microbiology services user manual - pat user...general information the microbiology services...

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Microbiology Department Microbiology Services User Manual

Revision 11 Issue Date: May 2019

Authorised by: Microbiology Management Team

Microbiology Services User Manual

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GENERAL INFORMATION .................................................................................................. 4

GUIDELINES FOR ON-CALL SERVICE ............................................................................. 7

QUALITY ASSURANCE ...................................................................................................... 8

HOW TO ORDER SPECIMEN CONTAINERS ................................................................... 10

COLLECTION AND DELIVERY SERVICE ........................................................................ 10

SPECIMEN COLLECTION ................................................................................................ 11

TRANSPORT OF SPECIMENS ......................................................................................... 12

SPECIMEN AND REQUEST LABELLING......................................................................... 15

HOW TO ACCESS LABORATORY RESULTS ................................................................. 23

PATIENT FLAGS ............................................................................................................... 25

BLOOD CULTURES .......................................................................................................... 27

URINE FOR URINALYSIS AND CULTURE ....................................................................... 28

URINE FOR SCHISTOSOMA ............................................................................................ 29

GENITAL SWABS ............................................................................................................. 30

WOUND SWABS, SKIN SWABS, TISSUE ETC. ............................................................... 32

THROAT SWABS .............................................................................................................. 33

MOUTH SWABS ................................................................................................................ 33

NOSE SWABS ................................................................................................................... 33

MRSA SCREENING SWABS ............................................................................................ 34

INFECTION SCREENING .................................................................................................. 34

CPE SCREENING.............................................................................................................. 34

NON-DIRECTED BRONCHIAL LAVAGE (NBLS) ............................................................. 35

PERNASAL SWABS FOR BORDETELLA PERTUSSIS/PARAPERTUSSIS .................... 35

SPUTUM FOR ROUTINE CULTURE ................................................................................. 36

INVESTIGATION OF INTRAVASCULAR CANNULAE & ASSOCIATED SPECIMENS .... 37

SWABS FROM STERILE SITES ....................................................................................... 38

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FLUIDS FROM STERILE SITES ........................................................................................ 39

CRYPTOCOCCAL ANTIGEN TESTING ............................................................................ 41

TB INVESTIGATIONS ....................................................................................................... 41

CORNEAL SCRAPES, INTRA-OCULAR FLUIDS AND CONTACT LENSES ................... 44

MYCOLOGY SPECIMENS ................................................................................................ 45

ENVIRONMENTAL SAMPLES .......................................................................................... 46

WATER TESTING.............................................................................................................. 47

ANTIMICROBIAL ASSAYS ............................................................................................... 48

THERAPEUTIC RANGES FOR ANTIMICROBIAL AGENTS ............................................ 48

LEGIONELLA/PNEUMOCOCCAL ANTIGEN TEST .......................................................... 49

HELICOBACTER PYLORI CULTURE ............................................................................... 49

HELICOBACTER STOOL ANTIGEN ................................................................................. 49

URINE PREGNANCY TESTING ........................................................................................ 50

VIRAL HAEMORRHAGIC FEVER ..................................................................................... 50

SEROLOGICAL TESTS..................................................................................................... 51

MOLECULAR TESTS ........................................................................................................ 51

APPENDIX 1: TRANSPORT DEPARTMENT HOSPITAL PATHOLOGY COLLECTION SCHEDULE ....................................................................................................................... 54

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General Information The Microbiology Services Department is located within the Pathology Laboratory at The Royal Oldham Hospital. The department provides a diagnostic service for the four hospitals within the Pennine Acute Hospitals NHS Trust: Fairfield General Hospital, North Manchester General Hospital, The Royal Oldham Hospital and Rochdale Infirmary. In addition, the department serves four local Care Commissioning Groups: Bury, Heywood, Middleton & Rochdale, Oldham, and North Manchester. This document is under constant review; if you have any comments regarding content or format, please contact one of the Microbiology Technical Managers, contact details are provided below. Full information about the repertoire of clinical investigations provided and details of external laboratories can be found in MC-MAN-5 Microbiology Services Tests Repertoire. Specimen retention times are stated in this document and indicate the timeframe available for requesting additional testing on specimens already received by the laboratory. Please note that in some circumstances, additional testing may not be possible; please contact the laboratory for advice. Specimens for investigations not performed in-house are referred to appropriate Reference or Specialist Laboratories. They are transported Monday to Friday by approved couriers in compliance with current Transport Regulations and MUST be received in Microbiology by 14:00 for same-day transportation. Specimens referred for testing at Manchester Medical Microbiology Partnership (MMMP) are transported by a scheduled Trust service twice per day Monday to Friday at 09:00 and 13:00. Postal Address

Microbiology Department Pathology Laboratory The Royal Oldham Hospital Rochdale Road Oldham OL1 2JH Telephone: 0161 627 8360 DX: 729540 (exchange 92 OL) UKAS Reference Number: 8913

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Clinical Advice

The Consultant Microbiologists, Consultant Virologists and Specialist Registrars are available on-site 09:00 to 17:00 Monday to Friday (see contact numbers below) and via the hospital switchboard on a rota basis at all other times including weekends and Bank holidays. They can provide advice on patient management, infection control and help with advice on selection of appropriate samples and the interpretation of laboratory reports. Technical Advice

The Biomedical Scientists (BMSs) are available on-site 08:00 to 20:00 (weekdays), 09:00 to 16:00 Saturdays/Sundays and Bank Holidays for technical advice (see contact numbers below). Outside these hours, the on-call BMS is available via the hospital switchboard. Urgent Requests

Please telephone the department on 0161 627 8360 during opening hours. Outside these hours the hospital switchboard will contact the ‘on call’ Biomedical Scientist. Please do not call switchboard to alert the on-call Biomedical Scientist until the specimen has been collected and transport to the laboratory is imminent. Always ensure a bleep or contact telephone number is stated on the request when sending urgent requests.

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Contact numbers

Hospital Switchboard 0161 624 0420

Microbiology General Enquiries 0161 627 (7)8360

Medical Staff

Dr. T.D.I. Cartmill Consultant Microbiologist [email protected]

0161 627 (7)8056

Dr J. Koreonos Consultant Microbiologist [email protected]

0161 656 (7)1644 (ROH)

Dr. M. Przybylo Consultant Microbiologist [email protected]

0161 627 (7)5059 (ROH)

Dr. Z. Fang (Locum) Consultant Microbiologist [email protected]

0161 656 (7)1643

Dr. J. Paul Consultant Virologist [email protected]

0161 656 (7)1673

Carol Edwards

PA to Consultant Microbiologists and Consultant Virologist. [email protected]

0161 656 (7)1641 0161 656 (7)1774 (FAX)

Joanne Fulton Amanda Corbitt

Microbiology Support Secretaries [email protected] [email protected]

0161 656 (7)1764 0161 656 (7)1642

Specialist Registrars 0161 627 (7)8362 (ROH) 0161 627 (7)1509 (ROH) 0161 720 (4)3794 (NMGH)

Technical Staff

Diane Dean Microbiology Service Manager [email protected]

0161 656 (7)1369 0161 656 (7)1774 (FAX)

Paul Loy Technical Manager [email protected]

0161 627 (7)8359 0161 656 (7)1774 (FAX)

Kate Whatmough Technical Manager [email protected]

Ravind Bhangal Tracy Howard Helen Irwin Christine Loy Janet Roche Paul Shilton Fiona Shufflebottom Peter Taft Cheryl Williams

Advanced Biomedical Scientists

0161 656 (7)1608

Infection Control

Linda Swanson Associate Director, I.P. & C. [email protected]

0161 656 (7)1782

Lorraine Durham Lead Nurse I.P.& C. (ROH) 0161 656 (7)1921

Mike Beesley Lead Nurse I.P.& C. (NMGH) 0161 720 (4)2935

Kevin Lawler

Lead Nurse I.P.& C. (FGH/RI)

0161 778 (8)2912

Lindsay Smith PA to Infection Control 0161 656 (7)1782

mailto:[email protected]












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Service availability details

Routine Opening Hours

Monday - Friday 08:00 to 20:00 Saturday, Sunday & Bank holidays 09:00 to 16:00 For any urgent investigations during these hours - contact the Lab on 0161 627 8360 (78360) On-Call Service

Monday – Friday After 20:00 Saturday, Sunday & Bank holiday After 16:00 For any urgent investigations during these hours, contact the Microbiology BMS on-call via the Hospital Switchboard.

