microbiology user manual - bhsct regional virus … · 2017-05-24 · microbiology user manual ......

Revision Number 7.0 Document Number M-3

Author/Reviewer V.Robinson

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Authoriser M McGimpsey

Active Date 07/12/16 Page Number of 35

Effective Date 07/12/16 Document Type Management Procedure

Belfast Trust Laboratories Microbiology

MICROBIOLOGY USER MANUAL

Additional Information & Cross References

Replaces Document Number MP 200 001

Change Management

Related Documents

C-345: BTL User Manual C-17: Instructions for the transport of specimens by pneumatic tube C-18: Instructions for the transport of specimens by road



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Microbiology Department General Information

Department of Medical Microbiology Kelvin Building, Royal Victoria Hospital, Grosvenor Road, Belfast, BT12 6BA DX 3864NR

Laboratory Contacts:

Laboratory Enquiries / Advice 028 9063 4140

Fax (028) 9031 1416

Virology Specific Enquiries 028 9063 5242

028 9063 2662

Clinical Lead Dr Anne Loughrey 028 9063 4112

Discipline Manager Mr Mark McGimpsey 028 9063 4125

Quality Officer Mrs Karen Shields 028 9063 8275

Operational Manager Bacteriology Mrs Nicola Wolseley 028 9063 2111

Operational Manager Molecular and Serology Services

Mr Ian Doherty 028 9063 3225

Medical Contacts:

Infection Control Doctor Dr Wesam Elbaz 028 9063 4020

Infection Control Nurses 028 9063 8160/8169

Duty Virologist (Clinical Virology advice Mon – Fri 9am – 5pm)

Dr Peter Coyle Dr Conall McCaughey Dr Susan Feeney Dr Tanya Curran Dr Alison Watt

07889086946

Medical Microbiology Registrars (clinical advice Mon – Fri 9am – 5pm)

Office 028 9063 4117

Pager (urgent only) 0425

Out of Hours Contacts:

Urgent Out of Hours Microbiology Laboratory Biomedical Scientist

028 9063 3607 or 07717731904

Virology Contact Switchboard

Medical Microbiologist Contact Switchboard

N. Ireland Public Health Laboratory:

Public Health Laboratory

NIPHL Belfast Health and Social Care Trust Lisburn Road Belfast Northern Ireland BT9 7AD

02890 263588

Laboratory Services The laboratory offers consultant-lead scientific and clinical advice and interpretation on a comprehensive range of tests for the microbiological investigation of patients. Microbiology service comprises:

General Bacteriology

N. Ireland Mycobacterial Reference Laboratory

Mycology

Regional Virology Services



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Serology

Molecular services (diagnostics, theranostics, epidemiology)

N. Ireland Public Health Laboratory (based on the City Hospital site)

Our aim is to provide the highest quality of service with prompt delivery of accurate results, (backed up by specialist medical and scientific expertise). Where specific tests are not available locally, they will be referred to colleagues in other centres. When test is sent to a reference laboratory, every effort is made to use a PHE recognised laboratory, the details of which will be published with the result received. Further information on the reference laboratories used can be obtained by contacting the Quality Officer. Comments and Complaints If you have a comment, compliment or complaint about our service, please let us know by contacting the quality officer who will try to help resolve the issue. The laboratory has documented policies on Data Protection, Protection of Personal Information and Complaints and Compliments available through the trust website http://www.belfasttrust.hscni.net/services/Laboratory-MortuaryServices.htm. Clinical Advice and Interpretation Clinical advice or interpretation of results is available at all times for Belfast Trust and Regional Users. See contact details provided above. During working hours (Mon-Fri 09:00-17:00): Contact the Laboratory Staff or Medical Microbiology team as appropriate. Out of hours: For urgent test requests: Contact the Biomedical Scientist out of hours For clinical advice: Bacteriology - Contact on-call Medical Microbiology via switchboard. Virology - Contact the in the first instance. If necessary, out of hours requests and requests for medical advice may be referred to a consultant virologist.

Test Request Information

Requests should be written on the green and white Microbiology request form with the exception of Regional Virology, Molecular and Serology, where dedicated forms for specific services are available from the documents section of the laboratory website: http://www.rvl-belfast.hscni.net. Requests can also be generated by order com. Place the request form in the extra pocket of the plastic sample bag or attach it outside with an elastic band. Do not staple the form to the bag.

http://www.rvl-belfast.hscni.net/



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Completion of Request Forms Please avoid the terms “viral screening”, “routine virology”, “viral studies” or “viral titres” as these terms are confusing and unhelpful. Instead, please provide brief patient clinical details and duration of illness, which allows us to choose appropriate tests. Minimum Patient Identifiers In order to fully identify a patient and send a full report back to the requesting source, the request must contain the following information:

Essential Desirable

Sample Unique Identification Number (E.g. H&C/ Hosp. / Client / WOC No.)

Forename

Surname

Date of Birth (dd/mm/yyyy)

Date & time

Request Form

Unique Identification Number (E.g. H&C/ Hosp. /Client/WOC No.)

Forename

Surname

Date of Birth (dd/mm/yyyy)

Test (s) Requested

Anatomical site and type of specimen

Destination for report

Sex

Name of Consultant or Gp

Identity of person collecting the sample

Date & time of sample collection (which is sometimes essential)

Patient’s address including postcode

MRSA/ESBL/CPO status etc. is desirable for Bacteriology requests

Relevant clinical information.

HTA Donor Sample: Request form and sample

Unique donor ID code (unique patient identification number e.g. H&C/Hosp. number)

Time

Place

Please indicate if an unusual or fragile organism is suspected as the causal agent, these may not be isolated by normal testing protocols and may require special media, special isolation conditions and prolonged incubation.



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Supplies Information All swabs, sample bags, request forms etc. can be obtained from the Belfast trust central stores (02890353418).

