Department of Microbiology Microbiology Services User Handbook Department of Microbiology Great Western Hospital Marlborough Road Swindon Wiltshire SN3 6BB DCN: MIC-P-006-10.0 November 2012 Page 1 of 18 Department of Microbiology Contents Document Control............................................................................................................................ 2 General Information ........................................................................................................................ 3 Contact Details ................................................................................................................................ 3 Service Availability ........................................................................................................................... 3 Laboratory Location ......................................................................................................................... 4 Results............................................................................................................................................. 5 Clinical Advice .................................................................................................................................. 5 Requesting Tests .............................................................................................................................. 5 Specimen Transport ......................................................................................................................... 5 Specimen Containers ............................................................................................................................... 5 Request Forms ......................................................................................................................................... 5 Health & Safety........................................................................................................................................ 6 Quality Management ....................................................................................................................... 7 External Quality Assurance...................................................................................................................... 7 Turnaround Times ................................................................................................................................... 7 Reference Laboratories .................................................................................................................... 7 External Service providers ................................................................................................................ 8 Bacteriology Tests ............................................................................................................................ 9 Virology Tests ................................................................................................................................ 14 DOCUMENT CONTROL This handbook is subject to the document control procedures used in the Pathology Directorate. As this version is controlled electronically, any printed hardcopy copy or locally-saved electronic copy will no longer be subject to the control procedures. Please ensure that any reference is made to the current active version of this document. DCN: MIC-P-006-10.0 November 2012 Page 2 of 18 Department of Microbiology GENERAL INFORMATION The Clinical Microbiology Service is provided by the laboratories at the Great Western Hospital, Swindon. We provide an analytical and interpretative service on a wide-range of clinical specimens, processing over 260,000 requests each year. The efficiency of the service we provide is reliant on the cooperation of our users with the necessary policies relating to safety, specimen transport and specimen identification. We hope that this handbook contains all the information you require to use our service. However, please feel free to contact us to discuss any problems or issues you may have. Any comments or suggestions about the User Handbook should be addressed to the Laboratory Manager, by email to penny.latham@gwh.nhs.uk. We aim to be a model of excellence in the delivery of a clinical pathology service. In order to achieve this, we are committed to the following: Service user involvement Good professional practice & evidence-based practice Efficient utilisation of our resources Valuing and developing our staff in order to realise their full potential Commitment