Microbiology and Virology User Handbook

Transcription

1 Please note; From July 4 th 2016, the microbiology laboratory at Lewisham hospital consolidated onto the Queen Elizabeth site. All microbiology samples from within the Lewisham and Greenwich NHS Trust, and all GP work from the Greenwich, Bexley and Lewisham boroughs will be analysed at the Queen Elizabeth site of the Lewisham and Greenwich NHS Trust from July 4 th. Subject Applicable to All Users of Lewisham and Greenwich NHS Trust Microbiology Services Date issued 4 th July, 2016 Next review date 4 th July, 2017 Author John Wright, Microbiology Quality Officer Owner Mick Brockwell, Microbiology Manager Approved by Breege Nicholson, Pathology Quality and Governance Manager Related documents Pathology General Information Handbook (PP-MP-009) Location of copies Master Q-Pulse 1 Microbiology Quality Management file 2 LGHT Intranet/internet Amendments on this SOP from previous version Updated to reflect the consolidation of LGT microbiology laboratories onto the QEW site. 3 Key personnel list updated to include Lewisham Microbiology clinicians 6.5 The department does not provide a service for seminal fluid analysis for infertility or post-vasectomy. 6.7 Revision of procedure for requesting additional tests 6.10 Contact number for South London HPT updated 7. Requirements for screening for resistant organisms revised. 7.1, 8.1, 9. Inclusion of reference ranges for tests where relevant 8. Virology and Molecular test repertoire revised Author John Wright Page 1 of 22

2 1. Introduction Key Personnel Opening Hours Core Opening Hours for the Laboratory are: Availability of Clinical Advice Urgent Requests Specimen Collection and Transport Specimen Requesting and Labelling Clinical Details Specimen Collection Specimen Transport Seminal Fluid Analysis for Infertility and Post-vasectomy Turnaround Times Requesting Additional Tests Telephoning of Results / Preliminary Results Antimicrobial Therapy and Prophylaxis Infection Prevention Virology Microbiology Test Repertoire References Ranges for Microbiology Tests Virology and Molecular Test Repertoire Reference Ranges for Virology and Molecular Tests Antimicrobial Drug Monitoring Test Repertoire Protection of Personal Information and Complaints Procedure Reference Laboratories Author John Wright Page 2 of 22

3 1. Introduction This handbook provides information about the services offered by the Microbiology laboratory at the Queen Elizabeth Hospital, Woolwich and has been compiled by the Medical and Scientific staff within Microbiology. We hope it enhances your knowledge of the services we provide and enables you to use them to their fullest potential. It has been our aim to set out in a clear and concise manner, and through consultation with you our users, guidance on how to obtain the maximum benefit from the different departmental services. The information contained within this guide is as accurate as possible but, as you will appreciate, new developments are occurring regularly. The department of microbiology at Queen Elizabeth hospital provides a comprehensive routine and specialised, diagnostic and clinical microbiology. This encompasses all aspects of microbial disease, bacterial, viral, fungal or parasitic, as well as infection prevention and control. The microbiology service is clinically based. The Critical Care Unit is usually attended on a daily basis and other patients are visited as appropriate. The Microbiologists will visit a ward to see patients, on request, and give advice on investigations and patient management. To take advantage of this service please telephone the Registrar or Consultants as detailed below. Clinical Advice on choice of investigations, interpretation of results, treatment and management of infection and infection control is available 24 hours a day, every day of the year. The quality of the service is monitored continuously by internal quality control and audit procedures and the department is fully accredited by Clinical Pathology Accreditation Ltd (CPA registration number 1015) and working towards ISO15189 accreditation. The department participates in all relevant, External Quality Assurance Schemes, where available, for the range of analytes measured. The configuration of laboratory services is under continuous review to encompass technical and analytical advances; including electronic requesting and reporting and automated analysers interfacing directly with the laboratory IT systems. This handbook is to be used in conjunction with the Pathology User Handbook which has details of Collecting samples, requesting and labelling of samples, transport of samples and Viewing the results. Please note; From July 4 th 2016, the microbiology laboratory at Lewisham hospital consolidated onto the Queen Elizabeth site. All microbiology samples from within the Lewisham and Greenwich NHS Trust, and all GP work from the Greenwich, Bexley and Lewisham boroughs will be analysed at the Queen Elizabeth site of the Lewisham and Greenwich NHS Trust from July 4 th. Author John Wright Page 3 of 22