Urgent Requests

It is essential that all request forms for emergency sample investigation are labeled accordingly and prior arrangements made with the laboratory by phoning the appropriate laboratory during normal working hours:

Department Extension No Working Hours

Bacteriology 33607 Mon – Fri 08:00 – 20:00

NIMRL 35798 Mon – Fri 09:00 – 16:00

Mycology 34166 Mon – Fri 09:00 – 17:00

Serology 35242 Mon – Fri 09:00 – 17:00

Molecular 33225 Mon – Fri 09:00 – 17:00

For urgent samples out of hours please contact Biomedical Scientist on the numbers listed. Requesting additional examinations If requesting a further test, this should be requested as soon as possible after receiving the original report and will be dependent on specimen retention, quality and volume requirement issues. Additional requests will be either added to the original request or a new request generated as appropriate. Labeling High Risk Samples For suspected or known Category 3 pathogens, hazard warning Category 3 pathogen labels should be affixed both to the container and the accompanying request form. If there is any doubt as to whether a specimen is high risk, please contact the Microbiology laboratory.

Hazard Group 3 is defined as a biological agent that may cause severe human disease and presents a serious hazard to employees; it may present a risk of spreading to the community, but there is usually effective prophylaxis or treatment available. NB: Hazard warning Category 3 pathogen labels should be affixed to ALL samples taken from patients with pyrexia of unknown origin (PUO) following foreign travel. Examples of Category 3 Pathogens Bacteria:-

Bacillus anthracis (Anthrax)

Brucella species

Escherichia coli, vero-cytotoxigenic strains (e.g: 0157: H7 and others)

Mycobacterium tuberculosis

Mycobacteria other than tuberculosis (MOTT)



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Salmonella typhi

Salmonella paratyphi

Shigella dysenteriae (Type 1) Fungi:-

Blastomyces dermatitidis

Coccidioides immitis

Histoplasma species

Paracoccidioides brasiliensis

Penicillium marneffei Viruses:-

All viral hepatitis (except Hepatitis A)

HIV

Severe Acute Respiratory Syndrome (SARS) Prion Proteins:-

Transmissible spongiform encephalopathies (TSE) e.g: the agents of Creutzfeldt-Jacob disease (CJD): variant Creutzfeldt-Jacob disease (vCJD)

Fatal familial insomnia

Gerstman-Straussler-Scheinker syndrome

Kuru Hazard Group 4 is defined as a biological agent that will cause severe human disease and is a serious hazard to employees; it is likely to spread to the community, and there is usually no effective prophylaxis or treatment available. Please contact the Medical Microbiology team immediately if you suspect a group 4 pathogen e.g. Lassa, Marburg, Ebola and Crimean. Under NO circumstances should any samples be taken from such patients without prior consultation with the Medical Microbiology team. Packaging and Transportation of Samples Advice on packaging samples for transport to the Laboratory Instructions can be found on the Belfast Trust website, or requested from the laboratory: C-17 - Pneumatic tube transport of specimens C-18 - Road transport of specimens The manager of every Ward, Clinic, or GP which sends specimens to the Belfast Trust Laboratories must read these and must ensure their unit complies with these directions. The Carriage of Dangerous Goods Regulations (2011) and ADR (2011) place a clear legal responsibility on the sender and any agent they use to transport diagnostic specimens by road. Internal transfer to the laboratories by the pneumatic tube system is subject to risk assessments made under the HSAW order and the COSHH regulations.



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Transportation of Samples There is a legal responsibility and a duty of care on anyone who dispatches clinical material (diagnostic specimens) to the Belfast Trust Laboratories. The legal responsibility is to ensure that if required, the specimens are packaged and labeled in compliance with the relevant road transport regulations (ADR/CDG). There is a further legal responsibility under COSHH regulations, since clinical materials may contain infectious agents, to ensure that the materials do not leak or injure anyone involved in the transportation or the wider public and environment. The duty of care (to the patient) is to ensure that the transport conditions do not damage the material being sent for testing or otherwise interfere with the validity of the test results, and to ensure the specimen reaches the laboratory in good condition within an appropriate time frame for good clinical management of the case. Specimens should be clearly labeled and dated. Place all specimens in leak proof containers in sealed plastic bags. NB: Category 3 samples should be double bagged and clearly identified.

Samples from the Royal Group of Hospitals can be sent via the vacuum tube system (except cat 3 samples) or by hospital courier.

Samples from other hospitals / GPs may be sent by the relevant dispatch systems.

Postal samples must be sent in accordance with the guidelines issued by the Post Office in respect of postal transmission of pathological specimens.

Any referring Unit, Hospital, Clinic, GP Practice or Trust transporting specimens by road (which includes postal services) should take professional advice and guidance on the packaging and labeling of any materials they hand over for transportation. The laboratories are not responsible for nor do they have any managerial control over the transportation of specimens between the shipper and the destination. The strong recommendation by Belfast Trust Microbiology is that all patient Clinical Specimens should be considered as potentially infectious and must therefore be categorised at the very minimum as UN3373 Biological Substance Category B and be packed and labeled according to Packing Instruction P650 in the ADR/CDG regulations. (The packaging standard comprises 3 layers, two leak proof layers, and a third outer rigid layer which provides protection against impact.) If fully compliant with P650 then the package, the transport vehicle and the driver are not subject to further specific requirements under ADR. THIS EXEMPTION MUST ALWAYS BE USED If the packaging is not P650 compliant then there is no exemption from the full ADR/CDG regs, and the shipper and the driver will probably be found in breach of a number of transport regulations and liable to prosecution.



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All users’ will be contacted immediately if specimens are received that do not meet with the stated packaging and transport requirements and informed as to how to eliminate recurrence. DX Courier Details DX address DX 3864NR Exchange: Belfast 14 Guidelines for Proper Specimen Collection and Factors Which May Affect the Quality of the Results:

Confirm the identity of the patient either verbally and/or by hospital identification wristband.