to the health, safety and welfare of our patients, staff and visitors Keeping a safe environment in compliance with current environmental legislation Working as teams and partnerships Continuous improvement CONTACT DETAILS Consultant Microbiologist Consultant Microbiologist Deputy General Manager Laboratory Manager Section Manager (Virology) Dr Melanie Wilson Dr Susan Dawson David Newell Penny Latham Helen Jones (01793) 604801 (01793) 604802 (01793) 605013 (01793) 604804 (01793) 604799 SERVICE AVAILABILITY The laboratories are open for receipt of specimens from 0845 to 1700 between Monday and Friday, 0800 to 1300 on Saturday mornings and 0845 to 1230 on Sunday mornings and Bank Holidays. There is a refrigerator in the Pathology Reception (and an incubator for blood culture bottles) for specimens that arrive outside the normal opening hours. Certain specimens may be sent direct to the laboratories using the pneumatic chute system (Pathology Address: 104). The on-call service is available outside normal hours. The use of the service should be restricted to those samples where it is essential to have a result before the next routine session. In general, samples normally accepted for the on-call service would include CSF, joint fluids, pleural fluids, ascitic fluids, pus DCN: MIC-P-006-10.0 November 2012 Page 3 of 18 Department of Microbiology and urine. To discuss an urgent specimen with the duty Biomedical Scientist, please contact switchboard at GWH (01793 604020). LABORATORY LOCATION The Department is part of the Directorate of Pathology, within the Great Western Hospitals NHS Foundation Trust. The department is sited on the fourth floor of the main hospital building (see diagram). The postal address is as follows: Department of Microbiology Great Western Hospitals NHS Foundation Trust The Great Western Hospital Marlborough Road Swindon Wiltshire SN3 6BB Department of Microbiology (67) Directorate of Pathology (69) DCN: MIC-P-006-10.0 November 2012 Page 4 of 18 Department of Microbiology RESULTS Please note that we need to establish the caller’s identity before giving results over the telephone. We are unable to give results directly to patients or their relatives. Authorised results are available on the Medway system and the Ward Enquiry system. Results may also be obtained by telephoning extension 4293 (direct dial 01793 604293). In general, results are not available until they have been authorised. In exceptional circumstances, preliminary results may be available direct from the relevant laboratory. However, please bear in mind that this may delay the testing of other samples. Microbiology Virology Extension 4798 Extension 4799 CLINICAL ADVICE For clinical advice on the interpretation of results, please contact the duty Consultant. During the outof-hours period, the duty Consultant can be contacted via GWH switchboard. Consultant Microbiologist Consultant Microbiologist Dr Melanie Wilson Dr Susan Dawson (01793) 604798 (01793) 604798 REQUESTING TESTS A list of tests provided by the Microbiology laboratory is provided in this document. All tests should be requested at the time of submitting the specimen to the laboratory. However, amendments to requests, or the need for additional tests, can still be discussed with the laboratory after processing has started. In general, additional tests must be requested within 48 hours of sample receipt within the laboratory. In some cases, additional tests may not be possible and a fresh specimen will be required. Further advice can be obtained from the laboratory. SPECIMEN TRANSPORT Refer to Specimen Transportation Policy available on the Trust intranet. Specimen Containers All patient specimen containers must be clearly labelled with the patient’s name, date of birth, the date of collection and the type of specimen. The hospital number should be included where possible. Request Forms All samples must be accompanied by a properly completed request form, giving relevant clinical information, including antibiotics (used or proposed), patient location and detailing the investigation DCN: MIC-P-006-10.0 November 2012 Page 5 of 18 Department of Microbiology required. Please note that inadequately labelled specimens and those without adequately completed request forms may not be processed. The laboratory assumes that patient consent has been obtained for the investigations requested. All requests for HIV investigations must include the Doctor’s signature on the request form. Health & Safety All specimens should be regarded as potentially