Guidelines for On-Call Service Please do not call switchboard to alert the on-call Biomedical Scientist until the specimen has been collected and transport to the laboratory is imminent. Only urgent specimens affecting the management of the patient will be processed during on-call hours. The list below is not exclusive but may include: CSF Joint Fluid if suspected septic arthritis Other fluids from normally sterile sites Pus from deep tissue abscess Other reasonable requests for an out of hours test should first be discussed with the Consultant Microbiologist/Virologist Clinical Advice Clinical advice is always available. The duty Consultant Microbiologist/Virologist can be contacted via the hospital switchboard. Urine Microscopy – this investigation is not normally available outside routine opening hours. If patient management depends on this result, please contact the Consultant Microbiologist/Virologist for advice. Blood Cultures – should be sent promptly to the laboratory. Do not contact the BMS on-call. Pregnancy Tests - request a serum hCG test via the Biochemistry department

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Quality Assurance The department subscribes to the following External Quality Assurance Schemes. General Bacteriology Antimicrobial susceptibility AAFB Microscopy Mycobacterial culture Faecal Parasitology Mycology Antifungal susceptibility Legionella/Pneumococcal Urinary Antigens MRSA Screening Clostridium difficile detection Helicobacter pylori antigen Cryptococcus antigen Urinary hCG Genital Pathogens Gram Staining Urine quantitative culture Rubella serology (IgG) Syphilis serology Hepatitis B serology Hepatitis C serology Diagnostic Hepatitis serology (Hep A IgM, CMV IgM, EBV) HIV serology Hepatitis B surface antibody detection Immunity screen Measles and Mumps IgG serology Toxoplasma serology Diagnostic Serology Exanthem (Rubella IgM) Hepatitis E serology C. trachomatis / N. gonorrhoeae Mycobacteria HBV DNA quantification HCV RNA detection and genotyping HIV-1 RNA quantification Viral Gastroenteritis Respiratory Viruses Viruses in CSF Legionella Isolation Endoscope Rinse Water Hospital Tap Water

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Quality Control

In addition, a rigorous internal quality control system is in place which covers all aspects of calibration and quality assessment. A comprehensive rolling calendar which includes audit of all procedures and policies is in place. All equipment is continuously monitored to ensure correct conditions are maintained and service contracts are in place for all essential machinery. Measurement Uncertainty

Many of the tests performed in Microbiology involve quantitative measurement of a parameter which may then be reported numerically or translated into a non-numeric result such as “Detected” or “Not Detected”. No measurement or test is perfect and imperfections give rise to “measurement uncertainty” (MU) which in essence means that if the same test is performed on the same sample several times, the results will differ slightly each time. When the value of the MU for a test is small and the results fall clearly within the positive or negative ranges for the test, the effect of MU on the result is less significant. However, close to the cut-off values for a test, MU can make the difference between the test being interpreted as positive or negative. For example, if a test has a MU value of 5% and is negative below a value of 1.0 and positive above a value of 1.0, a sample which is tested and gives a value of 0.96 would be interpreted as negative. Taking into account the MU, the test value is actually 0.96 plus or minus 5% so could have a value greater than 1.0 and therefore be positive. Similarly if the value had been 1.04, the report would say positive, when MU means that the actual value could have been less than 1.0 and therefore negative. MU has been calculated for all tests in Microbiology that involve a quantitative step and is considered before reporting the result; where required an interpretive clinical comment is added. Users may contact the lab to ask for further information on the specific MU for a particular test. Please Note:

Body fluids vary greatly in their consistency and sampling involves selection of a representative portion for submission to microbiology as a specimen. Where estimation of cell counts are performed on such specimens e.g. in sterile fluids such as CSF, the count is made available as part of the result issued and is intended only as a guide to clinicians. Further investigations on such specimens are performed regardless of cell counts.

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How to Order Specimen Containers All GP surgeries and wards/departments using Pennine Acute Hospitals NHS Trust Pathology services can obtain supplies of nearly all laboratory consumables from NHS Logistics by requisition via ROH Supplies Dept. The exceptions are Blood Culture bottles, Chlamydia collection kits, viral PCR collection kits and Dermapak collection kits for mycology specimens.

Chlamydia collection kits and Blood Culture bottles

Viral PCR kits (M4RT) and Dermapak

Bury FGH ESL Tel: 0161 778 (8)2597

ROH Microbiology Dept. Tel: 0161 627 (7)8360

North Manchester NMGH ESL Tel: 0161 720 (4)3288

Oldham & Rochdale

ROH Pathology Stores Tel: 0161 656 (7)1775 Fax: 0161 656 (7)1692

Collection and Delivery Service General Practitioners The laboratory offers a collection and delivery service designed as far as possible to meet the needs of your surgery. If you wish to take advantage of this service please contact the Trust Transport Department on 0161 720 4357 Hospitals A pneumatic tube system is available from most wards and departments to deliver specimens to the laboratory where there is one on site. Please contact Portering Services for transport of specimens not serviced by this system. When using the pneumatic tube systems, please ensure that all specimen containers are used in the correct manner & that lids are securely fastened. Please ensure that ALL specimens are placed inside securely sealed plastic bags and placed in a carrier pod. Do not use the pneumatic tube for unrepeatable samples. Special precautions for blood culture specimens sent by pneumatic tube: Ensure a maximum of TWO blood culture bottles are sent at a time. These bottles must be placed within the bag provided and the top of the bag sealed. This sealed bag must then be placed within a second bag before placing in the pneumatic tube carrier pod. Do not put any other pathology specimens in the carrier pod with blood culture bottles.

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Regular transport runs are in place to deliver specimens from Fairfield General Hospital, North Manchester General Hospital and Rochdale Infirmary to the Central Microbiology Laboratory at The Royal Oldham Hospital (see Appendix 1). On-Call specimens

When the specimen has been collected: Place the specimen in a UN3373 compliant packaging, ready for transport. At FGH, RI and NMGH organise a taxi to transport the specimen to Microbiology ROH. At ROH contact Portering Services to arrange delivery to the lab. When the specimen is on route, contact the Microbiology BMS on-call via the Hospital Switchboard.

Specimen Collection Whenever possible, specimens for microbiology should be collected prior to antibiotic therapy. Please refer to the tables and relevant sections below for further information on specimen collection. There are no facilities within the laboratory at ROH for the collection of patient specimens. Requests (cards or electronic) must indicate if there has been any variation from the normal procedure during collection of a specimen e.g. if antibiotics have been given prior to sampling. In order to ensure that appropriate investigations are performed, and to optimise quality of results it is vital that all relevant clinical information is provided with the request. Patient Consent

The laboratory staff have no involvement in direct collection of samples from patients. This is carried out by the clinicians and HealthCare workers requesting tests. It is assumed that arrival of a sample at the laboratory only occurs once the patient has consented to be tested for the investigations requested. Health & Safety Requirements

High Risk specimens Specimens that are from patients suspected of having a Viral Haemorrhagic Fever are always classified as ‘HIGH RISK’. There is a separate policy to cover the way that these specimens are handled depending on risk factors identified by the Infectious Diseases Consultant in charge of the patient. Please do not attempt to take any patient specimens until the VHF policy has been consulted. NB. Specimens for VHF investigations are dealt with by the Haematology Department. Microbiological culture specimens from individuals known or suspected of having Tuberculosis or Typhoid are considered ‘HIGH RISK’ and an appropriate hazard sticker

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MUST be attached to the specimen and the request form. The clinical details entered on the request card MUST be adequate to convey information of the suspected hazard to the staff handling the specimens. A recent Health and Safety Executive safety notice highlighting the importance of this can be accessed here: http://www.hse.gov.uk/safetybulletins/clinicalinformation.htm Specimens from individuals known or suspected to have Blood Borne Viruses i.e. HIV, Hepatitis B and Hepatitis C are NOT classified as ‘HIGH RISK’ in the laboratory. The infectious agents in these specimens are not propagated and routine specimen processing can be performed at Containment Level 2.