Complete the request form.

Check that the patient is appropriately prepared. This will obviously differ depending on the nature of the sample(s) being taken.

Ensure the specimen(s) is collected correctly. It is important that the laboratory receive good quality samples. Guidance on sample collection especially those samples that are naturally eliminated from the body and hence can often be collected by the patient can be found on the website http://labtestsonline.org.uk/ (further information can also be found by following the links in the specific sample types detailed below).

Collect specimen before administering antimicrobial agents when possible.

Check that the sample container is labeled correctly. Use sterile containers

and aseptic technique to collect specimens to prevent introduction of micro-

organisms during invasive procedures. Only laboratory approved, CE marked,

in vitro devices IVDs, must be used as primary specimen containers, no

substitutes or improvised containers.

Collect an adequate amount of specimen. Inadequate amounts of specimen may yield false-negative results. If multiple samples are collected at the same time ensure there is no interchange of samples.

Specimens obtained using needle aspiration should be transferred to a sterile container and transported to the laboratory as soon as possible. If there is only a small volume of material in the syringe, add some sterile preservative-free saline, mix and transfer to a sterile container. Do not send needle or syringe.

All materials used in specimen collection should be disposed of safely according to documented protocols.

All high risk samples MUST be identified to facilitate the correct processing of such samples by laboratory personnel.

Any spillages or breakages occurring during sample collection must be dealt with correctly according to a documented procedure.

All container tops must be firmly and properly closed, leakage adversely

affects not only that specimen but other specimens sharing the transit

http://labtestsonline.org.uk/



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The date and time of collection should be clearly stated (24 hr clock)

Fragile organisms may be affected by a delay in transport.

Specimens must be kept in a cool room awaiting dispatch, not in the sunlight

or near a radiator. Ensure the samples are stored under the appropriate

storage conditions for the investigation required.

Transit to the laboratory should be prompt and specimens must not be left in

uncontrolled vehicles (hot/cold) for any prolonged period.

If processing is delayed, refrigeration is preferable to storage at ambient temperature. Delays of over 48h are undesirable.

Indicate if an unusual or fragile organism is suspected as the causal agent, these may not be isolated by normal testing protocols & may require special media, special isolation conditions & prolonged incubation.

To minimise the risk and ensure the safety of the specimen collector, carrier, general public and the receiving laboratory, it is important that care is taken when collecting and handling clinical samples to ensure that the risk of infection to staff is kept to an absolute minimum. Therefore: o Samples must always be carried in closed sealed plastic bags placed in

closed sealed boxes. o Safe working practices shall be observed at all times. o All clinical samples must be placed inside a sealed plastic bag. o Should any urgent samples be sent outside of normal laboratory hours

(0900 – 1730) they will be transported in sealed plastic bags. o Samples must never be carried unprotected in the open hand or given to

other members of staff in this way. o Patient confidentiality must be preserved by the use of envelopes or

opaque plastic bags. o Samples must always be carried in closed boxes which are clearly marked

with a BIOHAZARD label. Samples must never be thrown into a large plastic bag and transported in this manner.

o The containment of samples within motor vehicles, used to transport samples, must be such as to restrain, retain and protect the contents in the event of an accident.



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Criteria for Rejection of Specimens Specimens may be rejected immediately if:

Form Received with no specimen

Discrepancy between the patient details on the form and the specimen

No patient details on either the request form or the specimen

Specimens which have leaked and are insufficient for testing

Specimens deemed unsuitable for testing by BMS or clinical scientist at the point of testing

Specimens accompanied by a request form with insufficient information to send out a report or to determine which test is required.

If a sample is unsuitable for testing a report will be sent to the requestor giving the reason and requesting another sample. When blood cultures are received that do not meet the minimum identifier set every effort will be used to contact the ward/department by telephone to advise that the sample is to be rejected and a repeat sample is necessary. The laboratory may choose to process a sample that may otherwise have been rejected by cooperating with users in clarifying the request. In the case of CSF, tissues, bronchial washes and irreplaceable fluids for TB culture and other such samples which cannot or are extremely difficult to repeat, the laboratory will contact the ward/department to clarify the patient identifier set. Note will be taken as to whom communication has been made and included as a laboratory comment on the report. In other instances, the final report will have a laboratory comment which indicates the problem and if caution need be applied when interpreting the result. Results

Reports for both routine and emergency requests can be viewed on labcentre or ECR and can be accessed in your ward/practice as soon as they are validated by laboratory personnel. Please make use of this facility. Please avoid phoning whenever possible. The issuing of results of a non-urgent nature over the phone is discouraged and must be kept to an essential minimum in the interests of safety as verbal reports may lead to transcription errors. If a phone enquiry is absolutely necessary, consult the laboratory computer system to obtain the on-screen laboratory test request number, if this is available. This is in order to validate that you are authorised to receive the confidential laboratory report in question and will assist laboratory staff in dealing with your enquiry more efficiently. All laboratory results should be interpreted in conjunction with the clinical



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state of the patient. If inappropriate results are received, please contact the laboratory and/or repeat the specimen. Frequency of requesting examinations How often a test should be repeated, if at all, should be based on a number of criteria:

The physiological properties

Biological half-life

Analytical aspects

Treatment and monitoring requirements

Established guidance The Royal College of Pathologists have published advice on the minimum retesting intervals in pathology: https://www.rcpath.org/asset/7A6DA597-181F-4482-B08303CE3907020D/ For further advice on the use of the services provided, please contact the laboratory.