infectious. Certain specimens from patients who are known or suspected to have the following diseases/conditions constitute a potential higher risk of infection to persons handling the specimens: Typhoid/paratyphoid fever (faecal specimens only) Dysentery (faecal specimens only) Tuberculosis (specimens from sites where tuberculosis infection is likely) Anthrax Brucellosis Transmissible Spongiform Encephalopathy (including CJD) Viral haemorrhagic fever Pandemic Flu To minimise the risks “Danger of Infection” labels should be attached to the specimen container and request form for all qualifying specimens (available from Phlebotomy Dept, GWH) and the nature of the risk specified on the request form. This is a necessary procedure to protect persons handling the specimens (nursing, portering, transport, reception and laboratory staff). The labels must be used in accordance with the Specimen Transportation Policy available on the Trust intranet. Samples thought to constitute a risk to laboratory staff because of inadequate packaging or warning may be rejected. The Consultant Microbiologist must be contacted BEFORE collecting specimens from a patient suspected of having a viral haemorrhagic fever, human avian influenza, SARS or CJD. These organisms require special transport arrangements and specialist laboratories designed for containment during manipulation of specimens and cultures. These lists are not exhaustive and rarely other biological agents that can cause severe human disease, and present a serious hazard to employees, may be present in specimens. If there is any suspicion of a high risk atypical organism advice on specimen collection and transport should be sought from the Consultant Microbiologist. DCN: MIC-P-006-10.0 November 2012 Page 6 of 18 Department of Microbiology QUALITY MANAGEMENT The Pathology Service is committed to maintaining accreditation for its quality management system. Accreditation is undertaken by Clinical Pathology Accreditation (UK) Ltd, an independent external organisation. Details of our accreditation, together with performance data, are available from the Laboratory Manager. In order to help us improve our service, we may ask you to complete a questionnaire. We greatly value the information obtained from these surveys, and we would like to thank you in anticipation of your assistance in completing the questionnaires. As part of our quality management system, we routinely monitor certain performance indicators. These include External Quality Assurance (EQA) scores and Turnaround Times (TAT). External Quality Assurance During 2011, our total EQA score was 98.6% (820 points out of a possible 834). The EQA scheme involves a series of simulated specimens being sent to our laboratory for testing. Our results are then scored against the intended results and compared to a national average. Each occasion in which we fail to report the intended result is investigated thoroughly within our quality improvement system. Turnaround Times We monitor the turnaround times for certain key tests every month. The time taken from receipt of specimen to the reporting of the result is analysed for a range of twelve key tests. Details of the target turnaround times for all tests are given in the test section later in this document. During 2011, our total TAT score for the twelve key tests was 98.1%. This meant that we met our target in 98.1% of cases. The total number of tests checked during this period was 239 510. Further details on our TAT performance can be obtained from the Laboratory Manager. REFERENCE LABORATORIES As part of the testing process, it may be necessary to refer some, or all, of the specimen to an external reference laboratory. We only use laboratories which have an accredited quality management system. The name of the reference laboratory used will be indicated on the test report. The reference laboratories currently used are: Anaerobe Reference Laboratory, Cardiff Antimicrobial Reference Unit, Bristol Cryptosporidium Reference Unit, Swansea Health Protection Agency, Birmingham Health Protection Agency, London Health Protection Agency, Bristol Health Protection Agency, Manchester Health Protection Agency, Porton Down Health Protection Agency, Southampton Immunology Department, Oxford DCN: MIC-P-006-10.0 November 2012 Page 7 of 18 Department of Microbiology Immunology Department, Bristol Insect Research & Development, Cambridge Lab 21 Clinical Laboratory, Cambridge Leptospira Reference Unit, Hereford Microbiology Department, Epsom Microbiology Department, Leeds