Transport of Specimens All specimens for Microbiology must be sent to the lab for processing without delay. Please refer to the transport schedule in Appendix 1 for inter-hospital samples. If a delay is unavoidable e.g. overnight or >24 hours for community samples, these should be refrigerated (4-8°C) except for blood cultures and Aptima containers for Chlamydia which should be stored at ambient/room temperature. For transport purposes, specimens are assigned to either Category A or Category B. Category A

A Category A substance is defined as an infectious substance which is capable of causing permanent disability, life-threatening or fatal disease in otherwise healthy humans or animals i.e. specimens from patients suspected to be at high risk of suffering from viral haemorrhagic fever following clinical risk assessment. Infectious substances meeting Category A criteria which cause disease in humans or both humans and animals are assigned the United Nations number UN2814. Specimens which fall into this category must be transported in Category A packaging by specialised courier following discussion with the Haematology Department. Category B

In the first instance, users should ensure that all specimen containers are securely fastened and placed into a sealed specimen bag prior to transportation. Infectious substances designated as Category B are assigned to UN3373 Packing Instructions P620, and must be transported in compliant packaging. This consists of an outer cardboard container and an internal hard plastic container with a screw lid, inside which the specimen container can be sealed. This type of packaging may be recycled & used again, provided it is not contaminated or damaged. All Trust Transport vehicles used to carry pathological specimens are equipped with compliant specimen transport cases.

http://www.hse.gov.uk/safetybulletins/clinicalinformation.htm

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Arrangements are in place for any specimens taken in the Bury, Rochdale and North Manchester areas to be transported to the hospitals in each area and then transported to ROH for testing. Specimens not picked up at Health Centres and GP surgeries on routine runs MUST be taken to the correct location in each of the hospitals or they risk being missed completely, or delayed significantly resulting in them being unsuitable for testing. Specimens MUST be dropped off as follows: Bury: at the Essential Services Laboratory (ESL) at F.G.H. Rochdale: at the Urgent Care Centre at R.I. North Manchester: at the Essential Services Laboratory (ESL) at N.M.G.H. As the specimens are to be transported to the above pick-up points by road, the packaging must conform to the legal requirements of the Carriage of Dangerous Goods Regulations which state that they must be packaged to a specific standard. Please ensure that specimens are transported correctly; suitable containers can be ordered via NHS Logistics (KCP139: 7 litre container) and (KCP140: 30 litre container), these are re-usable rigid red transport boxes or alternatively DGP PATHOPAK packaging is also available via NHS Logistics, these are single use. Arrangements are in place for any specimens taken in the Oldham area to be transported to ROH by means of an external courier company SRCL. Specimens not picked up at Health Centres and GP surgeries on routine runs MUST be taken directly to the ground floor reception at the ROH Pathology Laboratory. All specimens for referral to external laboratories MUST first be sent to the Microbiology Department where details will be recorded prior to collection by the dedicated tracked courier service (DX) or dedicated van services. Specimens that need to be transported from the FGH, NMGH and RI sites out of hours (on-call) must be packaged according to Category B instructions below. It is essential that patient identifiable information is NOT visible during transport. In certain exceptional circumstances, specimens may need to be sent directly to an external laboratory. In these cases, account must be taken of the type of specimen and whether it is Category A or B. It is the responsibility of the clinician requesting the test referral to ensure that all transport regulations are met and that the Microbiology Laboratory is sent a copy of the request form. Datix incidents will be raised in all instances where transport regulations are not followed. Limitations

The successful examination of specimens and the isolation of pathogens depend primarily upon the quality and quantity of specimen, the correct collection of specimens, their timely transportation to and processing within the laboratory.

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Additional Requests

For tests performed in-house the specimen retention time indicates the time limit for requesting additional tests. It must be recognised that the archived specimen available will have a limited volume, and in some circumstances a fresh specimen would be more appropriate. Specimens referred to other laboratories for testing will also be stored according to local protocol. Please contact the Microbiology Department to discuss. Microbiology will not undertake testing on any samples that have previously been tested in the Blood Sciences department; this is due to the risk of splash-contamination which may lead to false positive results.

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Specimen and Request Labelling The Microbiology Services Laboratory at Pennine uses 3 types of request card as well as 2 forms of electronic requesting (HealthViews and T-Quest). Please ensure that all the boxes are appropriately completed to ensure that the patient is fully identified, destination for report is stated, requester and source of sample is stated, date and time of collection is stated, sample type(s) and investigation(s) required are clear – this is essential to allow the lab to select appropriate investigations and report relevant results; relevant clinical information is also useful in guiding the selection of investigations performed and interpretation of results. Microbiology General Request Card

MRSA Screening Request Card

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Virology / Serology / Molecular Request Card

GP Electronic Requesting

Pennine Acute along with its CCG partners (Oldham, HMR, Bury and Manchester) has implemented an electronic system (t-Quest) which allows GPs to order Pathology Tests directly from their own GP systems. Results are sent back electronically and automatically to the requesting GP. This means that the process is more efficient, reduces the time in which results are made available, improves data quality immeasurably and reduces errors to an absolute minimum. These provide benefits to GP's, Laboratories and most importantly of all patients. To place an order for a Microbiology test, users should click on the order tab and then click on Microbiology at the bottom of the screen to open a view of the most common tests available. If the test required is not available on the main screen, click on “open Test Search” then Microbiology in the “All disciplines” drop-down box to be presented with a drop-down menu of all Microbiology tests available.

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Once a test/investigation has been selected and added, a new box will appear stating specimen-specific information if appropriate. Users should click on the drop-down arrow in the Anatomical Origin box to choose the specimen type, answer any questions and follow any instructions presented on screen then click on save. NB. If the specimen type required is not in the list it is probable that an incorrect test has been selected, users should return to the main selection screen & select the appropriate test. 3 generic serology tests are listed, bacterial serology, fungal serology and viral serology. Please select one of these tests if the serology test required is not available in any of the lists on screen and give full details of the exact test(s) required in the box available. Users should contact the department if unsure of how to use the system or if any issues arise. The reverse side of the card attached to the specimen bag can be used to manually enter patient and specimen details if the electronic ordering system is unavailable.

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Hospital Electronic Requesting

Pennine Acute hospital wards and departments have implemented an electronic ordering system (CSC HealthViews) which allows clinicians to request Pathology tests directly from the patient record. Results are sent back electronically from the lab system to HealthViews and users are able to acknowledge receipt of the report and print a hard-copy if required. This has benefits similar to those of the GP electronic system in that the process is more efficient, reduces the time in which results are made available, improves data quality immeasurably and reduces errors to an absolute minimum. Training has been rolled out by the Trust I.T. training team; below is a brief guide on requesting a Microbiology investigation. To place an order for a Microbiology test click on the Microbiology tab to display the screen of commonly requested investigations in three columns, General Microbiology, Serology and Molecular.

Click in the adjacent box to request an investigation; information and warnings can be seen by hovering the cursor over the yellow triangles and green circles respectively. If more than one specimen type exists for the investigation, users will be presented with a drop-down list and should select the appropriate option. N.B. If the specimen type required is not in the list it is probable that an incorrect test has been selected, users should return to the main selection screen & select the appropriate test.

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Select the “General” tab and complete all the yellow boxes with particular attention to clinical details which are essential to ensure that correct procedures are carried out by the lab.

When all fields are completed, click on the order button and a summary of the order is displayed. If all details are correct, users can choose to finish and print labels to send the specimen immediately, or can choose to save the order for future collection e.g. by the phlebotomy service.

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All wards and departments have access to barcode label printers for HealthViews orders. Labels should be attached to the specimen (barcode) and the transport bag and sent to Microbiology without delay. Users should contact the department if unsure of how to use the system or if any issues arise. The reverse side of the card attached to the specimen bag can be used to manually enter patient and specimen details if the electronic ordering system is unavailable. Specimen Labelling

For a full explanation of Pathology labelling policy, please see document number CPDI061 Pathology Specimen and Request Card Labelling Policy, which is available within the Pathology pages on the Trust web-site. The most commonly encountered source of error and incident in Pathology Departments is unlabelled/mislabelled specimens. Pathology staff must establish minimum identification criteria prior to performing investigations on a specimen. Table 1 below outlines the absolute minimum criteria allowed for a request to be accepted; specimens failing to meet these minimum criteria will only be processed in exceptional circumstances. Table 2 below outlines the information required to provide a full quality examination of the specimen received. Failure to provide all this relevant information will not result in the request not being processed, but the results and clinical advice given might not be as comprehensive without the relevant information.

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Table 1

Specimen

Request Card

Minimum Required Information

Minimum Required Information

Patients full Surname / Family Name First or Forename Date of Birth or Unique identification Number i.e. Hospital or NHS Number

Blood Culture bottles should be labelled as follows.

☺Full Name

# Patient Hospital Number

Date and Time of Collection

Patients full Name i.e. Surname/ Family name and Forename. Date of Birth Hospital Number or NHS Number* Test / Tests Required Name of requestor (not initials) Location for report

Table 2

Specimen

Request Card

The Specimen MUST be labelled whilst with the patient

Required Information

Required Information

Addressograph labels must not be used to label specimens * Patients full Name** Date of Birth. Hospital Number / NHS Number. Date & Time of Collection. Destination for Report

Blood Culture bottles should be labelled as follows.

☺Full Name

# Patient Hospital Number

Date and Time of Collection

All sections of the appropriate request card should be completed, including: Patients full Name or Unique coded identifier. Date of Birth & Gender. Hospital number & NHS number Test / Tests required. Name (not initials) & Location of requestor. Location for the report Specimen type and location site if appropriate. Date & Time of collection. Relevant drug therapy (dose & time) Telephone / Fax number / Bleep number for results. Clinical details. NHS / Private Patient.

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*Labels generated whilst in the presence of the patient using a unique label printer are acceptable, these must contain all of the required information for specimen labelling and must only cover the tube manufacturer’s primary label. If you are considering introducing a system please inform the Pathology department. ** In certain circumstances Unique Coded identifiers might be used e.g. GUM patients, major incidents and when a name is unobtainable. Pre-printed barcode labels must be affixed to samples near to the top and along the longitudinal axis as follows:

This is especially important for blood and urine samples as these are tested directly on analysers.

