriform 2-5 x 3-13 um (average 34-53 um) in size and have smooth thin walls [7C (ii)] Identification of Scedosporium prolificans to

species level is very important due to its intrinsic resistance to most antifungal drugs It may be distinguished from other members of the genus in particular the human pathogen S apiospermum by its basally swollen (inflated) flask-shaped annellides conidia borne in small groups rather than singly and by not growing on media containing cycloheximide (actidione) DNA sequencing (ITS region) will also definitively identify Scedosporium species Three laboratories reported Sporothrix schenckii which is easily distinguished from Scedosporium spp because it is a dimorphic pathogen with a yeast-like phase when grown at 37degC

2

1

1

1

1

2

3

3

2

1

9

86

0 10 20 30 40 50 60 70 80 90 100

Unable to identify- refer

Chaetomium species

Hortaea werneckii

Ochroconis gallopava

Wangiella species

Exophiala species

Exophiala dermatitidis

Sporothrix schenckii

Scedosporium species

Scedosporium aurantiacum

Scedosporium apiospermum (sensu stricto)

Scedosporium prolificans

7C (i) 7C (ii)

Page 5: FINAL RESULTS AND COMMENTS D6-2013 …dataentry.rcpaqap.com.au/micro/reports/uploadedfiles/fnl2013-6.pdf · FINAL RESULTS AND COMMENTS D6/2013 ... This item contained a pure growth

copy2013 RCPA Quality Assurance Programs Pty Limited 5 Date of issue 13th November 2013

IdentificationmdashEscherichia coli

Ninety eight percent of participants correctly reported Escherichia coli for this item The two results of Pmirabilis and the ldquoUnable to identify-referrdquo were transposed results The participant reporting Kpneumoniae used ldquoRapid Onerdquo kit Two other participants used this same kit and reported correctly Eighty five participants reported the use of chromogenic agar Commercial kitssystems were used by 182 participants All kits performed well Thirty five participants used MALDI-TOF with all reporting Ecoli

Ecoli Item 1B Susceptibilities

(all methods)

Antibiotic S IRS R

Amikacin 40 - -

AmpicillinAmoxycillin 233 - 5

Augmentin 217 2 2

Cefaclor 16 - -

Cefazolin 37 - -

Cefepime 12 - -

CefoperzoneSulbactum 1 - -

Cefotaxime 49 - -

Cefoxitin 20 - -

Ceftazidime 54 - -

Ceftriaxone 53 - -

Cefuroxime 56 - -

Cephalexin 93 - 1

Cephalothin 53 3 -

Chloramphenicol 5 - -

Ciprofloxacin 80 - -

Cotrimoxazole 91 - 1

Ertapenem 12 - -

Gentamicin 180 1 -

Imipenem 50 - -

Levofloxacin 13 - -

Meropenem 57 - -

Nalidixic acid 6 - -

Nitrofurantoin 209 - 2

Norfloxacin 133 - 1

Piperacillintazobactam 37 1 -

Polymyxin B 2 - -

Tetracycline 6 - -

Timentin 10 - -

Tobramycin 8 - -

Trimethoprim 191 - 1

Table 4 Escherichia coli susceptibilities (all methods)

1B Escherichia coli

260 981

1 04

2 04

1 04

1 04

1

1

2

1

260

0 50 100 150 200 250 300

Sent to Reference Lab

Unable to Identify - Refer

Proteus mirabilis

Klebsiella pneumoniae

Escherichia coli

Susceptibility testingndash Escherichia coli Susceptibility testing was performed well with the majority of participants reporting susceptible to the commonly reported antibiotics for gram-negative urine isolates

copy2013 RCPA Quality Assurance Programs Pty Limited 6 Date of issue 13th November 2013

ITEM 201362 NOSE SWAB

includes presumptive identifications

ITEM 201362 Nose swab Quality Control This item represented an infection control nose swab containing Methicillin resistant Staphylococcus aureus (MRSA) and Staphylococcus epidermidis Counts for MRSA remained above 10 x 1010 CFUL throughout the survey Homogeneity and stability testing were satisfactory Culture and identification results Two hundred and forty seven participants returned results with 242 (98) reporting MRSA This isolate was a non multi-resistant MRSA (NMRSA) with a susceptibility pattern as follows Resistant to ampicillin Augmentin cefotaxime cefoxitin cephalothin oxacillin and penicillin susceptible to ciprofloxacin clindamycin erythromycin fusidic acid gentamicin rifampicin and tetracycline Many laboratories screened using chromogenic agars Follow up tests included Gram stain (gram-positive cocci) catalase (positive) DNAase (positive) slidetube coagulase (positive) and conventional susceptibility testing or other method to confirm MRSA Staphylococcus aureus agglutination kits used are shown in Table 5 below Identification kitssystems employed are also shown below in Table 6 Most kitssystems accurately identified S aureus Three laboratories reporting S aureus mentioned that it was MRSA in the comments box One of the four laboratories reporting S aureus (only) reported it oxacillin susceptible in the comments box The other three gave no indication of it being or possibly being MRSA

239 968

3 12

4 16

1 04 1

4

3

239

0 50 100 150 200 250 300

Staphylococcus coag negative

Staphylococcus aureus

Staphylococcus aureus (MRSA in comments)

MRSA or Staphylococcus aureus (MRSA)

Most common kits used

Number of users

Biomerieux Slidex Staph 5

Bio-Rad 6

Omega Avipath 2

Oxoid Staphylase 4

Oxoid Staphytect Plus 7

Pastorex Staph Plus 25

Phadebact 9

Prolex Staph 8

Remel BactiStaph 7

Remel Staphaurex (Plus) 20

Table 5 Staphylococcus aureus agglutination kits Table 6 Identification kitssystems

Most common kits used Number of users

API StaphmdashBiomerieux 2

BBL Crystal-BD Gram Positive ID Kit 2

MALDI-TOF Bruker 25

MALDI-TOF VITEK MS 9

Microbact 12S 2

Microscan 1

Phadebact 1

Phoenix 7

RapID Staph Plus 1

SAM-PCR 1

VITEK2 GPmdashBiomerieux 23

copy2013 RCPA Quality Assurance Programs Pty Limited 7 Date of issue 13th November 2013

ITEM 201363 SKIN SWAB

36 146

109 441

29 117

3 12

24 97

1 04

30 121

8 32

5 20

1 04

1 04

Aeromonas veronii biovar sobria (formally A sobria)

ITEM 201363

Quality Control This item contained the pure isolate Aeromonas veronii bv sobria Homogeneity and stability testing were satisfactory with the bacterial count for the A veronii bv sobria remaining above 41 X 109 CFUL during the 3 week survey period Identification

Two hundred and forty seven participants submitted results with 246 (996) reporting an Aeromonas species The most frequently isolated Aeromonas species of clinical significance in humans are A veronii bv sobria A hydrophila and A caviae1 2 A sobria reported by the majority of participants now refers to the organism originally described by Popoff and Veacuteron in 1976 and is primarily a fish pathogen Aldquosobriardquo that are negative for aesculin hydrolysis salicin KCN L-arabinose and ornithine decarboxylase (ODC) and positive for arginine dihydrolase (ADH) should be designated A veronii bv sobria 2 3 A ichthiosmia reported by one laboratory is identical to A veronii bv sobria using gene sequencing2 A liquefaciens (one laboratory) is exclusively a fish pathogen4 Laboratories identified using Gram stain (gram-negative rods) oxidase reaction (positive) and a variety of identification kitssystems the most commonly used being API 20E (n=49) API 20NE (n=52) MALDI-TOFBruker (n=36) MALDI-TOFVITEK MS (n=10) and VITEK2 GN (n=68)

Susceptibility testing Aeromonas veronii bv sobria

Most discrepancies occurred in the reporting of Augmentin and the carbapenems for this isolate The CDS susceptibility method acknowledges the presence of chromosomally-linked β-lactamases (A1 and A2) in Aeromonas species5678 A1 is an inducible cephalosporinase which is inhibited by aztreonam but not by clavulanic acid and which hydrolyses cephalosporins and cephamycins but not carbapenems (AmpCBush group 1) It is detected by adjacent disc testing in the CDS method (Figure 3a) A2 is a carbapenemase which hydrolyses carbapenems but not cephalosporins or cephamycins It may show heterogeneous expression of resistance and so resistance to imipenem and meropenem may not be detectable by conventional methods unless a heavy inoculum is used 6789 and inaccurate reporting of sensitivity to carbapenems may ensue(Figure 3b) CDS users should report A veronii bv sobria as resistant to both Augmentin and carbapenems and are directed to Table 104a of the current CDS guidelines For CLSI users standard M45-A2 states that ldquointerpretive breakpoints for cefazolin and for ertapenem imipenem and meropenem for the Enterobacteriaceae were voted to be changed by the Subcommittee on Antimicrobial Susceptibility Testing subsequent to final approval of this edition of M45 It is anticipated that these modified breakpoints will be adopted for use with Aeromonas spp and Vibrio spp in the next edition of M45 or possibly in a future supplementrdquo10 The CLSI standard inoculum equivalent of 05 McFarland would likely fail to detect carbapenem resistance in Aeromonas species

Antibiotic

Aeromonas veronii bv sobria susceptibilities (all methods)

Susc IntRS Res

Amikacin 42 - 1

AmpicillinAmoxycillin - - 146

Augmentin 28 17 98

Cefazolin 9 - 18

Cefepime 21 - 1

Cefotaxime 51 - 2

Cefoxitin 11 - 1

Ceftazidime 82 - 3

Ceftriaxone 75 - 10

Cefuroxime 43 - -

Cephalexin 6 - 7

Cephalothin 9 - 5

Chloramphenicol 15 - -

Ciprofloxacin 213 - 1

Cotrimoxazole 153 2 3

Gentamicin 198 - 1

Imipenem 25 5 26

Levofloxacin 13 - -

Meropenem 40 2 43

Piperacillin 6 - -

Piperacillintazobactam 44 - 15

Sulphafurazole 8 - -

Tetracycline 29 - -

Timentin 5 - 19

Tobramycin 12 - -

Trimethoprim 19 - 1

Table 7 Aeromonas veronii bv sobria

1

1

5

8

30

1

24

3

29

109

36

0 20 40 60 80 100 120

Citrobacter freundii

Aeromonas liquefaciens

Aeromonas hydrophilacaviae

Aeromonas hydrophila group

Aeromonas hydrophila

Aeromonas ichthiosmia

Aeromonas species

Aeromonas veronii

Aeromonas veronii complex

Aeromonas sobria

Aeromonas veronii bv sobria

copy2013 RCPA Quality Assurance Programs Pty Limited 8 Date of issue 13th November 2013

Figure 3a A hydrophilia with cephalosporinase A1 amp carbapenemase A2 copy South Eastern Area Laboratory Services httpwebmedunsweduaucdstest

Figure 3b A sobria with carbapenemase A2 but lacking cephalosporinase A1 copy South Eastern Area Laboratory Services httpwebmedunsweduaucdstest

References Item 3 1 Parker JL and Shaw JG Aeromonas spp clinical microbiology and disease Journal of infection 201162 109-118 httpwwwsciencedirectcomsciencearticlepiiS0163445310003543bbib10 2 Janda JM and Abbott SL The genus Aeromonas taxonomy pathogenicity and infection Clin Microbiol Rev 201023 35ndash73 httpwwwncbinlmnihgovpmcarticlesPMC2806660 3 Horneman AJ and Afsar A Aeromonas Ch 38 In Versalovic J Carroll KC Funke G Jorgensen JH Landry ML WarnockDW(ed) Manual of clinical

microbiology 10th ed ASM Press Washington DC 4 Bullock GL The identification and separation of Aeromonas liquefaciens from Pseudomonas fluorescens and related organisms occurring in dis-

eased fish Appl Microbiol 19619 587ndash590 httpwwwncbinlmnihgovpmcarticlesPMC1057793 5 Antibiotic susceptibility testing by the CDS method httpwebmedunsweduaucdstest 6 Walsh TR et al Distribution and expression of β-lactamase genes among Aeromonas spp Journal of Antimicrobial Chemotherapy 199740 171ndash

178 httpjacoxfordjournalsorgcontent402171fullpdf 7 Wu C-J et al Distribution and phenotypic and genotypic detection of a metallo-b-lactamase CphA among bacteraemic Aeromonas isolates Jour-

nal of Medical Microbiology 201261 712ndash719 httpwwwncbinlmnihgovpubmed22322339 8 Aravena-Romaacuten M et al Antimicrobial susceptibilities of Aeromonas strains isolated from clinical and environmental sources to 26 antimicrobial

agents J Med Microbiol 201261 712-9 httpaacasmorgcontent5621110 9 Rossolini GM et al The Aeromonas metallo-β-lactamases genetics enzymology and contribution to drug resistance Microb Drug Resist 1996 2

245-252 httponlineliebertpubcomdoiabs101089mdr19962245

10 CLSI standard A45-A2 Methods for antimicrobial dilution and disk susceptibility testing for infrequently isolated or fastidious bacteria approved guidelinemdashsecond edition August 2010

copy2013 RCPA Quality Assurance Programs Pty Limited 9 Date of issue 13th November 2013

ITEM 201364ABCD CULTURE AND MICROSCOPY FOR AFB

Reference laboratory report

Culture results C D

Mycobacterium species isolated 59 0

Mycobacterium species not isolated 10 70

Not result reported 2 1

Participant smear results A B

Negative 17 178

1 - 9100 HPF 115 3

10 - 99100 HPF 47 2

1 - 10HPF 4 -

Table 11 Results for mediamethods used for specimen 4C

Table 9 Participant smear results

Table 10 Participant culture results

Table 12 Molecular Diagnostics

Molecular Diagnostics

C D

Mycobacterium TB Complex DNA amplification Positive

13 0

Mycobacterium TB Complex DNA amplification Negative

1 12

No result reported 1 3

Media Total no inoculated

Number positive

BacTALERT amp 3D 9 6

BD BACTEC MGIT 960 System 43 38

BD BBL MGIT 5 3

Brown amp Buckle 3 1

LJ 32 21

LJ Glycerol 6 5

LJ Pyruvate 15 8

LJ Pyruvate Glycerol 4 3

Ogawa 6 2

Other 10 7

Test A B

AFB stain Ziehl Neelsen

Positive 1-9100 HPF

No AFB seen

C D

Culture Bactec MGIT 960 (BD)L-J

Mycobacterium tuberculosis

present

Mycobacterium species absent

Microscopy Results Slides were prepared in this survey using sputum seeded with Mycobacterium tuberculosis H37Ra The sputum used was examined before inoculation with the M tuberculosis strain using a Ziehl-Neelsen stain and tested for M tuberculosis and MAC by molecular methods and found to be negative Smear 4A Slide 4A contained scanty (1-9100HPF) numbers of AFB It was examined by a reference laboratory and a RCPAQAP scientist The three smears examined by the reference laboratory were confirmed positive and contained 4 1 and 3 AFB100HPF Ten randomly selected smears examined by RCPAQAP contained from 4 to 9 AFB100HPF Most laboratories (91 or 92 when transcription errors were included) reported a positive result with the majority (63) reporting 1-9 AFB100 HPF Three transcription errors were apparent among the 17 negative results reported It is recommended these laboratories carefully review their smears Participants are requested to report AFB counts based on acid fast stains rather than on fluorescent stains Smear 4B Smear 4B contained no AFB and this was confirmed by the reference laboratory and 10 smears examined by a RCPAQAP scientist As already mentioned 3 of the 5 laboratories reporting positive results transcribed them in error The other 2 reported positive results in both smears Culture Results Item 4C Sample 4C contained Mycobacterium tuberculosis and organisms representing normal upper respiratory tract flora such as Staphylococcus epidermidis Neisseria subflava and alpha-haemolytic streptococci Of the 69 participants returning a result the majority (86) reported this sample positive Item 4D Sample 4D contained the above upper respiratory organisms only and no Mycobacteria species All participants returning a result reported it negative for Mycobacteria species Molecular Diagnostics Results Fifteen laboratories performed molecular diagnostics for M tuberculosis (14 laboratories returned results on sample 4C and 12 on 4D) Please refer to Table 12 for participant results All methods used are listed below Gene Expert 2 HAIN (MTBDR) 1 HAIN (Mycobacterium CM) 1 Inhouse PCR 3 ProbeTec 2 qPCR 1 Roche Cobas 1 Seegene 1 Taqman 2 Not stated 1

Table 8 4A-D expected results

copy2013 RCPA Quality Assurance Programs Pty Limited 10 Date of issue 13th November 2013

includes presumptive identification(s)

ITEM 201365 ISOLATE FOR IDENTIFICATION

includes presumptive identification(s)

103 475

1 05

72 332

4 18

3 14

2 09

7 32

1 05

1 05

1 05

1 05

1 05

1 05

2 09

1 05

1 05

1 05

14 65

Fig 5b H haemolyticus on HBA copy 2013 RCPA QAP

ITEM 201365 Haemophilus haemolyticus This item contained a pure growth of Haemophilus haemolyticus Homogeneity and stability testing for this organism was satisfactory with bacterial counts for the H haemolyticus remaining above 10 x 1010CFUL throughout the survey

This organism represented an isolate from blood culture collected from a patient with endocarditis H haemolyticus is a human commensal of the nasopharynx in some individuals Some authors find its pathogenicity debatable but it has occasionally been implicated in disease 123 Phenotypically and genotypically it is difficult to distinguish from non-typeable H influenzae except for β-haemolysis on blood agar in the case of H haemolyticus 45678 But even this can be an unreliable characteristic as non-haemolytic strains occur and upon repeated sub-culture this trait may disappear 5910 For this reason it has been suggested that H haemolyticus is more commonly misidentified as H influenzae than is recognised5 Like H influenzae H haemolyticus is a fastidious facultative anaerobe XV-dependent oxidase and catalase positive gram-negative coccobacillus

Fig 5a H haemolyticus on Chocolate Agar copy 2013 RCPA QAP

14

1

1

1

2

1

1

1

1

1

1

7

2

3

4

72

1

103

0 20 40 60 80 100 120

Unable to Identify - Refer

Psychrobacter phenylpyruvicus

Pasteurella species

Other

Kingella kingae

Gram negative rod

Francisella tularensis

Corynebacterium jeikeium

Brucella spp

Bacteroides ureolyticus

Actinobacillus actinomycetemcomitans

Haemophilus species

Haemophilus parainfluenzae

Haemophilus parahaemolyticus

Haemophilus influenzae type B

Haemophilus influenzae

Haemophilus aegyptius

Haemophilus haemolyticus

copy2013 RCPA Quality Assurance Programs Pty Limited 11 Date of issue 13th November 2013

SUMMARY OF PHENOTYPIC AND BIOCHEMICAL RESULTS 811

Phenotypic characteristics

Gram stain Small gram-positive rods and coccobacilli

Motility RT (BHI broth) non-motile

Colonial appearance on Chocolate agar (CA) 24hrs 10mm beige shiny round entire colonies

Colonial appearance on Horse Blood agar (HBA) 24hrs pinpoint translucent shiny round entire colonies

Pigment pale yellow

Haemolysis β (key distinguishing test if apparent) This isolate was haemolytic on HBA

Catalase positive

Oxidase positive

KIA slope NCNC gas negative

Satellitism XV + V - X - Growth conditions

Growth on HBA 35degC in O2 +

Growth on HBA 35degC in CO2 ++

Growth on HBA 35degC in ANO2 +

Growth on CA 35degC 35degC +++

Growth on MacConkey agar no growth Biochemical tests Rapid substrate utilisation

Urease positive

Nitrate positive

Indole negative

Aesculin negative

ADH negative

LDC negative

ODC negative

Glucose positive

Xylose negative

Mannitol negative

Lactose positive (weak) 11

Sucrose negative

Maltose positive (weak) 11 16S rRNA gene analysis by PCR H haemolyticus with a 99 match Although standard genetic testing may be inadequate to distinguish H influenzae and H haemolyticus because of their genetic similarity1012 the demonstration of β-haemolysis on HBA for this isolate supports the PCR findings A few other Haemophilus species are known to display β-haemolysis on blood agar but they are not X and V-dependent 8 Participant results Two hundred and seventeen participants submitted results for this item with 192 (88) correctly identifying to genus level Under half were able to fully speciate The graph on the previous page illustrates participantsrsquo results Some biochemical tests commonly used by participants to identify include catalase (+) oxidase (+) indole (-) urea (+) growth on MacConkey agar (-) and XV-dependency (+) Many participants correctly identifying H haemolyticus observed the β-haemolytic activity of this isolate on blood agar and made note of it in their comments Identification kitssystems used and success rates in the hands of the users are listed below Please note that success rates may have been influenced by the observation (or lack thereof) of β-haemolysis

API NHmdashBiomerieux 1236 (33) correct H influenzae (24)

BBL Crystal-BD NeisseriaHaemophilus ID Kit 22 (100) correct

MALDI-TOF (Bruker ) 423(17) correct Pasteurella species (1) H influenzae (17) gram-negative rod (1)

MALDI-TOF (VITEK MS) 914 (64) correct H influenzae (4) Haemophilus species (1)

Rapid NH 1528 (54) correct Kingella kingae (1) H aegypticus (1) Haemophilus species (2) H influenzae (8) H parainfluenzae (1)

Sequencing 16S rRNA 78 (88) correct H influenzae (1)

VITEK2 GN 56 (83) correct H influenzae (1)

VITEK2 NH 3150 (62) correct Haemophilus species (1) Unable to identify-refer (1) H influenzae (17)

VITEK NHI 45 (80) correct H influenzae (1)

copy2013 RCPA Quality Assurance Programs Pty Limited 12 Date of issue 13th November 2013

References Item 5 1 McCrea KW et al Relationships of nontypeable Haemophilus influenzae strains to hemolytic and nonhemolytic Haemophilus haemolyticus strains J Clin

Microbiol 200846 406ndash416 httpwwwncbinlmnihgovpmcarticlesPMC2238123

2 Jordan IK et al Genome sequences for five strains of the emerging pathogen Haemophilus haemolyticus J Bacteriol 2011193 5879ndash5880

httpwwwncbinlmnihgovpmcarticlesPMC3187195

3 Anderson R et al Haemophilus haemolyticus isolates causing clinical disease J Clin Microbiol 201250 2462-5

httpwwwncbinlmnihgovpubmed22573587

4 Morton DJ et al An invasive Haemophilus haemolyticus isolate J Clin Microbiol 201250 1502ndash1503

httpwwwncbinlmnihgovpmcarticlesPMC3318549

5 Agrawal A Murphy TF Haemophilus influenzae infections in the H influenzae type b conjugate vaccine era J Clin Microbiol 201149 3728ndash3732

httpwwwncbinlmnihgovpmcarticlesPMC3209133

6 Kilian M A taxonomic study of the genus Haemophilus with the proposal of a new species J Gen Microbiol 197693 9ndash62

httpwwwncbinlmnihgovpubmed772168

7 Kilian M 2005 Genus III Haemophilus Winslow Broadhurst Buchanan Krumweide Rogers and Smith 1917 561 p 883ndash904 In Brenner DJ Krieg NR Staley JT (ed) Bergeyrsquos manual of systematic bacteriology 2nd ed vol 2 Springer New York NY

8 Ledeboer NA Doern GV 2012 Haemophilus In Versalovic J Carroll KC Funke G Jorgensen JH Landry ML WarnockDW(ed) Manual of clinical microbiology 10th ed ASM Press Washington DC

9 McCrea KW et al Relationships of nontypeable Haemophilus influenzae strains to hemolytic and nonhemolytic Haemophilus haemolyticus strains J Clin Microbiol 200846 406ndash416 httpwwwncbinlmnihgovpmcarticlesPMC2238123

10 Murphy TF et al Haemophilus haemolyticus a human respiratory tract commensal to be distinguished from Haemophilus influenzae J Infect Dis 2007195 81ndash 89 httpwwwncbinlmnihgovpubmed17152011

11 Identification Reference Laboratory Centre for Infectious Diseases and Microbiology ICPMR Westmead Hospital 12 Binks MJ et al Molecular Surveillance of True Nontypeable Haemophilus influenzae An Evaluation of PCR Screening Assays PLOS

httpwwwplosoneorgarticleinfo3Adoi2F1013712Fjournalpone0034083

13 Duerden B Bennet KW and Faulkner J Isolation of Bacteroides ureolyticus (B corrodens) from clinical infections J Clin Pathol 1982 35 309-312 httpjcpbmjcomcontent353309fullpdf