4 2. Key Personnel Contact Telephone Base Dr Tacim Karadag Head of Department Consultant 3264 Microbiologist Dr Martino Dall Antonia Lead Consultant Microbiologist QEW Dr Juliet Uwagwu Consultant Microbiologist Dr Sarah Starkey Consultant Microbiologist Dr Geraldine Fernando Consultant Microbiologist Dr Sarjana Jain Consultant Microbiologist Microbiology Specialist Registrar Mick Brockwell Laboratory Manager Lewisham Queen Elizabeth Queen Elizabeth Queen Elizabeth Lewisham Lewisham Queen Elizabeth Queen Elizabeth Laboratory Enquiries Telephone ext. Results and General Enquiries 5738 Bacteriology/Mycology 5692 Virology/Serology/Molecular Opening Hours 3.1 Core Opening Hours for the Laboratory are: to (Monday to Friday) to (Saturday/Sunday/Bank Holidays) An emergency only service is available outside these hours. 3.2 Availability of Clinical Advice Clinical advice concerning the interpretation of results or management of patients and antimicrobial use is available to Monday to Friday. Author John Wright Page 4 of 22

5 Outside of these times an on-call Consultant Microbiologist can be contacted via the switchboard. 4. Urgent Requests To request an urgent investigation during normal working hours please telephone extension 5695 for Virology/Serology and extension 5692 for Microbiology. Outside routine working hours for all requests telephone extension 5692 or bleep 270. After midnight, please do not make contact until the specimen has been collected. Some requests may be referred to a Clinical Microbiologist before the laboratory will proceed. Please ensure that only genuinely urgent tests are requested in this way, otherwise routine working will be disrupted and results delayed. Tests which have not been requested as urgent by telephone may not be processed urgently. Please ensure that you give adequate contact information in order that the result can be provided as soon as it is available. The following tests may be requested urgently: Microscopy and culture Acid fast bacilli Antigen detection Viral serology Cerebro-spinal fluid (CSF) and other normally sterile body fluids e.g. pleural, joint, ascites Tissue and surgically drained pus and other aspirates Bronchial washings and NBL Urine Sputum and other appropriate specimens Urine for legionella and pneumococcal antigen Nasopharngeal aspirate for RSV HIV, Hepatitis B and C serology if clinically indicated. Following a needlestick injury: HIV, Hepatitis C and Hepatitis B status tested for the donor, and Hepatitis B immunity checked for the recipient and Hepatitis C RNA should the donor be positive. VZV IgG following chickenpox contact in pregnancy or if patient immuno-compromised. Gentamicin and vancomycin assays are performed in the Blood Sciences Department, and they should be contacted directly. Samples for other antibiotic assays, e.g. amikacin, tobramycin, should be collected as early as possible in the day to allow time for the sample(s) to be dispatched to a referral laboratory. Author John Wright Page 5 of 22

6 Blood cultures are processed automatically throughout the day every day and evening. The duty Clinical Microbiologist is informed of all positive cultures for assessment and further action. 5. Specimen Collection and Transport 5.1 Specimen Requesting and Labelling Please refer to the Pathology General Information Handbook for full details of specimen requesting and labelling requirements. In addition to these instructions, it is important for result interpretation in Microbiology that the site and nature of a specimen is adequately documented. For example, simply stating "wound" does not provide sufficient information, please be specific. 5.2 Clinical Details Requests for Microbiology and Virology tests must be accompanied by a request form, including icare requests. Supplying relevant clinical details and medical history is essential to ensure that all relevant investigations are performed and the significance of results can be assessed. Simply stating "unwell" may result in essential investigations not being carried out. Relevant clinical information may include: Date of onset and duration of illness Antimicrobial therapy Travel history (stating countries visited) Post-operative (please give details of operation) Pyrexial, septic, shock, raised WBC count Diarrhoea, weight loss Renal impairment Diabetes Productive/dry cough 5.3 Specimen Collection The best results are obtained when an appropriate, well taken specimen, in the correct specimen container, is delivered to the laboratory promptly. Sterile containers must be used for microbiology requests. Specimens should be collected before antimicrobial agents have been administered whenever possible. An adequate quantity of material should be collected for the examination required. Always send pus if available rather than a swab that has been immersed in pus, as the former is better for the preservation of anaerobes. If the Author John Wright Page 6 of 22