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How to access Laboratory Results Results for test performed in-house are reported in the Laboratory Information Management System (LIMS) which is CliniSys LabCentre and in the Trust system HealthViews. Results for tests performed externally are issued to users on the original Reference Laboratory report form, with the exception of: Antimicrobial/antifungal assays and susceptibility tests (transcribed into the LIMS). Significant virus results (transcribed into the LIMS and original Reference Laboratory reports issued). Please attempt to find your results electronically. If you cannot find the one you want, contact the Microbiology Lab (0161 627 (7)8360) where the staff will be able to help you. Additional paper copies of reference lab reports can be obtained by telephoning this laboratory. Please do not contact reference labs directly. There are several ways in which test results may be viewed and the best method is dependent upon the ease of your access to the different systems. All systems require each user to have a unique logon, in order for appropriate and authorised access to the results required. Pennine Acute Hospital Clinicians & Staff Please access the Pathology Results system via the Interactive page of the Intranet, or via this link - Access to Results To review how to use the Pathology Results system, please click on the links below to follow e-Learning modules covering most of the basic concepts and suggested efficient ways to search for patient records upon the Pathology system :- Pathology ELearning module How to search for patient pathology records If you require access and you are not yet authorised to do so, please complete the form using this link - Systems Access form - and then submit the completed form to the IT Department for processing. GP and Community based Clinicians and Staff It is much simpler and more efficient to view results directly from within your own GP systems, where you have access to both GP and acute services test results in T Quest Review. This has been rolled out to all GP Practices within our districts. If you require access, please contact your relevant CCG for further details.

http://159.170.208.54:42001/labcentreweb/login.asp

http://nm-ashanti/Uploads/ELearning/Pathology/index.html

http://nm-ashanti/Uploads/ELearning/Pathology2/Path_Search_by_DOB_demo.htm

http://nww.pat.nhs.uk/online-forms.htm

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Other Clinicians & Services If you require access to results, but are not covered by any of the options above, please contact the Trust I.T. Helpdesk on 0161 604 5678 Telephone Enquiries

In order to reduce the risk of error in the oral transmission of results, standard procedures are in place within the laboratory. Results will be read to you by a suitably trained member of staff, you will be asked to repeat the results back as a check of accuracy.

Result Reporting The laboratory reports results in the following ways: Bacterial cultures (pathogens and commensals) Detection of pathogens using molecular methods Serological tests (numerical values and their interpretation) Antimicrobial susceptibility profiles Interpretive comments: these may be added automatically or by medical staff. Other comments pertaining to Susceptibility testing and reporting

The laboratory follows current EUCAST guidelines for reporting and interpretation of bacterial and fungal susceptibilities. In 2019, EUCAST have changed the definitions of susceptibility testing categories S, I and R as shown below: S – Susceptible, standard dosing regimen: A microorganism is categorised as “Susceptible, standard dosing regimen” when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent. I – Susceptible, increased exposure*: A microorganism is categorised as “Susceptible, increased exposure” when there is a high likelihood of therapeutic success because exposure to the agent in increased by adjusting the dosing regimen or by its concentration at the site of infection. R – Resistant: A microorganism is categorised as “Resistant” when there is a high likelihood of therapeutic failure even when there is increased exposure. *Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.

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Patient Flags These are used in the LIMS (LabCentre) to highlight patients that have been identified as being positive for certain important pathogens at some point in time. As this flag is associated with the patient record rather than individual specimens received it will be present at the top right hand corner of enquiry screens in the web-enquiry software or the top left hand corner in the live LabCentre system for all specimens from the patient and may not be a finding for the particular specimen on-screen at the time or that patient episode.

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Common Patient Flags in use are:

AMP AMP C Positive

CDT C.difficile TOXIN Positive

CPE Carbapenemase Producing Enterobacteriaceae

EBL ESBL Positive

GDH C.difficile organism present

HIV HIV Positive

HPB Hepatitis B Positive

HPC Hepatitis C Positive

MBL Metallo beta lactamase Positive

MRS MRSA Positive

PVL PVL Positive S.aureus present

TB M.tuberculosis Positive

VRE Glycopeptide Resistant Enterococcus Positive

Other flags are in use, please contact Microbiology for clarification if required.

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Blood Cultures

Specimen collection This is one of the most important investigations performed in Microbiology. It is important to take extra care and pay meticulous attention to detail when collecting blood cultures if results are to be reliable Blood Cultures taken in Pennine Acute are processed using the bioMerieux Virtuo System. Only bottles which are compatible with this system are acceptable.

Bottle type

Colour Code Volume of blood Incubation

Aerobic Anaerobic

Blue Top & Lid Burgundy Top & Lid

5-10 ml 5-10 ml

5 days* 5 days*

Paediatric ** Yellow Top & Lid 1-3 ml 5 days*

* Incubation period increased to 10 days if bacterial endocarditis is suspected. ** Use the Paediatric bottle for adult patients if only a small volume of blood is available.

Collection procedure See Trust document CPDI085 ‘Standard Operational Procedures for the Collection of Blood Cultures’ available on the Trust Intranet.

Precautions Label the bottles with the patient name & hospital number and/or date of birth and date & time of collection. All efforts to avoid contamination of the bottle with skin organisms must be made. Contamination of the specimens can result in patients having unnecessary antibiotic treatment, or incorrect treatment when contaminants mask true pathogens.

Laboratory procedure Blood cultures are continuously monitored using automated instrumentation. If a bottle flags ‘positive’, results are telephoned and entered onto the laboratory computer system (available for remote access via the web based enquiry browser) at the earliest opportunity. Please note that Gram stain results are telephoned as soon as they are available and are provisional until culture results are known. Occasionally liquid culture/antibiotic treatment may produce atypical organism morphology upon microscopy. This may mean that the culture does not always match the initial Gram result and should be interpreted with care.

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Urine for Urinalysis and Culture

Specimen collection

To minimise contamination, fresh mid-stream specimens (MSU) should be collected using standard methods. MSU samples are prone to contamination and the patient has to be instructed to cleanse the area of the urethra thoroughly with soap and water before collecting after voiding the initial portion of urine to reduce the contamination rate. Specimens should be collected before starting antibiotic therapy whenever possible.

The preferred container for collection is the green Sarstedt primary urine monovette tube (order code KTH123), alternatively a 30 ml red topped universal container (KCP885) can be used. The preservative in these tubes ensures that results reflect the bacteria present at the time of sample collection and therefore minimizes the effect of any delays in transport on bacterial overgrowth and has the additional benefit of reducing the unnecessary use of antibiotics in patients whose samples show moderate bacterial growth where results are often difficult to interpret in conjunction with the clinical picture. Specimens in containers without preservative will be processed however clinicians should be aware that the quality of the result may be adversely affected.

Samples delayed longer than 48 hours will be tested, however comment will be made on the report to indicate that the quality of the result will be reduced and may not reflect the condition of the patient, due to overgrowth or death of any organisms present at the time of collection.

A minimum of 3 ml is required. Do NOT overfill the container. Catheter Specimen Urine (CSU) – Urine from catheterised patients should only be taken when there is a clear indication for antibiotic treatment. Catheter specimens should be collected from the sampling port on the catheter, not from the bag. Results from catheter specimens of urine are difficult to interpret as cultures are often misleading. For this reason, antibiotic sensitivity results are not routinely reported from CSU but are available on request from the laboratory. Supra pubic aspirate (SPA) – specimens collected in this manner should be clearly indicated on the request card as an SPA. SPA specimens are processed and interpreted differently from routine urine. Ensure the container is securely fastened. Label the container/tube with name and date of birth and date of collection. Affix the printed sample label if using electronic ordering. Place the specimen bottle into the plastic bag attached to the request card. Seal the bag following the written instructions on the card.

Automated quantitative urinalysis is performed on all specimens for: White cells Red cells Epithelial cells Casts Bacteria (not reported) Conductivity (not reported)

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Differentiation of pathological casts is only performed if specifically requested. This is done by manual microscopy. Tests for Goodpasture Syndrome are not performed.

Culture Cultures are only performed if indicated by the urinalysis results (i.e. if either the white cell count and/or bacterial count are above the validated threshold) and for the following patient groups: Patients <16 years old Immunocompromised patients (includes patients on critical care wards) Pregnant women

Urine for Schistosoma

Specimen collection Urine specimen in a plain 30ml universal container is required. This should ideally be a midday urine specimen (between 10.00 and 14.00 hours).