The most common misidentification by participants was H influenzae (35) because of the phenotypicgenetic similarity of the two species and because of the failure of all kitsidentification systems to differentiate between them Reliance on one type of identification system is discouraged and may lead to incorrect identification of some organisms In this instance β-haemolysis on blood agar facilitated an accurate identification if detected however as already noted it may not always be displayed in this species even in primary cultures H parahaemolyticus reported by three laboratories is also β-haemolytic but unlike H haemolyticus it is V-dependent only (and δ-Aminolevulinic acid (ALA) test negative) as is H parainfluenzae reported by two laboratories which is not β-haemolytic All other false identifications reported do not exhibit X+V dependency or X- or V-dependency The laboratory reporting Corynebacterium jeikeium should note that this is a gram-positive rod B ureolyticus reported by one laboratory is an anaerobic organism with corroding colonies on agar plates 13 Brucella and Francisella tularensis are slow-growing fastidious organisms (also not XV-dependent) that would not be dispatched in this type of QAP

ITEM 201364C CLERICAL ERROR

Clerical Errors reported in Item 201364C Number labs (71)

No error reported 6

Error first name only (correct) in 4C 60(85)

Error first name only in 4D (incorrect) 1

Error first name (correct) + last name (incorrect) 1

Error first name (correct) + unit number (incorrect) 1

Error last name (incorrect) 2

Table 13 Clerical errors reported

Specimen label Karina DANIELS UN 831248 Paperwork Amelia DANIELS UN 831248

The clerical error was placed in item 201364C Mycobacteriology culture As only 95 participants receive 4C and 4D culture vials and only 71 performed testing this clerical error has not been scored

copy2013 RCPA Quality Assurance Programs Pty Limited 13 Date of issue 13th November 2013

ITEM 201367ABC MYCOLOGY

7A This item contained Trichophyton interdigitale [zoophilic] (previously T mentagrophytes) 973 correct to genus level 634 correct to species level (required) The Trichophyton species have undergone extensive reclassification in the last 5 years This is because there exists much phenotypic variation but genetic variation is low Most of the species formerly known as T mentagrophytes are now classified within T interdigitale T mentagrophytes still exists but encompasses only the organism previously known as T quinckeanum (T mentagrophytes var quinckeanum) which is associated with mice T interdigitale is recognised as having two ecological groups the anthropophilic and the zoophilic group with the former T mentagrophytes species falls into the zoophilic group For this item T interdigitale and T mentagrophytes were both marked as correct This newly merged species encompasses a wide range of phenotypes which may or may not be observed for a given specimen Sequencing of the internal transcribed spacer (ITS) region is the gold standard for identification using reference strains that are correctly named according to the revised taxonomy Chen et al have published a useful book chapter with phenotypic descriptions and recommendations for molecular identification of the revised Trichophyton species1

7A Trichophyton interdigitale [zoophilic]

Figures 7A (i-iii) Trichophyton interdigitale [zoophilic group] (previously T mentagrophytes) may have [7A(i)] numerous single-celled microconidia often in dense clusters along with smooth thin-walled cigar-shaped multicelled macroconidia Microconidia are hyaline smooth-walled and are predominantly spherical to subspherical in shape however occasional clavate to pyriform forms may occur [7A(ii)] varying numbers of spherical chlamydoconidia and [7A (iii)] spiral hyphae may also be observed The zoophilic form of the species tends to have powdery-granular colonies on Sabouraudrsquos lactritmel and 1 peptone media while the anthropophilic form has suede-downy textured colonies

1

1

1

1

1

2

2

5

6

7

14

1

31

1

5

20

13

0 5 10 15 20 25 30 35

Chrysosporium tropicum

Microsporum gypseum

Microsporum persicolor

Trichophyton equinum

Trichophyton terrestre

Trichophyton erinacei

Trichophyton verrucosum

Trichophyton species

Trichophyton rubrum [Worldwide population]

Trichophyton tonsurans

Trichophyton rubrum

Trichophyton mentagrophytes complex

Trichophyton mentagrophytes

Trichophyton interdigitale [anthropophilic] and [zoophilic]

Trichophyton interdigitale [anthropophilic]

Trichophyton interdigitale

Trichophyton interdigitale [zoophilic]

13 116

20 179

5 45

1 09

31 277

1 09

14 125

7 63

6 54

5 45

2 18

2 18

1 09

1 09

1 09

1 09

1 09

7A (i)

7A (ii) 7A (iii)

copy2013 RCPA Quality Assurance Programs Pty Limited 14 Date of issue 13th November 2013

7B Cryptococcus neoformans

82 732

8 71

1 09

1 09

5 45

11 98

1 09

1 09

1 09

1 09

7B This item contained Cryptococcus neoformans 964 correct to genus level 812 correct to species level (required) Cryptococcosis is typically caused by either Cryptococcus neoformans or Cryptococcus gattii although occasionally other Cryptococcus species have been implicated C neoformans typically infects the immunocompromised host frequently in the setting of HIV with gt1 million new cases and~600000 deaths per year globally C neoformans is a yeast-like basidiomycete fungus with a distinctive polysaccharide capsule Differentiation from the closely related C gattii is important Presumptive identification is by India Ink stain to highlight the capsule and birdseed agar to observe dark brown colonies

Figure 7B (i-iii) [7B (i)] India Ink stain highlighting the capsule of C neoformansgattii [7B(ii)] Dark brown colonies of C neoformansgattii mixed with white colonies of Candida albicans on birdseed agar [7B(iii)] Canavanine glycine bromothyol blue (CGB) media for distinguishing C neoformans (left) from C gattii (right)

1

1

1

1

11

5

1

1

8

82

0 10 20 30 40 50 60 70 80 90

Unable to identify- refer

Candida (not albicans)

Candida glabrata complex

Candida krusei

Cryptococcus neoformansgattii- unable to speciate

Cryptococcus species

Cryptococcus laurentii

Cryptococcus neoformans var grubii

Cryptococcus neoformans var neoformans

Cryptococcus neoformans

81 of labs correctly reported this isolate as Cryptococcus neoformans While no lab reported C gattii 11 labs were unable to differentiate C neoformans from C gattii Epidemiology risk factors and treatment of infections caused by these species are different and accurate identification is important for effective management All labs should seek to differentiate these species using CGB media a validated molecular method or by referral to a reference laboratory API ID32C and Vitek-2 does not distinguish C neoformans from C gattii These species may be differentiated by a number of DNA-based assays MALDI-ToF and canavanine-glycine-bromothymol blue (CGB) media C neoformans does not grow on CGB media which remains yellow whereas C gattii will grow triggering a blue colour change reaction in the media usually within 3 days It is worth noting that some slow growing C gattii isolates may take as long as 10 days to effect the blue colour change and may initially be mis-identified as C neoformans Nine labs unnecessarily attempted to further identify the C neoformans isolate to variety level either Cn var grubii (serotype A molecular types VNI and VNII) or Cn var neoformans (serotype D molecular type VNIV) It is not clear what methods were used to achieve this varietal identification but 8 of the 9 labs incorrectly reported Cn var neoformans In fact the isolate was confirmed by molecular methods to be Cryptococcus neoformans var grubii molecular type VNI The 8 reports of Cn var neoformans may reflect persistence of the now obsolete classification of Cryptococcus neoformans having two varieties var neoformans and var gattii If it is the normal practice of these labs to report to varietal level it would be worthwhile reviewing methods interpretation and reporting procedures

7B (i) 7B (ii) 7B(iii)

copy2013 RCPA Quality Assurance Programs Pty Limited 15 Date of issue 13th November 2013

Reference item 7

1 Chen SC DH Ellis TC Sorrell and W Meyer Chapter 44 Trichophyton In ldquoMolecular Detection of Human Fungal Pathogensrdquo Dongyou Liu (Ed) CRC Press 2011

All mycology isolates were identified by both conventional and molecular techniques

86 768

9 80

1 09

2 18

3 27

3 27

2 18

1 09

1 09

1 09

1 09

2 18

7C Scedosporium prolificans

This item contained Scedosporium prolificans 875 correct to genus level 768 correct to species level (required) Colonies are rapid growing flat spreading olive-grey to black (the culture may contain a mixture of the colurs depending on the age) and have a suede-like to downy surface texture [7C (i)] Conidia are borne in small groups on distinctive basally swollen flask-shaped annellides which occur singly or in clusters along the vegetative hyphae Conidia are single-celled hyaline to pale-brown ovoid to pyriform 2-5 x 3-13 um (average 34-53 um) in size and have smooth thin walls [7C (ii)] Identification of Scedosporium prolificans to

species level is very important due to its intrinsic resistance to most antifungal drugs It may be distinguished from other members of the genus in particular the human pathogen S apiospermum by its basally swollen (inflated) flask-shaped annellides conidia borne in small groups rather than singly and by not growing on media containing cycloheximide (actidione) DNA sequencing (ITS region) will also definitively identify Scedosporium species Three laboratories reported Sporothrix schenckii which is easily distinguished from Scedosporium spp because it is a dimorphic pathogen with a yeast-like phase when grown at 37degC

2

1

1

1

1

2

3

3

2

1

9

86

0 10 20 30 40 50 60 70 80 90 100

Unable to identify- refer

Chaetomium species

Hortaea werneckii

Ochroconis gallopava

Wangiella species

Exophiala species

Exophiala dermatitidis

Sporothrix schenckii

Scedosporium species

Scedosporium aurantiacum

Scedosporium apiospermum (sensu stricto)

Scedosporium prolificans

7C (i) 7C (ii)

Page 6: FINAL RESULTS AND COMMENTS D6-2013 …dataentry.rcpaqap.com.au/micro/reports/uploadedfiles/fnl2013-6.pdf · FINAL RESULTS AND COMMENTS D6/2013 ... This item contained a pure growth

copy2013 RCPA Quality Assurance Programs Pty Limited 6 Date of issue 13th November 2013

ITEM 201362 NOSE SWAB

includes presumptive identifications

ITEM 201362 Nose swab Quality Control This item represented an infection control nose swab containing Methicillin resistant Staphylococcus aureus (MRSA) and Staphylococcus epidermidis Counts for MRSA remained above 10 x 1010 CFUL throughout the survey Homogeneity and stability testing were satisfactory Culture and identification results Two hundred and forty seven participants returned results with 242 (98) reporting MRSA This isolate was a non multi-resistant MRSA (NMRSA) with a susceptibility pattern as follows Resistant to ampicillin Augmentin cefotaxime cefoxitin cephalothin oxacillin and penicillin susceptible to ciprofloxacin clindamycin erythromycin fusidic acid gentamicin rifampicin and tetracycline Many laboratories screened using chromogenic agars Follow up tests included Gram stain (gram-positive cocci) catalase (positive) DNAase (positive) slidetube coagulase (positive) and conventional susceptibility testing or other method to confirm MRSA Staphylococcus aureus agglutination kits used are shown in Table 5 below Identification kitssystems employed are also shown below in Table 6 Most kitssystems accurately identified S aureus Three laboratories reporting S aureus mentioned that it was MRSA in the comments box One of the four laboratories reporting S aureus (only) reported it oxacillin susceptible in the comments box The other three gave no indication of it being or possibly being MRSA

239 968

3 12

4 16

1 04 1

4

3

239

0 50 100 150 200 250 300

Staphylococcus coag negative

Staphylococcus aureus

Staphylococcus aureus (MRSA in comments)

MRSA or Staphylococcus aureus (MRSA)

Most common kits used

Number of users

Biomerieux Slidex Staph 5

Bio-Rad 6

Omega Avipath 2

Oxoid Staphylase 4

Oxoid Staphytect Plus 7

Pastorex Staph Plus 25

Phadebact 9

Prolex Staph 8

Remel BactiStaph 7

Remel Staphaurex (Plus) 20

Table 5 Staphylococcus aureus agglutination kits Table 6 Identification kitssystems

Most common kits used Number of users

API StaphmdashBiomerieux 2

BBL Crystal-BD Gram Positive ID Kit 2

MALDI-TOF Bruker 25

MALDI-TOF VITEK MS 9

Microbact 12S 2

Microscan 1

Phadebact 1

Phoenix 7

RapID Staph Plus 1

SAM-PCR 1

VITEK2 GPmdashBiomerieux 23

copy2013 RCPA Quality Assurance Programs Pty Limited 7 Date of issue 13th November 2013

ITEM 201363 SKIN SWAB

36 146

109 441

29 117

3 12

24 97

1 04

30 121

8 32

5 20

1 04

1 04

Aeromonas veronii biovar sobria (formally A sobria)

ITEM 201363

Quality Control This item contained the pure isolate Aeromonas veronii bv sobria Homogeneity and stability testing were satisfactory with the bacterial count for the A veronii bv sobria remaining above 41 X 109 CFUL during the 3 week survey period Identification

Two hundred and forty seven participants submitted results with 246 (996) reporting an Aeromonas species The most frequently isolated Aeromonas species of clinical significance in humans are A veronii bv sobria A hydrophila and A caviae1 2 A sobria reported by the majority of participants now refers to the organism originally described by Popoff and Veacuteron in 1976 and is primarily a fish pathogen Aldquosobriardquo that are negative for aesculin hydrolysis salicin KCN L-arabinose and ornithine decarboxylase (ODC) and positive for arginine dihydrolase (ADH) should be designated A veronii bv sobria 2 3 A ichthiosmia reported by one laboratory is identical to A veronii bv sobria using gene sequencing2 A liquefaciens (one laboratory) is exclusively a fish pathogen4 Laboratories identified using Gram stain (gram-negative rods) oxidase reaction (positive) and a variety of identification kitssystems the most commonly used being API 20E (n=49) API 20NE (n=52) MALDI-TOFBruker (n=36) MALDI-TOFVITEK MS (n=10) and VITEK2 GN (n=68)

Susceptibility testing Aeromonas veronii bv sobria

Most discrepancies occurred in the reporting of Augmentin and the carbapenems for this isolate The CDS susceptibility method acknowledges the presence of chromosomally-linked β-lactamases (A1 and A2) in Aeromonas species5678 A1 is an inducible cephalosporinase which is inhibited by aztreonam but not by clavulanic acid and which hydrolyses cephalosporins and cephamycins but not carbapenems (AmpCBush group 1) It is detected by adjacent disc testing in the CDS method (Figure 3a) A2 is a carbapenemase which hydrolyses carbapenems but not cephalosporins or cephamycins It may show heterogeneous expression of resistance and so resistance to imipenem and meropenem may not be detectable by conventional methods unless a heavy inoculum is used 6789 and inaccurate reporting of sensitivity to carbapenems may ensue(Figure 3b) CDS users should report A veronii bv sobria as resistant to both Augmentin and carbapenems and are directed to Table 104a of the current CDS guidelines For CLSI users standard M45-A2 states that ldquointerpretive breakpoints for cefazolin and for ertapenem imipenem and meropenem for the Enterobacteriaceae were voted to be changed by the Subcommittee on Antimicrobial Susceptibility Testing subsequent to final approval of this edition of M45 It is anticipated that these modified breakpoints will be adopted for use with Aeromonas spp and Vibrio spp in the next edition of M45 or possibly in a future supplementrdquo10 The CLSI standard inoculum equivalent of 05 McFarland would likely fail to detect carbapenem resistance in Aeromonas species

Antibiotic

Aeromonas veronii bv sobria susceptibilities (all methods)

Susc IntRS Res

Amikacin 42 - 1

AmpicillinAmoxycillin - - 146

Augmentin 28 17 98

Cefazolin 9 - 18

Cefepime 21 - 1

Cefotaxime 51 - 2

Cefoxitin 11 - 1

Ceftazidime 82 - 3

Ceftriaxone 75 - 10

Cefuroxime 43 - -

Cephalexin 6 - 7

Cephalothin 9 - 5

Chloramphenicol 15 - -

Ciprofloxacin 213 - 1

Cotrimoxazole 153 2 3

Gentamicin 198 - 1

Imipenem 25 5 26

Levofloxacin 13 - -

Meropenem 40 2 43

Piperacillin 6 - -

Piperacillintazobactam 44 - 15

Sulphafurazole 8 - -

Tetracycline 29 - -

Timentin 5 - 19

Tobramycin 12 - -

Trimethoprim 19 - 1

Table 7 Aeromonas veronii bv sobria

1

1

5

8

30

1

24

3

29

109

36

0 20 40 60 80 100 120

Citrobacter freundii

Aeromonas liquefaciens

Aeromonas hydrophilacaviae

Aeromonas hydrophila group

Aeromonas hydrophila

Aeromonas ichthiosmia

Aeromonas species

Aeromonas veronii

Aeromonas veronii complex

Aeromonas sobria

Aeromonas veronii bv sobria

copy2013 RCPA Quality Assurance Programs Pty Limited 8 Date of issue 13th November 2013

Figure 3a A hydrophilia with cephalosporinase A1 amp carbapenemase A2 copy South Eastern Area Laboratory Services httpwebmedunsweduaucdstest

Figure 3b A sobria with carbapenemase A2 but lacking cephalosporinase A1 copy South Eastern Area Laboratory Services httpwebmedunsweduaucdstest

References Item 3 1 Parker JL and Shaw JG Aeromonas spp clinical microbiology and disease Journal of infection 201162 109-118 httpwwwsciencedirectcomsciencearticlepiiS0163445310003543bbib10 2 Janda JM and Abbott SL The genus Aeromonas taxonomy pathogenicity and infection Clin Microbiol Rev 201023 35ndash73 httpwwwncbinlmnihgovpmcarticlesPMC2806660 3 Horneman AJ and Afsar A Aeromonas Ch 38 In Versalovic J Carroll KC Funke G Jorgensen JH Landry ML WarnockDW(ed) Manual of clinical

microbiology 10th ed ASM Press Washington DC 4 Bullock GL The identification and separation of Aeromonas liquefaciens from Pseudomonas fluorescens and related organisms occurring in dis-

eased fish Appl Microbiol 19619 587ndash590 httpwwwncbinlmnihgovpmcarticlesPMC1057793 5 Antibiotic susceptibility testing by the CDS method httpwebmedunsweduaucdstest 6 Walsh TR et al Distribution and expression of β-lactamase genes among Aeromonas spp Journal of Antimicrobial Chemotherapy 199740 171ndash

178 httpjacoxfordjournalsorgcontent402171fullpdf 7 Wu C-J et al Distribution and phenotypic and genotypic detection of a metallo-b-lactamase CphA among bacteraemic Aeromonas isolates Jour-

nal of Medical Microbiology 201261 712ndash719 httpwwwncbinlmnihgovpubmed22322339 8 Aravena-Romaacuten M et al Antimicrobial susceptibilities of Aeromonas strains isolated from clinical and environmental sources to 26 antimicrobial

agents J Med Microbiol 201261 712-9 httpaacasmorgcontent5621110 9 Rossolini GM et al The Aeromonas metallo-β-lactamases genetics enzymology and contribution to drug resistance Microb Drug Resist 1996 2

245-252 httponlineliebertpubcomdoiabs101089mdr19962245

10 CLSI standard A45-A2 Methods for antimicrobial dilution and disk susceptibility testing for infrequently isolated or fastidious bacteria approved guidelinemdashsecond edition August 2010

copy2013 RCPA Quality Assurance Programs Pty Limited 9 Date of issue 13th November 2013

ITEM 201364ABCD CULTURE AND MICROSCOPY FOR AFB

Reference laboratory report

Culture results C D

Mycobacterium species isolated 59 0

Mycobacterium species not isolated 10 70

Not result reported 2 1

Participant smear results A B

Negative 17 178

1 - 9100 HPF 115 3

10 - 99100 HPF 47 2

1 - 10HPF 4 -

Table 11 Results for mediamethods used for specimen 4C

Table 9 Participant smear results

Table 10 Participant culture results

Table 12 Molecular Diagnostics

Molecular Diagnostics

C D

Mycobacterium TB Complex DNA amplification Positive

13 0

Mycobacterium TB Complex DNA amplification Negative

1 12

No result reported 1 3

Media Total no inoculated

Number positive

BacTALERT amp 3D 9 6

BD BACTEC MGIT 960 System 43 38

BD BBL MGIT 5 3

Brown amp Buckle 3 1

LJ 32 21

LJ Glycerol 6 5

LJ Pyruvate 15 8

LJ Pyruvate Glycerol 4 3

Ogawa 6 2

Other 10 7

Test A B

AFB stain Ziehl Neelsen

Positive 1-9100 HPF

No AFB seen

C D

Culture Bactec MGIT 960 (BD)L-J

Mycobacterium tuberculosis

present

Mycobacterium species absent

Microscopy Results Slides were prepared in this survey using sputum seeded with Mycobacterium tuberculosis H37Ra The sputum used was examined before inoculation with the M tuberculosis strain using a Ziehl-Neelsen stain and tested for M tuberculosis and MAC by molecular methods and found to be negative Smear 4A Slide 4A contained scanty (1-9100HPF) numbers of AFB It was examined by a reference laboratory and a RCPAQAP scientist The three smears examined by the reference laboratory were confirmed positive and contained 4 1 and 3 AFB100HPF Ten randomly selected smears examined by RCPAQAP contained from 4 to 9 AFB100HPF Most laboratories (91 or 92 when transcription errors were included) reported a positive result with the majority (63) reporting 1-9 AFB100 HPF Three transcription errors were apparent among the 17 negative results reported It is recommended these laboratories carefully review their smears Participants are requested to report AFB counts based on acid fast stains rather than on fluorescent stains Smear 4B Smear 4B contained no AFB and this was confirmed by the reference laboratory and 10 smears examined by a RCPAQAP scientist As already mentioned 3 of the 5 laboratories reporting positive results transcribed them in error The other 2 reported positive results in both smears Culture Results Item 4C Sample 4C contained Mycobacterium tuberculosis and organisms representing normal upper respiratory tract flora such as Staphylococcus epidermidis Neisseria subflava and alpha-haemolytic streptococci Of the 69 participants returning a result the majority (86) reported this sample positive Item 4D Sample 4D contained the above upper respiratory organisms only and no Mycobacteria species All participants returning a result reported it negative for Mycobacteria species Molecular Diagnostics Results Fifteen laboratories performed molecular diagnostics for M tuberculosis (14 laboratories returned results on sample 4C and 12 on 4D) Please refer to Table 12 for participant results All methods used are listed below Gene Expert 2 HAIN (MTBDR) 1 HAIN (Mycobacterium CM) 1 Inhouse PCR 3 ProbeTec 2 qPCR 1 Roche Cobas 1 Seegene 1 Taqman 2 Not stated 1

Table 8 4A-D expected results

copy2013 RCPA Quality Assurance Programs Pty Limited 10 Date of issue 13th November 2013

includes presumptive identification(s)

ITEM 201365 ISOLATE FOR IDENTIFICATION

includes presumptive identification(s)

103 475

1 05

72 332

4 18

3 14

2 09

7 32

1 05

1 05

1 05

1 05

1 05

1 05

2 09

1 05

1 05

1 05

14 65

Fig 5b H haemolyticus on HBA copy 2013 RCPA QAP

ITEM 201365 Haemophilus haemolyticus This item contained a pure growth of Haemophilus haemolyticus Homogeneity and stability testing for this organism was satisfactory with bacterial counts for the H haemolyticus remaining above 10 x 1010CFUL throughout the survey

This organism represented an isolate from blood culture collected from a patient with endocarditis H haemolyticus is a human commensal of the nasopharynx in some individuals Some authors find its pathogenicity debatable but it has occasionally been implicated in disease 123 Phenotypically and genotypically it is difficult to distinguish from non-typeable H influenzae except for β-haemolysis on blood agar in the case of H haemolyticus 45678 But even this can be an unreliable characteristic as non-haemolytic strains occur and upon repeated sub-culture this trait may disappear 5910 For this reason it has been suggested that H haemolyticus is more commonly misidentified as H influenzae than is recognised5 Like H influenzae H haemolyticus is a fastidious facultative anaerobe XV-dependent oxidase and catalase positive gram-negative coccobacillus

Fig 5a H haemolyticus on Chocolate Agar copy 2013 RCPA QAP

14

1

1

1

2

1

1

1

1

1

1

7

2

3

4

72

1

103

0 20 40 60 80 100 120

Unable to Identify - Refer

Psychrobacter phenylpyruvicus

Pasteurella species

Other

Kingella kingae

Gram negative rod

Francisella tularensis

Corynebacterium jeikeium

Brucella spp

Bacteroides ureolyticus

Actinobacillus actinomycetemcomitans

Haemophilus species

Haemophilus parainfluenzae

Haemophilus parahaemolyticus

Haemophilus influenzae type B

Haemophilus influenzae

Haemophilus aegyptius

Haemophilus haemolyticus

copy2013 RCPA Quality Assurance Programs Pty Limited 11 Date of issue 13th November 2013

SUMMARY OF PHENOTYPIC AND BIOCHEMICAL RESULTS 811

Phenotypic characteristics

Gram stain Small gram-positive rods and coccobacilli

Motility RT (BHI broth) non-motile

Colonial appearance on Chocolate agar (CA) 24hrs 10mm beige shiny round entire colonies

Colonial appearance on Horse Blood agar (HBA) 24hrs pinpoint translucent shiny round entire colonies

Pigment pale yellow

Haemolysis β (key distinguishing test if apparent) This isolate was haemolytic on HBA