7 Pathology Department sample has been aspirated, it must be sent in a universal container, not in a syringe. Specimens should be collected from an appropriate site and, if relevant, at an appropriate time. Care must be taken to avoid contamination of specimens by normal flora from skin or alimentary tract. Sterile equipment and aseptic technique must be used when collecting specimens, in particular for those sites that are normally sterile. Specimens must be collected using the appropriate container as stated in Sections 6,7and 8 of this handbook. 5.4 Specimen Transport Please refer to Pathology General Information Handbook for full details of specimen transport arrangements for microbiology specimens. All sample containers must be properly closed and packed in the airtight polythene bag supplied, with the request form/flimsy in the attached unsealed pouch. Samples from different patients must be sent in separate bags. If more than one patient s samples are received in a single bag, or samples have been sent with another patient s request form (however generated), they will be rejected for analysis. Specimens must be transported to the laboratory as soon as possible after collection. Blood and urine samples that cannot be transported on the day of collection must be refrigerated at 4-8 O C overnight. They may not be suitable for processing if left in a refrigerator over a weekend. Swabs can be kept at room temperature (providing the temperature is monitored), but again should be transported to the laboratory within 24 hours of collection. Normally sterile body fluid specimens (e.g. CSF) must be transported to the laboratory promptly after collection. Specimens collected within the hospital should be sent to the laboratory using the pneumatic tube system with the exception of: o CSF o Blood Cultures o Respiratory tract specimens (Sputum, bronchial washings, NBL) and any other specimen patient where a mycobacterial infection is suspected o Specimens from patient with known or suspected arbovirus, viral haemorrhagic fever infection e.g. Ebola virus, or with emerging infectious diseases Author John Wright Page 7 of 22

8 5.5 Seminal Fluid Analysis for Infertility and Post-vasectomy This service is not provided by the Pathology Department of Lewisham and Greenwich NHS Trust. Patients should refer to their GP practice and/or hospital Consultant with regards to the services available for these investigations. 5.6 Turnaround Times These vary according to the type of specimen, tests requested, whether results are negative or positive and require confirmation, the complexity of the findings, the time required for organisms isolated to grow and whether the test is a "one off" or done as a batch (more common with virology and molecular tests). As in all laboratories, more highly specialised investigations are referred on to national reference laboratories for processing (listed in Section 10 of this handbook). For some tests, e.g. ASOT and toxoplasma, a screening test is done locally to identify samples that warrant referral for further more detailed investigation. For others, e.g. HIV, a national reference centre must confirm local test results. In these situations, care must be taken as to what the patient is told about the initial unconfirmed result pending a definitive answer. 5.7 Requesting Additional Tests Most requests for microbiology investigation are best performed on a fresh specimen, however a number of specimen types (except urine for culture) are stored under temperature controlled conditions for 7 days after receipt. Blood specimens are stored frozen for up to 2 years after collection, depending on patient category. Any additional investigations must be communicated by telephone to the relevant laboratory: for Bacteriology tests ext for Virology and Molecular tests ext Requests may be referred to the microbiology clinical team to discuss clinical aspects and/or the suitability of the specimen for further investigation. Additional tests must be requested electronically by users of icare and tquest systems or with a request form for all other users. Additional tests can be performed on the following specimens within the stated time frames: Specimen type Urine Swabs Sputum and other lower respiratory specimens Faeces Sterile fluids Serum Time limit from collection 24 hr 48 hr 24 hr 48 hr 1 week Antenatal and needlestick specimens 2 years Other blood specimens 1 year. Author John Wright Page 8 of 22

9 Please note, due to the instability of bacteria over time and the processing required for some specimens, requesting culture for additional organisms may not be possible. Wherever possible a repeat sample should be collected. 5.8 Telephoning of Results / Preliminary Results Some results e.g. those which require interpretation, will be telephoned by the Medical Microbiologist to the requesting clinician or team. Similarly, results which indicate acute severe infection, e.g. positive blood culture or CSF, requiring prompt treatment or a change of management will be telephoned to the appropriate person. Other, less clinically urgent reports may contain a comment providing appropriate advice. Preliminary culture results, if significant, will be available on icare, Review or alternative primary care reporting systems following authorisation and usually within 24 hours of initial specimen processing. 5.9 Antimicrobial Therapy and Prophylaxis There is a useful four page summary of Treatment and Prophylaxis at the beginning of the Infection Section of the British National Formulary. The antimicrobial prescribing policy for Lewisham and Greenwich NHS Trust (LGHT) is provided on the LGHT intranet/internet and as a booklet available from the laboratory. Further information and advice is available from the Pharmacy Department, or a Consultant Microbiologist. If you are in doubt or your patient's condition is complicated please do not hesitate to CONTACT A CLINICAL MICROBIOLOGIST. Refer to Section 8 of this handbook for a list of antimicrobial drug monitoring tests available Infection Prevention Notification of Infectious Diseases Infectious disease, including Mycobacterium tuberculosis, must be notified by the clinician caring for the patient by completion of an electronic Infectious Disease Notification form, currently located on the Policies menu of the SHLT legacy intranet. These forms are London Borough specific and must be ed to the address provided. The Microbiology Department will in addition notify cases of enteric fever, meningitis etc. which are CULTURE POSITIVE, but we cannot notify SUSPECTED CASES. The clinician caring for the patient must also inform the South London Health Protection Team by telephone on if there is a serious risk of cross infection which needs urgent attention in the community, e.g. cases of meningococcal meningitis. The Hospital Infection Prevention Team must also be informed of such cases Infection Prevention and Control Policies Author John Wright Page 9 of 22