Test Repertoire: The Microbiology laboratory is a UKAS accredited testing laboratory No. 8704 The test schedule listing accredited tests can be found on the UKAS website: www.ukas.com/search-accredited-organisations/ Service Agreement Each request accepted by the Microbiology Laboratory for examination(s) shall be deemed to be an agreement by the user for the Belfast Health & Social Care Laboratory services, or other accredited laboratories as may be used to perform testing outside repertoire, to carry out the necessary testing and reporting function. It also implies an acceptance of the conditions of preparation and transport as outlined in this manual. Please Note: Tests and specimen types listed below are for guidance only. For tests not listed below, or specimen types not listed within a particular test please contact the laboratory to discuss clinical requirements.

https://www.rcpath.org/asset/7A6DA597-181F-4482-B08303CE3907020D/

http://www.ukas.com/search-accredited-organisations/



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Bacteriology

Test Sample Type Container

Further information TAT (Working

Days)

Antibiotic Assay

5mls Clotted blood sample

red top bottle

60Gentamycin, Vancomycin, Amikacin, Tobramycin, Teicoplanin Performed in Biochemistry Laboratory For antibiotic guidelines follow the link below. http://www.bcare.nbt.nhs.uk/wp-content/uploads/Antibiotic-Assay-Guideline-Ranges-20151.pdf Other Antibiotics Sent to reference laboratory

See Biochemistry user manual

Blood culture Adult – set of culture bottles 8-10mls Blood in each NB: In cases of endocarditis a maximal volume of blood should be added Paediatric – single bottle 1-3ml Blood Blood Culture bottles are available to order from microbiology specimen reception (Tel. 02890633507)

Aerobic – Green top Anaerobic – Orange top Yellow top

Blood cultures should be taken aseptically according to Trust policy. A maximum delay of 4 hours has been stipulated by National UK Standards, PHE between inoculation of blood culture bottles at the bedside and incubation of these in the lab. Blood culture bottles should be inoculated before other containers Repeated cultures increase sensitivity and help to distinguish contaminants from clinically relevant organisms. Three sets, taken not less than one hour apart, will give a success rate of 99%. In cases of suspected intravascular catheter related sepsis, separate blood cultures should be taken from the various lines or line ports. An additional blood culture from a peripheral venipuncture should be taken also. Blood Cultures must NOT be refrigerated.

“No growth” will be reported in 5 days Results of possible pathogens will be telephoned by medical staff as a priority.

http://www.bcare.nbt.nhs.uk/wp-content/uploads/Antibiotic-Assay-Guideline-Ranges-20151.pdf

http://www.bcare.nbt.nhs.uk/wp-content/uploads/Antibiotic-Assay-Guideline-Ranges-20151.pdf



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CSF A minimum volume of 1ml CSF should be collected using an aseptic technique.

Sterile universal container

CSF should be received into the laboratory within 1 hr. of being taken. In cases of suspected meningitis, the following should also be considered:

Blood culture

EDTA blood sample 2.5mls for meningococcal and pneumococcal PCR

Cryptococcus CSF/blood antigen if relevant

Throat swab for meningococcal culture

Haemorrhagic skin rash swab and glass slide (pinch the lesion to exclude circulating blood and puncture

with a sterile needle. Squeeze a drop of fluid and smear on a slide.

Microscopy/cell count – Same Day Culture – Negative & preliminary results available after 2 days

Ear Swab Blue cap swab

Before sampling, remove debris with sterile saline under direct vision

Negative & preliminary results available after 2 days

Eye -Conjunctiva

Swab

Blue cap swab


Eye -Corneal scrape

Corneal scraping should be accompanied by a conjunctival swab The first corneal scraping should be spread on a glass slide for gram staining The second scraping sample should

Glass slide and brain heart infusion container

Microscopy and culture (bacterial and fungal) is routinely performed on corneal scrapings.

If Acanthamoeba infection is suspected, please send a punch biopsy or corneal scrape (without the blade)

Microscopy – Same Day Culture – Negative & preliminary results available after 2 days



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be added with the blade to a brain heart infusion container [supplied by the lab]

in approximately 200µl of sterile saline to the laboratory.

If Chlamydial or viral infection is suspected, please send an additional conjunctival swab to the Regional Virus Laboratory.

If mycobacterial infection is suspected, an extra slide should be sent for ZN stain and a further sample in a sterile universal container mixed with one ml of sterile preservative-free saline

Suspected Acanthamoeba specimens sent to reference lab.

Faeces Diarrhoeal samples which flow to assume the shape of the container

Blue top universal container with plastic spoon

Enteric Pathogens

Diarrhoeal Samples are routinely tested for salmonella, shigella, campylobacter, verotoxigenic E. coli, cryptosporidium and giardia. C. difficile:

Specimens from ICU patients and patients above 65 years will be routinely tested for C.difficile . Otherwise, this needs to be specifically requested. C. difficile is tested once daily including weekends . Samples should be received by 11:45am and should be less than 24 hours old. Parasitology:

Faeces will only be tested for other parasites on request and in the presence of appropriate history ie foreign travel.

If you suspect a viral etiology please refer to molecular section

http://labtestsonline.org.uk/understanding/analytes/ocp/tab/sample

Negative & preliminary results available after 2 days C difficle – 1 day Parasitology – 1 Week





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Fluid [pleural] Aseptically collect 20 ml of pleural fluid. If TB is suspected, a larger volume is required (up to 250 ml if possible) If a small volume of material is obtained in the syringe, add some sterile preservative-free saline, mix and transfer to a sterile container.

Sterile universal container or any large sterile container.

Microscopy (Gram and ZN stains) and culture (bacterial and mycobacterial) is performed routinely. Please refer to the mycobacterial section

Cell count will be performed on request only.


Fluid [joint] Fluid should be collected under complete aseptic conditions If only a small volume of material is obtained, add some sterile preservative-free saline, mix and transfer to a sterile container.

Sterile universal container only. For cell count please send EDTA sample

Crystal analysis will be performed on request only.

Cell count will be performed on request only.

If septic arthritis is suspected, a blood culture should be sent.

If reactive arthritis is suspected, faecal culture may be considered for salmonella, shigella, campylobacter and yersinia; Paired sera for antibody testing are also required.