Catalase positive

Oxidase positive

KIA slope NCNC gas negative

Satellitism XV + V - X - Growth conditions

Growth on HBA 35degC in O2 +

Growth on HBA 35degC in CO2 ++

Growth on HBA 35degC in ANO2 +

Growth on CA 35degC 35degC +++

Growth on MacConkey agar no growth Biochemical tests Rapid substrate utilisation

Urease positive

Nitrate positive

Indole negative

Aesculin negative

ADH negative

LDC negative

ODC negative

Glucose positive

Xylose negative

Mannitol negative

Lactose positive (weak) 11

Sucrose negative

Maltose positive (weak) 11 16S rRNA gene analysis by PCR H haemolyticus with a 99 match Although standard genetic testing may be inadequate to distinguish H influenzae and H haemolyticus because of their genetic similarity1012 the demonstration of β-haemolysis on HBA for this isolate supports the PCR findings A few other Haemophilus species are known to display β-haemolysis on blood agar but they are not X and V-dependent 8 Participant results Two hundred and seventeen participants submitted results for this item with 192 (88) correctly identifying to genus level Under half were able to fully speciate The graph on the previous page illustrates participantsrsquo results Some biochemical tests commonly used by participants to identify include catalase (+) oxidase (+) indole (-) urea (+) growth on MacConkey agar (-) and XV-dependency (+) Many participants correctly identifying H haemolyticus observed the β-haemolytic activity of this isolate on blood agar and made note of it in their comments Identification kitssystems used and success rates in the hands of the users are listed below Please note that success rates may have been influenced by the observation (or lack thereof) of β-haemolysis

API NHmdashBiomerieux 1236 (33) correct H influenzae (24)

BBL Crystal-BD NeisseriaHaemophilus ID Kit 22 (100) correct

MALDI-TOF (Bruker ) 423(17) correct Pasteurella species (1) H influenzae (17) gram-negative rod (1)

MALDI-TOF (VITEK MS) 914 (64) correct H influenzae (4) Haemophilus species (1)

Rapid NH 1528 (54) correct Kingella kingae (1) H aegypticus (1) Haemophilus species (2) H influenzae (8) H parainfluenzae (1)

Sequencing 16S rRNA 78 (88) correct H influenzae (1)

VITEK2 GN 56 (83) correct H influenzae (1)

VITEK2 NH 3150 (62) correct Haemophilus species (1) Unable to identify-refer (1) H influenzae (17)

VITEK NHI 45 (80) correct H influenzae (1)

copy2013 RCPA Quality Assurance Programs Pty Limited 12 Date of issue 13th November 2013

References Item 5 1 McCrea KW et al Relationships of nontypeable Haemophilus influenzae strains to hemolytic and nonhemolytic Haemophilus haemolyticus strains J Clin

Microbiol 200846 406ndash416 httpwwwncbinlmnihgovpmcarticlesPMC2238123

2 Jordan IK et al Genome sequences for five strains of the emerging pathogen Haemophilus haemolyticus J Bacteriol 2011193 5879ndash5880

httpwwwncbinlmnihgovpmcarticlesPMC3187195

3 Anderson R et al Haemophilus haemolyticus isolates causing clinical disease J Clin Microbiol 201250 2462-5

httpwwwncbinlmnihgovpubmed22573587

4 Morton DJ et al An invasive Haemophilus haemolyticus isolate J Clin Microbiol 201250 1502ndash1503

httpwwwncbinlmnihgovpmcarticlesPMC3318549

5 Agrawal A Murphy TF Haemophilus influenzae infections in the H influenzae type b conjugate vaccine era J Clin Microbiol 201149 3728ndash3732

httpwwwncbinlmnihgovpmcarticlesPMC3209133

6 Kilian M A taxonomic study of the genus Haemophilus with the proposal of a new species J Gen Microbiol 197693 9ndash62

httpwwwncbinlmnihgovpubmed772168

7 Kilian M 2005 Genus III Haemophilus Winslow Broadhurst Buchanan Krumweide Rogers and Smith 1917 561 p 883ndash904 In Brenner DJ Krieg NR Staley JT (ed) Bergeyrsquos manual of systematic bacteriology 2nd ed vol 2 Springer New York NY

8 Ledeboer NA Doern GV 2012 Haemophilus In Versalovic J Carroll KC Funke G Jorgensen JH Landry ML WarnockDW(ed) Manual of clinical microbiology 10th ed ASM Press Washington DC

9 McCrea KW et al Relationships of nontypeable Haemophilus influenzae strains to hemolytic and nonhemolytic Haemophilus haemolyticus strains J Clin Microbiol 200846 406ndash416 httpwwwncbinlmnihgovpmcarticlesPMC2238123

10 Murphy TF et al Haemophilus haemolyticus a human respiratory tract commensal to be distinguished from Haemophilus influenzae J Infect Dis 2007195 81ndash 89 httpwwwncbinlmnihgovpubmed17152011

11 Identification Reference Laboratory Centre for Infectious Diseases and Microbiology ICPMR Westmead Hospital 12 Binks MJ et al Molecular Surveillance of True Nontypeable Haemophilus influenzae An Evaluation of PCR Screening Assays PLOS

httpwwwplosoneorgarticleinfo3Adoi2F1013712Fjournalpone0034083

13 Duerden B Bennet KW and Faulkner J Isolation of Bacteroides ureolyticus (B corrodens) from clinical infections J Clin Pathol 1982 35 309-312 httpjcpbmjcomcontent353309fullpdf

The most common misidentification by participants was H influenzae (35) because of the phenotypicgenetic similarity of the two species and because of the failure of all kitsidentification systems to differentiate between them Reliance on one type of identification system is discouraged and may lead to incorrect identification of some organisms In this instance β-haemolysis on blood agar facilitated an accurate identification if detected however as already noted it may not always be displayed in this species even in primary cultures H parahaemolyticus reported by three laboratories is also β-haemolytic but unlike H haemolyticus it is V-dependent only (and δ-Aminolevulinic acid (ALA) test negative) as is H parainfluenzae reported by two laboratories which is not β-haemolytic All other false identifications reported do not exhibit X+V dependency or X- or V-dependency The laboratory reporting Corynebacterium jeikeium should note that this is a gram-positive rod B ureolyticus reported by one laboratory is an anaerobic organism with corroding colonies on agar plates 13 Brucella and Francisella tularensis are slow-growing fastidious organisms (also not XV-dependent) that would not be dispatched in this type of QAP

ITEM 201364C CLERICAL ERROR

Clerical Errors reported in Item 201364C Number labs (71)

No error reported 6

Error first name only (correct) in 4C 60(85)

Error first name only in 4D (incorrect) 1

Error first name (correct) + last name (incorrect) 1

Error first name (correct) + unit number (incorrect) 1

Error last name (incorrect) 2

Table 13 Clerical errors reported

Specimen label Karina DANIELS UN 831248 Paperwork Amelia DANIELS UN 831248

The clerical error was placed in item 201364C Mycobacteriology culture As only 95 participants receive 4C and 4D culture vials and only 71 performed testing this clerical error has not been scored

copy2013 RCPA Quality Assurance Programs Pty Limited 13 Date of issue 13th November 2013

ITEM 201367ABC MYCOLOGY

7A This item contained Trichophyton interdigitale [zoophilic] (previously T mentagrophytes) 973 correct to genus level 634 correct to species level (required) The Trichophyton species have undergone extensive reclassification in the last 5 years This is because there exists much phenotypic variation but genetic variation is low Most of the species formerly known as T mentagrophytes are now classified within T interdigitale T mentagrophytes still exists but encompasses only the organism previously known as T quinckeanum (T mentagrophytes var quinckeanum) which is associated with mice T interdigitale is recognised as having two ecological groups the anthropophilic and the zoophilic group with the former T mentagrophytes species falls into the zoophilic group For this item T interdigitale and T mentagrophytes were both marked as correct This newly merged species encompasses a wide range of phenotypes which may or may not be observed for a given specimen Sequencing of the internal transcribed spacer (ITS) region is the gold standard for identification using reference strains that are correctly named according to the revised taxonomy Chen et al have published a useful book chapter with phenotypic descriptions and recommendations for molecular identification of the revised Trichophyton species1

7A Trichophyton interdigitale [zoophilic]

Figures 7A (i-iii) Trichophyton interdigitale [zoophilic group] (previously T mentagrophytes) may have [7A(i)] numerous single-celled microconidia often in dense clusters along with smooth thin-walled cigar-shaped multicelled macroconidia Microconidia are hyaline smooth-walled and are predominantly spherical to subspherical in shape however occasional clavate to pyriform forms may occur [7A(ii)] varying numbers of spherical chlamydoconidia and [7A (iii)] spiral hyphae may also be observed The zoophilic form of the species tends to have powdery-granular colonies on Sabouraudrsquos lactritmel and 1 peptone media while the anthropophilic form has suede-downy textured colonies

1

1

1

1

1

2

2

5

6

7

14

1

31

1

5

20

13

0 5 10 15 20 25 30 35

Chrysosporium tropicum

Microsporum gypseum

Microsporum persicolor

Trichophyton equinum

Trichophyton terrestre

Trichophyton erinacei

Trichophyton verrucosum

Trichophyton species

Trichophyton rubrum [Worldwide population]

Trichophyton tonsurans

Trichophyton rubrum

Trichophyton mentagrophytes complex

Trichophyton mentagrophytes

Trichophyton interdigitale [anthropophilic] and [zoophilic]

Trichophyton interdigitale [anthropophilic]

Trichophyton interdigitale

Trichophyton interdigitale [zoophilic]

13 116

20 179

5 45

1 09

31 277

1 09

14 125

7 63

6 54

5 45

2 18

2 18

1 09

1 09

1 09

1 09

1 09

7A (i)

7A (ii) 7A (iii)

copy2013 RCPA Quality Assurance Programs Pty Limited 14 Date of issue 13th November 2013

7B Cryptococcus neoformans

82 732

8 71

1 09

1 09

5 45

11 98

1 09

1 09

1 09

1 09

7B This item contained Cryptococcus neoformans 964 correct to genus level 812 correct to species level (required) Cryptococcosis is typically caused by either Cryptococcus neoformans or Cryptococcus gattii although occasionally other Cryptococcus species have been implicated C neoformans typically infects the immunocompromised host frequently in the setting of HIV with gt1 million new cases and~600000 deaths per year globally C neoformans is a yeast-like basidiomycete fungus with a distinctive polysaccharide capsule Differentiation from the closely related C gattii is important Presumptive identification is by India Ink stain to highlight the capsule and birdseed agar to observe dark brown colonies

Figure 7B (i-iii) [7B (i)] India Ink stain highlighting the capsule of C neoformansgattii [7B(ii)] Dark brown colonies of C neoformansgattii mixed with white colonies of Candida albicans on birdseed agar [7B(iii)] Canavanine glycine bromothyol blue (CGB) media for distinguishing C neoformans (left) from C gattii (right)

1

1

1

1

11

5

1

1

8

82

0 10 20 30 40 50 60 70 80 90

Unable to identify- refer

Candida (not albicans)

Candida glabrata complex

Candida krusei

Cryptococcus neoformansgattii- unable to speciate

Cryptococcus species

Cryptococcus laurentii

Cryptococcus neoformans var grubii

Cryptococcus neoformans var neoformans

Cryptococcus neoformans

81 of labs correctly reported this isolate as Cryptococcus neoformans While no lab reported C gattii 11 labs were unable to differentiate C neoformans from C gattii Epidemiology risk factors and treatment of infections caused by these species are different and accurate identification is important for effective management All labs should seek to differentiate these species using CGB media a validated molecular method or by referral to a reference laboratory API ID32C and Vitek-2 does not distinguish C neoformans from C gattii These species may be differentiated by a number of DNA-based assays MALDI-ToF and canavanine-glycine-bromothymol blue (CGB) media C neoformans does not grow on CGB media which remains yellow whereas C gattii will grow triggering a blue colour change reaction in the media usually within 3 days It is worth noting that some slow growing C gattii isolates may take as long as 10 days to effect the blue colour change and may initially be mis-identified as C neoformans Nine labs unnecessarily attempted to further identify the C neoformans isolate to variety level either Cn var grubii (serotype A molecular types VNI and VNII) or Cn var neoformans (serotype D molecular type VNIV) It is not clear what methods were used to achieve this varietal identification but 8 of the 9 labs incorrectly reported Cn var neoformans In fact the isolate was confirmed by molecular methods to be Cryptococcus neoformans var grubii molecular type VNI The 8 reports of Cn var neoformans may reflect persistence of the now obsolete classification of Cryptococcus neoformans having two varieties var neoformans and var gattii If it is the normal practice of these labs to report to varietal level it would be worthwhile reviewing methods interpretation and reporting procedures

7B (i) 7B (ii) 7B(iii)

copy2013 RCPA Quality Assurance Programs Pty Limited 15 Date of issue 13th November 2013

Reference item 7

1 Chen SC DH Ellis TC Sorrell and W Meyer Chapter 44 Trichophyton In ldquoMolecular Detection of Human Fungal Pathogensrdquo Dongyou Liu (Ed) CRC Press 2011

All mycology isolates were identified by both conventional and molecular techniques

86 768

9 80

1 09

2 18

3 27

3 27

2 18

1 09

1 09

1 09

1 09

2 18

7C Scedosporium prolificans

This item contained Scedosporium prolificans 875 correct to genus level 768 correct to species level (required) Colonies are rapid growing flat spreading olive-grey to black (the culture may contain a mixture of the colurs depending on the age) and have a suede-like to downy surface texture [7C (i)] Conidia are borne in small groups on distinctive basally swollen flask-shaped annellides which occur singly or in clusters along the vegetative hyphae Conidia are single-celled hyaline to pale-brown ovoid to pyriform 2-5 x 3-13 um (average 34-53 um) in size and have smooth thin walls [7C (ii)] Identification of Scedosporium prolificans to

species level is very important due to its intrinsic resistance to most antifungal drugs It may be distinguished from other members of the genus in particular the human pathogen S apiospermum by its basally swollen (inflated) flask-shaped annellides conidia borne in small groups rather than singly and by not growing on media containing cycloheximide (actidione) DNA sequencing (ITS region) will also definitively identify Scedosporium species Three laboratories reported Sporothrix schenckii which is easily distinguished from Scedosporium spp because it is a dimorphic pathogen with a yeast-like phase when grown at 37degC

2

1

1

1

1

2

3

3

2

1

9

86

0 10 20 30 40 50 60 70 80 90 100

Unable to identify- refer

Chaetomium species

Hortaea werneckii

Ochroconis gallopava

Wangiella species

Exophiala species

Exophiala dermatitidis

Sporothrix schenckii

Scedosporium species

Scedosporium aurantiacum

Scedosporium apiospermum (sensu stricto)

Scedosporium prolificans

7C (i) 7C (ii)

Page 7: FINAL RESULTS AND COMMENTS D6-2013 …dataentry.rcpaqap.com.au/micro/reports/uploadedfiles/fnl2013-6.pdf · FINAL RESULTS AND COMMENTS D6/2013 ... This item contained a pure growth

copy2013 RCPA Quality Assurance Programs Pty Limited 7 Date of issue 13th November 2013

ITEM 201363 SKIN SWAB

36 146

109 441

29 117

3 12

24 97

1 04

30 121

8 32

5 20

1 04

1 04

Aeromonas veronii biovar sobria (formally A sobria)

ITEM 201363

Quality Control This item contained the pure isolate Aeromonas veronii bv sobria Homogeneity and stability testing were satisfactory with the bacterial count for the A veronii bv sobria remaining above 41 X 109 CFUL during the 3 week survey period Identification

Two hundred and forty seven participants submitted results with 246 (996) reporting an Aeromonas species The most frequently isolated Aeromonas species of clinical significance in humans are A veronii bv sobria A hydrophila and A caviae1 2 A sobria reported by the majority of participants now refers to the organism originally described by Popoff and Veacuteron in 1976 and is primarily a fish pathogen Aldquosobriardquo that are negative for aesculin hydrolysis salicin KCN L-arabinose and ornithine decarboxylase (ODC) and positive for arginine dihydrolase (ADH) should be designated A veronii bv sobria 2 3 A ichthiosmia reported by one laboratory is identical to A veronii bv sobria using gene sequencing2 A liquefaciens (one laboratory) is exclusively a fish pathogen4 Laboratories identified using Gram stain (gram-negative rods) oxidase reaction (positive) and a variety of identification kitssystems the most commonly used being API 20E (n=49) API 20NE (n=52) MALDI-TOFBruker (n=36) MALDI-TOFVITEK MS (n=10) and VITEK2 GN (n=68)

Susceptibility testing Aeromonas veronii bv sobria

Most discrepancies occurred in the reporting of Augmentin and the carbapenems for this isolate The CDS susceptibility method acknowledges the presence of chromosomally-linked β-lactamases (A1 and A2) in Aeromonas species5678 A1 is an inducible cephalosporinase which is inhibited by aztreonam but not by clavulanic acid and which hydrolyses cephalosporins and cephamycins but not carbapenems (AmpCBush group 1) It is detected by adjacent disc testing in the CDS method (Figure 3a) A2 is a carbapenemase which hydrolyses carbapenems but not cephalosporins or cephamycins It may show heterogeneous expression of resistance and so resistance to imipenem and meropenem may not be detectable by conventional methods unless a heavy inoculum is used 6789 and inaccurate reporting of sensitivity to carbapenems may ensue(Figure 3b) CDS users should report A veronii bv sobria as resistant to both Augmentin and carbapenems and are directed to Table 104a of the current CDS guidelines For CLSI users standard M45-A2 states that ldquointerpretive breakpoints for cefazolin and for ertapenem imipenem and meropenem for the Enterobacteriaceae were voted to be changed by the Subcommittee on Antimicrobial Susceptibility Testing subsequent to final approval of this edition of M45 It is anticipated that these modified breakpoints will be adopted for use with Aeromonas spp and Vibrio spp in the next edition of M45 or possibly in a future supplementrdquo10 The CLSI standard inoculum equivalent of 05 McFarland would likely fail to detect carbapenem resistance in Aeromonas species

Antibiotic

Aeromonas veronii bv sobria susceptibilities (all methods)

Susc IntRS Res

Amikacin 42 - 1

AmpicillinAmoxycillin - - 146

Augmentin 28 17 98

Cefazolin 9 - 18

Cefepime 21 - 1

Cefotaxime 51 - 2

Cefoxitin 11 - 1

Ceftazidime 82 - 3

Ceftriaxone 75 - 10

Cefuroxime 43 - -

Cephalexin 6 - 7

Cephalothin 9 - 5

Chloramphenicol 15 - -

Ciprofloxacin 213 - 1

Cotrimoxazole 153 2 3

Gentamicin 198 - 1

Imipenem 25 5 26

Levofloxacin 13 - -

Meropenem 40 2 43

Piperacillin 6 - -

Piperacillintazobactam 44 - 15

Sulphafurazole 8 - -

Tetracycline 29 - -

Timentin 5 - 19

Tobramycin 12 - -

Trimethoprim 19 - 1

Table 7 Aeromonas veronii bv sobria

1

1

5

8

30

1

24

3

29

109

36

0 20 40 60 80 100 120

Citrobacter freundii

Aeromonas liquefaciens

Aeromonas hydrophilacaviae

Aeromonas hydrophila group

Aeromonas hydrophila

Aeromonas ichthiosmia

Aeromonas species

Aeromonas veronii

Aeromonas veronii complex

Aeromonas sobria

Aeromonas veronii bv sobria

copy2013 RCPA Quality Assurance Programs Pty Limited 8 Date of issue 13th November 2013

Figure 3a A hydrophilia with cephalosporinase A1 amp carbapenemase A2 copy South Eastern Area Laboratory Services httpwebmedunsweduaucdstest

Figure 3b A sobria with carbapenemase A2 but lacking cephalosporinase A1 copy South Eastern Area Laboratory Services httpwebmedunsweduaucdstest

References Item 3 1 Parker JL and Shaw JG Aeromonas spp clinical microbiology and disease Journal of infection 201162 109-118 httpwwwsciencedirectcomsciencearticlepiiS0163445310003543bbib10 2 Janda JM and Abbott SL The genus Aeromonas taxonomy pathogenicity and infection Clin Microbiol Rev 201023 35ndash73 httpwwwncbinlmnihgovpmcarticlesPMC2806660 3 Horneman AJ and Afsar A Aeromonas Ch 38 In Versalovic J Carroll KC Funke G Jorgensen JH Landry ML WarnockDW(ed) Manual of clinical

microbiology 10th ed ASM Press Washington DC 4 Bullock GL The identification and separation of Aeromonas liquefaciens from Pseudomonas fluorescens and related organisms occurring in dis-

eased fish Appl Microbiol 19619 587ndash590 httpwwwncbinlmnihgovpmcarticlesPMC1057793 5 Antibiotic susceptibility testing by the CDS method httpwebmedunsweduaucdstest 6 Walsh TR et al Distribution and expression of β-lactamase genes among Aeromonas spp Journal of Antimicrobial Chemotherapy 199740 171ndash

178 httpjacoxfordjournalsorgcontent402171fullpdf 7 Wu C-J et al Distribution and phenotypic and genotypic detection of a metallo-b-lactamase CphA among bacteraemic Aeromonas isolates Jour-

nal of Medical Microbiology 201261 712ndash719 httpwwwncbinlmnihgovpubmed22322339 8 Aravena-Romaacuten M et al Antimicrobial susceptibilities of Aeromonas strains isolated from clinical and environmental sources to 26 antimicrobial

agents J Med Microbiol 201261 712-9 httpaacasmorgcontent5621110 9 Rossolini GM et al The Aeromonas metallo-β-lactamases genetics enzymology and contribution to drug resistance Microb Drug Resist 1996 2

245-252 httponlineliebertpubcomdoiabs101089mdr19962245

10 CLSI standard A45-A2 Methods for antimicrobial dilution and disk susceptibility testing for infrequently isolated or fastidious bacteria approved guidelinemdashsecond edition August 2010

copy2013 RCPA Quality Assurance Programs Pty Limited 9 Date of issue 13th November 2013

ITEM 201364ABCD CULTURE AND MICROSCOPY FOR AFB

Reference laboratory report

Culture results C D

Mycobacterium species isolated 59 0

Mycobacterium species not isolated 10 70

Not result reported 2 1

Participant smear results A B

Negative 17 178

1 - 9100 HPF 115 3

10 - 99100 HPF 47 2

1 - 10HPF 4 -

Table 11 Results for mediamethods used for specimen 4C

Table 9 Participant smear results

Table 10 Participant culture results

Table 12 Molecular Diagnostics

Molecular Diagnostics

C D

Mycobacterium TB Complex DNA amplification Positive

13 0

Mycobacterium TB Complex DNA amplification Negative

1 12

No result reported 1 3

Media Total no inoculated

Number positive

BacTALERT amp 3D 9 6

BD BACTEC MGIT 960 System 43 38

BD BBL MGIT 5 3

Brown amp Buckle 3 1

LJ 32 21

LJ Glycerol 6 5

LJ Pyruvate 15 8

LJ Pyruvate Glycerol 4 3

Ogawa 6 2

Other 10 7

Test A B

AFB stain Ziehl Neelsen

Positive 1-9100 HPF

No AFB seen

C D

Culture Bactec MGIT 960 (BD)L-J

Mycobacterium tuberculosis

present

Mycobacterium species absent

Microscopy Results Slides were prepared in this survey using sputum seeded with Mycobacterium tuberculosis H37Ra The sputum used was examined before inoculation with the M tuberculosis strain using a Ziehl-Neelsen stain and tested for M tuberculosis and MAC by molecular methods and found to be negative Smear 4A Slide 4A contained scanty (1-9100HPF) numbers of AFB It was examined by a reference laboratory and a RCPAQAP scientist The three smears examined by the reference laboratory were confirmed positive and contained 4 1 and 3 AFB100HPF Ten randomly selected smears examined by RCPAQAP contained from 4 to 9 AFB100HPF Most laboratories (91 or 92 when transcription errors were included) reported a positive result with the majority (63) reporting 1-9 AFB100 HPF Three transcription errors were apparent among the 17 negative results reported It is recommended these laboratories carefully review their smears Participants are requested to report AFB counts based on acid fast stains rather than on fluorescent stains Smear 4B Smear 4B contained no AFB and this was confirmed by the reference laboratory and 10 smears examined by a RCPAQAP scientist As already mentioned 3 of the 5 laboratories reporting positive results transcribed them in error The other 2 reported positive results in both smears Culture Results Item 4C Sample 4C contained Mycobacterium tuberculosis and organisms representing normal upper respiratory tract flora such as Staphylococcus epidermidis Neisseria subflava and alpha-haemolytic streptococci Of the 69 participants returning a result the majority (86) reported this sample positive Item 4D Sample 4D contained the above upper respiratory organisms only and no Mycobacteria species All participants returning a result reported it negative for Mycobacteria species Molecular Diagnostics Results Fifteen laboratories performed molecular diagnostics for M tuberculosis (14 laboratories returned results on sample 4C and 12 on 4D) Please refer to Table 12 for participant results All methods used are listed below Gene Expert 2 HAIN (MTBDR) 1 HAIN (Mycobacterium CM) 1 Inhouse PCR 3 ProbeTec 2 qPCR 1 Roche Cobas 1 Seegene 1 Taqman 2 Not stated 1