10 Trust policies and procedures are available on the LGHT intranet in relation to Infection prevention and control. Contact the Infection Prevention and Control team or Consultant Microbiologist for advice Needle-stick Injuries and Other Occupational Health Issues Please inform Occupational Health as soon as possible if you have an infectious disease which you believe may be hazardous to other patients. e.g. chicken pox; sore throats; diarrhoea etc. A Safeguard incident report form should be completed for all injuries acquired through work, especially for those caused by needlesticks/sharps. Please refer to LGHT intranet for Trust Inoculation, Needlestick and Sharps Policy. All appropriate staff should have been vaccinated against Hepatitis B and be aware of their immune status. A specimen of clotted blood is required from the RECIPIENT for SERUM STORAGE, and when appropriate, re-testing of hepatitis antibody levels. A specimen of clotted blood is required from the DONOR for testing for bloodborne viruses Virology Paired Sera Paired sera should be collected to diagnose certain infections, e.g. atypical pneumonia etc, as a measurable rise in antibody level is diagnostic. Please send an acute serum, clearly stating date of onset and a further convalescent specimen days after onset. Please refer to the accession number of the acute specimen when sending the convalescent specimen. A clotted blood sample should be taken. Acute sera will not routinely be tested on their own. Please contact the department should you require advice about which infections require the taking of paired sera, or if you wish for acute serum samples to be tested without the accompanying convalescent specimen Special Samples Samples requiring molecular detection of pathogens may require special transport media or collection requirements. Please refer to the Virology and Molecular test Repertoire section and if in doubt contact the laboratory for advice before taking the sample. For virus antigen detection, e.g. RSV, a minimum specimen volume of 0.5ml is required. Author John Wright Page 10 of 22

11 6. Microbiology Test Repertoire Sample/ Investigation Sample Requirements/Comments Turnaround Times* Antral washings Sterile universal container. Gram stain and Microscopy <24 hr culture performed. Culture 48 hr Ascitic/Peritoneal fluid Sterile universal container. Gram stain, neutrophil count and culture performed. Microscopy <24 hr Culture 48 hr Blood culture Adult set: Aerobic (blue top) and Anaerobic (gold top) bottles. Blood volume: 8-10ml Paediatric: Silver top bottle. Blood volume 1-3ml. Instructions and a butterfly needle for blood collection are provided with each set. Preliminary report 48 hr Final report 5 days Biopsy Sterile universal container. A small volume of Microscopy <24 hr sterile saline may be added if a small Direct culture 48 hr amount of tissue collected. Gram stain and Enrichment 5 days culture performed. These samples should be collected in a Bronchial washings specimen trap using suction apparatus. AFB Microscopy <24 hr stain and TB culture will be performed in Culture 48 hr addition to Gram stain and routine culture. Ideally 2-3ml in each of three sterile universal containers labelled 1, 2 and 3. Gram stain, cell count and culture Cerebro-spinal fluid Microscopy<24 hr performed. Further investigations for viral/tb (CSF) Culture 48 hr infection or other pathogens may be undertaken based on clinical information provided and cell count. Sterile swab in transport medium (Amies) for culture for gonococci and for investigation of Cervical swab PID. For molecular detection of chlamydia Microscopy <24 hr and gonococcal infections an endocervical Culture 48hr swab must be taken using a collection kit (available from the laboratory). Cough swab Sterile swab in transport medium (Amies). Cystic fibrosis patients. Culture 5 days Ear swab Sterile swab in transport medium (Amies). Culture 48 hr Eye swab Sterile swab in transport medium (Amies). If chlamydia or gonococcal infection suspected and additional conjunctival swab must be taken using a ProbeTec collection kit (available from the laboratory). Culture 48 hr Author John Wright Page 11 of 22