If rheumatic fever is suspected, a throat swab and a clotted blood sample for antistreptolysin O titre are appropriate.

If a sexually transmitted aetiology is suspected, please refer to the genital swab section of user manual

Cell count will be performed on request only. If TB peritonitis is suspected, ZN stain and TB culture should be specifically requested. See mycobacterial section.


Helicobacter Gastric Biopsy

a vial of Dents

The test is performed by the Laboratory of Gastrointestinal Pathogens (HPA Coilndale). The ref

15 days from receipt in ref. lab.



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Please give the laboratory previous notice that this test is to be performed so that the Dents media can be supplied for day of testing.

media lab supply ‘Dents’ , which is a preservation media used for Helicobacter. Anyone requesting this will now obtain a vial of Dents media and a referral form from the lab. Return the biopsy in it and the referral form for dispatch. It is important that this is dispatched ASAP as samples over 96hrs old are not suitable for culture. Consultants requesting this have been advised to get samples to the lab no later than midday Thursday.

Pus (exudates) Any volume of pus is preferable to a swab of pus. If a small volume is obtained, add some sterile preservative-free saline, mix and transfer to a sterile container.


Routine bacterial culture will be performed on all samples.

Gram stain will be performed on request only.

If an unusual infection is suspected eg TB, this should be highlighted and requested specifically.


Sputum Purulent and mucopurulent samples are ideal Salivary samples may be rejected Samples should be taken prior to starting antibiotic therapy. Sputum production may be enhanced with physiotherapy or saline inhalation. If TB is suspected, three early

Wide neck sputum container

Blood culture and pleural fluid culture may aid with the diagnosis of pneumonia.

Urine for legionella and pneumococcal antigens should be considered especially in community acquired pneumonia.

If Legionnaires` disease is suspected, sputum culture and PCR should be requested.

ZN stain and mycobacterial culture will be performed on request only.

In immunosupressed patients or patients with a history of foreign travel where unusual mould




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morning sputum samples on consecutive days should be sent – please refer to the mycobacterial section

infections are suspected, fungal culture should also be specifically requested.

Suspected ureaplasma/ mycoplasma hominis pneumonia in ventilated neonates: send ET or tracheal secretions to microbiology (0.5mls).

Inform microbiology registrar prior to sending secretions so that laboratory is aware that sample is being sent.

Cystic Fibrosis: The form must be clearly marked “Cystic Fibrosis” or “CF” so that the sample can be processed appropriately.

http://labtestsonline.org.uk/understanding/analytes/sputum-culture/tab/sample

Bronchoalveolar lavage (BAL) and associated specimens

Where possible all specimens should be fresh and taken before antimicrobial treatment. Use aseptic technique.

A sterile leak proof universal container

Numbers and frequency of specimens collected are dependent on the clinical condition of patient.

Culture for Mycobacterium species will be performed on all BAL specimens with the exception of PICU.

Preliminary results available after 2 days.

Swabs [Cough Swab] (Cystic Fibrosis)

If possible the sample is taken after physiotherapy. The swab is rubbed over the high pharyngeal area after the patient has been asked to cough.

Blue cap clear transwab

These swabs are from Cystic Fibrosis patients unable to produce a sputum sample. Swabs will be cultured for typical CF pathogens. The form must be clearly marked “Cystic Fibrosis” or “CF” so that the sample can be processed appropriately.


Swabs [genital tract]

Females High Vaginal swab Cervical Swab Males Urethral Swab


Routine bacterial culture will be performed on high vaginal swabs.

Gonococcal culture will be performed on request only.

Clue cells will only be tested for on request, or if there is an appropriate history of bacterial vaginosis

Trichomonas testing performed on request only.






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Swabs [Chlamydia]

For investigation, please refer to the Molecular diagnostics Section.

NB. When taking a genital tract specimen which may have particular legal significance, you may need to contact a genito-urinary physician for advice.

Swabs [Screening: MRSA MSSA GRE CPO]

- Nasal swab - Perineum swab [groin] - All wounds - Aseptic catheter sample of

urine if catheterized - Vascular access site if signs of

infection are present- Sputum

- Faeces / Rectal Swab +/- urine (CPO/GRE)


Swabs from other sites are not helpful for screening and will be rejected. NB. The swab should be moistened with sterile saline 0.9% solution before use. Throat/axilla swabs are not required for routine MRSA screening and therefore not normally processed in the laboratory. If a patient is to receive treatment in another hospital and throat/axilla swabs are requested by that establishment, it is imperative that the requirement and reasons for this is made clear on the request form, otherwise the swabs will not be processed.


Swabs [skin and soft tissue]

Pus and tissue samples are superior to swabs


Before sampling, remove debris with sterile saline or water. Rub the swab over the base of the lesion.


Swabs [throat]

Rub the swab over the tonsillar areas and the posterior pharyngeal wall. Rotate the swab to ensure that all the infected mucosa is sampled


It is important to swab the infected area. Swabs will be cultured for Haemolytic Streptococci and relevant Corynebacterium species. Specimens will be examined for Vincent`s organisms if clinical history is suggestive.


Tips [intravascular]

Clean the skin with antiseptic solution before withdrawal of the catheter. Send a 5cm length of tip


Intravascular line tips should only be sent if line related sepsis is suspected. They should not be sent for routine culture. Intravascular line tips should be accompanied by peripheral blood cultures




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Tips [others] Sterile universal container

Urinary catheter tip is not an appropriate sample and will be rejected. Aspirated fluid is superior to drain tips.


Tissue

For small samples, add a minimal volume of sterile preservative-free saline to avoid dryness of the sample.

Sterile container

Samples should ideally be sent prior to starting antimicrobial chemotherapy

Microscopy – Same Day Culture–Negative & preliminary available after 2 days

Tissue [bone] For orthopedic patients: Five separate samples should be taken intra-operatively and put in five separate containers.