Table 8 4A-D expected results

copy2013 RCPA Quality Assurance Programs Pty Limited 10 Date of issue 13th November 2013

includes presumptive identification(s)

ITEM 201365 ISOLATE FOR IDENTIFICATION

includes presumptive identification(s)

103 475

1 05

72 332

4 18

3 14

2 09

7 32

1 05

1 05

1 05

1 05

1 05

1 05

2 09

1 05

1 05

1 05

14 65

Fig 5b H haemolyticus on HBA copy 2013 RCPA QAP

ITEM 201365 Haemophilus haemolyticus This item contained a pure growth of Haemophilus haemolyticus Homogeneity and stability testing for this organism was satisfactory with bacterial counts for the H haemolyticus remaining above 10 x 1010CFUL throughout the survey

This organism represented an isolate from blood culture collected from a patient with endocarditis H haemolyticus is a human commensal of the nasopharynx in some individuals Some authors find its pathogenicity debatable but it has occasionally been implicated in disease 123 Phenotypically and genotypically it is difficult to distinguish from non-typeable H influenzae except for β-haemolysis on blood agar in the case of H haemolyticus 45678 But even this can be an unreliable characteristic as non-haemolytic strains occur and upon repeated sub-culture this trait may disappear 5910 For this reason it has been suggested that H haemolyticus is more commonly misidentified as H influenzae than is recognised5 Like H influenzae H haemolyticus is a fastidious facultative anaerobe XV-dependent oxidase and catalase positive gram-negative coccobacillus

Fig 5a H haemolyticus on Chocolate Agar copy 2013 RCPA QAP

14

1

1

1

2

1

1

1

1

1

1

7

2

3

4

72

1

103

0 20 40 60 80 100 120

Unable to Identify - Refer

Psychrobacter phenylpyruvicus

Pasteurella species

Other

Kingella kingae

Gram negative rod

Francisella tularensis

Corynebacterium jeikeium

Brucella spp

Bacteroides ureolyticus

Actinobacillus actinomycetemcomitans

Haemophilus species

Haemophilus parainfluenzae

Haemophilus parahaemolyticus

Haemophilus influenzae type B

Haemophilus influenzae

Haemophilus aegyptius

Haemophilus haemolyticus

copy2013 RCPA Quality Assurance Programs Pty Limited 11 Date of issue 13th November 2013

SUMMARY OF PHENOTYPIC AND BIOCHEMICAL RESULTS 811

Phenotypic characteristics

Gram stain Small gram-positive rods and coccobacilli

Motility RT (BHI broth) non-motile

Colonial appearance on Chocolate agar (CA) 24hrs 10mm beige shiny round entire colonies

Colonial appearance on Horse Blood agar (HBA) 24hrs pinpoint translucent shiny round entire colonies

Pigment pale yellow

Haemolysis β (key distinguishing test if apparent) This isolate was haemolytic on HBA

Catalase positive

Oxidase positive

KIA slope NCNC gas negative

Satellitism XV + V - X - Growth conditions

Growth on HBA 35degC in O2 +

Growth on HBA 35degC in CO2 ++

Growth on HBA 35degC in ANO2 +

Growth on CA 35degC 35degC +++

Growth on MacConkey agar no growth Biochemical tests Rapid substrate utilisation

Urease positive

Nitrate positive

Indole negative

Aesculin negative

ADH negative

LDC negative

ODC negative

Glucose positive

Xylose negative

Mannitol negative

Lactose positive (weak) 11

Sucrose negative

Maltose positive (weak) 11 16S rRNA gene analysis by PCR H haemolyticus with a 99 match Although standard genetic testing may be inadequate to distinguish H influenzae and H haemolyticus because of their genetic similarity1012 the demonstration of β-haemolysis on HBA for this isolate supports the PCR findings A few other Haemophilus species are known to display β-haemolysis on blood agar but they are not X and V-dependent 8 Participant results Two hundred and seventeen participants submitted results for this item with 192 (88) correctly identifying to genus level Under half were able to fully speciate The graph on the previous page illustrates participantsrsquo results Some biochemical tests commonly used by participants to identify include catalase (+) oxidase (+) indole (-) urea (+) growth on MacConkey agar (-) and XV-dependency (+) Many participants correctly identifying H haemolyticus observed the β-haemolytic activity of this isolate on blood agar and made note of it in their comments Identification kitssystems used and success rates in the hands of the users are listed below Please note that success rates may have been influenced by the observation (or lack thereof) of β-haemolysis

API NHmdashBiomerieux 1236 (33) correct H influenzae (24)

BBL Crystal-BD NeisseriaHaemophilus ID Kit 22 (100) correct

MALDI-TOF (Bruker ) 423(17) correct Pasteurella species (1) H influenzae (17) gram-negative rod (1)

MALDI-TOF (VITEK MS) 914 (64) correct H influenzae (4) Haemophilus species (1)

Rapid NH 1528 (54) correct Kingella kingae (1) H aegypticus (1) Haemophilus species (2) H influenzae (8) H parainfluenzae (1)

Sequencing 16S rRNA 78 (88) correct H influenzae (1)

VITEK2 GN 56 (83) correct H influenzae (1)

VITEK2 NH 3150 (62) correct Haemophilus species (1) Unable to identify-refer (1) H influenzae (17)

VITEK NHI 45 (80) correct H influenzae (1)

copy2013 RCPA Quality Assurance Programs Pty Limited 12 Date of issue 13th November 2013

References Item 5 1 McCrea KW et al Relationships of nontypeable Haemophilus influenzae strains to hemolytic and nonhemolytic Haemophilus haemolyticus strains J Clin

Microbiol 200846 406ndash416 httpwwwncbinlmnihgovpmcarticlesPMC2238123

2 Jordan IK et al Genome sequences for five strains of the emerging pathogen Haemophilus haemolyticus J Bacteriol 2011193 5879ndash5880

httpwwwncbinlmnihgovpmcarticlesPMC3187195

3 Anderson R et al Haemophilus haemolyticus isolates causing clinical disease J Clin Microbiol 201250 2462-5

httpwwwncbinlmnihgovpubmed22573587

4 Morton DJ et al An invasive Haemophilus haemolyticus isolate J Clin Microbiol 201250 1502ndash1503

httpwwwncbinlmnihgovpmcarticlesPMC3318549

5 Agrawal A Murphy TF Haemophilus influenzae infections in the H influenzae type b conjugate vaccine era J Clin Microbiol 201149 3728ndash3732

httpwwwncbinlmnihgovpmcarticlesPMC3209133

6 Kilian M A taxonomic study of the genus Haemophilus with the proposal of a new species J Gen Microbiol 197693 9ndash62

httpwwwncbinlmnihgovpubmed772168

7 Kilian M 2005 Genus III Haemophilus Winslow Broadhurst Buchanan Krumweide Rogers and Smith 1917 561 p 883ndash904 In Brenner DJ Krieg NR Staley JT (ed) Bergeyrsquos manual of systematic bacteriology 2nd ed vol 2 Springer New York NY

8 Ledeboer NA Doern GV 2012 Haemophilus In Versalovic J Carroll KC Funke G Jorgensen JH Landry ML WarnockDW(ed) Manual of clinical microbiology 10th ed ASM Press Washington DC

9 McCrea KW et al Relationships of nontypeable Haemophilus influenzae strains to hemolytic and nonhemolytic Haemophilus haemolyticus strains J Clin Microbiol 200846 406ndash416 httpwwwncbinlmnihgovpmcarticlesPMC2238123

10 Murphy TF et al Haemophilus haemolyticus a human respiratory tract commensal to be distinguished from Haemophilus influenzae J Infect Dis 2007195 81ndash 89 httpwwwncbinlmnihgovpubmed17152011

11 Identification Reference Laboratory Centre for Infectious Diseases and Microbiology ICPMR Westmead Hospital 12 Binks MJ et al Molecular Surveillance of True Nontypeable Haemophilus influenzae An Evaluation of PCR Screening Assays PLOS

httpwwwplosoneorgarticleinfo3Adoi2F1013712Fjournalpone0034083

13 Duerden B Bennet KW and Faulkner J Isolation of Bacteroides ureolyticus (B corrodens) from clinical infections J Clin Pathol 1982 35 309-312 httpjcpbmjcomcontent353309fullpdf

The most common misidentification by participants was H influenzae (35) because of the phenotypicgenetic similarity of the two species and because of the failure of all kitsidentification systems to differentiate between them Reliance on one type of identification system is discouraged and may lead to incorrect identification of some organisms In this instance β-haemolysis on blood agar facilitated an accurate identification if detected however as already noted it may not always be displayed in this species even in primary cultures H parahaemolyticus reported by three laboratories is also β-haemolytic but unlike H haemolyticus it is V-dependent only (and δ-Aminolevulinic acid (ALA) test negative) as is H parainfluenzae reported by two laboratories which is not β-haemolytic All other false identifications reported do not exhibit X+V dependency or X- or V-dependency The laboratory reporting Corynebacterium jeikeium should note that this is a gram-positive rod B ureolyticus reported by one laboratory is an anaerobic organism with corroding colonies on agar plates 13 Brucella and Francisella tularensis are slow-growing fastidious organisms (also not XV-dependent) that would not be dispatched in this type of QAP

ITEM 201364C CLERICAL ERROR

Clerical Errors reported in Item 201364C Number labs (71)

No error reported 6

Error first name only (correct) in 4C 60(85)

Error first name only in 4D (incorrect) 1

Error first name (correct) + last name (incorrect) 1

Error first name (correct) + unit number (incorrect) 1

Error last name (incorrect) 2

Table 13 Clerical errors reported

Specimen label Karina DANIELS UN 831248 Paperwork Amelia DANIELS UN 831248

The clerical error was placed in item 201364C Mycobacteriology culture As only 95 participants receive 4C and 4D culture vials and only 71 performed testing this clerical error has not been scored

copy2013 RCPA Quality Assurance Programs Pty Limited 13 Date of issue 13th November 2013

ITEM 201367ABC MYCOLOGY

7A This item contained Trichophyton interdigitale [zoophilic] (previously T mentagrophytes) 973 correct to genus level 634 correct to species level (required) The Trichophyton species have undergone extensive reclassification in the last 5 years This is because there exists much phenotypic variation but genetic variation is low Most of the species formerly known as T mentagrophytes are now classified within T interdigitale T mentagrophytes still exists but encompasses only the organism previously known as T quinckeanum (T mentagrophytes var quinckeanum) which is associated with mice T interdigitale is recognised as having two ecological groups the anthropophilic and the zoophilic group with the former T mentagrophytes species falls into the zoophilic group For this item T interdigitale and T mentagrophytes were both marked as correct This newly merged species encompasses a wide range of phenotypes which may or may not be observed for a given specimen Sequencing of the internal transcribed spacer (ITS) region is the gold standard for identification using reference strains that are correctly named according to the revised taxonomy Chen et al have published a useful book chapter with phenotypic descriptions and recommendations for molecular identification of the revised Trichophyton species1

7A Trichophyton interdigitale [zoophilic]

Figures 7A (i-iii) Trichophyton interdigitale [zoophilic group] (previously T mentagrophytes) may have [7A(i)] numerous single-celled microconidia often in dense clusters along with smooth thin-walled cigar-shaped multicelled macroconidia Microconidia are hyaline smooth-walled and are predominantly spherical to subspherical in shape however occasional clavate to pyriform forms may occur [7A(ii)] varying numbers of spherical chlamydoconidia and [7A (iii)] spiral hyphae may also be observed The zoophilic form of the species tends to have powdery-granular colonies on Sabouraudrsquos lactritmel and 1 peptone media while the anthropophilic form has suede-downy textured colonies

1

1

1

1

1

2

2

5

6

7

14

1

31

1

5

20

13

0 5 10 15 20 25 30 35

Chrysosporium tropicum

Microsporum gypseum

Microsporum persicolor

Trichophyton equinum

Trichophyton terrestre

Trichophyton erinacei

Trichophyton verrucosum

Trichophyton species

Trichophyton rubrum [Worldwide population]

Trichophyton tonsurans

Trichophyton rubrum

Trichophyton mentagrophytes complex

Trichophyton mentagrophytes

Trichophyton interdigitale [anthropophilic] and [zoophilic]

Trichophyton interdigitale [anthropophilic]

Trichophyton interdigitale

Trichophyton interdigitale [zoophilic]

13 116

20 179

5 45

1 09

31 277

1 09

14 125

7 63

6 54

5 45

2 18

2 18

1 09

1 09

1 09

1 09

1 09

7A (i)

7A (ii) 7A (iii)

copy2013 RCPA Quality Assurance Programs Pty Limited 14 Date of issue 13th November 2013

7B Cryptococcus neoformans

82 732

8 71

1 09

1 09

5 45

11 98

1 09

1 09

1 09

1 09

7B This item contained Cryptococcus neoformans 964 correct to genus level 812 correct to species level (required) Cryptococcosis is typically caused by either Cryptococcus neoformans or Cryptococcus gattii although occasionally other Cryptococcus species have been implicated C neoformans typically infects the immunocompromised host frequently in the setting of HIV with gt1 million new cases and~600000 deaths per year globally C neoformans is a yeast-like basidiomycete fungus with a distinctive polysaccharide capsule Differentiation from the closely related C gattii is important Presumptive identification is by India Ink stain to highlight the capsule and birdseed agar to observe dark brown colonies

Figure 7B (i-iii) [7B (i)] India Ink stain highlighting the capsule of C neoformansgattii [7B(ii)] Dark brown colonies of C neoformansgattii mixed with white colonies of Candida albicans on birdseed agar [7B(iii)] Canavanine glycine bromothyol blue (CGB) media for distinguishing C neoformans (left) from C gattii (right)

1

1

1

1

11

5

1

1

8

82

0 10 20 30 40 50 60 70 80 90

Unable to identify- refer

Candida (not albicans)

Candida glabrata complex

Candida krusei

Cryptococcus neoformansgattii- unable to speciate

Cryptococcus species

Cryptococcus laurentii

Cryptococcus neoformans var grubii

Cryptococcus neoformans var neoformans

Cryptococcus neoformans

81 of labs correctly reported this isolate as Cryptococcus neoformans While no lab reported C gattii 11 labs were unable to differentiate C neoformans from C gattii Epidemiology risk factors and treatment of infections caused by these species are different and accurate identification is important for effective management All labs should seek to differentiate these species using CGB media a validated molecular method or by referral to a reference laboratory API ID32C and Vitek-2 does not distinguish C neoformans from C gattii These species may be differentiated by a number of DNA-based assays MALDI-ToF and canavanine-glycine-bromothymol blue (CGB) media C neoformans does not grow on CGB media which remains yellow whereas C gattii will grow triggering a blue colour change reaction in the media usually within 3 days It is worth noting that some slow growing C gattii isolates may take as long as 10 days to effect the blue colour change and may initially be mis-identified as C neoformans Nine labs unnecessarily attempted to further identify the C neoformans isolate to variety level either Cn var grubii (serotype A molecular types VNI and VNII) or Cn var neoformans (serotype D molecular type VNIV) It is not clear what methods were used to achieve this varietal identification but 8 of the 9 labs incorrectly reported Cn var neoformans In fact the isolate was confirmed by molecular methods to be Cryptococcus neoformans var grubii molecular type VNI The 8 reports of Cn var neoformans may reflect persistence of the now obsolete classification of Cryptococcus neoformans having two varieties var neoformans and var gattii If it is the normal practice of these labs to report to varietal level it would be worthwhile reviewing methods interpretation and reporting procedures

7B (i) 7B (ii) 7B(iii)

copy2013 RCPA Quality Assurance Programs Pty Limited 15 Date of issue 13th November 2013

Reference item 7

1 Chen SC DH Ellis TC Sorrell and W Meyer Chapter 44 Trichophyton In ldquoMolecular Detection of Human Fungal Pathogensrdquo Dongyou Liu (Ed) CRC Press 2011

All mycology isolates were identified by both conventional and molecular techniques

86 768

9 80

1 09

2 18

3 27

3 27

2 18

1 09

1 09

1 09

1 09

2 18

7C Scedosporium prolificans

This item contained Scedosporium prolificans 875 correct to genus level 768 correct to species level (required) Colonies are rapid growing flat spreading olive-grey to black (the culture may contain a mixture of the colurs depending on the age) and have a suede-like to downy surface texture [7C (i)] Conidia are borne in small groups on distinctive basally swollen flask-shaped annellides which occur singly or in clusters along the vegetative hyphae Conidia are single-celled hyaline to pale-brown ovoid to pyriform 2-5 x 3-13 um (average 34-53 um) in size and have smooth thin walls [7C (ii)] Identification of Scedosporium prolificans to

species level is very important due to its intrinsic resistance to most antifungal drugs It may be distinguished from other members of the genus in particular the human pathogen S apiospermum by its basally swollen (inflated) flask-shaped annellides conidia borne in small groups rather than singly and by not growing on media containing cycloheximide (actidione) DNA sequencing (ITS region) will also definitively identify Scedosporium species Three laboratories reported Sporothrix schenckii which is easily distinguished from Scedosporium spp because it is a dimorphic pathogen with a yeast-like phase when grown at 37degC

2

1

1

1

1

2

3

3

2

1

9

86

0 10 20 30 40 50 60 70 80 90 100

Unable to identify- refer

Chaetomium species

Hortaea werneckii

Ochroconis gallopava

Wangiella species

Exophiala species

Exophiala dermatitidis

Sporothrix schenckii

Scedosporium species

Scedosporium aurantiacum

Scedosporium apiospermum (sensu stricto)

Scedosporium prolificans

7C (i) 7C (ii)

Page 8: FINAL RESULTS AND COMMENTS D6-2013 …dataentry.rcpaqap.com.au/micro/reports/uploadedfiles/fnl2013-6.pdf · FINAL RESULTS AND COMMENTS D6/2013 ... This item contained a pure growth

copy2013 RCPA Quality Assurance Programs Pty Limited 8 Date of issue 13th November 2013

Figure 3a A hydrophilia with cephalosporinase A1 amp carbapenemase A2 copy South Eastern Area Laboratory Services httpwebmedunsweduaucdstest

Figure 3b A sobria with carbapenemase A2 but lacking cephalosporinase A1 copy South Eastern Area Laboratory Services httpwebmedunsweduaucdstest

References Item 3 1 Parker JL and Shaw JG Aeromonas spp clinical microbiology and disease Journal of infection 201162 109-118 httpwwwsciencedirectcomsciencearticlepiiS0163445310003543bbib10 2 Janda JM and Abbott SL The genus Aeromonas taxonomy pathogenicity and infection Clin Microbiol Rev 201023 35ndash73 httpwwwncbinlmnihgovpmcarticlesPMC2806660 3 Horneman AJ and Afsar A Aeromonas Ch 38 In Versalovic J Carroll KC Funke G Jorgensen JH Landry ML WarnockDW(ed) Manual of clinical

microbiology 10th ed ASM Press Washington DC 4 Bullock GL The identification and separation of Aeromonas liquefaciens from Pseudomonas fluorescens and related organisms occurring in dis-

eased fish Appl Microbiol 19619 587ndash590 httpwwwncbinlmnihgovpmcarticlesPMC1057793 5 Antibiotic susceptibility testing by the CDS method httpwebmedunsweduaucdstest 6 Walsh TR et al Distribution and expression of β-lactamase genes among Aeromonas spp Journal of Antimicrobial Chemotherapy 199740 171ndash

178 httpjacoxfordjournalsorgcontent402171fullpdf 7 Wu C-J et al Distribution and phenotypic and genotypic detection of a metallo-b-lactamase CphA among bacteraemic Aeromonas isolates Jour-

nal of Medical Microbiology 201261 712ndash719 httpwwwncbinlmnihgovpubmed22322339 8 Aravena-Romaacuten M et al Antimicrobial susceptibilities of Aeromonas strains isolated from clinical and environmental sources to 26 antimicrobial

agents J Med Microbiol 201261 712-9 httpaacasmorgcontent5621110 9 Rossolini GM et al The Aeromonas metallo-β-lactamases genetics enzymology and contribution to drug resistance Microb Drug Resist 1996 2

245-252 httponlineliebertpubcomdoiabs101089mdr19962245

10 CLSI standard A45-A2 Methods for antimicrobial dilution and disk susceptibility testing for infrequently isolated or fastidious bacteria approved guidelinemdashsecond edition August 2010

copy2013 RCPA Quality Assurance Programs Pty Limited 9 Date of issue 13th November 2013

ITEM 201364ABCD CULTURE AND MICROSCOPY FOR AFB

Reference laboratory report

Culture results C D

Mycobacterium species isolated 59 0

Mycobacterium species not isolated 10 70

Not result reported 2 1

Participant smear results A B

Negative 17 178

1 - 9100 HPF 115 3

10 - 99100 HPF 47 2

1 - 10HPF 4 -

Table 11 Results for mediamethods used for specimen 4C

Table 9 Participant smear results

Table 10 Participant culture results

Table 12 Molecular Diagnostics

Molecular Diagnostics

C D

Mycobacterium TB Complex DNA amplification Positive

13 0

Mycobacterium TB Complex DNA amplification Negative

1 12

No result reported 1 3

Media Total no inoculated

Number positive

BacTALERT amp 3D 9 6

BD BACTEC MGIT 960 System 43 38

BD BBL MGIT 5 3

Brown amp Buckle 3 1

LJ 32 21

LJ Glycerol 6 5

LJ Pyruvate 15 8

LJ Pyruvate Glycerol 4 3

Ogawa 6 2

Other 10 7

Test A B

AFB stain Ziehl Neelsen

Positive 1-9100 HPF

No AFB seen

C D

Culture Bactec MGIT 960 (BD)L-J

Mycobacterium tuberculosis

present

Mycobacterium species absent

Microscopy Results Slides were prepared in this survey using sputum seeded with Mycobacterium tuberculosis H37Ra The sputum used was examined before inoculation with the M tuberculosis strain using a Ziehl-Neelsen stain and tested for M tuberculosis and MAC by molecular methods and found to be negative Smear 4A Slide 4A contained scanty (1-9100HPF) numbers of AFB It was examined by a reference laboratory and a RCPAQAP scientist The three smears examined by the reference laboratory were confirmed positive and contained 4 1 and 3 AFB100HPF Ten randomly selected smears examined by RCPAQAP contained from 4 to 9 AFB100HPF Most laboratories (91 or 92 when transcription errors were included) reported a positive result with the majority (63) reporting 1-9 AFB100 HPF Three transcription errors were apparent among the 17 negative results reported It is recommended these laboratories carefully review their smears Participants are requested to report AFB counts based on acid fast stains rather than on fluorescent stains Smear 4B Smear 4B contained no AFB and this was confirmed by the reference laboratory and 10 smears examined by a RCPAQAP scientist As already mentioned 3 of the 5 laboratories reporting positive results transcribed them in error The other 2 reported positive results in both smears Culture Results Item 4C Sample 4C contained Mycobacterium tuberculosis and organisms representing normal upper respiratory tract flora such as Staphylococcus epidermidis Neisseria subflava and alpha-haemolytic streptococci Of the 69 participants returning a result the majority (86) reported this sample positive Item 4D Sample 4D contained the above upper respiratory organisms only and no Mycobacteria species All participants returning a result reported it negative for Mycobacteria species Molecular Diagnostics Results Fifteen laboratories performed molecular diagnostics for M tuberculosis (14 laboratories returned results on sample 4C and 12 on 4D) Please refer to Table 12 for participant results All methods used are listed below Gene Expert 2 HAIN (MTBDR) 1 HAIN (Mycobacterium CM) 1 Inhouse PCR 3 ProbeTec 2 qPCR 1 Roche Cobas 1 Seegene 1 Taqman 2 Not stated 1

Table 8 4A-D expected results

copy2013 RCPA Quality Assurance Programs Pty Limited 10 Date of issue 13th November 2013

includes presumptive identification(s)

ITEM 201365 ISOLATE FOR IDENTIFICATION

includes presumptive identification(s)

103 475

1 05

72 332

4 18

3 14

2 09

7 32

1 05

1 05

1 05

1 05

1 05

1 05

2 09

1 05

1 05

1 05

14 65

Fig 5b H haemolyticus on HBA copy 2013 RCPA QAP

ITEM 201365 Haemophilus haemolyticus This item contained a pure growth of Haemophilus haemolyticus Homogeneity and stability testing for this organism was satisfactory with bacterial counts for the H haemolyticus remaining above 10 x 1010CFUL throughout the survey