12 Sample/ Investigation Faeces Faeces (Clostridium difficile) Faeces (Helicobacter antigen) Fungal culture for dermatophytes High vaginal swab Intra-uterine contraceptive device Joint fluids Legionella/ Pneumococcal antigen Intravascular lines, tips and drains Nasal swab Pernasal swab Placental swabs /Bartholins abscess Sample Requirements/Comments Sterile universal container with spatula (blue top). Include any mucus, pus or blood present in the sample. Rectal swabs generally unsuitable. Routine culture performed for salmonella, shigella, campylobacter and E. coli O157. Additional investigations may be performed based on clinical information provided and age of patient e.g. foreign travel. Microscopy for ova, cysts and parasites should be requested if required. Sterile universal container with spatula (blue top). Note that this test will only be performed on Bristol stool types 5, 6 and 7. Sterile universal container with spatula (blue top). Skin scrapings, nails, hair samples collected using a Dermapak envelopes or equivalent or into a sterile universal container. A swab in transport medium required if candida suspected. Sterile swab in transport medium (Amies). For candida, trichomonas, bacterial vaginosis, routine culture. Sterile universal container. Direct microscopy for actinomyces and culture. Sterile universal container. Gram stain, routine culture and microscopy for crystals performed. Urine in sterile universal container. Aseptically place tip into a sterile universal container. Note: urinary catheters are unsuitable for culture. Sterile swab in transport medium (Amies). Post-nasal swab indicated for detection of staphylococcal or meningococcal carriage. Sterile pernasal swab in transport medium (fine wire swab) supplied by laboratory. For isolation of Bordetella pertussis (whooping cough). Sterile swab in transport medium (Amies). Collect maternal and foetal side swabs. Routine and gonococcal culture performed. Turnaround Times* Microscopy 1-5 Culture 3 Significant bacterial isolates are referred for speciation and typing 7, with a TAT of days depending on testing required. If required parasites are referred 16 for confirmation of identification with a TAT of 24 hr. <24 hrs 1-3 days Microscopy 1-2 days Culture 2 weeks Microscopy <24hr Culture 48hr Microscopy <24 hrs Culture 2 weeks Microscopy <24 hr Culture 48 hr <4 hrs Culture 48 hr Culture 48 hr 7 days Culture 48 hr Author John Wright Page 12 of 22

13 Sample/ Investigation Pleural fluid Pus Screening swabs (MRSA, VRE, CRE, ESBL, Multiresistant Acinetobacter) Sample Requirements/Comments Sterile universal container. AFB stain and TB culture will be performed in addition to Gram stain and routine culture. Aspirate with a sterile syringe into a sterile universal container. A sample of pus always preferable to a pus swab. Sterile swabs in transport medium (Amies) together with any other relevant sites e.g. urine, sputum, lines, fluids. MRSA: Admission screen: nose, throat and groin. Ward/Bay screen: nose, throat, groin and any suspect sites. Note: groin NOT perineum is the preferred site. Repeat swabs from positive sitesfor clearance. CRE: Rectal swab required. ESBL: Requests for neonates >2 days old will also be screened for other potential pathogens. Ciprofloxacin/Gentamicin resistant organisms: Rectal swab and urine required. Turnaround Times* Microscopy <24 hr Culture 48 hr Microscopy <24 hr Direct culture 48 hr Enrichment 7 days Culture 24 hr Screening swabs (Neonatal) Schistosomiasis (Bilharzia) Skin swab Sputum Ticks and lice Tissues Sterile swabs in transport medium (Amies). Ear, nose, umbilicus. Routine screen if <=2 days, ESBL screen if >=3 days old. It is preferable to collect the total urine produced between the hours of 10 am and 2 pm as it has been shown that the maximum concentration of eggs are excreted during this period. Please obtain a plain 24 hour urine container and instructions from Pathology Reception for this purpose. The specimen must be taken to Pathology on the day of collection and preferably within 1 hour. Sterile swabs in transport medium (Amies). Nappy rash, eczema, impetigo, paronychia. Sterile universal container. Gram stain and routine culture performed. If mycobacterial culture required send 3 consecutive early morning samples. Sterile universal container. Specimen will be referred if cannot be identified in-house Sterile universal container. Gram stain and routine culture performed. Culture 24 hr 1-2 hrs Culture 48 hr Threadworm Sellotape slide collected from perianal area. <24 hr Microscopy <24hr Culture 48 hr Microscopy <24 hr Direct culture 48 hr Enrichment 7 days Author John Wright Page 13 of 22