Microbiology Department, Exeter Toxoplasma Reference Unit, Swansea Veterinary Laboratory Agency, Surrey EXTERNAL SERVICE PROVIDERS Specimens for Mycology and Mycobacterium investigation are referred to an external service provider, Southampton University Hospitals NHS Trust (SUHT), for processing. DCN: MIC-P-006-10.0 November 2012 Page 8 of 18 Department of Microbiology BACTERIOLOGY TESTS Test Sample (Volume) Container Antibiotic Levels Antibiotic Assay Clotted blood (2-6mls) Vacutainer (red-top) Ascitic Fluid Culture Cell count, Gram stain & Culture Ascitic fluid (<20mls) Universal (white top) Blood Cultures (Adults) Gram stain & Culture Blood (5-10mls) Blood Cultures (Children) Gram stain & Culture Blood (<4mls) Paediatric blood culture bottle C. difficile Toxin Toxin Detection Faeces (<20mls) Universal with spoon (blue top) Corneal Scrape Culture Gram stain & Culture Corneal scrape CSF Culture Cell count, Gram stain & Culture CSF (1-2mls) Ear Swab Culture Culture Eye Swab Culture Culture Investigation DCN: MIC-P-006-10.0 TAT Limitations Out-of-Hours 3 days Requests must be discussed with the Consultant Microbiologist no 4 days, plus 2 days for cell counts performed enrichment on SBP patients only culture yes, by arrangement 1-5 days, Adult blood culture depending on set positivity samples should be collected before antibiotic treatment bottles should be sent to the incubator located in Pathology reception 1-5 days, depending on positivity samples should be collected before antibiotic treatment bottles should be sent to the incubator located in Pathology reception 1 day not performed on formed stools; not performed if a positive result within previous 28 days no 2 hrs for Direct inoculation microscopy onto plates and slide 2-5 days for culture requires good amount of cellular material yes, by arrangement 3 sterile universal containers (white top), labelled 1,2,3 2 hrs for microscopy 2 days for culture cell counts cannot be performed on clotted samples yes, by arrangement Ear swab Transport swab (blue top) 4 days none no Eye swab Transport swab (blue top) 4 days none no November 2012 Page 9 of 18 Department of Microbiology Investigation Test Sample (Volume) Container TAT Limitations Out-of-Hours Faeces Culture Microscopy & Culture Faeces (<20mls) Universal with spoon (blue top) 4 days clinical details are essential for processing no Fungal Culture Microscopy & Culture Skin, hair, nails none no Gonococcal Culture Culture Urethral swab Transport swab (orange top) 3 days transport delay may reduce sensitivity of test no Gonococcal Culture Culture Endocervical swab Transport swab (blue top) 3 days transport delay may reduce sensitivity of test no Gynaecological Culture Microscopy & Culture Endocervical swab Transport swab (blue top) 4 days clinical details are essential for processing no no 1 week for fungal culture kit / microscopy universal (white top) 4 weeks for culture Gynaecological Culture Microscopy & Culture Vaginal swab Transport swab (blue top) 4 days clinical details are essential for processing please send endocervical swab if gonococcal culture is required IV Cannulae Culture Culture End of cannula tip (2-5cm length) Universal (white top) 4 days none no Joint Fluid Culture Gram stain, Crystals & Culture Joint fluid (<20mls) Universal (white top) 4 days, plus 2 days for enrichment culture none yes, by arrangement Lavage Culture Gram stain & Culture Broncho-alveolar lavage (<20mls) Universal (white top) 4 days none no DCN: MIC-P-006-10.0 November 2012 Page 10 of 18 Department of Microbiology Investigation Test Sample (Volume) Container TAT Limitations Out-of-Hours Leg Ulcer Swab Culture Culture Leg ulcer swab Transport swab (blue top) 4 days routine swabbing is unnecessary unless there is indication of infection no Mouth Swab Culture Culture Mouth swab Transport swab (blue top) 4 days Culture directed to Candida sp. no MRSA Culture Culture for MRSA only Swab / urine Transport swab (blue top) / universal container 3 days Culture directed to MRSA only No MRSA PCR Rapid test for MRSA Swab Transport swab (red top) 2-4 hours Limited to Aldbourne patients and patients who have missed conventional tetsing No Neonatal Screen Culture Culture Swabs & gastric aspirate Transport swab (blue top) / universal container 4 days swabs from throat, umbilicus and ear no Nose Swab Culture Culture for Staph. aureus only Nose swab Transport swab (blue top) 4 days pernasal swabs are required for the isolation of Pertussis sp. no Parasitology Microscopy for Schistosomiasis Urine (<20mls) Universal (white top) 2 days Collection of urine between 10am and 2pm no Parasitology Microscopy Faeces (<20mls) Universal with spoon (blue top) 2 days none no Parasitology (Pinworm) Microscopy Sellotape slide Collection kits available from laboratory 2 days none no DCN: MIC-P-006-10.0 November 2012 Page 11 of 18 Department of Microbiology Investigation Test Sample (Volume) Container PD Fluid Culture Cell count, Gram stain & Culture Peritoneal dialysis fluid (<20mls) Universal (white top) 7 days none no TAT Limitations 4 days, plus 2 differential cell counts days for performed on raised enrichment WBC counts culture Out-of-Hours yes, by arrangement Pertussis Culture Culture Pernasal swab Pernasal swab (orange top) obtained from laboratory Pleural Fluid Culture Gram stain & Culture Pleural fluid (<20mls) Universal (white top) 4 days, plus 2 days for enrichment culture none yes, by arrangement Pus Culture Gram stain & Culture Pus (<20mls) Universal (white top) 4 days, plus 2 days for enrichment culture none yes, by arrangement Faeces (<20mls) Universal with spoon (blue top) 1 day limited to children <4years no Rotavirus Detection Antigen Detection Skin Swab Culture Culture Skin swab Transport swab (blue top) 4 days none no Sputum Culture Gram stain & Culture Sputum (<20mls) Universal (white top) 4 days samples should be collected early morning or after physio no TB Culture Culture Early Morning Urine (3x250mls) 250ml bottles obtained from laboratory 6 weeks no microscopy performed on urine TB samples no TB Culture Microscopy & Culture Sputum / BAL (<20mls) Universal (white top) 2 days for microscopy; 6 weeks for culture none no DCN: MIC-P-006-10.0 November 2012 Page 12 of 18 Department of Microbiology Sample (Volume) Container TAT Limitations Out-of-Hours Microscopy & Culture Tissue Universal (white top) 2 days for microscopy; 6 weeks for culture none no Teicoplanin Levels Antibiotic Assay Clotted blood (2-6mls) Vacutainer (red-top) 3 days Requests must be discussed with the Consultant Microbiologist no Throat Swab Culture Culture Throat swab Transport swab (blue top) 4 days Isolation of Neisseria sp only on request no Tissue Culture Gram stain & Culture Tissue Universal (white top) 4 days, plus 2 days for enrichment culture none yes, by arrangement Urine Culture Microscopy & Culture Urine (<20mls) Universal with boric acid (red top) 3 days none yes, by arrangement Urine Legionella Test Antigen Detection Urine (5-20mls) Universal (white top) <1 day please contact lab if urgent processing required Saturday and Sunday morning, by arrangement only Urine Pneumococcal Antigen Detection Test Urine (5-20mls) Universal (white top) <1 day please contact lab if urgent processing required Saturday and Sunday morning, by arrangement only Wound swab Transport swab (blue top) 4 days pus sample should be sent, if available no Investigation Test TB Culture Wound Swab Culture DCN: MIC-P-006-10.0 Culture November 2012 Page 13 of 18 Department of Microbiology VIROLOGY TESTS Investigation Test Sample Container TAT Limitations Out-of-Hours Antenatal Serology Antibody Detection Clotted blood (2-6mls) Vacutainer (red-top) 7 days requests for HIV test must be clearly indicated and signed no ASO Titres Antibody Detection Clotted blood (2-6mls) Vacutainer (red-top) 14 days clinical details are essential for processing no Broncho-alveolar lavage (<20mls) Universal (white top) 1 day please contact lab if urgent processing is required for PCP no Atypical Pneumonia Antigen Detection Atypical Serology Antibody Detection Clotted blood (2-6mls) Vacutainer (red-top) 14 days clinical details and date of onset are essential for processing no Bone Donor Screen Antigen & Antibody Detection Clotted blood (2-6mls) Vacutainer (red-top) 7 days clinical details are essential for processing no Cardiac Virus Serology Antibody Detection Clotted blood (2-6mls) Vacutainer (red-top) 14 days clinical details and date of onset are essential for processing no Cardiac Virus PCR DNA Detection by PCR EDTA sample (2-3mls) 14 days clinical details and date of onset are essential for processing no Chickenpox Serology Antibody Detection Clotted blood (2-6mls) Vacutainer (red-top) 1 day (urgent) 7 days (normal) please contact lab if urgent processing is required no CMV Serology Antibody Detection Clotted blood (2-6mls) Vacutainer (red-top) 14 days clinical details are essential for processing no DCN: MIC-P-006-10.0 Vacutainer (purple-top) November 2012 Page 14 of 18 Department of Microbiology Investigation Test Sample CMV PCR DNA