This organism represented an isolate from blood culture collected from a patient with endocarditis H haemolyticus is a human commensal of the nasopharynx in some individuals Some authors find its pathogenicity debatable but it has occasionally been implicated in disease 123 Phenotypically and genotypically it is difficult to distinguish from non-typeable H influenzae except for β-haemolysis on blood agar in the case of H haemolyticus 45678 But even this can be an unreliable characteristic as non-haemolytic strains occur and upon repeated sub-culture this trait may disappear 5910 For this reason it has been suggested that H haemolyticus is more commonly misidentified as H influenzae than is recognised5 Like H influenzae H haemolyticus is a fastidious facultative anaerobe XV-dependent oxidase and catalase positive gram-negative coccobacillus

Fig 5a H haemolyticus on Chocolate Agar copy 2013 RCPA QAP

14

1

1

1

2

1

1

1

1

1

1

7

2

3

4

72

1

103

0 20 40 60 80 100 120

Unable to Identify - Refer

Psychrobacter phenylpyruvicus

Pasteurella species

Other

Kingella kingae

Gram negative rod

Francisella tularensis

Corynebacterium jeikeium

Brucella spp

Bacteroides ureolyticus

Actinobacillus actinomycetemcomitans

Haemophilus species

Haemophilus parainfluenzae

Haemophilus parahaemolyticus

Haemophilus influenzae type B

Haemophilus influenzae

Haemophilus aegyptius

Haemophilus haemolyticus

copy2013 RCPA Quality Assurance Programs Pty Limited 11 Date of issue 13th November 2013

SUMMARY OF PHENOTYPIC AND BIOCHEMICAL RESULTS 811

Phenotypic characteristics

Gram stain Small gram-positive rods and coccobacilli

Motility RT (BHI broth) non-motile

Colonial appearance on Chocolate agar (CA) 24hrs 10mm beige shiny round entire colonies

Colonial appearance on Horse Blood agar (HBA) 24hrs pinpoint translucent shiny round entire colonies

Pigment pale yellow

Haemolysis β (key distinguishing test if apparent) This isolate was haemolytic on HBA

Catalase positive

Oxidase positive

KIA slope NCNC gas negative

Satellitism XV + V - X - Growth conditions

Growth on HBA 35degC in O2 +

Growth on HBA 35degC in CO2 ++

Growth on HBA 35degC in ANO2 +

Growth on CA 35degC 35degC +++

Growth on MacConkey agar no growth Biochemical tests Rapid substrate utilisation

Urease positive

Nitrate positive

Indole negative

Aesculin negative

ADH negative

LDC negative

ODC negative

Glucose positive

Xylose negative

Mannitol negative

Lactose positive (weak) 11

Sucrose negative

Maltose positive (weak) 11 16S rRNA gene analysis by PCR H haemolyticus with a 99 match Although standard genetic testing may be inadequate to distinguish H influenzae and H haemolyticus because of their genetic similarity1012 the demonstration of β-haemolysis on HBA for this isolate supports the PCR findings A few other Haemophilus species are known to display β-haemolysis on blood agar but they are not X and V-dependent 8 Participant results Two hundred and seventeen participants submitted results for this item with 192 (88) correctly identifying to genus level Under half were able to fully speciate The graph on the previous page illustrates participantsrsquo results Some biochemical tests commonly used by participants to identify include catalase (+) oxidase (+) indole (-) urea (+) growth on MacConkey agar (-) and XV-dependency (+) Many participants correctly identifying H haemolyticus observed the β-haemolytic activity of this isolate on blood agar and made note of it in their comments Identification kitssystems used and success rates in the hands of the users are listed below Please note that success rates may have been influenced by the observation (or lack thereof) of β-haemolysis

API NHmdashBiomerieux 1236 (33) correct H influenzae (24)

BBL Crystal-BD NeisseriaHaemophilus ID Kit 22 (100) correct

MALDI-TOF (Bruker ) 423(17) correct Pasteurella species (1) H influenzae (17) gram-negative rod (1)

MALDI-TOF (VITEK MS) 914 (64) correct H influenzae (4) Haemophilus species (1)

Rapid NH 1528 (54) correct Kingella kingae (1) H aegypticus (1) Haemophilus species (2) H influenzae (8) H parainfluenzae (1)

Sequencing 16S rRNA 78 (88) correct H influenzae (1)

VITEK2 GN 56 (83) correct H influenzae (1)

VITEK2 NH 3150 (62) correct Haemophilus species (1) Unable to identify-refer (1) H influenzae (17)

VITEK NHI 45 (80) correct H influenzae (1)

copy2013 RCPA Quality Assurance Programs Pty Limited 12 Date of issue 13th November 2013

References Item 5 1 McCrea KW et al Relationships of nontypeable Haemophilus influenzae strains to hemolytic and nonhemolytic Haemophilus haemolyticus strains J Clin

Microbiol 200846 406ndash416 httpwwwncbinlmnihgovpmcarticlesPMC2238123

2 Jordan IK et al Genome sequences for five strains of the emerging pathogen Haemophilus haemolyticus J Bacteriol 2011193 5879ndash5880

httpwwwncbinlmnihgovpmcarticlesPMC3187195

3 Anderson R et al Haemophilus haemolyticus isolates causing clinical disease J Clin Microbiol 201250 2462-5

httpwwwncbinlmnihgovpubmed22573587

4 Morton DJ et al An invasive Haemophilus haemolyticus isolate J Clin Microbiol 201250 1502ndash1503

httpwwwncbinlmnihgovpmcarticlesPMC3318549

5 Agrawal A Murphy TF Haemophilus influenzae infections in the H influenzae type b conjugate vaccine era J Clin Microbiol 201149 3728ndash3732

httpwwwncbinlmnihgovpmcarticlesPMC3209133

6 Kilian M A taxonomic study of the genus Haemophilus with the proposal of a new species J Gen Microbiol 197693 9ndash62

httpwwwncbinlmnihgovpubmed772168

7 Kilian M 2005 Genus III Haemophilus Winslow Broadhurst Buchanan Krumweide Rogers and Smith 1917 561 p 883ndash904 In Brenner DJ Krieg NR Staley JT (ed) Bergeyrsquos manual of systematic bacteriology 2nd ed vol 2 Springer New York NY

8 Ledeboer NA Doern GV 2012 Haemophilus In Versalovic J Carroll KC Funke G Jorgensen JH Landry ML WarnockDW(ed) Manual of clinical microbiology 10th ed ASM Press Washington DC

9 McCrea KW et al Relationships of nontypeable Haemophilus influenzae strains to hemolytic and nonhemolytic Haemophilus haemolyticus strains J Clin Microbiol 200846 406ndash416 httpwwwncbinlmnihgovpmcarticlesPMC2238123

10 Murphy TF et al Haemophilus haemolyticus a human respiratory tract commensal to be distinguished from Haemophilus influenzae J Infect Dis 2007195 81ndash 89 httpwwwncbinlmnihgovpubmed17152011

11 Identification Reference Laboratory Centre for Infectious Diseases and Microbiology ICPMR Westmead Hospital 12 Binks MJ et al Molecular Surveillance of True Nontypeable Haemophilus influenzae An Evaluation of PCR Screening Assays PLOS

httpwwwplosoneorgarticleinfo3Adoi2F1013712Fjournalpone0034083

13 Duerden B Bennet KW and Faulkner J Isolation of Bacteroides ureolyticus (B corrodens) from clinical infections J Clin Pathol 1982 35 309-312 httpjcpbmjcomcontent353309fullpdf

The most common misidentification by participants was H influenzae (35) because of the phenotypicgenetic similarity of the two species and because of the failure of all kitsidentification systems to differentiate between them Reliance on one type of identification system is discouraged and may lead to incorrect identification of some organisms In this instance β-haemolysis on blood agar facilitated an accurate identification if detected however as already noted it may not always be displayed in this species even in primary cultures H parahaemolyticus reported by three laboratories is also β-haemolytic but unlike H haemolyticus it is V-dependent only (and δ-Aminolevulinic acid (ALA) test negative) as is H parainfluenzae reported by two laboratories which is not β-haemolytic All other false identifications reported do not exhibit X+V dependency or X- or V-dependency The laboratory reporting Corynebacterium jeikeium should note that this is a gram-positive rod B ureolyticus reported by one laboratory is an anaerobic organism with corroding colonies on agar plates 13 Brucella and Francisella tularensis are slow-growing fastidious organisms (also not XV-dependent) that would not be dispatched in this type of QAP

ITEM 201364C CLERICAL ERROR

Clerical Errors reported in Item 201364C Number labs (71)

No error reported 6

Error first name only (correct) in 4C 60(85)

Error first name only in 4D (incorrect) 1

Error first name (correct) + last name (incorrect) 1

Error first name (correct) + unit number (incorrect) 1

Error last name (incorrect) 2

Table 13 Clerical errors reported

Specimen label Karina DANIELS UN 831248 Paperwork Amelia DANIELS UN 831248

The clerical error was placed in item 201364C Mycobacteriology culture As only 95 participants receive 4C and 4D culture vials and only 71 performed testing this clerical error has not been scored

copy2013 RCPA Quality Assurance Programs Pty Limited 13 Date of issue 13th November 2013

ITEM 201367ABC MYCOLOGY

7A This item contained Trichophyton interdigitale [zoophilic] (previously T mentagrophytes) 973 correct to genus level 634 correct to species level (required) The Trichophyton species have undergone extensive reclassification in the last 5 years This is because there exists much phenotypic variation but genetic variation is low Most of the species formerly known as T mentagrophytes are now classified within T interdigitale T mentagrophytes still exists but encompasses only the organism previously known as T quinckeanum (T mentagrophytes var quinckeanum) which is associated with mice T interdigitale is recognised as having two ecological groups the anthropophilic and the zoophilic group with the former T mentagrophytes species falls into the zoophilic group For this item T interdigitale and T mentagrophytes were both marked as correct This newly merged species encompasses a wide range of phenotypes which may or may not be observed for a given specimen Sequencing of the internal transcribed spacer (ITS) region is the gold standard for identification using reference strains that are correctly named according to the revised taxonomy Chen et al have published a useful book chapter with phenotypic descriptions and recommendations for molecular identification of the revised Trichophyton species1

7A Trichophyton interdigitale [zoophilic]

Figures 7A (i-iii) Trichophyton interdigitale [zoophilic group] (previously T mentagrophytes) may have [7A(i)] numerous single-celled microconidia often in dense clusters along with smooth thin-walled cigar-shaped multicelled macroconidia Microconidia are hyaline smooth-walled and are predominantly spherical to subspherical in shape however occasional clavate to pyriform forms may occur [7A(ii)] varying numbers of spherical chlamydoconidia and [7A (iii)] spiral hyphae may also be observed The zoophilic form of the species tends to have powdery-granular colonies on Sabouraudrsquos lactritmel and 1 peptone media while the anthropophilic form has suede-downy textured colonies

1

1

1

1

1

2

2

5

6

7

14

1

31

1

5

20

13

0 5 10 15 20 25 30 35

Chrysosporium tropicum

Microsporum gypseum

Microsporum persicolor

Trichophyton equinum

Trichophyton terrestre

Trichophyton erinacei

Trichophyton verrucosum

Trichophyton species

Trichophyton rubrum [Worldwide population]

Trichophyton tonsurans

Trichophyton rubrum

Trichophyton mentagrophytes complex

Trichophyton mentagrophytes

Trichophyton interdigitale [anthropophilic] and [zoophilic]

Trichophyton interdigitale [anthropophilic]

Trichophyton interdigitale

Trichophyton interdigitale [zoophilic]

13 116

20 179

5 45

1 09

31 277

1 09

14 125

7 63

6 54

5 45

2 18

2 18

1 09

1 09

1 09

1 09

1 09

7A (i)

7A (ii) 7A (iii)

copy2013 RCPA Quality Assurance Programs Pty Limited 14 Date of issue 13th November 2013

7B Cryptococcus neoformans

82 732

8 71

1 09

1 09

5 45

11 98

1 09

1 09

1 09

1 09

7B This item contained Cryptococcus neoformans 964 correct to genus level 812 correct to species level (required) Cryptococcosis is typically caused by either Cryptococcus neoformans or Cryptococcus gattii although occasionally other Cryptococcus species have been implicated C neoformans typically infects the immunocompromised host frequently in the setting of HIV with gt1 million new cases and~600000 deaths per year globally C neoformans is a yeast-like basidiomycete fungus with a distinctive polysaccharide capsule Differentiation from the closely related C gattii is important Presumptive identification is by India Ink stain to highlight the capsule and birdseed agar to observe dark brown colonies

Figure 7B (i-iii) [7B (i)] India Ink stain highlighting the capsule of C neoformansgattii [7B(ii)] Dark brown colonies of C neoformansgattii mixed with white colonies of Candida albicans on birdseed agar [7B(iii)] Canavanine glycine bromothyol blue (CGB) media for distinguishing C neoformans (left) from C gattii (right)

1

1

1

1

11

5

1

1

8

82

0 10 20 30 40 50 60 70 80 90

Unable to identify- refer

Candida (not albicans)

Candida glabrata complex

Candida krusei

Cryptococcus neoformansgattii- unable to speciate

Cryptococcus species

Cryptococcus laurentii

Cryptococcus neoformans var grubii

Cryptococcus neoformans var neoformans

Cryptococcus neoformans

81 of labs correctly reported this isolate as Cryptococcus neoformans While no lab reported C gattii 11 labs were unable to differentiate C neoformans from C gattii Epidemiology risk factors and treatment of infections caused by these species are different and accurate identification is important for effective management All labs should seek to differentiate these species using CGB media a validated molecular method or by referral to a reference laboratory API ID32C and Vitek-2 does not distinguish C neoformans from C gattii These species may be differentiated by a number of DNA-based assays MALDI-ToF and canavanine-glycine-bromothymol blue (CGB) media C neoformans does not grow on CGB media which remains yellow whereas C gattii will grow triggering a blue colour change reaction in the media usually within 3 days It is worth noting that some slow growing C gattii isolates may take as long as 10 days to effect the blue colour change and may initially be mis-identified as C neoformans Nine labs unnecessarily attempted to further identify the C neoformans isolate to variety level either Cn var grubii (serotype A molecular types VNI and VNII) or Cn var neoformans (serotype D molecular type VNIV) It is not clear what methods were used to achieve this varietal identification but 8 of the 9 labs incorrectly reported Cn var neoformans In fact the isolate was confirmed by molecular methods to be Cryptococcus neoformans var grubii molecular type VNI The 8 reports of Cn var neoformans may reflect persistence of the now obsolete classification of Cryptococcus neoformans having two varieties var neoformans and var gattii If it is the normal practice of these labs to report to varietal level it would be worthwhile reviewing methods interpretation and reporting procedures

7B (i) 7B (ii) 7B(iii)

copy2013 RCPA Quality Assurance Programs Pty Limited 15 Date of issue 13th November 2013

Reference item 7

1 Chen SC DH Ellis TC Sorrell and W Meyer Chapter 44 Trichophyton In ldquoMolecular Detection of Human Fungal Pathogensrdquo Dongyou Liu (Ed) CRC Press 2011

All mycology isolates were identified by both conventional and molecular techniques

86 768

9 80

1 09

2 18

3 27

3 27

2 18

1 09

1 09

1 09

1 09

2 18

7C Scedosporium prolificans

This item contained Scedosporium prolificans 875 correct to genus level 768 correct to species level (required) Colonies are rapid growing flat spreading olive-grey to black (the culture may contain a mixture of the colurs depending on the age) and have a suede-like to downy surface texture [7C (i)] Conidia are borne in small groups on distinctive basally swollen flask-shaped annellides which occur singly or in clusters along the vegetative hyphae Conidia are single-celled hyaline to pale-brown ovoid to pyriform 2-5 x 3-13 um (average 34-53 um) in size and have smooth thin walls [7C (ii)] Identification of Scedosporium prolificans to

species level is very important due to its intrinsic resistance to most antifungal drugs It may be distinguished from other members of the genus in particular the human pathogen S apiospermum by its basally swollen (inflated) flask-shaped annellides conidia borne in small groups rather than singly and by not growing on media containing cycloheximide (actidione) DNA sequencing (ITS region) will also definitively identify Scedosporium species Three laboratories reported Sporothrix schenckii which is easily distinguished from Scedosporium spp because it is a dimorphic pathogen with a yeast-like phase when grown at 37degC

2

1

1

1

1

2

3

3

2

1

9

86

0 10 20 30 40 50 60 70 80 90 100

Unable to identify- refer

Chaetomium species

Hortaea werneckii

Ochroconis gallopava

Wangiella species

Exophiala species

Exophiala dermatitidis

Sporothrix schenckii

Scedosporium species

Scedosporium aurantiacum

Scedosporium apiospermum (sensu stricto)

Scedosporium prolificans

7C (i) 7C (ii)

Page 9: FINAL RESULTS AND COMMENTS D6-2013 …dataentry.rcpaqap.com.au/micro/reports/uploadedfiles/fnl2013-6.pdf · FINAL RESULTS AND COMMENTS D6/2013 ... This item contained a pure growth

copy2013 RCPA Quality Assurance Programs Pty Limited 9 Date of issue 13th November 2013

ITEM 201364ABCD CULTURE AND MICROSCOPY FOR AFB

Reference laboratory report

Culture results C D

Mycobacterium species isolated 59 0

Mycobacterium species not isolated 10 70

Not result reported 2 1

Participant smear results A B

Negative 17 178

1 - 9100 HPF 115 3

10 - 99100 HPF 47 2

1 - 10HPF 4 -

Table 11 Results for mediamethods used for specimen 4C

Table 9 Participant smear results

Table 10 Participant culture results

Table 12 Molecular Diagnostics

Molecular Diagnostics

C D

Mycobacterium TB Complex DNA amplification Positive

13 0

Mycobacterium TB Complex DNA amplification Negative

1 12

No result reported 1 3

Media Total no inoculated

Number positive

BacTALERT amp 3D 9 6

BD BACTEC MGIT 960 System 43 38

BD BBL MGIT 5 3

Brown amp Buckle 3 1

LJ 32 21

LJ Glycerol 6 5

LJ Pyruvate 15 8

LJ Pyruvate Glycerol 4 3

Ogawa 6 2

Other 10 7

Test A B

AFB stain Ziehl Neelsen

Positive 1-9100 HPF

No AFB seen

C D

Culture Bactec MGIT 960 (BD)L-J

Mycobacterium tuberculosis

present

Mycobacterium species absent

Microscopy Results Slides were prepared in this survey using sputum seeded with Mycobacterium tuberculosis H37Ra The sputum used was examined before inoculation with the M tuberculosis strain using a Ziehl-Neelsen stain and tested for M tuberculosis and MAC by molecular methods and found to be negative Smear 4A Slide 4A contained scanty (1-9100HPF) numbers of AFB It was examined by a reference laboratory and a RCPAQAP scientist The three smears examined by the reference laboratory were confirmed positive and contained 4 1 and 3 AFB100HPF Ten randomly selected smears examined by RCPAQAP contained from 4 to 9 AFB100HPF Most laboratories (91 or 92 when transcription errors were included) reported a positive result with the majority (63) reporting 1-9 AFB100 HPF Three transcription errors were apparent among the 17 negative results reported It is recommended these laboratories carefully review their smears Participants are requested to report AFB counts based on acid fast stains rather than on fluorescent stains Smear 4B Smear 4B contained no AFB and this was confirmed by the reference laboratory and 10 smears examined by a RCPAQAP scientist As already mentioned 3 of the 5 laboratories reporting positive results transcribed them in error The other 2 reported positive results in both smears Culture Results Item 4C Sample 4C contained Mycobacterium tuberculosis and organisms representing normal upper respiratory tract flora such as Staphylococcus epidermidis Neisseria subflava and alpha-haemolytic streptococci Of the 69 participants returning a result the majority (86) reported this sample positive Item 4D Sample 4D contained the above upper respiratory organisms only and no Mycobacteria species All participants returning a result reported it negative for Mycobacteria species Molecular Diagnostics Results Fifteen laboratories performed molecular diagnostics for M tuberculosis (14 laboratories returned results on sample 4C and 12 on 4D) Please refer to Table 12 for participant results All methods used are listed below Gene Expert 2 HAIN (MTBDR) 1 HAIN (Mycobacterium CM) 1 Inhouse PCR 3 ProbeTec 2 qPCR 1 Roche Cobas 1 Seegene 1 Taqman 2 Not stated 1

Table 8 4A-D expected results

copy2013 RCPA Quality Assurance Programs Pty Limited 10 Date of issue 13th November 2013

includes presumptive identification(s)

ITEM 201365 ISOLATE FOR IDENTIFICATION

includes presumptive identification(s)

103 475

1 05

72 332

4 18

3 14

2 09

7 32

1 05

1 05

1 05

1 05

1 05

1 05

2 09

1 05

1 05

1 05

14 65

Fig 5b H haemolyticus on HBA copy 2013 RCPA QAP

ITEM 201365 Haemophilus haemolyticus This item contained a pure growth of Haemophilus haemolyticus Homogeneity and stability testing for this organism was satisfactory with bacterial counts for the H haemolyticus remaining above 10 x 1010CFUL throughout the survey

This organism represented an isolate from blood culture collected from a patient with endocarditis H haemolyticus is a human commensal of the nasopharynx in some individuals Some authors find its pathogenicity debatable but it has occasionally been implicated in disease 123 Phenotypically and genotypically it is difficult to distinguish from non-typeable H influenzae except for β-haemolysis on blood agar in the case of H haemolyticus 45678 But even this can be an unreliable characteristic as non-haemolytic strains occur and upon repeated sub-culture this trait may disappear 5910 For this reason it has been suggested that H haemolyticus is more commonly misidentified as H influenzae than is recognised5 Like H influenzae H haemolyticus is a fastidious facultative anaerobe XV-dependent oxidase and catalase positive gram-negative coccobacillus

Fig 5a H haemolyticus on Chocolate Agar copy 2013 RCPA QAP

14

1

1

1

2

1

1

1

1

1

1

7

2

3

4

72

1

103

0 20 40 60 80 100 120

Unable to Identify - Refer

Psychrobacter phenylpyruvicus

Pasteurella species

Other

Kingella kingae

Gram negative rod

Francisella tularensis

Corynebacterium jeikeium

Brucella spp

Bacteroides ureolyticus

Actinobacillus actinomycetemcomitans

Haemophilus species

Haemophilus parainfluenzae

Haemophilus parahaemolyticus

Haemophilus influenzae type B

Haemophilus influenzae

Haemophilus aegyptius

Haemophilus haemolyticus

copy2013 RCPA Quality Assurance Programs Pty Limited 11 Date of issue 13th November 2013

SUMMARY OF PHENOTYPIC AND BIOCHEMICAL RESULTS 811

Phenotypic characteristics

Gram stain Small gram-positive rods and coccobacilli

Motility RT (BHI broth) non-motile

Colonial appearance on Chocolate agar (CA) 24hrs 10mm beige shiny round entire colonies

Colonial appearance on Horse Blood agar (HBA) 24hrs pinpoint translucent shiny round entire colonies

Pigment pale yellow

Haemolysis β (key distinguishing test if apparent) This isolate was haemolytic on HBA

Catalase positive

Oxidase positive

KIA slope NCNC gas negative

Satellitism XV + V - X - Growth conditions

Growth on HBA 35degC in O2 +

Growth on HBA 35degC in CO2 ++

Growth on HBA 35degC in ANO2 +

Growth on CA 35degC 35degC +++

Growth on MacConkey agar no growth Biochemical tests Rapid substrate utilisation

Urease positive

Nitrate positive

Indole negative

Aesculin negative

ADH negative

LDC negative

ODC negative

Glucose positive

Xylose negative

Mannitol negative

Lactose positive (weak) 11

Sucrose negative

Maltose positive (weak) 11 16S rRNA gene analysis by PCR H haemolyticus with a 99 match Although standard genetic testing may be inadequate to distinguish H influenzae and H haemolyticus because of their genetic similarity1012 the demonstration of β-haemolysis on HBA for this isolate supports the PCR findings A few other Haemophilus species are known to display β-haemolysis on blood agar but they are not X and V-dependent 8 Participant results Two hundred and seventeen participants submitted results for this item with 192 (88) correctly identifying to genus level Under half were able to fully speciate The graph on the previous page illustrates participantsrsquo results Some biochemical tests commonly used by participants to identify include catalase (+) oxidase (+) indole (-) urea (+) growth on MacConkey agar (-) and XV-dependency (+) Many participants correctly identifying H haemolyticus observed the β-haemolytic activity of this isolate on blood agar and made note of it in their comments Identification kitssystems used and success rates in the hands of the users are listed below Please note that success rates may have been influenced by the observation (or lack thereof) of β-haemolysis

API NHmdashBiomerieux 1236 (33) correct H influenzae (24)