Laboratory procedure Microscopic examination for presence of ova

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Genital Swabs

Specimen collection Low vaginal swabs (LVS) – Specimens will provide information about the perineal flora only. High vaginal swabs (HVS) - HVS should be collected with the aid of a speculum to avoid perineal contamination. (N.B. If a speculum has NOT been used, please label the specimen as LVS or Vaginal only). A HVS is suitable for the isolation of Candida spp. and the diagnosis of bacterial vaginosis. Swabs should be placed in bacterial transport media. A HVS is NOT a suitable specimen for the isolation of Neisseria gonorrhoeae. Cervical swabs - Always use a speculum to collect cervical swabs. Insert the swab approximately 1 cm into the cervical canal rotating it several times. Withdraw the swab without touching the vaginal wall and place the swab in bacterial transport media. Cervical swabs are suitable for the isolation of Neisseria gonorrhoeae. Urethral swabs - From male patients, these specimens should be collected using a fine wire swab. Insert the swab into the urethra, rotate several times and withdraw, place the swab into bacterial transport media.

Laboratory Procedure

Microscopic examination White blood cells Bacterial vaginosis (Hays criteria) Trichomonas vaginalis Culture will be performed for relevant organisms as appropriate depending on clinical details, Haemolytic group B streptococcus is considered to be part of the normal vaginal flora if the patient is not pregnant or has had no recent surgical intervention or invasive procedures, it is therefore essential that full clinical details are stated on the request for accurate interpretation of culture results and relevant reporting of findings.

Antibiotic sensitivity testing Significant isolates are tested against appropriate antibiotics. Please indicate on the request if the patient has been prescribed antibiotics and state which.

IUCD specimens In addition to routine culture, IUCDs are cultured for Actinomyces spp. This may take up to 14 days.

GBS screening Screening is offered to antenatal patients with previous high risk (i.e. carriers of GBS in previous pregnancies). Vaginal/anorectal swabs are inoculated into enrichment media for 24h then sub-culture to selective media for isolation of Group B Streptococci.

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Enteric specimens

Specimen collection Faeces specimens should be collected into a ‘blue top’ faeces container with spoon. To help ensure that the appropriate laboratory investigations are performed, the following clinical details must be stated on the request card: Date of onset Details of any current or previous antibiotic therapy Details of any recent travel history Date of admission to hospital (in-patients only)

Threadworm (Enterobius vermicularis) Specimens of faeces are unsuitable for threadworm investigations. Use a *sterile swab. Moisten with sterile saline and swab the anal area. Break off the swab into a universal container & seal securely.* A swab out of a standard transport swab kit can be used.

Laboratory procedures

Clinical Indications Target Pathogens

*All Specimens Salmonella spp. Shigella spp. E coli 0157 Campylobacter spp. Microscopy for Cryptosporidium

Mesenteric adenitis Acute abdominal pain Persistent / recurrent diarrhoea Reactive arthritis Contact with animals Foreign travel with abdominal pain

Yersinia spp

Relevant Foreign Travel. Sea Food Poisoning.

Vibrio spp.

Relevant clinical history. Relevant travel history. Specific request.

Concentration for Ova, Cysts and Parasites

All in-patients over the age of 2 years with diarrhoeal stool

Clostridium difficile investigation

All community patients aged 65 and over with diarrhoeal stool or aged under 65 with diarrhoeal stool where specifically requested.

Clostridium difficile investigation

Outbreak where routine pathogens are not detected.

Consult Infection Control for advice on further investigations (e.g. Norovirus)

*A Clostridium difficile investigation only is performed on in-patients admitted 3 or more days ago. Although cultures are not routinely performed on these patients, they will be performed if relevant clinical information is provided e.g. known consumption of food from an external source or suspected carriage of an enteric pathogen.

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C.difficile Investigation A three-step algorithm is in place to aid infection prevention measures within the hospital setting. Specimens are first screened for the presence of C.difficile bacteria (GDH test) and then positives tested for the presence of toxin. Samples from in-patients that test positive for C. difficile bacteria and negative for toxin will be tested for the presence of the toxin gene to indicate risk of organism to produce toxin. Currently there is no capacity to extend this toxin gene testing to the community.

Wound swabs, Skin swabs, Tissue etc.

Specimen collection Pus, when present, is preferable to a swab, particularly from deep seated infection sites. Swabs are acceptable where no pus is readily available or where the area to be sampled superficial. Swabs taken from ulcers should, where possible, be taken deep under the margin of the ulcer. Swabs should be placed in bacterial transport media.

Laboratory procedures Swabs are cultured onto appropriate culture media depending on specimen site and clinical details.

Pus / Tissue All pus specimens have a direct Gram film, standard culture + extended anaerobic culture.


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Throat swabs

Specimen collection Take the swab by depressing the tongue with a spatula, direct the swab to the back of the throat and rotate the swab to sample the tonsillar area on both sides. Try to avoid touching the mouth or tongue and contaminating the swab with normal oral flora. Place the swab in bacterial transport medium. It is important to include details of any recent travel history in the clinical details.

Laboratory procedures All throat swabs are cultured for Haemolytic Streptococci, culture for Corynebacterium spp. will only be performed if specifically requested. Whilst the commonest form of bacterial throat infection is caused by Haemolytic Streptococci, the majority of sore throats are caused by viruses. Culture for anaerobes will only be performed if relevant clinical details are recorded.

Mouth swabs All mouth swabs are processed for Candida spp. only.

Nose swabs Unless otherwise stated, nose swabs are processed to screen for Staphylococcal carriage only.


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MRSA screening swabs Methicillin resistant Staphylococcus aureus (MRSA) are multi-drug resistant strains of S. aureus that are resistant to all beta lactam antibiotics and in most cases other groups too.

MRSA strains are a continuing and increasing problem in healthcare settings, with outbreaks now occurring in the community. Screening for MRSA provides a means of identifying patients who may be at risk of infection and/or involved in transmission of the organism. Specimen Collection Routine screening includes a nose, throat, and perineum/groin swab. Other lesion sites may also be included as part of a screen. MRSA screening for elective admissions will have as a minimum nose and perineum/groin swabs; and day cases a nose swab only. Emergency admissions will be risk assessed and a variable swabbing regime utilised following the assessment. Please complete a Pennine MRSA request card. Laboratory procedure MRSA swabs are cultured onto special selective chromogenic agar and incubated for 18-24 hours.

Infection Screening Specimen Collection ITU surveillance specimens include swabs from nose, throat and perineum/groin. Other specimens may be sent if applicable e.g. wound swabs, urine and catheter sites. Laboratory Procedure Specimens are cultured onto appropriate media and incubated for 24-48 hours.

CPE Screening CPE stands for Carbapenemase Producing Enterobacteriaceae. The term “carbapenemase” is used to describe any β-lactamase enzyme that hydrolyses carbapenem antibiotics (doripenem, ertapenem, imipenem and meropenem). These carbapenems are antimicrobial drugs of last resort and are crucial for preventing and treating life-threatening nosocomial infections of clinical concern. Many carbapenemases confer resistance or reduced susceptibility to all or nearly all members of the β-lactam class along with other antibiotic classes. Most carbapenemases are acquired and are passed between bacteria by small sections of DNA called plasmids. This gives potential for spread between different strains, species and genera of bacteria. Specimen collection

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Rectal swabs or faecal specimens should be sent following appropriate risk assessment on admission and to aid in infection prevention and patient management. Laboratory Procedure Specimens are cultured onto special selective chromogenic agar and incubated for 18-24 hours.

Non-Directed Bronchial Lavage (NBLs)

Currently only received from HICU at ROH. Specimen Collection 20ml of 0.9% saline should be instilled through a catheter transiently placed in the bronchial tree through an endotracheal tube. Immediately aspirate back into a syringe yielding a sample of 5-10ml. Laboratory Procedure Microscopical examination for white blood cells and organisms (Gram stain). Specimens are diluted to give a semi-quantitative bacterial count. Plates are incubated for up to 48 hours and significant isolates reported.

Pernasal swabs for Bordetella pertussis/parapertussis

Specimen Collection A special swab with a fine wire flexible shaft should be used. Guide the fine wire swab through a nostril until resistance is felt at the naso-pharyngeal wall. Rotate the swab once or twice and remove, place into transport media and send to the laboratory.

Laboratory Procedure Swabs are cultured onto selective charcoal agar and incubated for 5 days. Positive isolates are referred for confirmation and typing.

Antibiotic sensitivity testing Significant isolates are tested against appropriate antibiotics. Please indicate on the request if the patient has been prescribed antibiotics and state which. Bordetella pertussis can also be detected using molecular testing. Swabs should be sent using a Remel M4RT viral collection kit. Refer to page 51 for molecular testing.

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Sputum for routine culture

Specimen Collection A fresh specimen of purulent or mucopurulent sputum should be collected into a 60ml wide mouth container. Mucoid or salivary specimens should only be submitted from immunocompromised patients. Specimens collected by bronchoscopy must not be transported in containers with the suction tubes attached to the lid. Collection packs are available which include a second sealed lid. This should be applied to the container prior to transportation to the laboratory. Whenever possible, specimens should be collected before the administration of antibiotics. Please include any anticipated antibiotic therapy on the request card. Clinical details are important; please ensure relevant information is given e.g. Community Acquired Pneumonia, COPD, bronchiectasis, VAP, CAP etc. to allow the lab to select suitable investigations and report relevant results. Where a delay in processing the specimen is expected, store the specimen at 4oC. Care must be taken to ensure that the lid is properly screwed down to avoid contamination of the outside of the container.