Sterile saline and beads container

Samples should ideally be sent prior to starting antimicrobial chemotherapy

Blood culture may aid with the diagnosis, particularly in acute presentations.

Mycobacterial culture will be performed only on request.

Microscopy– Same Day Culture – Negative & preliminary results available after 2 days

Urine

Mid-stream specimen of urine (MSSU) [Cleanse the genital area with soap and water before micturition prior to collecting an MSSU] Catheter specimen of urine (CSU) [To collect a CSU, clamp the drainage tubing below the sampling port and aspirate sample with a sterile needle and syringe. Unclamp.Do not collect from drainage bag)

Monovette container (yellow cap) Monovette with Boric acid container (green cap) if sample is not transported immediately

All urines undergo screening by automated microscopy which counts cells and bacteria. Only those specimens reaching a certain threshold number of cells and bacteria undergo culture. Specific patient groups where a false negative screening result is particularly high risk will undergo culture irrespective of the screening result. These are: children <16 years, pregnant women, urology patients, neutropenic patients, transplant recipients, and patients undergoing repeat testing following a previous equivocal culture result or for persistent symptoms. To ensure that all such patients’ urine specimens

Microscopy – Same Day Culture – Negative & preliminary results available after 1 day



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Clean catch/pad specimen of urine (paediatrics)

(must fill to line)

routinely undergo culture please indicate clearly on the request form when a patient belongs to one of these groups. http://labtestsonline.org.uk/understanding/analytes/urine-culture/tab/sample

Urine Legionella antigen Streptococcus pneumoniae antigen

As above Sterile container

Same Day

Mycobacterial Laboratory

Test Sample Type Container Further information TAT(Working

Days) Auramine Stain Culture Sensitivities on all MTBC primary isolates. Sensitivities on MOTT on request.

Sputum Minimum 5ml

Wide neck sputum container

Three fresh purulent samples should be collected at intervals of 8-24 hours, including one early morning sample. Samples taken closer together may be combined into one request.

Samples without date and time information may also be combined. Samples must be sent promptly to the lab.

Auramine Stain 1 Working Day of receipt of sample Culture Negative results in 10weeks.

Bronchial washing/Broncho-alveolar washing Minimum 5ml

Plain sterile container

Urine -The entire volume passed


Three early morning samples on three consecutive days should be collected.

http://labtestsonline.org.uk/understanding/analytes/urine-culture/tab/sample

http://labtestsonline.org.uk/understanding/analytes/urine-culture/tab/sample



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Days)

BORIC ACID PRESERVATIVE MUST NOT BE USED

24hr collections of urine are not satisfactory. Positive culture results are reported as they arise. r PCR for MTBC/Rif resistance detection on direct positive results within 1 working day. MTBC Sensitivities 14-21 days from positive culture identification.

Aspirated fluid and pus Volume required, up to 250ml

plain sterile container

Pleural and pericardial fluids are not very satisfactory samples due to the low number of bacilli present. Pleural and pericardial biopsies taken with the fluid give better results. Swabs dipped in pus are rarely satisfactory and should only be used when very small amounts of material are available.

Tissue HISTOLOGICAL FIXITIVES MUST NOT BE USED Small biopsies may be sent in sterile preservative-free saline to prevent drying out.

Universal containers, sputum jars or larger glass jars may be used, depending on the size of specimen.

HISTOLOGICAL FIXITIVES MUST NOT BE USED

CSF Volume required,>6ml For Neonates 2-4ml Smaller volume will be tested down to a minimum of 1.0ml, but the sensitivity of the results will be low (see Further Information)


The British Infection Society guidelines for the diagnosis of tuberculosis meningitis recommends approximately 10% of the total CSF volume can be taken exclusively for mycobacterial testing. Positive laboratory results are associated with large volume for CSF submitted(>6.0ml)

Blood and bone marrow Maximum 5ml

Special culture bottles are available on request from the



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Days) Microbiology lab. A separate sample of bone marrow should also be sent in a plain sterile container

Gastric washings Minimum 5ml Plain sterile container

Collect samples early in the morning (before breakfast) on three consecutive days. Samples should be delivered to the TB lab within 4 hours or neutralised with sterile 6.8ph phosphate buffer.(available from the TB lab)

Faeces

The HPA does not recommend culture of faeces for mycobacteria.

Please contact the TB lab for advice.

Antibiotic Assay (Rifampicin, Ethambutol, Isoniaizid, Pyrazinamide, Streptomycin and Cycloserine)

Contact NIMRL Contact NIMRL Sent to Reference Lab, Contact NIMRL for instructions on testing protocols.

2-4 working days



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Days) IGRA QuantiFERON®

Blood Quantiferon® TB Gold-Plus (4 tubes)

This test is performed in areas of the hospital where prior arrangements have been made. Otherwise it is only available on a case by case basis following approval by the Consultant Microbiologist. Please contact bacteriology (028 90634281) for blood collection tubes and guidelines on collection, storage and transportation of this test. Samples are to be sent Mon-Wed only and by 16:00 hrs. on the day of venepuncture. Otherwise for test approval in individual cases please phone the duty micro SPR on 02890634139.

2 Weeks Samples are referred to the Mycobacterial Reference laboratory (MRL), London where they are processed on a weekly batched basis.

Adenosine Deaminase (ADA)

2-5 mL pleural, ascitic or pericardial fluid, 1ml CSF

ADA is raised in pleural/ascitic fluid and CSF of patients with TB. This sample is sent to the Purine Research lab, St Thomas’ Hospital, London. Please contact them on 020 7188 1266 for any further information.

1 Week



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Mycology Laboratory

Test Sample type Container Further information TAT(Working

Days) Isolation of dermatophyte fungi for the diagnosis of dermatophyte infections.