BBL Crystal-BD NeisseriaHaemophilus ID Kit 22 (100) correct

MALDI-TOF (Bruker ) 423(17) correct Pasteurella species (1) H influenzae (17) gram-negative rod (1)

MALDI-TOF (VITEK MS) 914 (64) correct H influenzae (4) Haemophilus species (1)

Rapid NH 1528 (54) correct Kingella kingae (1) H aegypticus (1) Haemophilus species (2) H influenzae (8) H parainfluenzae (1)

Sequencing 16S rRNA 78 (88) correct H influenzae (1)

VITEK2 GN 56 (83) correct H influenzae (1)

VITEK2 NH 3150 (62) correct Haemophilus species (1) Unable to identify-refer (1) H influenzae (17)

VITEK NHI 45 (80) correct H influenzae (1)

copy2013 RCPA Quality Assurance Programs Pty Limited 12 Date of issue 13th November 2013

References Item 5 1 McCrea KW et al Relationships of nontypeable Haemophilus influenzae strains to hemolytic and nonhemolytic Haemophilus haemolyticus strains J Clin

Microbiol 200846 406ndash416 httpwwwncbinlmnihgovpmcarticlesPMC2238123

2 Jordan IK et al Genome sequences for five strains of the emerging pathogen Haemophilus haemolyticus J Bacteriol 2011193 5879ndash5880

httpwwwncbinlmnihgovpmcarticlesPMC3187195

3 Anderson R et al Haemophilus haemolyticus isolates causing clinical disease J Clin Microbiol 201250 2462-5

httpwwwncbinlmnihgovpubmed22573587

4 Morton DJ et al An invasive Haemophilus haemolyticus isolate J Clin Microbiol 201250 1502ndash1503

httpwwwncbinlmnihgovpmcarticlesPMC3318549

5 Agrawal A Murphy TF Haemophilus influenzae infections in the H influenzae type b conjugate vaccine era J Clin Microbiol 201149 3728ndash3732

httpwwwncbinlmnihgovpmcarticlesPMC3209133

6 Kilian M A taxonomic study of the genus Haemophilus with the proposal of a new species J Gen Microbiol 197693 9ndash62

httpwwwncbinlmnihgovpubmed772168

7 Kilian M 2005 Genus III Haemophilus Winslow Broadhurst Buchanan Krumweide Rogers and Smith 1917 561 p 883ndash904 In Brenner DJ Krieg NR Staley JT (ed) Bergeyrsquos manual of systematic bacteriology 2nd ed vol 2 Springer New York NY

8 Ledeboer NA Doern GV 2012 Haemophilus In Versalovic J Carroll KC Funke G Jorgensen JH Landry ML WarnockDW(ed) Manual of clinical microbiology 10th ed ASM Press Washington DC

9 McCrea KW et al Relationships of nontypeable Haemophilus influenzae strains to hemolytic and nonhemolytic Haemophilus haemolyticus strains J Clin Microbiol 200846 406ndash416 httpwwwncbinlmnihgovpmcarticlesPMC2238123

10 Murphy TF et al Haemophilus haemolyticus a human respiratory tract commensal to be distinguished from Haemophilus influenzae J Infect Dis 2007195 81ndash 89 httpwwwncbinlmnihgovpubmed17152011

11 Identification Reference Laboratory Centre for Infectious Diseases and Microbiology ICPMR Westmead Hospital 12 Binks MJ et al Molecular Surveillance of True Nontypeable Haemophilus influenzae An Evaluation of PCR Screening Assays PLOS

httpwwwplosoneorgarticleinfo3Adoi2F1013712Fjournalpone0034083

13 Duerden B Bennet KW and Faulkner J Isolation of Bacteroides ureolyticus (B corrodens) from clinical infections J Clin Pathol 1982 35 309-312 httpjcpbmjcomcontent353309fullpdf

The most common misidentification by participants was H influenzae (35) because of the phenotypicgenetic similarity of the two species and because of the failure of all kitsidentification systems to differentiate between them Reliance on one type of identification system is discouraged and may lead to incorrect identification of some organisms In this instance β-haemolysis on blood agar facilitated an accurate identification if detected however as already noted it may not always be displayed in this species even in primary cultures H parahaemolyticus reported by three laboratories is also β-haemolytic but unlike H haemolyticus it is V-dependent only (and δ-Aminolevulinic acid (ALA) test negative) as is H parainfluenzae reported by two laboratories which is not β-haemolytic All other false identifications reported do not exhibit X+V dependency or X- or V-dependency The laboratory reporting Corynebacterium jeikeium should note that this is a gram-positive rod B ureolyticus reported by one laboratory is an anaerobic organism with corroding colonies on agar plates 13 Brucella and Francisella tularensis are slow-growing fastidious organisms (also not XV-dependent) that would not be dispatched in this type of QAP

ITEM 201364C CLERICAL ERROR

Clerical Errors reported in Item 201364C Number labs (71)

No error reported 6

Error first name only (correct) in 4C 60(85)

Error first name only in 4D (incorrect) 1

Error first name (correct) + last name (incorrect) 1

Error first name (correct) + unit number (incorrect) 1

Error last name (incorrect) 2

Table 13 Clerical errors reported

Specimen label Karina DANIELS UN 831248 Paperwork Amelia DANIELS UN 831248

The clerical error was placed in item 201364C Mycobacteriology culture As only 95 participants receive 4C and 4D culture vials and only 71 performed testing this clerical error has not been scored

copy2013 RCPA Quality Assurance Programs Pty Limited 13 Date of issue 13th November 2013

ITEM 201367ABC MYCOLOGY

7A This item contained Trichophyton interdigitale [zoophilic] (previously T mentagrophytes) 973 correct to genus level 634 correct to species level (required) The Trichophyton species have undergone extensive reclassification in the last 5 years This is because there exists much phenotypic variation but genetic variation is low Most of the species formerly known as T mentagrophytes are now classified within T interdigitale T mentagrophytes still exists but encompasses only the organism previously known as T quinckeanum (T mentagrophytes var quinckeanum) which is associated with mice T interdigitale is recognised as having two ecological groups the anthropophilic and the zoophilic group with the former T mentagrophytes species falls into the zoophilic group For this item T interdigitale and T mentagrophytes were both marked as correct This newly merged species encompasses a wide range of phenotypes which may or may not be observed for a given specimen Sequencing of the internal transcribed spacer (ITS) region is the gold standard for identification using reference strains that are correctly named according to the revised taxonomy Chen et al have published a useful book chapter with phenotypic descriptions and recommendations for molecular identification of the revised Trichophyton species1

7A Trichophyton interdigitale [zoophilic]

Figures 7A (i-iii) Trichophyton interdigitale [zoophilic group] (previously T mentagrophytes) may have [7A(i)] numerous single-celled microconidia often in dense clusters along with smooth thin-walled cigar-shaped multicelled macroconidia Microconidia are hyaline smooth-walled and are predominantly spherical to subspherical in shape however occasional clavate to pyriform forms may occur [7A(ii)] varying numbers of spherical chlamydoconidia and [7A (iii)] spiral hyphae may also be observed The zoophilic form of the species tends to have powdery-granular colonies on Sabouraudrsquos lactritmel and 1 peptone media while the anthropophilic form has suede-downy textured colonies

1

1

1

1

1

2

2

5

6

7

14

1

31

1

5

20

13

0 5 10 15 20 25 30 35

Chrysosporium tropicum

Microsporum gypseum

Microsporum persicolor

Trichophyton equinum

Trichophyton terrestre

Trichophyton erinacei

Trichophyton verrucosum

Trichophyton species

Trichophyton rubrum [Worldwide population]

Trichophyton tonsurans

Trichophyton rubrum

Trichophyton mentagrophytes complex

Trichophyton mentagrophytes

Trichophyton interdigitale [anthropophilic] and [zoophilic]

Trichophyton interdigitale [anthropophilic]

Trichophyton interdigitale

Trichophyton interdigitale [zoophilic]

13 116

20 179

5 45

1 09

31 277

1 09

14 125

7 63

6 54

5 45

2 18

2 18

1 09

1 09

1 09

1 09

1 09

7A (i)

7A (ii) 7A (iii)

copy2013 RCPA Quality Assurance Programs Pty Limited 14 Date of issue 13th November 2013

7B Cryptococcus neoformans

82 732

8 71

1 09

1 09

5 45

11 98

1 09

1 09

1 09

1 09

7B This item contained Cryptococcus neoformans 964 correct to genus level 812 correct to species level (required) Cryptococcosis is typically caused by either Cryptococcus neoformans or Cryptococcus gattii although occasionally other Cryptococcus species have been implicated C neoformans typically infects the immunocompromised host frequently in the setting of HIV with gt1 million new cases and~600000 deaths per year globally C neoformans is a yeast-like basidiomycete fungus with a distinctive polysaccharide capsule Differentiation from the closely related C gattii is important Presumptive identification is by India Ink stain to highlight the capsule and birdseed agar to observe dark brown colonies

Figure 7B (i-iii) [7B (i)] India Ink stain highlighting the capsule of C neoformansgattii [7B(ii)] Dark brown colonies of C neoformansgattii mixed with white colonies of Candida albicans on birdseed agar [7B(iii)] Canavanine glycine bromothyol blue (CGB) media for distinguishing C neoformans (left) from C gattii (right)

1

1

1

1

11

5

1

1

8

82

0 10 20 30 40 50 60 70 80 90

Unable to identify- refer

Candida (not albicans)

Candida glabrata complex

Candida krusei

Cryptococcus neoformansgattii- unable to speciate

Cryptococcus species

Cryptococcus laurentii

Cryptococcus neoformans var grubii

Cryptococcus neoformans var neoformans

Cryptococcus neoformans

81 of labs correctly reported this isolate as Cryptococcus neoformans While no lab reported C gattii 11 labs were unable to differentiate C neoformans from C gattii Epidemiology risk factors and treatment of infections caused by these species are different and accurate identification is important for effective management All labs should seek to differentiate these species using CGB media a validated molecular method or by referral to a reference laboratory API ID32C and Vitek-2 does not distinguish C neoformans from C gattii These species may be differentiated by a number of DNA-based assays MALDI-ToF and canavanine-glycine-bromothymol blue (CGB) media C neoformans does not grow on CGB media which remains yellow whereas C gattii will grow triggering a blue colour change reaction in the media usually within 3 days It is worth noting that some slow growing C gattii isolates may take as long as 10 days to effect the blue colour change and may initially be mis-identified as C neoformans Nine labs unnecessarily attempted to further identify the C neoformans isolate to variety level either Cn var grubii (serotype A molecular types VNI and VNII) or Cn var neoformans (serotype D molecular type VNIV) It is not clear what methods were used to achieve this varietal identification but 8 of the 9 labs incorrectly reported Cn var neoformans In fact the isolate was confirmed by molecular methods to be Cryptococcus neoformans var grubii molecular type VNI The 8 reports of Cn var neoformans may reflect persistence of the now obsolete classification of Cryptococcus neoformans having two varieties var neoformans and var gattii If it is the normal practice of these labs to report to varietal level it would be worthwhile reviewing methods interpretation and reporting procedures

7B (i) 7B (ii) 7B(iii)

copy2013 RCPA Quality Assurance Programs Pty Limited 15 Date of issue 13th November 2013

Reference item 7

1 Chen SC DH Ellis TC Sorrell and W Meyer Chapter 44 Trichophyton In ldquoMolecular Detection of Human Fungal Pathogensrdquo Dongyou Liu (Ed) CRC Press 2011

All mycology isolates were identified by both conventional and molecular techniques

86 768

9 80

1 09

2 18

3 27

3 27

2 18

1 09

1 09

1 09

1 09

2 18

7C Scedosporium prolificans

This item contained Scedosporium prolificans 875 correct to genus level 768 correct to species level (required) Colonies are rapid growing flat spreading olive-grey to black (the culture may contain a mixture of the colurs depending on the age) and have a suede-like to downy surface texture [7C (i)] Conidia are borne in small groups on distinctive basally swollen flask-shaped annellides which occur singly or in clusters along the vegetative hyphae Conidia are single-celled hyaline to pale-brown ovoid to pyriform 2-5 x 3-13 um (average 34-53 um) in size and have smooth thin walls [7C (ii)] Identification of Scedosporium prolificans to

species level is very important due to its intrinsic resistance to most antifungal drugs It may be distinguished from other members of the genus in particular the human pathogen S apiospermum by its basally swollen (inflated) flask-shaped annellides conidia borne in small groups rather than singly and by not growing on media containing cycloheximide (actidione) DNA sequencing (ITS region) will also definitively identify Scedosporium species Three laboratories reported Sporothrix schenckii which is easily distinguished from Scedosporium spp because it is a dimorphic pathogen with a yeast-like phase when grown at 37degC

2

1

1

1

1

2

3

3

2

1

9

86

0 10 20 30 40 50 60 70 80 90 100

Unable to identify- refer

Chaetomium species

Hortaea werneckii

Ochroconis gallopava

Wangiella species

Exophiala species

Exophiala dermatitidis

Sporothrix schenckii

Scedosporium species

Scedosporium aurantiacum

Scedosporium apiospermum (sensu stricto)

Scedosporium prolificans

7C (i) 7C (ii)

Page 10: FINAL RESULTS AND COMMENTS D6-2013 …dataentry.rcpaqap.com.au/micro/reports/uploadedfiles/fnl2013-6.pdf · FINAL RESULTS AND COMMENTS D6/2013 ... This item contained a pure growth

copy2013 RCPA Quality Assurance Programs Pty Limited 10 Date of issue 13th November 2013

includes presumptive identification(s)

ITEM 201365 ISOLATE FOR IDENTIFICATION

includes presumptive identification(s)

103 475

1 05

72 332

4 18

3 14

2 09

7 32

1 05

1 05

1 05

1 05

1 05

1 05

2 09

1 05

1 05

1 05

14 65

Fig 5b H haemolyticus on HBA copy 2013 RCPA QAP

ITEM 201365 Haemophilus haemolyticus This item contained a pure growth of Haemophilus haemolyticus Homogeneity and stability testing for this organism was satisfactory with bacterial counts for the H haemolyticus remaining above 10 x 1010CFUL throughout the survey

This organism represented an isolate from blood culture collected from a patient with endocarditis H haemolyticus is a human commensal of the nasopharynx in some individuals Some authors find its pathogenicity debatable but it has occasionally been implicated in disease 123 Phenotypically and genotypically it is difficult to distinguish from non-typeable H influenzae except for β-haemolysis on blood agar in the case of H haemolyticus 45678 But even this can be an unreliable characteristic as non-haemolytic strains occur and upon repeated sub-culture this trait may disappear 5910 For this reason it has been suggested that H haemolyticus is more commonly misidentified as H influenzae than is recognised5 Like H influenzae H haemolyticus is a fastidious facultative anaerobe XV-dependent oxidase and catalase positive gram-negative coccobacillus

Fig 5a H haemolyticus on Chocolate Agar copy 2013 RCPA QAP

14

1

1

1

2

1

1

1

1

1

1

7

2

3

4

72

1

103

0 20 40 60 80 100 120

Unable to Identify - Refer

Psychrobacter phenylpyruvicus

Pasteurella species

Other

Kingella kingae

Gram negative rod

Francisella tularensis

Corynebacterium jeikeium

Brucella spp

Bacteroides ureolyticus

Actinobacillus actinomycetemcomitans

Haemophilus species

Haemophilus parainfluenzae

Haemophilus parahaemolyticus

Haemophilus influenzae type B

Haemophilus influenzae

Haemophilus aegyptius

Haemophilus haemolyticus

copy2013 RCPA Quality Assurance Programs Pty Limited 11 Date of issue 13th November 2013

SUMMARY OF PHENOTYPIC AND BIOCHEMICAL RESULTS 811

Phenotypic characteristics

Gram stain Small gram-positive rods and coccobacilli

Motility RT (BHI broth) non-motile

Colonial appearance on Chocolate agar (CA) 24hrs 10mm beige shiny round entire colonies

Colonial appearance on Horse Blood agar (HBA) 24hrs pinpoint translucent shiny round entire colonies

Pigment pale yellow

Haemolysis β (key distinguishing test if apparent) This isolate was haemolytic on HBA

Catalase positive

Oxidase positive

KIA slope NCNC gas negative

Satellitism XV + V - X - Growth conditions

Growth on HBA 35degC in O2 +

Growth on HBA 35degC in CO2 ++

Growth on HBA 35degC in ANO2 +

Growth on CA 35degC 35degC +++

Growth on MacConkey agar no growth Biochemical tests Rapid substrate utilisation

Urease positive

Nitrate positive

Indole negative

Aesculin negative

ADH negative

LDC negative

ODC negative

Glucose positive

Xylose negative

Mannitol negative

Lactose positive (weak) 11

Sucrose negative

Maltose positive (weak) 11 16S rRNA gene analysis by PCR H haemolyticus with a 99 match Although standard genetic testing may be inadequate to distinguish H influenzae and H haemolyticus because of their genetic similarity1012 the demonstration of β-haemolysis on HBA for this isolate supports the PCR findings A few other Haemophilus species are known to display β-haemolysis on blood agar but they are not X and V-dependent 8 Participant results Two hundred and seventeen participants submitted results for this item with 192 (88) correctly identifying to genus level Under half were able to fully speciate The graph on the previous page illustrates participantsrsquo results Some biochemical tests commonly used by participants to identify include catalase (+) oxidase (+) indole (-) urea (+) growth on MacConkey agar (-) and XV-dependency (+) Many participants correctly identifying H haemolyticus observed the β-haemolytic activity of this isolate on blood agar and made note of it in their comments Identification kitssystems used and success rates in the hands of the users are listed below Please note that success rates may have been influenced by the observation (or lack thereof) of β-haemolysis

API NHmdashBiomerieux 1236 (33) correct H influenzae (24)

BBL Crystal-BD NeisseriaHaemophilus ID Kit 22 (100) correct

MALDI-TOF (Bruker ) 423(17) correct Pasteurella species (1) H influenzae (17) gram-negative rod (1)

MALDI-TOF (VITEK MS) 914 (64) correct H influenzae (4) Haemophilus species (1)

Rapid NH 1528 (54) correct Kingella kingae (1) H aegypticus (1) Haemophilus species (2) H influenzae (8) H parainfluenzae (1)

Sequencing 16S rRNA 78 (88) correct H influenzae (1)

VITEK2 GN 56 (83) correct H influenzae (1)

VITEK2 NH 3150 (62) correct Haemophilus species (1) Unable to identify-refer (1) H influenzae (17)

VITEK NHI 45 (80) correct H influenzae (1)

copy2013 RCPA Quality Assurance Programs Pty Limited 12 Date of issue 13th November 2013

References Item 5 1 McCrea KW et al Relationships of nontypeable Haemophilus influenzae strains to hemolytic and nonhemolytic Haemophilus haemolyticus strains J Clin

Microbiol 200846 406ndash416 httpwwwncbinlmnihgovpmcarticlesPMC2238123

2 Jordan IK et al Genome sequences for five strains of the emerging pathogen Haemophilus haemolyticus J Bacteriol 2011193 5879ndash5880

httpwwwncbinlmnihgovpmcarticlesPMC3187195

3 Anderson R et al Haemophilus haemolyticus isolates causing clinical disease J Clin Microbiol 201250 2462-5

httpwwwncbinlmnihgovpubmed22573587

4 Morton DJ et al An invasive Haemophilus haemolyticus isolate J Clin Microbiol 201250 1502ndash1503

httpwwwncbinlmnihgovpmcarticlesPMC3318549

5 Agrawal A Murphy TF Haemophilus influenzae infections in the H influenzae type b conjugate vaccine era J Clin Microbiol 201149 3728ndash3732

httpwwwncbinlmnihgovpmcarticlesPMC3209133

6 Kilian M A taxonomic study of the genus Haemophilus with the proposal of a new species J Gen Microbiol 197693 9ndash62

httpwwwncbinlmnihgovpubmed772168

7 Kilian M 2005 Genus III Haemophilus Winslow Broadhurst Buchanan Krumweide Rogers and Smith 1917 561 p 883ndash904 In Brenner DJ Krieg NR Staley JT (ed) Bergeyrsquos manual of systematic bacteriology 2nd ed vol 2 Springer New York NY

8 Ledeboer NA Doern GV 2012 Haemophilus In Versalovic J Carroll KC Funke G Jorgensen JH Landry ML WarnockDW(ed) Manual of clinical microbiology 10th ed ASM Press Washington DC

9 McCrea KW et al Relationships of nontypeable Haemophilus influenzae strains to hemolytic and nonhemolytic Haemophilus haemolyticus strains J Clin Microbiol 200846 406ndash416 httpwwwncbinlmnihgovpmcarticlesPMC2238123

10 Murphy TF et al Haemophilus haemolyticus a human respiratory tract commensal to be distinguished from Haemophilus influenzae J Infect Dis 2007195 81ndash 89 httpwwwncbinlmnihgovpubmed17152011

11 Identification Reference Laboratory Centre for Infectious Diseases and Microbiology ICPMR Westmead Hospital 12 Binks MJ et al Molecular Surveillance of True Nontypeable Haemophilus influenzae An Evaluation of PCR Screening Assays PLOS

httpwwwplosoneorgarticleinfo3Adoi2F1013712Fjournalpone0034083

13 Duerden B Bennet KW and Faulkner J Isolation of Bacteroides ureolyticus (B corrodens) from clinical infections J Clin Pathol 1982 35 309-312 httpjcpbmjcomcontent353309fullpdf

The most common misidentification by participants was H influenzae (35) because of the phenotypicgenetic similarity of the two species and because of the failure of all kitsidentification systems to differentiate between them Reliance on one type of identification system is discouraged and may lead to incorrect identification of some organisms In this instance β-haemolysis on blood agar facilitated an accurate identification if detected however as already noted it may not always be displayed in this species even in primary cultures H parahaemolyticus reported by three laboratories is also β-haemolytic but unlike H haemolyticus it is V-dependent only (and δ-Aminolevulinic acid (ALA) test negative) as is H parainfluenzae reported by two laboratories which is not β-haemolytic All other false identifications reported do not exhibit X+V dependency or X- or V-dependency The laboratory reporting Corynebacterium jeikeium should note that this is a gram-positive rod B ureolyticus reported by one laboratory is an anaerobic organism with corroding colonies on agar plates 13 Brucella and Francisella tularensis are slow-growing fastidious organisms (also not XV-dependent) that would not be dispatched in this type of QAP

ITEM 201364C CLERICAL ERROR

Clerical Errors reported in Item 201364C Number labs (71)

No error reported 6

Error first name only (correct) in 4C 60(85)

Error first name only in 4D (incorrect) 1

Error first name (correct) + last name (incorrect) 1

Error first name (correct) + unit number (incorrect) 1

Error last name (incorrect) 2

Table 13 Clerical errors reported

Specimen label Karina DANIELS UN 831248 Paperwork Amelia DANIELS UN 831248

The clerical error was placed in item 201364C Mycobacteriology culture As only 95 participants receive 4C and 4D culture vials and only 71 performed testing this clerical error has not been scored

copy2013 RCPA Quality Assurance Programs Pty Limited 13 Date of issue 13th November 2013

ITEM 201367ABC MYCOLOGY

7A This item contained Trichophyton interdigitale [zoophilic] (previously T mentagrophytes) 973 correct to genus level 634 correct to species level (required) The Trichophyton species have undergone extensive reclassification in the last 5 years This is because there exists much phenotypic variation but genetic variation is low Most of the species formerly known as T mentagrophytes are now classified within T interdigitale T mentagrophytes still exists but encompasses only the organism previously known as T quinckeanum (T mentagrophytes var quinckeanum) which is associated with mice T interdigitale is recognised as having two ecological groups the anthropophilic and the zoophilic group with the former T mentagrophytes species falls into the zoophilic group For this item T interdigitale and T mentagrophytes were both marked as correct This newly merged species encompasses a wide range of phenotypes which may or may not be observed for a given specimen Sequencing of the internal transcribed spacer (ITS) region is the gold standard for identification using reference strains that are correctly named according to the revised taxonomy Chen et al have published a useful book chapter with phenotypic descriptions and recommendations for molecular identification of the revised Trichophyton species1

7A Trichophyton interdigitale [zoophilic]

Figures 7A (i-iii) Trichophyton interdigitale [zoophilic group] (previously T mentagrophytes) may have [7A(i)] numerous single-celled microconidia often in dense clusters along with smooth thin-walled cigar-shaped multicelled macroconidia Microconidia are hyaline smooth-walled and are predominantly spherical to subspherical in shape however occasional clavate to pyriform forms may occur [7A(ii)] varying numbers of spherical chlamydoconidia and [7A (iii)] spiral hyphae may also be observed The zoophilic form of the species tends to have powdery-granular colonies on Sabouraudrsquos lactritmel and 1 peptone media while the anthropophilic form has suede-downy textured colonies