14 Sample/ Investigation Sample Requirements/Comments Turnaround Times* Throat swab Sterile swab in transport medium (Amies). Culture 48 hr Appropriate sample depends on site of AFB stain infection: 3 consecutive early morning <24 hr (respiratory Mycobacteria sputum or urine samples, bronchial washing, samples) 48 hr (other culture pus, tissue. Blood culture bottles for samples) mycobacteria are available from the Culture 6 weeks. laboratory. Sterile plain universal container. Preferred Urine (MSU) sample for diagnosis of urinary tract Urine (CSU) Urine (supra pubic aspirate) Urine (ureteric) Urethral swab infection. Sterile universal container. Routine culture rarely indicated for patients with long term catheters. Sterile universal container. Preferred sample for very young children. Sterile universal container Sterile swab in transport medium (Amies). If chlamydia or gonococcal infection suspected and additional swab must be taken using a collection kit (available from the laboratory). Microscopy <24 hr Culture 24 hr Microscopy <24 hr Culture 48hr Wound swabs Sterile swab in transport medium (Amies) Culture 48 hr This list is not exhaustive, please contact the laboratory if further information required. Swabs and specimen containers are available from the central stores at Queen Elizabeth Hospital, unless otherwise stated. Swabs and specimen containers are available from the pathology stores at Lewisham hospital. *Turnaround times are for negative cultures from receipt in the laboratory to issue of the final report (confirmation of significant cultures may require more time). 6.1 References Ranges for Microbiology Tests Urine Microscopy Analyte WBC >50 RBC >10 Organisms >200 Abnormal Result (Units x10 3 /ml) Author John Wright Page 14 of 22

15 7. Virology and Molecular Test Repertoire Investigation Sample Requirements/Comments (All tests require 6 ml BUFF top clotted blood sample unless otherwise stated) Adenovirus Faeces <24 hr Adenovirus DNA 4 ml blood MAUVE top EDTA, any respiratory specimen, CSF, eye, throat swabs in viral 48 hr transport medium. Referred test 11 Amoebic antibody Referred test 15 <2 Turnaround Times (working days) Anthrax PCR Referred test hr urgent 1-2 request Anti-streptolysin O (ASOT) Arbovirus and Viral Haemorrhagic Fevers including Ebola PCR Aspergillus antigen (Galactomannan) Bordetella pertussis serology & PCR Borrelia antibody (Lyme disease) Positive tests referred 8 for confirmatory testing 5 (14 if confirmation required) Referred tests hr urgent requests Referred test Referred test 8 (in patients only) Note: a pernasal swab or nasopharyngeal aspirate required for PCR and test only available for children <12 months old. Referred test 17 4 Brucella antibody Referred test 3 5 Candida antibody Referred test Candida antigen Referred test Chlamydia trachomatis/ Neisseria gonorrhoeae DNA Endocervix, urethral, rectal, eye swabs, urine Only use the collection kits supplied by the laboratory. Coxiella antibody Referred test 9 14 CMV DNA Urine, 4 ml blood MAUVE top EDTA. Referred test 11 CMV IgG and IgM 5 Cryptococcus antigen Referred test 13 1 Cysticercosis antibody CSF or serum. Referred test hr Diphtheria immunity Referred test 8 21 unless urgent EBV (EBNA IgG, VCA-IgG, VCA IgM) Enterovirus IgM Referred test Author John Wright Page 15 of 22

16 Investigation Enterovirus RNA Sample Requirements/Comments (All tests require 6 ml BUFF top clotted blood sample unless otherwise stated) CSF, swab, faeces. 4ml blood MAUVE top EDTA may be useful in suspected meningitis cases 11 Fasciola antibody Referred test Filaria antibody Referred test Hepatitis A IgG, IgM 5 Hepatitis B markers (HBs antibody, HBs antigen, core antibody, core IgM, HBe antigen, anti-hbe) Hepatitis B DNA 4ml blood MAUVE top EDTA 5 Hepatitis C antibody 5 Turnaround Times (working days) 24 hr Hepatitis C RNA 4ml blood MAUVE top EDTA, referred test hr Hepatitis D IgG (delta virus) 5 Hepatitis D IgM Referred test 21 Contact laboratory Hepatitis E IgG Referred test 21 8 Herpes simplex DNA CSF, vesicle fluid, genital, skin, eye swabs collected in viral transport medium. Genital and 1-7 skin specimen tested in-house all others referred 11 Histoplasma antibody Referred test 13 Contact laboratory HIV Ag-Ab 5 HIV-1 proviral DNA Referred test 21 8 HIV resistance test 4ml blood MAUVE top EDTA. Referred test HIV RNA viral load 2 x 4ml or 1 x 6ml blood MAUVE top EDTA 5 HIV TDM 6ml blood GREEN top Li heparin must be separated within 4 hrs of collection. Referred test 6. HTLV antibody Referred test 21 8 Hydatid serology CSF or serum. Referred test Influenza A & B antigen Nasopharyngeal aspirate <4 hrs Influenza antibody Referred test 9 14 Influenza A & B PCR Nasopharyngeal aspirate, Nose or throat swabs collected into viral transport medium. Referred test Legionella antigen Urine <4 hrs Leishmania antibody Referred test 15 6 Leptospira antibody Referred test Measles IgG, IgM 5 5 Author John Wright Page 16 of 22