Laboratory Procedures

All specimens are cultured for: Streptococcus pneumoniae Haemophilus spp. Moraxella catarrhalis Staphylococcus aureus and Gram Negative organisms / other organisms will be reported where appropriate


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Investigation of Intravascular Cannulae & Associated Specimens Specimen Collection Disinfect the skin around the cannula entry site, remove cannula using aseptic technique, and cut off 4cm of the tip into a sterile container using sterile scissors. Send newly removed cannulae in a sterile leak proof container in a sealed plastic bag. Swabs in a sealed plastic bag Laboratory Procedure These samples will be cultured onto appropriate media. Tips/cannulae will be inoculated and interpreted in a semi-quantitative manner. Antibiotic Sensitivity Testing Will be performed only when appropriate and when the number of Colony Forming Units (CFU’s) of the organisms grown indicates this is necessary. Limitations Delays in transportation may affect the viability of fastidious organisms. Poor aseptic technique at specimen collection or processing may lead to erroneous results. Urinary catheters are unsuitable for microbiological investigation of UTI, please send a urine specimen.

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Swabs from sterile sites Specimen Collection Any available pus should be sampled as well as the lesion of interest. Specimens should be transported and processed ASAP. Swabs should be transported in Amies transport medium with charcoal. For investigation of fungal infection, scrapings of material from the ear canal are preferred although swabs can also be used. Laboratory Procedure Swabs/ pus are cultured onto appropriate media for the common pathogens associated with these sites. Clinical details should be as detailed as possible to ensure correct investigations are carried out. Please indicate in the clinical details if ophthalmia neonatorum is clinically suspected in neonates. Antibiotic Sensitivity Testing Significant isolates are tested against appropriate antibiotics. Please indicate on the request if the patient has been prescribed antibiotics and state which. Limitations Delays in transportation may affect the viability of fastidious organisms.

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Fluids from sterile sites CSF

Specimen collection

As a standard, the CSF should be collected into 3 universal containers + a yellow top (fluoride) glucose container. In situations where specimen collection is difficult, it may not be possible to complete all the investigations requested. Clearly label the containers 1, 2 and 3 in the order they were collected. Send all the specimens together with the completed Microbiology and Biochemistry request cards/order to Microbiology at ROH. Microbiology will then distribute the specimens as required to Biochemistry. If xanthochromia is required: obtain a fourth specimen and send in a black sample bag directly to Biochemistry, using request form BC-FORM-148. All requests for CSF investigations should be accompanied by a telephone call to the appropriate testing laboratory. Outside normal working hours, it is the responsibility of the requesting clinician to inform the Microbiology BMS on-call via switchboard that a CSF sample is being sent. Laboratory procedure

Standard tests

Macroscopic examination for turbidity and presence of blood Red cell count Differential white cell count Culture

Supplementary tests as clinically indicated Gram stain Cryptococcal antigen Bacterial antigen AAFB stain and TB Culture Viral PCR Meningococcal PCR (Referred) TB PCR (Referred) Syphilis (Referred) If meningococcal meningitis is suspected an EDTA specimen should also be sent for meningococcal PCR Xanthochromia (Quantitative) – performed in Biochemistry. Please send CSF in an extra universal container (specimen 4) inside a black mini-grip bag to minimise light deterioration of the specimen prior to testing.

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Transmissible Spongiform Encephalopathy’s (TSE, CJD)

Investigations into TSE are performed at the National CJD Surveillance Unit and the contact numbers are shown. Clinical Office Tel: 0131 537 2128/3103 Pathology Tel: 0131 537 3084 CSF Referrals: 0131 343 1404 There are strict guidelines that must be followed to ensure that specimens are processed correctly and Microbiology must be informed immediately to ensure that these procedures are followed. Please refer to the Trust document CPDI024 Management of Transmissible Spongiform Encephalopathies (TSE) including Creutzfeldt Jakob Disease (CJD). Synovial / Joint fluid

Specimen collection For routine culture and microscopy - send 5 - 10 ml in a universal container. Where possible, an aerobic blood culture bottle can be aseptically inoculated with between 5 and 10 ml of the fluid. For crystals and differential cell counts - send approximately 1 ml in a paediatric lithium heparin container. Examination for crystals will only be performed when specifically requested. Laboratory procedures

Gram stain and culture Microscopy for crystals and differential cell count are referred to the Cell Path Department ROH.

Pleural fluid / Bronchial wash Specimen collection

Collect 10-15 ml in a universal or special collection trap with secure screw cap. Containers with aspiration tubes attached to the lid are not acceptable. Laboratory procedure

Gram stain and culture

Ascitic and Peritoneal Fluid Specimen collection

Collect 10-15 ml of fluid in a universal container. Where possible, an aerobic blood culture bottle can be aseptically inoculated with between 5 and 10 ml of the fluid.

Laboratory procedures Gram stain Quantitative differential white cell count Culture

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Cryptococcal Antigen Testing Specimen collection Blood specimens: the sample must not contain anti-coagulants as this will invalidate the test. Samples must be sent in a serum gel bottle. CSF: samples should be collected according to local protocols. Laboratory Procedure Appropriate specimens are screened using a serological assay. Any samples which screen positive will be referred to the Regional Mycology Lab at Wythenshawe for further testing. Limitations of the Test A negative test does not exclude the possibility of cryptococcal infection, particularly when a single patient specimen has been tested and the patient has symptoms consistent with cryptococcosis. False-negative reactions may be caused by low titres, very high concentrations, early infection, presence of immune complexes, or poorly encapsulated strains with low production of polysaccharide. Presence of other artefacts in the specimen may result in false-positive reactions.

TB Investigations Specimen collection

Sputum – collect sputum specimen into a wide mouth 60ml container or universal. If other investigations are required, please send a separate specimen with an appropriate request/order. Urine – collect early morning urine into a universal. As a minimum, 3 early morning urine specimens on 3 consecutive days are recommended. Bronchial aspirate / wash – collect fluid into a universal or similar screw capped container. Containers with aspiration tubes attached to the lid are not acceptable. Other fluids – collect specimen into a universal For neonates and young children who have difficulty producing sputum, a gastric aspirate may be an appropriate alternative specimen. Collect the specimen into a universal and send to the laboratory immediately. Laboratory procedure

Auramine stain for AAFB (not performed on urine specimens) Traditional culture onto LJ slopes (up to 12 weeks) Automated liquid based culture (continuously monitored for up to 8 weeks)

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TB PCR

PCR testing for species identification and resistance genes to isoniazid and rifampicin is performed in-house on all positive cultures. These are also referred to the Regional TB Reference Laboratory (PHE Birmingham) for full susceptibility testing. After discussion with the laboratory TB PCR can be performed directly on smear positive sputum specimens. TB Blood Culture

Blood Cultures for Mycobacteria investigations taken in Pennine Acute are processed using the Bactec FX system. Only bottles which are compatible with this system are acceptable, these are available from Pathology stores. NB. These bottles can also be used for investigation of fungal septicaemia.

Bottle type

Colour Code Volume of blood Incubation

Myco-F-Lytic Red Top 5-10 ml

42 days

Collection procedure

See Trust document CPDI085 ‘Standard Operational Procedures for the Collection of Blood Cultures’ available on the Trust intranet.

Precautions Label the bottles with the patient name & hospital number and/or date of birth and date & time of collection. All efforts to avoid contamination of the bottle with skin organisms must be made. Laboratory procedure

Blood cultures are continuously monitored using automated instrumentation. If a bottle flags ‘positive’, results are telephoned and entered onto the laboratory computer system (available for remote access via the web based enquiry browser) at the earliest opportunity. TB Quantiferon Test

Use of interferon gamma blood tests as the front line test for latent TB infection is replacing the skin test, especially in immunocompromised patients. Blood tests should be used as a secondary, confirmatory test in cases where the tuberculin skin test is positive. In this case, the blood test is used as a means of screening out false positives. Blood tests also have a role to play in the diagnosis of TB disease, especially in non-pulmonary TB and as a rule-out test in TB suspects. This test is currently not performed in-house. All specimens are referred to the Department of Immunology at Manchester Royal Infirmary.