1

1

1

1

1

2

2

5

6

7

14

1

31

1

5

20

13

0 5 10 15 20 25 30 35

Chrysosporium tropicum

Microsporum gypseum

Microsporum persicolor

Trichophyton equinum

Trichophyton terrestre

Trichophyton erinacei

Trichophyton verrucosum

Trichophyton species

Trichophyton rubrum [Worldwide population]

Trichophyton tonsurans

Trichophyton rubrum

Trichophyton mentagrophytes complex

Trichophyton mentagrophytes

Trichophyton interdigitale [anthropophilic] and [zoophilic]

Trichophyton interdigitale [anthropophilic]

Trichophyton interdigitale

Trichophyton interdigitale [zoophilic]

13 116

20 179

5 45

1 09

31 277

1 09

14 125

7 63

6 54

5 45

2 18

2 18

1 09

1 09

1 09

1 09

1 09

7A (i)

7A (ii) 7A (iii)

copy2013 RCPA Quality Assurance Programs Pty Limited 14 Date of issue 13th November 2013

7B Cryptococcus neoformans

82 732

8 71

1 09

1 09

5 45

11 98

1 09

1 09

1 09

1 09

7B This item contained Cryptococcus neoformans 964 correct to genus level 812 correct to species level (required) Cryptococcosis is typically caused by either Cryptococcus neoformans or Cryptococcus gattii although occasionally other Cryptococcus species have been implicated C neoformans typically infects the immunocompromised host frequently in the setting of HIV with gt1 million new cases and~600000 deaths per year globally C neoformans is a yeast-like basidiomycete fungus with a distinctive polysaccharide capsule Differentiation from the closely related C gattii is important Presumptive identification is by India Ink stain to highlight the capsule and birdseed agar to observe dark brown colonies

Figure 7B (i-iii) [7B (i)] India Ink stain highlighting the capsule of C neoformansgattii [7B(ii)] Dark brown colonies of C neoformansgattii mixed with white colonies of Candida albicans on birdseed agar [7B(iii)] Canavanine glycine bromothyol blue (CGB) media for distinguishing C neoformans (left) from C gattii (right)

1

1

1

1

11

5

1

1

8

82

0 10 20 30 40 50 60 70 80 90

Unable to identify- refer

Candida (not albicans)

Candida glabrata complex

Candida krusei

Cryptococcus neoformansgattii- unable to speciate

Cryptococcus species

Cryptococcus laurentii

Cryptococcus neoformans var grubii

Cryptococcus neoformans var neoformans

Cryptococcus neoformans

81 of labs correctly reported this isolate as Cryptococcus neoformans While no lab reported C gattii 11 labs were unable to differentiate C neoformans from C gattii Epidemiology risk factors and treatment of infections caused by these species are different and accurate identification is important for effective management All labs should seek to differentiate these species using CGB media a validated molecular method or by referral to a reference laboratory API ID32C and Vitek-2 does not distinguish C neoformans from C gattii These species may be differentiated by a number of DNA-based assays MALDI-ToF and canavanine-glycine-bromothymol blue (CGB) media C neoformans does not grow on CGB media which remains yellow whereas C gattii will grow triggering a blue colour change reaction in the media usually within 3 days It is worth noting that some slow growing C gattii isolates may take as long as 10 days to effect the blue colour change and may initially be mis-identified as C neoformans Nine labs unnecessarily attempted to further identify the C neoformans isolate to variety level either Cn var grubii (serotype A molecular types VNI and VNII) or Cn var neoformans (serotype D molecular type VNIV) It is not clear what methods were used to achieve this varietal identification but 8 of the 9 labs incorrectly reported Cn var neoformans In fact the isolate was confirmed by molecular methods to be Cryptococcus neoformans var grubii molecular type VNI The 8 reports of Cn var neoformans may reflect persistence of the now obsolete classification of Cryptococcus neoformans having two varieties var neoformans and var gattii If it is the normal practice of these labs to report to varietal level it would be worthwhile reviewing methods interpretation and reporting procedures

7B (i) 7B (ii) 7B(iii)

copy2013 RCPA Quality Assurance Programs Pty Limited 15 Date of issue 13th November 2013

Reference item 7

1 Chen SC DH Ellis TC Sorrell and W Meyer Chapter 44 Trichophyton In ldquoMolecular Detection of Human Fungal Pathogensrdquo Dongyou Liu (Ed) CRC Press 2011

All mycology isolates were identified by both conventional and molecular techniques

86 768

9 80

1 09

2 18

3 27

3 27

2 18

1 09

1 09

1 09

1 09

2 18

7C Scedosporium prolificans

This item contained Scedosporium prolificans 875 correct to genus level 768 correct to species level (required) Colonies are rapid growing flat spreading olive-grey to black (the culture may contain a mixture of the colurs depending on the age) and have a suede-like to downy surface texture [7C (i)] Conidia are borne in small groups on distinctive basally swollen flask-shaped annellides which occur singly or in clusters along the vegetative hyphae Conidia are single-celled hyaline to pale-brown ovoid to pyriform 2-5 x 3-13 um (average 34-53 um) in size and have smooth thin walls [7C (ii)] Identification of Scedosporium prolificans to

species level is very important due to its intrinsic resistance to most antifungal drugs It may be distinguished from other members of the genus in particular the human pathogen S apiospermum by its basally swollen (inflated) flask-shaped annellides conidia borne in small groups rather than singly and by not growing on media containing cycloheximide (actidione) DNA sequencing (ITS region) will also definitively identify Scedosporium species Three laboratories reported Sporothrix schenckii which is easily distinguished from Scedosporium spp because it is a dimorphic pathogen with a yeast-like phase when grown at 37degC

2

1

1

1

1

2

3

3

2

1

9

86

0 10 20 30 40 50 60 70 80 90 100

Unable to identify- refer

Chaetomium species

Hortaea werneckii

Ochroconis gallopava

Wangiella species

Exophiala species

Exophiala dermatitidis

Sporothrix schenckii

Scedosporium species

Scedosporium aurantiacum

Scedosporium apiospermum (sensu stricto)

Scedosporium prolificans

7C (i) 7C (ii)

Page 11: FINAL RESULTS AND COMMENTS D6-2013 …dataentry.rcpaqap.com.au/micro/reports/uploadedfiles/fnl2013-6.pdf · FINAL RESULTS AND COMMENTS D6/2013 ... This item contained a pure growth

copy2013 RCPA Quality Assurance Programs Pty Limited 11 Date of issue 13th November 2013

SUMMARY OF PHENOTYPIC AND BIOCHEMICAL RESULTS 811

Phenotypic characteristics

Gram stain Small gram-positive rods and coccobacilli

Motility RT (BHI broth) non-motile

Colonial appearance on Chocolate agar (CA) 24hrs 10mm beige shiny round entire colonies

Colonial appearance on Horse Blood agar (HBA) 24hrs pinpoint translucent shiny round entire colonies

Pigment pale yellow

Haemolysis β (key distinguishing test if apparent) This isolate was haemolytic on HBA

Catalase positive

Oxidase positive

KIA slope NCNC gas negative

Satellitism XV + V - X - Growth conditions

Growth on HBA 35degC in O2 +

Growth on HBA 35degC in CO2 ++

Growth on HBA 35degC in ANO2 +

Growth on CA 35degC 35degC +++

Growth on MacConkey agar no growth Biochemical tests Rapid substrate utilisation

Urease positive

Nitrate positive

Indole negative

Aesculin negative

ADH negative

LDC negative

ODC negative

Glucose positive

Xylose negative

Mannitol negative

Lactose positive (weak) 11

Sucrose negative

Maltose positive (weak) 11 16S rRNA gene analysis by PCR H haemolyticus with a 99 match Although standard genetic testing may be inadequate to distinguish H influenzae and H haemolyticus because of their genetic similarity1012 the demonstration of β-haemolysis on HBA for this isolate supports the PCR findings A few other Haemophilus species are known to display β-haemolysis on blood agar but they are not X and V-dependent 8 Participant results Two hundred and seventeen participants submitted results for this item with 192 (88) correctly identifying to genus level Under half were able to fully speciate The graph on the previous page illustrates participantsrsquo results Some biochemical tests commonly used by participants to identify include catalase (+) oxidase (+) indole (-) urea (+) growth on MacConkey agar (-) and XV-dependency (+) Many participants correctly identifying H haemolyticus observed the β-haemolytic activity of this isolate on blood agar and made note of it in their comments Identification kitssystems used and success rates in the hands of the users are listed below Please note that success rates may have been influenced by the observation (or lack thereof) of β-haemolysis

API NHmdashBiomerieux 1236 (33) correct H influenzae (24)

BBL Crystal-BD NeisseriaHaemophilus ID Kit 22 (100) correct

MALDI-TOF (Bruker ) 423(17) correct Pasteurella species (1) H influenzae (17) gram-negative rod (1)

MALDI-TOF (VITEK MS) 914 (64) correct H influenzae (4) Haemophilus species (1)

Rapid NH 1528 (54) correct Kingella kingae (1) H aegypticus (1) Haemophilus species (2) H influenzae (8) H parainfluenzae (1)

Sequencing 16S rRNA 78 (88) correct H influenzae (1)

VITEK2 GN 56 (83) correct H influenzae (1)

VITEK2 NH 3150 (62) correct Haemophilus species (1) Unable to identify-refer (1) H influenzae (17)

VITEK NHI 45 (80) correct H influenzae (1)

copy2013 RCPA Quality Assurance Programs Pty Limited 12 Date of issue 13th November 2013

References Item 5 1 McCrea KW et al Relationships of nontypeable Haemophilus influenzae strains to hemolytic and nonhemolytic Haemophilus haemolyticus strains J Clin

Microbiol 200846 406ndash416 httpwwwncbinlmnihgovpmcarticlesPMC2238123

2 Jordan IK et al Genome sequences for five strains of the emerging pathogen Haemophilus haemolyticus J Bacteriol 2011193 5879ndash5880

httpwwwncbinlmnihgovpmcarticlesPMC3187195

3 Anderson R et al Haemophilus haemolyticus isolates causing clinical disease J Clin Microbiol 201250 2462-5

httpwwwncbinlmnihgovpubmed22573587

4 Morton DJ et al An invasive Haemophilus haemolyticus isolate J Clin Microbiol 201250 1502ndash1503

httpwwwncbinlmnihgovpmcarticlesPMC3318549

5 Agrawal A Murphy TF Haemophilus influenzae infections in the H influenzae type b conjugate vaccine era J Clin Microbiol 201149 3728ndash3732

httpwwwncbinlmnihgovpmcarticlesPMC3209133

6 Kilian M A taxonomic study of the genus Haemophilus with the proposal of a new species J Gen Microbiol 197693 9ndash62

httpwwwncbinlmnihgovpubmed772168

7 Kilian M 2005 Genus III Haemophilus Winslow Broadhurst Buchanan Krumweide Rogers and Smith 1917 561 p 883ndash904 In Brenner DJ Krieg NR Staley JT (ed) Bergeyrsquos manual of systematic bacteriology 2nd ed vol 2 Springer New York NY

8 Ledeboer NA Doern GV 2012 Haemophilus In Versalovic J Carroll KC Funke G Jorgensen JH Landry ML WarnockDW(ed) Manual of clinical microbiology 10th ed ASM Press Washington DC

9 McCrea KW et al Relationships of nontypeable Haemophilus influenzae strains to hemolytic and nonhemolytic Haemophilus haemolyticus strains J Clin Microbiol 200846 406ndash416 httpwwwncbinlmnihgovpmcarticlesPMC2238123

10 Murphy TF et al Haemophilus haemolyticus a human respiratory tract commensal to be distinguished from Haemophilus influenzae J Infect Dis 2007195 81ndash 89 httpwwwncbinlmnihgovpubmed17152011

11 Identification Reference Laboratory Centre for Infectious Diseases and Microbiology ICPMR Westmead Hospital 12 Binks MJ et al Molecular Surveillance of True Nontypeable Haemophilus influenzae An Evaluation of PCR Screening Assays PLOS

httpwwwplosoneorgarticleinfo3Adoi2F1013712Fjournalpone0034083

13 Duerden B Bennet KW and Faulkner J Isolation of Bacteroides ureolyticus (B corrodens) from clinical infections J Clin Pathol 1982 35 309-312 httpjcpbmjcomcontent353309fullpdf

The most common misidentification by participants was H influenzae (35) because of the phenotypicgenetic similarity of the two species and because of the failure of all kitsidentification systems to differentiate between them Reliance on one type of identification system is discouraged and may lead to incorrect identification of some organisms In this instance β-haemolysis on blood agar facilitated an accurate identification if detected however as already noted it may not always be displayed in this species even in primary cultures H parahaemolyticus reported by three laboratories is also β-haemolytic but unlike H haemolyticus it is V-dependent only (and δ-Aminolevulinic acid (ALA) test negative) as is H parainfluenzae reported by two laboratories which is not β-haemolytic All other false identifications reported do not exhibit X+V dependency or X- or V-dependency The laboratory reporting Corynebacterium jeikeium should note that this is a gram-positive rod B ureolyticus reported by one laboratory is an anaerobic organism with corroding colonies on agar plates 13 Brucella and Francisella tularensis are slow-growing fastidious organisms (also not XV-dependent) that would not be dispatched in this type of QAP

ITEM 201364C CLERICAL ERROR

Clerical Errors reported in Item 201364C Number labs (71)

No error reported 6

Error first name only (correct) in 4C 60(85)

Error first name only in 4D (incorrect) 1

Error first name (correct) + last name (incorrect) 1

Error first name (correct) + unit number (incorrect) 1

Error last name (incorrect) 2

Table 13 Clerical errors reported

Specimen label Karina DANIELS UN 831248 Paperwork Amelia DANIELS UN 831248

The clerical error was placed in item 201364C Mycobacteriology culture As only 95 participants receive 4C and 4D culture vials and only 71 performed testing this clerical error has not been scored

copy2013 RCPA Quality Assurance Programs Pty Limited 13 Date of issue 13th November 2013

ITEM 201367ABC MYCOLOGY

7A This item contained Trichophyton interdigitale [zoophilic] (previously T mentagrophytes) 973 correct to genus level 634 correct to species level (required) The Trichophyton species have undergone extensive reclassification in the last 5 years This is because there exists much phenotypic variation but genetic variation is low Most of the species formerly known as T mentagrophytes are now classified within T interdigitale T mentagrophytes still exists but encompasses only the organism previously known as T quinckeanum (T mentagrophytes var quinckeanum) which is associated with mice T interdigitale is recognised as having two ecological groups the anthropophilic and the zoophilic group with the former T mentagrophytes species falls into the zoophilic group For this item T interdigitale and T mentagrophytes were both marked as correct This newly merged species encompasses a wide range of phenotypes which may or may not be observed for a given specimen Sequencing of the internal transcribed spacer (ITS) region is the gold standard for identification using reference strains that are correctly named according to the revised taxonomy Chen et al have published a useful book chapter with phenotypic descriptions and recommendations for molecular identification of the revised Trichophyton species1

7A Trichophyton interdigitale [zoophilic]

Figures 7A (i-iii) Trichophyton interdigitale [zoophilic group] (previously T mentagrophytes) may have [7A(i)] numerous single-celled microconidia often in dense clusters along with smooth thin-walled cigar-shaped multicelled macroconidia Microconidia are hyaline smooth-walled and are predominantly spherical to subspherical in shape however occasional clavate to pyriform forms may occur [7A(ii)] varying numbers of spherical chlamydoconidia and [7A (iii)] spiral hyphae may also be observed The zoophilic form of the species tends to have powdery-granular colonies on Sabouraudrsquos lactritmel and 1 peptone media while the anthropophilic form has suede-downy textured colonies

1

1

1

1

1

2

2

5

6

7

14

1

31

1

5

20

13

0 5 10 15 20 25 30 35

Chrysosporium tropicum

Microsporum gypseum

Microsporum persicolor

Trichophyton equinum

Trichophyton terrestre

Trichophyton erinacei

Trichophyton verrucosum

Trichophyton species

Trichophyton rubrum [Worldwide population]

Trichophyton tonsurans

Trichophyton rubrum

Trichophyton mentagrophytes complex

Trichophyton mentagrophytes

Trichophyton interdigitale [anthropophilic] and [zoophilic]

Trichophyton interdigitale [anthropophilic]

Trichophyton interdigitale

Trichophyton interdigitale [zoophilic]

13 116

20 179

5 45

1 09

31 277

1 09

14 125

7 63

6 54

5 45

2 18

2 18

1 09

1 09

1 09

1 09

1 09

7A (i)

7A (ii) 7A (iii)

copy2013 RCPA Quality Assurance Programs Pty Limited 14 Date of issue 13th November 2013

7B Cryptococcus neoformans

82 732

8 71

1 09

1 09

5 45

11 98

1 09

1 09

1 09

1 09

7B This item contained Cryptococcus neoformans 964 correct to genus level 812 correct to species level (required) Cryptococcosis is typically caused by either Cryptococcus neoformans or Cryptococcus gattii although occasionally other Cryptococcus species have been implicated C neoformans typically infects the immunocompromised host frequently in the setting of HIV with gt1 million new cases and~600000 deaths per year globally C neoformans is a yeast-like basidiomycete fungus with a distinctive polysaccharide capsule Differentiation from the closely related C gattii is important Presumptive identification is by India Ink stain to highlight the capsule and birdseed agar to observe dark brown colonies

Figure 7B (i-iii) [7B (i)] India Ink stain highlighting the capsule of C neoformansgattii [7B(ii)] Dark brown colonies of C neoformansgattii mixed with white colonies of Candida albicans on birdseed agar [7B(iii)] Canavanine glycine bromothyol blue (CGB) media for distinguishing C neoformans (left) from C gattii (right)

1

1

1

1

11

5

1

1

8

82

0 10 20 30 40 50 60 70 80 90

Unable to identify- refer

Candida (not albicans)

Candida glabrata complex

Candida krusei

Cryptococcus neoformansgattii- unable to speciate

Cryptococcus species

Cryptococcus laurentii

Cryptococcus neoformans var grubii

Cryptococcus neoformans var neoformans

Cryptococcus neoformans

81 of labs correctly reported this isolate as Cryptococcus neoformans While no lab reported C gattii 11 labs were unable to differentiate C neoformans from C gattii Epidemiology risk factors and treatment of infections caused by these species are different and accurate identification is important for effective management All labs should seek to differentiate these species using CGB media a validated molecular method or by referral to a reference laboratory API ID32C and Vitek-2 does not distinguish C neoformans from C gattii These species may be differentiated by a number of DNA-based assays MALDI-ToF and canavanine-glycine-bromothymol blue (CGB) media C neoformans does not grow on CGB media which remains yellow whereas C gattii will grow triggering a blue colour change reaction in the media usually within 3 days It is worth noting that some slow growing C gattii isolates may take as long as 10 days to effect the blue colour change and may initially be mis-identified as C neoformans Nine labs unnecessarily attempted to further identify the C neoformans isolate to variety level either Cn var grubii (serotype A molecular types VNI and VNII) or Cn var neoformans (serotype D molecular type VNIV) It is not clear what methods were used to achieve this varietal identification but 8 of the 9 labs incorrectly reported Cn var neoformans In fact the isolate was confirmed by molecular methods to be Cryptococcus neoformans var grubii molecular type VNI The 8 reports of Cn var neoformans may reflect persistence of the now obsolete classification of Cryptococcus neoformans having two varieties var neoformans and var gattii If it is the normal practice of these labs to report to varietal level it would be worthwhile reviewing methods interpretation and reporting procedures

7B (i) 7B (ii) 7B(iii)

copy2013 RCPA Quality Assurance Programs Pty Limited 15 Date of issue 13th November 2013

Reference item 7

1 Chen SC DH Ellis TC Sorrell and W Meyer Chapter 44 Trichophyton In ldquoMolecular Detection of Human Fungal Pathogensrdquo Dongyou Liu (Ed) CRC Press 2011

All mycology isolates were identified by both conventional and molecular techniques

86 768

9 80

1 09

2 18

3 27

3 27

2 18

1 09

1 09

1 09

1 09

2 18

7C Scedosporium prolificans

This item contained Scedosporium prolificans 875 correct to genus level 768 correct to species level (required) Colonies are rapid growing flat spreading olive-grey to black (the culture may contain a mixture of the colurs depending on the age) and have a suede-like to downy surface texture [7C (i)] Conidia are borne in small groups on distinctive basally swollen flask-shaped annellides which occur singly or in clusters along the vegetative hyphae Conidia are single-celled hyaline to pale-brown ovoid to pyriform 2-5 x 3-13 um (average 34-53 um) in size and have smooth thin walls [7C (ii)] Identification of Scedosporium prolificans to

species level is very important due to its intrinsic resistance to most antifungal drugs It may be distinguished from other members of the genus in particular the human pathogen S apiospermum by its basally swollen (inflated) flask-shaped annellides conidia borne in small groups rather than singly and by not growing on media containing cycloheximide (actidione) DNA sequencing (ITS region) will also definitively identify Scedosporium species Three laboratories reported Sporothrix schenckii which is easily distinguished from Scedosporium spp because it is a dimorphic pathogen with a yeast-like phase when grown at 37degC

2

1

1

1

1

2

3

3

2

1

9

86

0 10 20 30 40 50 60 70 80 90 100

Unable to identify- refer

Chaetomium species

Hortaea werneckii

Ochroconis gallopava

Wangiella species

Exophiala species

Exophiala dermatitidis

Sporothrix schenckii

Scedosporium species

Scedosporium aurantiacum

Scedosporium apiospermum (sensu stricto)

Scedosporium prolificans

7C (i) 7C (ii)

Page 12: FINAL RESULTS AND COMMENTS D6-2013 …dataentry.rcpaqap.com.au/micro/reports/uploadedfiles/fnl2013-6.pdf · FINAL RESULTS AND COMMENTS D6/2013 ... This item contained a pure growth

copy2013 RCPA Quality Assurance Programs Pty Limited 12 Date of issue 13th November 2013

References Item 5 1 McCrea KW et al Relationships of nontypeable Haemophilus influenzae strains to hemolytic and nonhemolytic Haemophilus haemolyticus strains J Clin

Microbiol 200846 406ndash416 httpwwwncbinlmnihgovpmcarticlesPMC2238123

2 Jordan IK et al Genome sequences for five strains of the emerging pathogen Haemophilus haemolyticus J Bacteriol 2011193 5879ndash5880

httpwwwncbinlmnihgovpmcarticlesPMC3187195

3 Anderson R et al Haemophilus haemolyticus isolates causing clinical disease J Clin Microbiol 201250 2462-5

httpwwwncbinlmnihgovpubmed22573587

4 Morton DJ et al An invasive Haemophilus haemolyticus isolate J Clin Microbiol 201250 1502ndash1503

httpwwwncbinlmnihgovpmcarticlesPMC3318549

5 Agrawal A Murphy TF Haemophilus influenzae infections in the H influenzae type b conjugate vaccine era J Clin Microbiol 201149 3728ndash3732

httpwwwncbinlmnihgovpmcarticlesPMC3209133

6 Kilian M A taxonomic study of the genus Haemophilus with the proposal of a new species J Gen Microbiol 197693 9ndash62

httpwwwncbinlmnihgovpubmed772168

7 Kilian M 2005 Genus III Haemophilus Winslow Broadhurst Buchanan Krumweide Rogers and Smith 1917 561 p 883ndash904 In Brenner DJ Krieg NR Staley JT (ed) Bergeyrsquos manual of systematic bacteriology 2nd ed vol 2 Springer New York NY

8 Ledeboer NA Doern GV 2012 Haemophilus In Versalovic J Carroll KC Funke G Jorgensen JH Landry ML WarnockDW(ed) Manual of clinical microbiology 10th ed ASM Press Washington DC

9 McCrea KW et al Relationships of nontypeable Haemophilus influenzae strains to hemolytic and nonhemolytic Haemophilus haemolyticus strains J Clin Microbiol 200846 406ndash416 httpwwwncbinlmnihgovpmcarticlesPMC2238123

10 Murphy TF et al Haemophilus haemolyticus a human respiratory tract commensal to be distinguished from Haemophilus influenzae J Infect Dis 2007195 81ndash 89 httpwwwncbinlmnihgovpubmed17152011

11 Identification Reference Laboratory Centre for Infectious Diseases and Microbiology ICPMR Westmead Hospital 12 Binks MJ et al Molecular Surveillance of True Nontypeable Haemophilus influenzae An Evaluation of PCR Screening Assays PLOS

httpwwwplosoneorgarticleinfo3Adoi2F1013712Fjournalpone0034083

13 Duerden B Bennet KW and Faulkner J Isolation of Bacteroides ureolyticus (B corrodens) from clinical infections J Clin Pathol 1982 35 309-312 httpjcpbmjcomcontent353309fullpdf