Detection by PCR EDTA sample (2-3mls) Conjunctival DNA Detection by Chlamydia Infection PCR Container TAT Limitations Out-of-Hours Vacutainer (purple-top) 7 days clinical details are essential for processing no Conjunctival swab Chlamydia transport swab 1-2 days none no EBV Serology Antibody Detection Clotted blood (2-6mls) Vacutainer (red-top) 14 days clinical details are essential for processing no EBV PCR Antigen Detection EDTA sample (2-3mls) Vacutainer (purple-top) 7 days clinical details are essential for processing no Genital Chlamydia Infection DNA Detection by PCR Urine (<20mls) Universal (white top) 4 days patient should not have urinated for 2 hours prior to specimen collection no Genital Chlamydia Infection DNA Detection by PCR Endocervical swab Chlamydia transport swab 4 days none no Helicobacter Serology Antibody Detection Clotted blood (2-6mls) Vacutainer (red-top) 7 days clinical details are essential for processing no Hepatitis A Serology Antibody Detection Clotted blood (2-6mls) Vacutainer (red-top) 7 days clinical details are essential for processing, especially onset date no Hepatitis B Antibody Antibody Detection Clotted blood (2-6mls) Vacutainer (red-top) 7 days vaccination history required for full interpretation of result no DCN: MIC-P-006-10.0 November 2012 Page 15 of 18 Department of Microbiology Investigation Test Sample Container TAT Limitations Out-of-Hours Hepatitis B Core Antibody Antibody Detection Clotted blood (2-6mls) Vacutainer (red-top) 7 days clinical details are essential for processing no Hepatitis B Surface Antigen Antibody Detection Clotted blood (2-6mls) Vacutainer (red-top) 7 days requests must be clearly indicated and signed on the request form no Hepatitis B (DNA) Viral Load DNA Detection by PCR EDTA sample (2-3mls) Vacutainer (purple-top) 14 days clinical details are essential for processing no Hepatitis C Serology Antibody Detection Clotted blood (2-6mls) Vacutainer (red-top) 7 days requests must be clearly indicated and signed on the request form no Hepatitis C Viral Load / Genotype RNA Detection by PCR EDTA sample (2-3mls) Vacutainer (purple-top) 14 days clinical details are essential for processing no HIV Serology Antibody Detection Clotted blood (2-6mls) Vacutainer (red-top) 7days requests for HIV test must be clearly indicated and signed no HIV Viral Load DNA Detection by PCR EDTA sample (2-3mls) Vacutainer (purple-top) 10 days clinical details are essential for processing no HSV Serology Antibody Detection Clotted blood (2-6mls) Vacutainer (red-top) 14 days clinical details are essential for processing no Leptospira Serology Antibody Detection Clotted blood (2-6mls) Vacutainer (red-top) 10 days clinical details, date of onset and exposure history are essential for processing no DCN: MIC-P-006-10.0 November 2012 Page 16 of 18 Department of Microbiology Investigation Test Sample Container TAT Limitations Out-of-Hours Lymes Serology Antibody Detection Clotted blood (2-6mls) Vacutainer (red-top) 10 days clinical details, tick exposure and date of onset are essential for processing no Meningococcal PCR DNA Detection by PCR EDTA sample (2-3mls) 14 days clinical details are essential for processing no Parasite Serology Antibody Detection Clotted blood (2-6mls) Vacutainer (red-top) 14 days clinical details, date of onset and travel history are essential for processing no Parvovirus Serology Antibody Detection Clotted blood (2-6mls) Vacutainer (red-top) 14 days clinical details are essential for processing no Pneumococcal PCR DNA Detection by PCR EDTA sample (2-3mls) Vacutainer (purple-top) 14 days clinical details are essential for processing no RSV Detection Antigen Detection Nasopharyngeal aspirate (5-10mls) Trap bottle <1day none Saturday and Sunday morning, by arrangement only Rubella Serology Antibody Detection Clotted blood (2-6mls) Vacutainer (red-top) 7 days clinical details are essential for processing no Syphilis Serology Antibody Detection Clotted blood (2-6mls) Vacutainer (red-top) 7 days clinical details are essential for processing no Toxoplasma Serology Antibody Detection Clotted blood (2-6mls) Vacutainer (red-top) 7 days clinical details are essential for processing no DCN: MIC-P-006-10.0 Vacutainer (purple-top) November 2012 Page 17 of 18 Department of Microbiology Investigation Virus Detection Test Sample DNA Detection by Viral transport swab PCR DCN: MIC-P-006-10.0 Container TAT Limitations Out-of-Hours Transport swab (green top) 14 days clinical details are essential for processing no November 2012 Page 18 of 18