Skin Hair Nails

Skin lesions are sampled by scraping with a blunt scalpel and collecting the scales in folded paper, which is then folded again and made secure with a paper clip, with hairs and nails also being collected in this manner. MycoTans or similar paper packs designed for this purpose may also be used.

Factors affecting the quality of results:

Insufficient sample

Formaldehyde or preservatives used

Scrapings stuck to selotape Identification, usually to species level. Yeasts are identified by a combination of morphological and nutritional/enzymatic tests. Moulds are usually identified on the basis of macroscopic and microscopic morphology. Fungi not considered to be clinically significant may not be identified.

2 Weeks

Cryptococcal antigen.

CSF Serum or CSF, 300μl minimum or 2mls of clotted

4 Days



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Days) blood.

Isolation of yeasts such as Candida species for the diagnosis of candidosis

Swabs, urine, Fluids, exudates See General bacteriology section

3 Working Days

Antifungal sensitivity testing

Isolates of yeasts

Sabouraud’s slope in a bijoux or universal

Candida krusei is intrinsically resistant to fluconazole and is therefore not tested against this antifungal. Sensitivity testing for moulds is not generally indicated.

5 Days

Isolation of moulds such as Aspergillus species for the diagnosis of aspergillosis

Sputa and bronchoalveolar lavage See General bacteriology section

1 Week

significant moulds

Fluids, exudates See General bacteriology section

1 Week

Isolation of moulds such as Sporothrix schenkii for the diagnosis of mycetoma.

Biopsy and tissue See General bacteriology section

4 Weeks

Antifungal drug susceptibility testing of moulds

Isolates of moulds Sent to reference lab. BHSCT only

7 Days



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Days) Candida Antigen

clotted blood 5-10mls

red top bottle Sent to reference lab. BHSCT only

7 Days

Antifungal Assays (Flucytosine, Itraconazole, Voriconazole)


red top bottle Sent to reference lab BHSCT only

2 Days

Serology: Histoplasma serology Coccidioides serology Paracoccidioides serology Blastomyces serology Aspergillus antigen


red top bottle Sent to reference lab. Travel history essential BHSCT only

14 Days



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Serology

Test Sample type Container Further information TAT(Working Days)

Antistreptolysin O

5-10mls clotted blood Gold or Red top bottle

Send sample a minimum of 7 days following a group A strep infection, and repeat sample after 14 days

2 Days

Arboviruses

5-10mls clotted blood

Gold or Red top bottle

Sent to reference lab bunyaviridae, flaviviridae, togaviridae

21 Days

ANTHRAX: Bacillus anthracis



Sent to reference lab 21 Days

Bartonella (Cat Sctatch)



Sent to reference lab. 21 Days

B. pertussis IgG



Sample should be taken > 3 weeks after onset for patients with a history of prolonged cough (Sent to reference lab.) Refer to molecular test if <3 weeks post onset.

21 Days

Borrelia burgdorferi IgG and IgM (Lyme Disease)



7 Days

Brucella IgG & IgM



Positive screening samples are sent to a reference laboratory for confirmation

Negative 7-Days Positive 21 Days

Clostridium tetani



Sent to reference lab. Tetanus immunity

21 Days

C. diphtheria 5-10mls clotted blood


Sent to reference lab Toxigenic C.diphtheriae are very uncommon within the UK and are almost always imported. A travel and immunisation history should always be obtained from suspected cases of diphtheria.

21 Days

Cytomegalovirus


Antibodies 2 Days



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Coxiella burnetii (Q fever)


Please state if suspected endocarditis or chronic infection, this will determine the serological tests.

2 Days

Enteric serodiagnosis



Sent to reference lab Yersinia / Yersinia biotyping E. coli including O157 Clostridium tetani

21 Days

Epstein-Barr virus (Infectious Mononucleosis)


Antibodies Only performed if patient <40years as specificity thereafter is poor. Monospot no longer performed

2 Days

Hantavirus 5-10mls clotted blood Gold or Red top bottle

Sent to reference lab Please give details of foreign travel

21 Days

Helicobacter pylori


Sent to reference lab For children or those unable to perform breath test ONLY

21 Days

Hepatitis A 5-10mls clotted blood Gold or Red top bottle

Antibodies 2 Days

Hepatitis B 5-10mls clotted blood Gold or Red top bottle

Current infection – HbsAg Pre-fertility/pre-biologics/immunosuppression/HIV baseline – HbsAg & core antibody Antibody titre post-vaccine - anti-HBsAg Core e Anti-e

2 Days

Hepatitis C 5-10mls clotted blood Gold or Red top bottle

Antibodies 2 Days

Hepatitis D 5-10mls clotted blood Gold or Red top bottle

Sent to reference lab only performed if Hepatitis B positive

21 Days

Hepatitis E 5-10mls clotted blood Gold or Red top bottle

Sent to reference lab 21 Days

Herpes simplex 5-10mls clotted blood Gold or Red IgG If pregnant to determine whether infection is primary or 21 Days



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virus (HSV) 1 & 2

top bottle reactivation - Sent to reference lab

HIV 5-10mls clotted blood Gold or Red top bottle

Screen - HIV 1&2 Antibodies and p24 Ag 2 Days

HTLV (Human T-cell lymphotropic virus)


Antibodies 2 Days

L.pneumophila Sg. 1-7 IgM



After about the 10th day post onset of disease, specific

antibodies are detectable, however seroconversion can take up to 14 weeks (generally 3-6 weeks). Consequently early diagnosis cannot be performed with serological methods.

7 Days

Leptospira IgM 5-10mls clotted blood


IgM antibodies can already be detected two days after the onset of symptoms. These antibodies are detectable in all patients up to five months after infection.