The most common misidentification by participants was H influenzae (35) because of the phenotypicgenetic similarity of the two species and because of the failure of all kitsidentification systems to differentiate between them Reliance on one type of identification system is discouraged and may lead to incorrect identification of some organisms In this instance β-haemolysis on blood agar facilitated an accurate identification if detected however as already noted it may not always be displayed in this species even in primary cultures H parahaemolyticus reported by three laboratories is also β-haemolytic but unlike H haemolyticus it is V-dependent only (and δ-Aminolevulinic acid (ALA) test negative) as is H parainfluenzae reported by two laboratories which is not β-haemolytic All other false identifications reported do not exhibit X+V dependency or X- or V-dependency The laboratory reporting Corynebacterium jeikeium should note that this is a gram-positive rod B ureolyticus reported by one laboratory is an anaerobic organism with corroding colonies on agar plates 13 Brucella and Francisella tularensis are slow-growing fastidious organisms (also not XV-dependent) that would not be dispatched in this type of QAP

ITEM 201364C CLERICAL ERROR

Clerical Errors reported in Item 201364C Number labs (71)

No error reported 6

Error first name only (correct) in 4C 60(85)

Error first name only in 4D (incorrect) 1

Error first name (correct) + last name (incorrect) 1

Error first name (correct) + unit number (incorrect) 1

Error last name (incorrect) 2

Table 13 Clerical errors reported

Specimen label Karina DANIELS UN 831248 Paperwork Amelia DANIELS UN 831248

The clerical error was placed in item 201364C Mycobacteriology culture As only 95 participants receive 4C and 4D culture vials and only 71 performed testing this clerical error has not been scored

copy2013 RCPA Quality Assurance Programs Pty Limited 13 Date of issue 13th November 2013

ITEM 201367ABC MYCOLOGY

7A This item contained Trichophyton interdigitale [zoophilic] (previously T mentagrophytes) 973 correct to genus level 634 correct to species level (required) The Trichophyton species have undergone extensive reclassification in the last 5 years This is because there exists much phenotypic variation but genetic variation is low Most of the species formerly known as T mentagrophytes are now classified within T interdigitale T mentagrophytes still exists but encompasses only the organism previously known as T quinckeanum (T mentagrophytes var quinckeanum) which is associated with mice T interdigitale is recognised as having two ecological groups the anthropophilic and the zoophilic group with the former T mentagrophytes species falls into the zoophilic group For this item T interdigitale and T mentagrophytes were both marked as correct This newly merged species encompasses a wide range of phenotypes which may or may not be observed for a given specimen Sequencing of the internal transcribed spacer (ITS) region is the gold standard for identification using reference strains that are correctly named according to the revised taxonomy Chen et al have published a useful book chapter with phenotypic descriptions and recommendations for molecular identification of the revised Trichophyton species1

7A Trichophyton interdigitale [zoophilic]

Figures 7A (i-iii) Trichophyton interdigitale [zoophilic group] (previously T mentagrophytes) may have [7A(i)] numerous single-celled microconidia often in dense clusters along with smooth thin-walled cigar-shaped multicelled macroconidia Microconidia are hyaline smooth-walled and are predominantly spherical to subspherical in shape however occasional clavate to pyriform forms may occur [7A(ii)] varying numbers of spherical chlamydoconidia and [7A (iii)] spiral hyphae may also be observed The zoophilic form of the species tends to have powdery-granular colonies on Sabouraudrsquos lactritmel and 1 peptone media while the anthropophilic form has suede-downy textured colonies

1

1

1

1

1

2

2

5

6

7

14

1

31

1

5

20

13

0 5 10 15 20 25 30 35

Chrysosporium tropicum

Microsporum gypseum

Microsporum persicolor

Trichophyton equinum

Trichophyton terrestre

Trichophyton erinacei

Trichophyton verrucosum

Trichophyton species

Trichophyton rubrum [Worldwide population]

Trichophyton tonsurans

Trichophyton rubrum

Trichophyton mentagrophytes complex

Trichophyton mentagrophytes

Trichophyton interdigitale [anthropophilic] and [zoophilic]

Trichophyton interdigitale [anthropophilic]

Trichophyton interdigitale

Trichophyton interdigitale [zoophilic]

13 116

20 179

5 45

1 09

31 277

1 09

14 125

7 63

6 54

5 45

2 18

2 18

1 09

1 09

1 09

1 09

1 09

7A (i)

7A (ii) 7A (iii)

copy2013 RCPA Quality Assurance Programs Pty Limited 14 Date of issue 13th November 2013

7B Cryptococcus neoformans

82 732

8 71

1 09

1 09

5 45

11 98

1 09

1 09

1 09

1 09

7B This item contained Cryptococcus neoformans 964 correct to genus level 812 correct to species level (required) Cryptococcosis is typically caused by either Cryptococcus neoformans or Cryptococcus gattii although occasionally other Cryptococcus species have been implicated C neoformans typically infects the immunocompromised host frequently in the setting of HIV with gt1 million new cases and~600000 deaths per year globally C neoformans is a yeast-like basidiomycete fungus with a distinctive polysaccharide capsule Differentiation from the closely related C gattii is important Presumptive identification is by India Ink stain to highlight the capsule and birdseed agar to observe dark brown colonies

Figure 7B (i-iii) [7B (i)] India Ink stain highlighting the capsule of C neoformansgattii [7B(ii)] Dark brown colonies of C neoformansgattii mixed with white colonies of Candida albicans on birdseed agar [7B(iii)] Canavanine glycine bromothyol blue (CGB) media for distinguishing C neoformans (left) from C gattii (right)

1

1

1

1

11

5

1

1

8

82

0 10 20 30 40 50 60 70 80 90

Unable to identify- refer

Candida (not albicans)

Candida glabrata complex

Candida krusei

Cryptococcus neoformansgattii- unable to speciate

Cryptococcus species

Cryptococcus laurentii

Cryptococcus neoformans var grubii

Cryptococcus neoformans var neoformans

Cryptococcus neoformans

81 of labs correctly reported this isolate as Cryptococcus neoformans While no lab reported C gattii 11 labs were unable to differentiate C neoformans from C gattii Epidemiology risk factors and treatment of infections caused by these species are different and accurate identification is important for effective management All labs should seek to differentiate these species using CGB media a validated molecular method or by referral to a reference laboratory API ID32C and Vitek-2 does not distinguish C neoformans from C gattii These species may be differentiated by a number of DNA-based assays MALDI-ToF and canavanine-glycine-bromothymol blue (CGB) media C neoformans does not grow on CGB media which remains yellow whereas C gattii will grow triggering a blue colour change reaction in the media usually within 3 days It is worth noting that some slow growing C gattii isolates may take as long as 10 days to effect the blue colour change and may initially be mis-identified as C neoformans Nine labs unnecessarily attempted to further identify the C neoformans isolate to variety level either Cn var grubii (serotype A molecular types VNI and VNII) or Cn var neoformans (serotype D molecular type VNIV) It is not clear what methods were used to achieve this varietal identification but 8 of the 9 labs incorrectly reported Cn var neoformans In fact the isolate was confirmed by molecular methods to be Cryptococcus neoformans var grubii molecular type VNI The 8 reports of Cn var neoformans may reflect persistence of the now obsolete classification of Cryptococcus neoformans having two varieties var neoformans and var gattii If it is the normal practice of these labs to report to varietal level it would be worthwhile reviewing methods interpretation and reporting procedures

7B (i) 7B (ii) 7B(iii)

copy2013 RCPA Quality Assurance Programs Pty Limited 15 Date of issue 13th November 2013

Reference item 7

1 Chen SC DH Ellis TC Sorrell and W Meyer Chapter 44 Trichophyton In ldquoMolecular Detection of Human Fungal Pathogensrdquo Dongyou Liu (Ed) CRC Press 2011

All mycology isolates were identified by both conventional and molecular techniques

86 768

9 80

1 09

2 18

3 27

3 27

2 18

1 09

1 09

1 09

1 09

2 18

7C Scedosporium prolificans

This item contained Scedosporium prolificans 875 correct to genus level 768 correct to species level (required) Colonies are rapid growing flat spreading olive-grey to black (the culture may contain a mixture of the colurs depending on the age) and have a suede-like to downy surface texture [7C (i)] Conidia are borne in small groups on distinctive basally swollen flask-shaped annellides which occur singly or in clusters along the vegetative hyphae Conidia are single-celled hyaline to pale-brown ovoid to pyriform 2-5 x 3-13 um (average 34-53 um) in size and have smooth thin walls [7C (ii)] Identification of Scedosporium prolificans to

species level is very important due to its intrinsic resistance to most antifungal drugs It may be distinguished from other members of the genus in particular the human pathogen S apiospermum by its basally swollen (inflated) flask-shaped annellides conidia borne in small groups rather than singly and by not growing on media containing cycloheximide (actidione) DNA sequencing (ITS region) will also definitively identify Scedosporium species Three laboratories reported Sporothrix schenckii which is easily distinguished from Scedosporium spp because it is a dimorphic pathogen with a yeast-like phase when grown at 37degC

2

1

1

1

1

2

3

3

2

1

9

86

0 10 20 30 40 50 60 70 80 90 100

Unable to identify- refer

Chaetomium species

Hortaea werneckii

Ochroconis gallopava

Wangiella species

Exophiala species

Exophiala dermatitidis

Sporothrix schenckii

Scedosporium species

Scedosporium aurantiacum

Scedosporium apiospermum (sensu stricto)

Scedosporium prolificans

7C (i) 7C (ii)

Page 13: FINAL RESULTS AND COMMENTS D6-2013 …dataentry.rcpaqap.com.au/micro/reports/uploadedfiles/fnl2013-6.pdf · FINAL RESULTS AND COMMENTS D6/2013 ... This item contained a pure growth

copy2013 RCPA Quality Assurance Programs Pty Limited 13 Date of issue 13th November 2013

ITEM 201367ABC MYCOLOGY

7A This item contained Trichophyton interdigitale [zoophilic] (previously T mentagrophytes) 973 correct to genus level 634 correct to species level (required) The Trichophyton species have undergone extensive reclassification in the last 5 years This is because there exists much phenotypic variation but genetic variation is low Most of the species formerly known as T mentagrophytes are now classified within T interdigitale T mentagrophytes still exists but encompasses only the organism previously known as T quinckeanum (T mentagrophytes var quinckeanum) which is associated with mice T interdigitale is recognised as having two ecological groups the anthropophilic and the zoophilic group with the former T mentagrophytes species falls into the zoophilic group For this item T interdigitale and T mentagrophytes were both marked as correct This newly merged species encompasses a wide range of phenotypes which may or may not be observed for a given specimen Sequencing of the internal transcribed spacer (ITS) region is the gold standard for identification using reference strains that are correctly named according to the revised taxonomy Chen et al have published a useful book chapter with phenotypic descriptions and recommendations for molecular identification of the revised Trichophyton species1

7A Trichophyton interdigitale [zoophilic]

Figures 7A (i-iii) Trichophyton interdigitale [zoophilic group] (previously T mentagrophytes) may have [7A(i)] numerous single-celled microconidia often in dense clusters along with smooth thin-walled cigar-shaped multicelled macroconidia Microconidia are hyaline smooth-walled and are predominantly spherical to subspherical in shape however occasional clavate to pyriform forms may occur [7A(ii)] varying numbers of spherical chlamydoconidia and [7A (iii)] spiral hyphae may also be observed The zoophilic form of the species tends to have powdery-granular colonies on Sabouraudrsquos lactritmel and 1 peptone media while the anthropophilic form has suede-downy textured colonies

1

1

1

1

1

2

2

5

6

7

14

1

31

1

5

20

13

0 5 10 15 20 25 30 35

Chrysosporium tropicum

Microsporum gypseum

Microsporum persicolor

Trichophyton equinum

Trichophyton terrestre

Trichophyton erinacei

Trichophyton verrucosum

Trichophyton species

Trichophyton rubrum [Worldwide population]

Trichophyton tonsurans

Trichophyton rubrum

Trichophyton mentagrophytes complex

Trichophyton mentagrophytes

Trichophyton interdigitale [anthropophilic] and [zoophilic]

Trichophyton interdigitale [anthropophilic]

Trichophyton interdigitale

Trichophyton interdigitale [zoophilic]

13 116

20 179

5 45

1 09

31 277

1 09

14 125

7 63

6 54

5 45

2 18

2 18

1 09

1 09

1 09

1 09

1 09

7A (i)

7A (ii) 7A (iii)

copy2013 RCPA Quality Assurance Programs Pty Limited 14 Date of issue 13th November 2013

7B Cryptococcus neoformans

82 732

8 71

1 09

1 09

5 45

11 98

1 09

1 09

1 09

1 09

7B This item contained Cryptococcus neoformans 964 correct to genus level 812 correct to species level (required) Cryptococcosis is typically caused by either Cryptococcus neoformans or Cryptococcus gattii although occasionally other Cryptococcus species have been implicated C neoformans typically infects the immunocompromised host frequently in the setting of HIV with gt1 million new cases and~600000 deaths per year globally C neoformans is a yeast-like basidiomycete fungus with a distinctive polysaccharide capsule Differentiation from the closely related C gattii is important Presumptive identification is by India Ink stain to highlight the capsule and birdseed agar to observe dark brown colonies

Figure 7B (i-iii) [7B (i)] India Ink stain highlighting the capsule of C neoformansgattii [7B(ii)] Dark brown colonies of C neoformansgattii mixed with white colonies of Candida albicans on birdseed agar [7B(iii)] Canavanine glycine bromothyol blue (CGB) media for distinguishing C neoformans (left) from C gattii (right)

1

1

1

1

11

5

1

1

8

82

0 10 20 30 40 50 60 70 80 90

Unable to identify- refer

Candida (not albicans)

Candida glabrata complex

Candida krusei

Cryptococcus neoformansgattii- unable to speciate

Cryptococcus species

Cryptococcus laurentii

Cryptococcus neoformans var grubii

Cryptococcus neoformans var neoformans

Cryptococcus neoformans

81 of labs correctly reported this isolate as Cryptococcus neoformans While no lab reported C gattii 11 labs were unable to differentiate C neoformans from C gattii Epidemiology risk factors and treatment of infections caused by these species are different and accurate identification is important for effective management All labs should seek to differentiate these species using CGB media a validated molecular method or by referral to a reference laboratory API ID32C and Vitek-2 does not distinguish C neoformans from C gattii These species may be differentiated by a number of DNA-based assays MALDI-ToF and canavanine-glycine-bromothymol blue (CGB) media C neoformans does not grow on CGB media which remains yellow whereas C gattii will grow triggering a blue colour change reaction in the media usually within 3 days It is worth noting that some slow growing C gattii isolates may take as long as 10 days to effect the blue colour change and may initially be mis-identified as C neoformans Nine labs unnecessarily attempted to further identify the C neoformans isolate to variety level either Cn var grubii (serotype A molecular types VNI and VNII) or Cn var neoformans (serotype D molecular type VNIV) It is not clear what methods were used to achieve this varietal identification but 8 of the 9 labs incorrectly reported Cn var neoformans In fact the isolate was confirmed by molecular methods to be Cryptococcus neoformans var grubii molecular type VNI The 8 reports of Cn var neoformans may reflect persistence of the now obsolete classification of Cryptococcus neoformans having two varieties var neoformans and var gattii If it is the normal practice of these labs to report to varietal level it would be worthwhile reviewing methods interpretation and reporting procedures

7B (i) 7B (ii) 7B(iii)

copy2013 RCPA Quality Assurance Programs Pty Limited 15 Date of issue 13th November 2013

Reference item 7

1 Chen SC DH Ellis TC Sorrell and W Meyer Chapter 44 Trichophyton In ldquoMolecular Detection of Human Fungal Pathogensrdquo Dongyou Liu (Ed) CRC Press 2011

All mycology isolates were identified by both conventional and molecular techniques

86 768

9 80

1 09

2 18

3 27

3 27

2 18

1 09

1 09

1 09

1 09

2 18

7C Scedosporium prolificans

This item contained Scedosporium prolificans 875 correct to genus level 768 correct to species level (required) Colonies are rapid growing flat spreading olive-grey to black (the culture may contain a mixture of the colurs depending on the age) and have a suede-like to downy surface texture [7C (i)] Conidia are borne in small groups on distinctive basally swollen flask-shaped annellides which occur singly or in clusters along the vegetative hyphae Conidia are single-celled hyaline to pale-brown ovoid to pyriform 2-5 x 3-13 um (average 34-53 um) in size and have smooth thin walls [7C (ii)] Identification of Scedosporium prolificans to

species level is very important due to its intrinsic resistance to most antifungal drugs It may be distinguished from other members of the genus in particular the human pathogen S apiospermum by its basally swollen (inflated) flask-shaped annellides conidia borne in small groups rather than singly and by not growing on media containing cycloheximide (actidione) DNA sequencing (ITS region) will also definitively identify Scedosporium species Three laboratories reported Sporothrix schenckii which is easily distinguished from Scedosporium spp because it is a dimorphic pathogen with a yeast-like phase when grown at 37degC

2

1

1

1

1

2

3

3

2

1

9

86

0 10 20 30 40 50 60 70 80 90 100

Unable to identify- refer

Chaetomium species

Hortaea werneckii

Ochroconis gallopava

Wangiella species

Exophiala species

Exophiala dermatitidis

Sporothrix schenckii

Scedosporium species

Scedosporium aurantiacum

Scedosporium apiospermum (sensu stricto)

Scedosporium prolificans

7C (i) 7C (ii)

Page 14: FINAL RESULTS AND COMMENTS D6-2013 …dataentry.rcpaqap.com.au/micro/reports/uploadedfiles/fnl2013-6.pdf · FINAL RESULTS AND COMMENTS D6/2013 ... This item contained a pure growth

copy2013 RCPA Quality Assurance Programs Pty Limited 14 Date of issue 13th November 2013

7B Cryptococcus neoformans

82 732

8 71

1 09

1 09

5 45

11 98

1 09

1 09

1 09

1 09

7B This item contained Cryptococcus neoformans 964 correct to genus level 812 correct to species level (required) Cryptococcosis is typically caused by either Cryptococcus neoformans or Cryptococcus gattii although occasionally other Cryptococcus species have been implicated C neoformans typically infects the immunocompromised host frequently in the setting of HIV with gt1 million new cases and~600000 deaths per year globally C neoformans is a yeast-like basidiomycete fungus with a distinctive polysaccharide capsule Differentiation from the closely related C gattii is important Presumptive identification is by India Ink stain to highlight the capsule and birdseed agar to observe dark brown colonies

Figure 7B (i-iii) [7B (i)] India Ink stain highlighting the capsule of C neoformansgattii [7B(ii)] Dark brown colonies of C neoformansgattii mixed with white colonies of Candida albicans on birdseed agar [7B(iii)] Canavanine glycine bromothyol blue (CGB) media for distinguishing C neoformans (left) from C gattii (right)

1

1

1

1

11

5

1

1

8

82

0 10 20 30 40 50 60 70 80 90

Unable to identify- refer

Candida (not albicans)

Candida glabrata complex

Candida krusei

Cryptococcus neoformansgattii- unable to speciate

Cryptococcus species

Cryptococcus laurentii

Cryptococcus neoformans var grubii

Cryptococcus neoformans var neoformans

Cryptococcus neoformans

81 of labs correctly reported this isolate as Cryptococcus neoformans While no lab reported C gattii 11 labs were unable to differentiate C neoformans from C gattii Epidemiology risk factors and treatment of infections caused by these species are different and accurate identification is important for effective management All labs should seek to differentiate these species using CGB media a validated molecular method or by referral to a reference laboratory API ID32C and Vitek-2 does not distinguish C neoformans from C gattii These species may be differentiated by a number of DNA-based assays MALDI-ToF and canavanine-glycine-bromothymol blue (CGB) media C neoformans does not grow on CGB media which remains yellow whereas C gattii will grow triggering a blue colour change reaction in the media usually within 3 days It is worth noting that some slow growing C gattii isolates may take as long as 10 days to effect the blue colour change and may initially be mis-identified as C neoformans Nine labs unnecessarily attempted to further identify the C neoformans isolate to variety level either Cn var grubii (serotype A molecular types VNI and VNII) or Cn var neoformans (serotype D molecular type VNIV) It is not clear what methods were used to achieve this varietal identification but 8 of the 9 labs incorrectly reported Cn var neoformans In fact the isolate was confirmed by molecular methods to be Cryptococcus neoformans var grubii molecular type VNI The 8 reports of Cn var neoformans may reflect persistence of the now obsolete classification of Cryptococcus neoformans having two varieties var neoformans and var gattii If it is the normal practice of these labs to report to varietal level it would be worthwhile reviewing methods interpretation and reporting procedures

7B (i) 7B (ii) 7B(iii)

copy2013 RCPA Quality Assurance Programs Pty Limited 15 Date of issue 13th November 2013

Reference item 7

1 Chen SC DH Ellis TC Sorrell and W Meyer Chapter 44 Trichophyton In ldquoMolecular Detection of Human Fungal Pathogensrdquo Dongyou Liu (Ed) CRC Press 2011

All mycology isolates were identified by both conventional and molecular techniques

86 768

9 80

1 09

2 18

3 27

3 27

2 18

1 09

1 09

1 09

1 09

2 18

7C Scedosporium prolificans

This item contained Scedosporium prolificans 875 correct to genus level 768 correct to species level (required) Colonies are rapid growing flat spreading olive-grey to black (the culture may contain a mixture of the colurs depending on the age) and have a suede-like to downy surface texture [7C (i)] Conidia are borne in small groups on distinctive basally swollen flask-shaped annellides which occur singly or in clusters along the vegetative hyphae Conidia are single-celled hyaline to pale-brown ovoid to pyriform 2-5 x 3-13 um (average 34-53 um) in size and have smooth thin walls [7C (ii)] Identification of Scedosporium prolificans to

species level is very important due to its intrinsic resistance to most antifungal drugs It may be distinguished from other members of the genus in particular the human pathogen S apiospermum by its basally swollen (inflated) flask-shaped annellides conidia borne in small groups rather than singly and by not growing on media containing cycloheximide (actidione) DNA sequencing (ITS region) will also definitively identify Scedosporium species Three laboratories reported Sporothrix schenckii which is easily distinguished from Scedosporium spp because it is a dimorphic pathogen with a yeast-like phase when grown at 37degC

2

1

1

1

1

2

3

3

2

1

9

86

0 10 20 30 40 50 60 70 80 90 100

Unable to identify- refer

Chaetomium species

Hortaea werneckii

Ochroconis gallopava

Wangiella species

Exophiala species

Exophiala dermatitidis

Sporothrix schenckii

Scedosporium species

Scedosporium aurantiacum

Scedosporium apiospermum (sensu stricto)

Scedosporium prolificans

7C (i) 7C (ii)

Page 15: FINAL RESULTS AND COMMENTS D6-2013 …dataentry.rcpaqap.com.au/micro/reports/uploadedfiles/fnl2013-6.pdf · FINAL RESULTS AND COMMENTS D6/2013 ... This item contained a pure growth

copy2013 RCPA Quality Assurance Programs Pty Limited 15 Date of issue 13th November 2013

Reference item 7

1 Chen SC DH Ellis TC Sorrell and W Meyer Chapter 44 Trichophyton In ldquoMolecular Detection of Human Fungal Pathogensrdquo Dongyou Liu (Ed) CRC Press 2011

All mycology isolates were identified by both conventional and molecular techniques

86 768

9 80

1 09

2 18

3 27

3 27

2 18

1 09

1 09

1 09

1 09

2 18

7C Scedosporium prolificans

This item contained Scedosporium prolificans 875 correct to genus level 768 correct to species level (required) Colonies are rapid growing flat spreading olive-grey to black (the culture may contain a mixture of the colurs depending on the age) and have a suede-like to downy surface texture [7C (i)] Conidia are borne in small groups on distinctive basally swollen flask-shaped annellides which occur singly or in clusters along the vegetative hyphae Conidia are single-celled hyaline to pale-brown ovoid to pyriform 2-5 x 3-13 um (average 34-53 um) in size and have smooth thin walls [7C (ii)] Identification of Scedosporium prolificans to

species level is very important due to its intrinsic resistance to most antifungal drugs It may be distinguished from other members of the genus in particular the human pathogen S apiospermum by its basally swollen (inflated) flask-shaped annellides conidia borne in small groups rather than singly and by not growing on media containing cycloheximide (actidione) DNA sequencing (ITS region) will also definitively identify Scedosporium species Three laboratories reported Sporothrix schenckii which is easily distinguished from Scedosporium spp because it is a dimorphic pathogen with a yeast-like phase when grown at 37degC

2

1

1

1

1

2

3

3

2

1

9

86

0 10 20 30 40 50 60 70 80 90 100

Unable to identify- refer

Chaetomium species

Hortaea werneckii

Ochroconis gallopava

Wangiella species

Exophiala species

Exophiala dermatitidis

Sporothrix schenckii

Scedosporium species

Scedosporium aurantiacum

Scedosporium apiospermum (sensu stricto)

Scedosporium prolificans

7C (i) 7C (ii)