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Please telephone the Immunology Department at MRI on 0161 276 6497 within normal working hours to order special tubes and request forms. Please note that Immunology does not accept specimens on weekends or Bank Holidays. The following instructions have been issued by the Immunology Department, and must be followed very carefully:

Tubes 4 tubes are provided for the TB Quantiferon test. The empty tubes may be stored either at room temperature or in the fridge until use or expiry. Blood

Blood must be collected into each of the red, purple and grey-topped vacutainer tubes to the fill line (that is all the tubes will draw). Mix the tubes gently. Do not remove the tops as this destroys the sterility and internal atmosphere. The specimens should be kept at room temperature. Telephone the Microbiology Laboratory at ROH to inform them that the specimens are being sent. Specimens must be received in Microbiology before 5pm. Please do not send specimens on the last day of the working week (usually Friday – except Bank Holidays) or at the weekend. Request Form

The details on the request form and tubes must conform to the Trust specimen acceptance policy and must be marked with the date and time taken. Please give information on previous TB and current symptoms and include the result of the skin test. For further information, please contact the Immunology Laboratory on 0161 276 6440

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Corneal scrapes, intra-ocular fluids and contact lenses Specimen collection

Corneal scrapings and intraocular fluids will be collected by an ophthalmic surgeon. Sterile needles may be used to aspirate or scrape material, and sterile scalpel blades to scrape material. It is important that material is collected into the appropriate media/container for the investigation required. Contact lenses and/or fluid can be sent in their original storage case. Samples are investigated on request for: Bacterial and fungal pathogens (culture) Viral pathogens Chlamydia Acanthamoeba (PCR) – referred to external labs for testing. Corneal scrape kit: Corneal scrape kits are held at Ophthalmology clinics across the Trust: Rochdale Infirmary: Ophthalmic Day Case Unit (2 kits) Clinical Assessment Unit (2 kits) Oldham: Eye clinic, Integrated Care Centre (1 kit) Fairfield: Eye clinic/ward, FGH (1 kit) New kits can be ordered by contacting the Microbiology lab. Each kit contains: 1ml Brain Heart Infusion broth in a minigrip bag with absorbent padding Chlamydia swab Viral transport media Minigrip bag, sterile bijou, universal and single-wrapped swab (Acanthamoeba PCR) Charcoal swab A copy of Appendix 2 of the procedure (MC-SOP-27) Return address label.

NB. Do not use the pneumatic air-tube system to transport these samples to the lab.

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Mycology specimens Specimen collection

Specimens should be collected into a Dermapak kit (available from the laboratory on request) or in to a universal container. The paper used in the Dermapak kit permits the specimen to dry out which helps reduce bacterial contamination. Specimens should not be stored in tightly closed containers, as any moisture present will stimulate the growth of contaminants and may prevent the isolation of dermatophytes. It may be helpful to clean lesions on the skin or scalp, and sometimes nail with surgical spirit or 70% alcohol prior to the collection of the specimen as this improves the chances of detecting the fungus microscopically and reduces the likelihood of contamination. Prior cleaning is essential if greasy ointment or powders have been applied to the region.

Nail Clippings should be taken from any discoloured, dystrophic or brittle parts of the nail. These should be cut as far back as possible from the free edge of the nail and include the full thickness, since some fungi are restricted to the lower parts. Where the nail is thickened, scrapings can also be taken from beneath the nail to supplement the clipping specimen. Fungus in the distal part of the nail is often non-viable and although still visible on microscopy it will fail to grow in between 40 and 50% of cases.

Skin Material from skin lesions should be collected by scraping outward from the lesion edge. This is where the most viable fungi are likely to be found

Hair Specimens from the scalp are best obtained by scraping with a blunt scalpel. The specimen should include hair stubs, the contents of plugged follicles and skin scales. Hairs may also be plucked from the scalp with forceps; infected hairs are easily removed this way. Hair cuttings are unsatisfactory as the focus of the infection is usually below or near the surface.

Unsuitable specimens Material that has been in fixative is unsuitable for culture. Swabs either dry or in transport media are also unsuitable with the exception of specimens for Candida culture. The following clinical details are useful when submitting specimens for Mycology Any therapy with antimicrobial, cytotoxic or immunosuppressive drugs Patient’s occupation History of travel or residence abroad Contact with animals

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Environmental Samples Specimen Collection This must be led by and at the request of the Microbiology medical team, and must include liaison with the Infection Prevention Team. The specimen collected will depend upon the investigation and the target organisms (e.g. swabs, contact plates). A PAT log number must be attached to all requests for environmental screens and this will be provided by the Infection Prevention / Microbiology team. Laboratory Procedure This will depend upon the organism of interest. Specimens will be inoculated onto appropriate media and incubated for the required time, dependant on the investigation required. Limitations Delays in transportation may affect the viability of fastidious organisms. Delays of over 48h are undesirable.

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Water Testing This includes the testing of hospital water for presence of Legionella or Pseudomonas and the testing of endoscope final rinse water for the presence of any organism. Hospital water for Legionella and Pseudomonas Specimen Collection Containers for collection of samples are available from Microbiology via an order form submitted to Pathology stores at ROH. Samples are collected by engineers from Trust Estates. Specimens should be transported without delay. If there is to be any delay then samples should be refrigerated (2-8°C) and transported as soon as possible (not more than 24 hours) using a cool-box. Lab Procedure Samples are filtered and cultured. Any isolates are identified. Legionella spp – reported with colony count Pseudomonas spp – reported with colony count Negatives are reported as Legionella or Pseudomonas NOT isolated Limitations This method is suitable for most types of aqueous samples except those with high turbidity which tend to block the membrane filter. This will limit the volume of sample that can be filtered. Accumulated deposit on the membrane filter may mask or inhibit the growth of target organisms. High numbers of competing organisms may inhibit the growth or detection of target organisms. Endoscope wash water Specimen Collection Water samples should be obtained from the EWD chamber or bowl and collected in 250ml sterile, chemically clean, single-use containers. The first 100 ml of sample taken at each sampling point should be run to waste. Specimens should be transported without delay. If there is to be any delay then samples should be refrigerated (2-8°C) and transported as soon as possible (not more than 24 hours) using a cool-box. Lab Procedure Samples are filtered and cultured. Any isolates are identified, counted and reported as <1 or the number of colony units present or >100cfu per 100ml as appropriate. Limitations This method is suitable for endoscope rinse waters except those with high turbidity, which tend to block the membrane filter. This will limit the volume of sample that can be filtered. Accumulated deposit on the membrane filter may mask or inhibit the growth of organisms. High numbers of competing organisms may inhibit the growth or detection of other organisms.

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Antimicrobial assays For comprehensive guidelines on antibiotic dosing and monitoring, refer to the Antibiotic Policies for Adults and Paediatrics/Neonates (EDT007 and EDT016) available on the Trust Intranet site. Gentamicin and Vancomycin testing is performed in the Biochemistry Dept at Pennine: Gentamicin assays are currently performed in Biochemistry at FGH, NMGH, and ROH. Vancomycin assays are currently performed in Biochemistry at NMGH and ROH. All other assays are referred for external testing; please send all specimens to Microbiology at ROH for recording and onward transport. A full list of external labs can be found in the Microbiology Test Repertoire. For all assay requests, please ensure that the date/time of dosage and date/time of specimen collection are stated in the request.

Therapeutic ranges for antimicrobial agents ‘Random’ or ‘time unspecified’ levels are difficult and may be impossible to interpret unless they are overtly above normal peak concentrations. Random levels taken to determine whether another dose should be given are strictly pre-dose levels. Samples are referred to the Antimicrobial Reference Lab, Severn Pathology, North Bristol NHS Trust, for assay procedure and therapeutic levels please see guidelines here:

Antimicrobial Ref Lab

https://www.nbt.nhs.uk/sites/default/files/Antibiotic%20Guideline%20Ranges%202018.pdf

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Legionella/Pneumococcal antigen test Specimen collection

Minimum of 1ml of urine collected into a universal container Laboratory procedure

Immunochromatographic membrane assays are used to detect Legionella pneumophila serogroup 1 and/or Streptococcus pneumoniae Limitations of the test

The Pneumococcal antigen kit is validated for urine and CSF specimens only The Legionella antigen kit is validated for urine only.

Helicobacter pylori culture Specimen collection

Gastric biopsy should be placed into a ‘Portagerm pylori’ container. This is a specific transport medium for the culture of Helicobacter pylori and is available from Microbiology on request. Laboratory procedure

Biopsy is cultured onto selective media for up to 5 days incubation.

Helicobacter Stool Antigen Specimen collection

Faeces specimens should be collected into a ‘blue top’ faeces container with spoon. If a delay in transporting to the laboratory is anticipated, please store at 4oC. Laboratory procedure

Processed in-house using Enzyme Immuno Assay (EIA) Please note: The serology test for H. pylori antibody is no longer available.

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Urine Pregnancy Testing (available for community patients only) Specimen collection

An early morning specimen of urine collected into a universal container. Specimens received in boric acid containers are unsuitable for pregnancy testing and will be rejected. Laboratory procedure

Immunochromatographic membrane assay (sensitivity is 25mIU/ml hCG) Limitations of the Test

This test provides a presumptive diagnosis of pregnancy. Physicians should evaluate all clinical and laboratory findings before making a definitive diagnosis.