17 Investigation Sample Requirements/Comments (All tests require 6 ml BUFF top clotted blood sample unless otherwise stated) Measles IgM Referred test Meningococcal and CSF, 4 ml blood MAUVE top EDTA. Referred Pneumococcal PCR test hr Mumps IgG 5 Mumps IgM Referred test Mycoplasma IgM Referred test 9 2 Turnaround Times (working days) Norovirus PCR Faeces 48 hr, same day if urgent or an outbreak Parvovirus B19 IgG, IgM 5 Pneumococcal antigen Urine <4 hrs Pneumocystis DNA Referred test hr Poliovirus antibodies Referred test 21 Contact laboratory Psittacosis antibody Referred test 9 14 Rabies virus Referred test 21 Contact laboratory Rickettsia antibodies Referred test Rotavirus Faeces <24 hrs RSV antigen Nasopharyngeal aspirate <4 hrs Rubella IgG, IgM 5 Schistosoma antibody CSF or serum. Referred test 15 7 Staphylococcal antibodies Referred test 2 12 Strongyloides antibody Referred test 15 7 Syphilis (RPR, TPPA, total antibody, IgM) T-Spot test for detection of latent TB Syphilis serology may also be performed on CSF if clinically indicated Referred test 14 by pre-arrangement with Consultant Microbiologist only. 6ml GREEN top Lithium heparin x 2 Toxocara antibody Referred test 15 7 Toxoplasma screen Positive screens referred for confirmation 5 Toxoplasma Dye test and IgM Referred test 18 7 Trichinella antibody Referred test 15 5 Trypanosomal antibody Referred test Varicella zoster IgG 5 Varicella zoster IgM Referred test Varicella zoster DNA Blood, CSF, vesicle fluid, swabs from lesions, skin, eye, endocervix, vulva, vagina, or penis in 5 48 hr 24 hr Author John Wright Page 17 of 22

18 Investigation Sample Requirements/Comments (All tests require 6 ml BUFF top clotted blood sample unless otherwise stated) viral transport medium 11 Yersinia antibody Referred test S rrna bacterial gene Any specimen preferably from normally sterile sites. Referred test 11 3 Turnaround Times (working days) These lists are not exhaustive, please contact the laboratory if further information required. Turnaround times for referred tests do not include specimen transit times. 7.1 Reference Ranges for Virology and Molecular Tests Included on patient report. 8. Antimicrobial Drug Monitoring Test Repertoire Investigation Amikacin Sample Requirements/Comments (All tests require 6 ml BUFF top clotted blood) Assayed by Blood Sciences Dept. Lewisham Turnaround Times (working days) < 6 hr Hospital Colistin Referred test hr Fluconazole Referred test hr Flucytosine Referred test hr Gentamicin Assay by Blood Science Department QEW Itraconazole Referred test 13 3 Posaconazole Referred test 13 3 Rifampicin Referred test 23 * Streptomycin Referred test 23 * Teicoplanin Referred test 23 * Tobramycin Referred test 23 * < 4 hr Vancomycin Assayed by Blood Science Department QEW <4 hr Voriconazle Referred test hr These lists are not exhaustive, please contact the laboratory if further information required. Turnaround times for referred tests do not include specimen transit times. *Results will be telephoned on the day of receipt for samples received between 9 am and 3 pm Monday to Friday and by am on a Saturday. 9. Protection of Personal Information and Complaints Procedure Please refer to the Pathology General Information Handbook. Author John Wright Page 18 of 22

19 10. Reference Laboratories Laboratory Address Service Details Anaerobe Reference Laboratory Antibiotic Resistance and Healthcare Associated Infections Reference Unit (ARMRHAI) Brucella Reference Unit (BRU) Clostridium difficile Ribotyping Service for London Region Cryptosporidium Reference Laboratory (CRL) 6 Lab21 Ltd 7 Gastrointestinal Bacteria Reference Unit (GBRU) NPHS Microbiology Cardiff University Hospital of Wales Heath Park Cardiff CF14 4XW Tel: Public Health England (PHE) 61 Colindale Avenue London NW9 5EQ Tel: Clinical Microbiology and PHE Collaborating Laboratory University Hospital Aintree Lower Lane, Liverpool L9 7AL Tel: PHE Collaborating Centre at UCL Hospitals NHS Trust Department of Microbiology 1st Floor, Windeyer Institute of Medical Sciences 46 Cleveland St, London W1T 4JF Singleton Hospital Sgeti Swansea, SA2 8QA Tel: Cambridge Science Park Cambridge CB4 0GA Tel: Public Health England (PHE) 61 Colindale Avenue London NW9 5EQ Tel: Anaerobe identification and susceptibility testing Detection and investigation of antibiotic resistance Serological diagnosis of Brucella infection Clostridium difficile ribotyping Differential diagnosis and confirmation of referred isolates of Cryptosporidium Genito-urinary medicine TDM tests Identification and typing of Salmonella, Shigella, Campylobacter, Esch. coli, Yersinia, Vibrios & Helicobacter Author John Wright Page 19 of 22