7Days

Measles 5-10mls clotted blood Gold or Red top bottle

Immunity 2 Days

Syphilis screening and Confirmation



Screen: Treponema pallidum Total Antibody Confirmation of positive screen:

Treponema pallidum IgM

RPR

TPPA

5 Days

Toxoplasma gondii IgM & IgG



Depending on clinical history and screening result samples may be sent off to the Toxoplasma reference Laboratory for confirmation and Dye Test

2 Days 21 Days reference lab report .

Rickettsia 5-10mls clotted blood Gold or Red Sent to reference lab 21 Days



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top bottle Ehrlichia, Typhus Group, Spotted Fever Group complete RIPL form with full clinical details available at http://www.rvl-belfast.hscni.net/)

Rubella 5-10mls clotted blood Gold or Red top bottle

Acute Infection – IgM Immunity – IgG

2 Days

Parasitic Diseases



Sent to reference lab Amoebiasis; Babesia; Cysticercosis; Fasciola; Filaria; Hydatid; Leishmania; Ehrlichia; Wuchereria bancrofti; Malaria; Schistosomiasis Strongyloides; Toxocara; Trichinella; Trypanosoma+ other tropical diseases as requested

21 Days

Parvovirus B19 (Slapped cheek)


2 Days

Staphylococcal & Streptococcal serodiagnosis



Sent to reference lab Includes anti-haemolysin or anti-nuclease titre, anti DNAse and anti-hyaluronidase

21 Days

TULARAEMIA: Francisella tularensis



Sent to reference lab

21 Days

Varicella Zoster Virus


Immunity (IgG) If pregnant but NOT immunosuppressed and there is a history of chickenpox then no testing is required and the lady can be reassured. If pregnant and no history of chickenpox or immunosuppressed regardless of history a serum sample should be sent to test for chickenpox immunity (VZV IgG). It is imperative to provide gestation and/or immunosuppression



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details along with the date and nature of the contact. A significant contact is face-face for any length of time or same room for 15 minutes. Exposure to shingles is only significant if the vesicles are on a body area that is exposed or if the shingles contact is immunosuppressed themselves as they will have increased viral shedding. For full and further info please see Immunisation against infectious disease: The Greenbook Chapter 34 on Varicella.

Molecular Diagnostics


Adenovirus EDTA Plasma or Serum Conjunctival Swabs Urine

Purple, Gold or Red top bottle Dry Swab Sterile container

2 Days

Chlamydia trachomatis and Neisseria gonorrhoea.

Females: Urine OR endocervical swab OR vulvovaginal swab Males: Urine Conjunctival swabs

Dedicated specimen collection kit

It is only necessary to send one specimen per patient

2 Days

Cytomegalovirus

EDTA Plasma Urine Colon Biopsies

Purple top bottle Sterile container Sterile

Plasma – Recommended specimen in adults. Urine - Recommended specimen in infants with suspected congenital CMV infection.

2 Days



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container Biopsy - Recommended specimen in suspected CMV colitis.

Epstein–Barr virus

EDTA Plasma Purple top bottle

2 Days

Hepatitis B EDTA Plasma Purple top bottle

Viral load 5 Days

Hepatitis C EDTA Plasma Purple top bottle

Viral load 5 Days

Herpes Simplex 1 & 2 Virus

Genital swab Skin Swab Conjunctival Swab Respiratory Samples CSF

Dry Swab Sterile container

2 Days

HIV EDTA Plasma Purple top bottle

Viral load Congenital transmission - pro-viral DNA Sent to reference lab Genotypic resistance testing - mutational analysis Sent to reference lab

5 Days 21 Days 21 Days

Respiratory Short Screen: Influenza A Influenza B Respiratory Syncytial A Respiratory Syncytial B

Respiratory Samples: Swab Washing Secretion


2 Days

Respiratory Screen: Metapneumovirus (A & B) Parainfluenza



2 Days



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(1,2 3, 4) Adenovirus Human rhinovirus Human Bocavirus Coronavirus

Influenza Typing



H1, H3, H5, H7, Coronavirus MERS 5 Days

Respiratory atypical screen: Mycoplasma pneumoniae Chlamydia pneumoniae Legionella pneumophila



2 Days

Additional respiratory targets: Bordetella pertussis Pneumocystis jirovecii Coxiella burnetii (Q fever)



2 Days

Gastroenteritis Screen:

Faeces Vomit

Sterile container

2 Days



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Norovirus Rota Virus Faecal Adenovirus Astrovirus

Meningeal and Sepsis Screen: Enterovirus Parechovirus Neiserria meningitidis Strep pneumonae Haemophilus influenzae

Respiratory Samples: Swab, Washing, Secretion Faeces CSF EDTA Plasma Serum

Sterile container Purple top bottle Gold or red top bottle

420ul of CSF is the optimal volume and will allow for re-testing of positive samples. A minimum of 220ul CSF is essential for molecular testing

2 Days

Measles Respiratory Samples: Swab Washing Secretion

Sterile container

Recommended specimen type is a throat swab. This test can only ensure reliable diagnosis if the sample is taken within 10 days of onset. For information regarding sampling beyond 10 days post onset, please contact the laboratory.

2 Days

Mumps

Saliva Buccal Swab Throat Swab

Sterile container Dry Swab

Recommended specimen type is a parotid duct or buccal membrane swab.

2 Days

Parvovirus B19 EDTA Plasma Serum Respiratory Samples Post Mortem Tissue

Purple top bottle Gold or red top bottle Sterile container

2 Days

Polyomavirus EDTA Plasma Purple top 2 Days



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BK Serum Urine

bottle Gold or red top bottle Sterile container

Syphilis

EDTA Plasma Serum Genital Swab Anal Swab Urine Respiratory Samples Post Mortem tissue

Purple top bottle Gold or red top bottle Sterile container

2 Days

Varicella zoster virus

Skin Swab Conjunctival Swab Respiratory Samples CSF


Current Chicken Pox or Shingles 2 Days

Molecular Typing Contact the typing service directly for further information on: Tel: 02890639389 Email: [email protected]