Viral Haemorrhagic Fever VHF investigations are processed by the Haematology Department. Please see Trust document below before collecting any specimens as the correct testing procedure will be determined by the clinical risk assessment. CPME089 ‘Integrated Care Pathway for Patients Assessed as Being at Risk of Viral Haemorrhagic Fever’

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Serological Tests

Serum or plasma (see Test Repertoire) specimens for serological tests should be submitted to the laboratory as soon as possible after collection and within 72 hours to prevent degradation of the analytes; if a delay is unavoidable, store at 2-8°C. Specimens which are highly haemolysed, hyperlipaemic or contain microbial contamination should not be sent. Needlestick Injuries

The Trust has an Accidental Inoculation Policy (Doc No CPDI018) which identifies the procedure to follow in the event of an inoculation injury. This includes needlestick/sharps injury, splashes to the eyes, mouth, mucous membranes or broken skin, and human bites. A 7.5ml gel tube (brown top) is the preferred sample type. A sample is required from both the source (donor) patient and the staff member (recipient) involved in the Needlestick Injury, it is imperative that the request clearly reflects this in order to ensure that the correct tests are performed. Needlestick Injuries occurring in an acute setting will be reported to the Trust Occupational Health Department. Community injuries will be reported to the requesting clinician.

Molecular Tests

Viral Loads EDTA plasma is preferable to serum as degradation of nucleic acid can occur in serum/clotted specimens which may result in under/over reporting of viral load. Specimens should be sent as soon as possible after collection, and if highly haemolysed, hyperlipaemic or contain microbial contamination should not be sent. For the HIV viral load test, plasma must be separated from cells within 24 hours of specimen collection to avoid degradation. For the Hepatitis B and Hepatitis C viral load tests, plasma must be separated from cells within 6 hours of specimen collection to avoid degradation. In order for effective audit of this requirement it is essential that the date and time of collection is recorded on the paper or electronic request. Please contact the Consultant Virologist should there be any concerns regarding results for viral load tests. Heparinised specimens or specimens from patients who have received heparin may give erroneous results and must not be sent, please contact the laboratory for advice.

Viral PCR Do not send dry swabs, charcoal swabs, swabs in bacterial transport media or swabs with wooden shafts, as all are unsuitable for molecular testing. Please send swabs using a Remel M4RT viral collection kit. Please give details of any antimicrobial therapy wherever possible. Multiplex PCR is performed in house for enteric viruses (faeces samples), respiratory viruses (nose/throat samples), CSF samples and swabs from non-GUM sources.

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Chlamydia / Neisseria gonorrhoeae Molecular Investigations Chlamydia / N. gonorrhoeae detection is performed using the Gen-Probe Tigris analyser. Only specimens collected into Gen-Probe Aptima collection kits (including urine specimens) are suitable to run on this analyser. Specimen Collection kits Unisex Swab Kit (Purple) - for collection of endocervical and urethral swabs. This collection kit can also be used for eye, throat and rectal swabs (see below). THIS COLLECTION KIT MUST NOT BE USED FOR HIGH VAGINAL OR VULVO-VAGINAL SPECIMENS. Vaginal Swab Kit (Orange) - for collection of high vaginal or vulvo-vaginal specimens. This specimen collection kit can be used by the patient for self-collection of specimen following guidance from clinician, nurse or care-provider. Urine Kit (Yellow) - for collection of “first-void” urine. A FIRST VOID URINE WILL CONTAIN THE MOST AMOUNT OF EPITHELIAL CELLS Specimen collection Chlamydia is an intracellular organism that infects the columnar epithelial surfaces of the human urethra and endocervix. To maximise detection rates, specimens from these sites should contain as many columnar epithelial cells as possible.

Endocervical swabs Prior to sampling the endocervix, using the white shaft cleaning swab provided in the kit, clean the cervical to remove excess mucous or pus. Insert the blue-shaft swab provided in the collection kit approximately 1 cm into the cervical canal, rotating several times for 10 to 30 seconds. Withdraw the swab without touching the vaginal surfaces and place in the tube containing the Chlamydia transport media. Carefully break the swab shaft at the score line and replace the tube lid securely.

Urethral swabs Insert the blue shaft swab included in the Chlamydia collection kit into the urethra for approximately 4 cm, rotating several times for 2 to 3 seconds. Withdraw the swab and place in the tube containing the Chlamydia transport media. Carefully break the swab shaft at the score line and replace the tube lid securely.

Urine Collect first void urine into a urine collection container free of any preservatives. Transfer 2ml of the urine into a urine collection tube using the pipette provided. The sample MUST be between the two black lines. DO NOT OVER OR UNDER FILL THE TUBE or the sample will be rejected. Replace the tube lid securely.

*Eye, Throat, Rectal and Ulcer Swabs Use the unisex (purple) collection kit.

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* The TMA assay used on the Gen-Probe Tigris instrument has not yet been validated for these swabs, these specimens will be processed and an appropriate comment added to the report. Laboratory procedure Examination for Chlamydia / N. gonorrhoeae is by a molecular amplification technique called ‘Transcription Mediated Amplification’ (TMA). The instrument used to perform this investigation is the Gen-Probe Tigris. Only specimens collected into Gen-Probe Aptima collection kits (including urine specimens) are suitable to run on this instrument. The kit used is a dual kit for the detection of both Chlamydia and Gonococcal nucleic acids. Results of both assays are reported. All positive assays for N. gonorrhoeae and positive assays for Chlamydia from un-validated specimen types are confirmed by repeat testing, as are low-level Chlamydia positives. The repeat test uses the same TMA technology but detects a different area of nucleic acid for both Chlamydia and Gonococci. Limitations of the assay Use only the swab and urine kits provided. Other types of swabs or urine containers may affect the performance of the assay and will therefore be rejected. It is critical that urine specimen containers are NOT overfilled or underfilled.

PVL Panton-Valentine leukocidin (PVL) is a cytotoxin produced by Staphylococcus aureus that causes leukocyte destruction and tissue necrosis. Although produced by <5% of S. aureus strains, the toxin is detected in large percentages of isolates that cause necrotic skin lesions and severe necrotizing pneumonia. PVL detection is performed in-house using molecular testing on cultures of Staphylococcus aureus isolated from specimens with the following clinical information: 1. Necrotising SSTI 2. Recurrent furunculosis or abscesses or non-recurrent pus from theatre 3. Clustering of SSTIs within a household or social group or Health Care group 4. Community-acquired necrotising/haemorrhagic pneumonia in previously fit young

people. 5. Myositis/pyomyositis/ acute haematogenous osteomyelitis or osteoarticular

infections.

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Appendix 1: Transport Department Hospital Pathology Collection Schedule

Pathology samples will be collected from each site at the approximate times detailed below by the Transport Department Monday to Friday for delivery to the Central Lab Royal Oldham Hospital unless otherwise indicated.

(http://nww.pat.nhs.uk/corporate-departments/Facilities/Transport/transport.htm)

Hospital/ Collection

NMGH FGH RI BH ROH to NMGH ROH to FGH ROH to RI NMGH Sat-Sun

FGH Sat-Sun

RI to ROH Sat

RI to ROH Sun

ROH Sat-Sun

1 08.40 08.40* 08.35* 09.10 9.15 09.20 08.10 8.40 09.10 8.30 2 09.50 10.15 9.45 10.25 10.45 9.15 9.40 10.10 9.40 9.40 9.50

3 10.20 11.20 10.55 14.10 13.00 12.35 10.25 10.55 11.25 10.40 10.40 11.00

4 11.20 12.40* 11.25* 14.10 13.45 11.40 11.55 12.25 11.55 11.55 12.00

5 12.25 13.05 12.25* 16.10 15.00 14.55 13.05 13.30 14.00 12.55 12.55 13.05

6 13.25 14.10 13.30 17.10 16.00 14.00 14.30 15.00 13.30 7 14.55* 15.00* 14.25*

15.05 15.45 16.15 14.30 14.30 14.50

8 15.25 15.35 15.35*

15.40 16.45 17.15 15.30 15.30 15.50

9 16.20 16.35 16.20

17.35 16.45 16.45 16.50

10 17.25 17.00

17.45 17.45 11 18.40 18.00#

12 19.40*

Collection Points / Comments

FGH - Pathology Lab. ● NMGH - Pathology Lab. ● RI - CAU collection point (plus collections from the GUM Clinic at 13.30 Wed/Thur & Mon - Fri 17.00 & at weekends from UCC) ● BH - 09.10 & 14.10 Floyd Unit & John Elliot Unit (via RI) 16.10 Floyd Unit (direct to ROH) ● * includes collection from theatres. (NMGH includes Main, Phase One & Day Services Theatres.) ● # non direct delivery

http://nww.pat.nhs.uk/corporate-departments/Facilities/Transport/transport.htm

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