20 Laboratory Address Service Details Respiratory and Vaccine Preventable Bacterial Reference Unit (RVPBRU) London South Specialist Virology Centre Meningococcal Reference Unit (MenRU) 11 Micropathology Ltd 12 Mycobacterium Reference Unit Public Health England (PHE) 61 Colindale Avenue London NW9 5EQ Tel: Viapath Kings College Hospital 2nd Floor Cheyne Wing Bessemer Road, London SE5 9RS Tel: Clinical Science Building 2 Manchester Royal Infirmary Oxford Road, Manchester M13 9WL Tel: University of Warwick Science Park Venture Centre Sir William Lyons Road Coventry CV4 7EZ Tel: Clinical Sciences Research Centre Centre for Infectious Disease Institute of Cell and Molecular Science (ICMS) Barts and The London Queen Mary's School of Medicine and Dentistry 2 Newark Street London E1 2AT Tel: Phenotypic and molecular epidemiological typing of bacteria causing respiratory, systemic and vaccine preventable infections Serological and/or molecular diagnosis of viral infection Isolate characterisation antigen and DNA detection and serodiagnosis Viral and bacterial pathogen molecular diagnosis Identification, genotyping Molecular diagnosis for rapid species identification and detection of resistance genes Drug susceptibility Molecular epidemiological studies Author John Wright Page 20 of 22

21 13 Laboratory Address Service Details Mycology Reference Laboratory PHE South West Laboratory Myrtle Road Kingsdown Bristol BS2 8EL Tel: Identification, serological diagnosis and drug susceptibility testing of yeast and other pathogenic fungi Oxford Diagnostic Laboratories Parasitology Reference Laboratory (PRL) Sexually Transmitted Bacteria Reference Unit (STBRU) Rare and Imported Pathogens Laboratory (RIPL) Toxoplasma Reference Laboratory (TRL) 19 Virology Department 94c Innovation Drive Milton Park Abingdon Oxfordshire OX14 4RY Tel: Department of Clinical Parasitology Hospital for Tropical Diseases Mortimer Market, Capper Street London, WC1E 6AU Tel: Public Health England (PHE) Centre for Infections 61 Colindale Avenue London NW9 5EQ Tel: Public Health England (PHE) Porton Down, Salisbury, Wiltshire SP4 0JG Tel: Singleton Hospital Sgeti, Swansea SA2 8QA Tel: Epsom and St Helier University Hospitals NHS Trust West Park Laboratory Horton Lane, Epsom Surrey KT19 8PB Tel: T-Spot for detection of latent TB Microscopic and serological diagnosis of parasitic and amoebic infections Identification, typing, serological and molecular diagnosis of sexually transmitted bacterial pathogens Diagnostic service for Arboviruses, Haemorrhagic Fever viruses, Rickettsiae, anthrax, Borrelia (Lyme Disease) Serological diagnosis of human leptospirosis and isolation of leptospires from clinical material Serological and molecular diagnosis of Toxoplasma infection Serological and molecular diagnosis of Enterovirus and Varicella zoster virus infection Author John Wright Page 21 of 22

22 Laboratory Address Service Details 20 Virology Department 21 Virus Reference Department (VRD) 22 Virology Laboratories Antimicrobial Reference Laboratory London School of Hygiene and Tropical Medicine Barts and Royal London Hospital 3rd Floor Pathology and Pharmacy Building, 80 Newark St. London E1 2ES Tel: Public Health England (PHE) 61 Colindale Avenue London NW9 5EQ Tel: Clinical Microbiology and Virology University College London Hospital 60 Whitfield St. London W1T 4EU Tel: Dept. of Medical Microbiology North Bristol NHS Trust Southmead Bristol BS10 5NB Tel: /5654 Keppel St Bloomsbury London WC1E 7HT Tel: Influenza A & B molecular screening Pertussis PCR Serological and/or molecular diagnosis of viral infection, including hepatitis and retroviruses HIV resistance testing Antimicrobial drug monitoring Identification of ticks and lice Author John Wright Page 22 of 22