Scottish Bacterial Sexually Transmitted Infections Reference Laboratory (SBSTIRL) User Manual Jan 2018

Transcription

1 Scottish Bacterial Sexually Transmitted Infections Reference Laboratory (SBSTIRL) User Manual Jan 2018 Page 1

2 Contents 1 Introduction Page 3 2 Contact details Page 4 3 Opening hours Page 4 4 Services provided Page 5 5 Samples Page 7 6 Results and turnaround times Page 9 7 Quality aspects Page 9 8 Request forms Page Page 2

3 Introduction The Scottish Bacterial Sexually Transmitted Infections Reference Laboratory (SBSTIRL) is commissioned by National Services Scotland (NSS) to provide a national reference service for the management of bacterial sexually transmitted infections throughout Scotland. It is located in the Department of Laboratory Medicine at the Royal Infirmary of Edinburgh, NHS Lothian and is accredited by the Clinical Pathology Accreditation (UK) Ltd. This User Manual describes the services provided by SBSTIRL, how to send samples to the laboratory and how to contact the laboratory. This Manual is intended for use by healthcare professionals working in Scotland accessing SBSTIRL s services. It is not intended for use by patients. Page 3

4 Contact details Postal address Scottish Bacterial STI Reference Laboratory (SBSTIRL) Microbiology Royal Infirmary of Edinburgh 51 Little France Crescent Edinburgh EH16 4SA HaysDX address DX , Edinburgh 96EH Office phone number Generic address NHS Lothian Department of Laboratory Medicine website Fax number We do not accept or send faxes. Staff contact details Dr Kate Templeton Director Dr Ewan Olson Medical lead Dr Kate Cuschieri R&D lead Dr Jill Shepherd Clinical Scientist Ms Anne-Marie Logue Administrator Opening hours Core working hours are Monday to Friday 09:00 to 17:00. The laboratory is not open on weekends or NHS Lothian public holidays. Page 4

5 Services provided The following services are provided for referred isolates of presumptive Neisseria gonorrhoeae: Identification of problem isolates Antibiotic resistance surveillance Molecular typing of gonococci by Neisseria gonorrhoeae multi-antigen sequence typing (NG-MAST) and, where appropriate, by other methods Characterisation of medico-legal isolates Identification of N. gonorrhoeae by nucleic acid amplification test (NAAT) for non-viable isolates. The following tests are performed on clinical specimens: Supplemental NAAT for N. gonorrhoeae (GC NAAT) NG-MAST on GC NAAT positive specimens Real-time PCR for Lymphogranuloma venereum (LGV) on Chlamydia-positive samples from cases of suspected LGV Detection of macrolide and quinolone resistance by sequencing in Mycoplasma genitalium-pcr positive samples The SBSTIRL also provides these general services: Clinical and microbiological advice Assessment and development of new methodologies Participation in national/international surveillance and quality assurance projects Education, training, audit and collaborative research Maintenance of isolate and sample archive to facilitate research and service development Please note that Treponema pallidum testing, either by serology or PCR is NOT part of the reference laboratory service. However, we are happy to provide general advice to laboratories regarding testing methodology. Tests N. gonorrhoeae susceptibility testing Susceptibility to 7 antibiotics (Azithromycin, Ceftriaxone, Cefixime, Penicillin, Ciprofloxacin, Spectinomycin and Tetracycline) is determined. EUCAST breakpoints are used. Supplemental NAAT for N. gonorrhoeae A second test that targets a different specific gene is required to ensure a true positive GC result. We provide alternative assays to ensure that whatever the first GC NAAT used at your laboratory, there will be a suitable second test available for supplemental testing. The assay currently in use is an in-house PCR which targets Page 5

6 the PorA pseudogene and the 16s rrna gene. This service is currently under review. Any changes made will communicated to all users. NG-MAST sequence typing A proportion of cultured isolate and NAAT positive specimens are selected for sequence typing by Sanger sequencing. LGV PCR A real-time PCR to detect the polymorphic membrane protein H gene is performed. M. genitalium resistance testing by sequencing Macrolide and quinoline resistance in clinical specimens is determined by Sanger sequencing. Referred tests Occasionally, specimens and isolates may be referred to Public Health England, Centre for Infections, Colindale, for further specialist testing unavailable in Scotland. All such referrals should be made through SBSTIRL in order to be funded by NSS. Additional testing Gonococcal isolates and medicolegal specimens are stored indefinitely, and DNA extracts from specimens for NAAT are stored for at least one year. For retrospective testing or typing within these time-frames, please contact the laboratory. Page 6

7 Samples Request information Please complete the relevant SBSTIRL request form (see end of Manual). There are separate request forms for submission of N. gonorrhoeae cultures, specimens for supplemental N. gonorrhoeae NAAT, for LGV real time PCR, and for M. genitalium resistance testing by sequencing. All specimens must be labelled with the following information: Unique Identifier (Surname & Forename/CHI number/nash number) Date of birth Sender s Laboratory Number All specimens must be accompanied by the appropriate request form with the following information: Patient s unique Identifier (Surname & Forename/CHI number/nash number) Patient s date of birth and gender Specimen type/site Sender s Laboratory Number Location of Sender Any relevant clinical information Samples not received with an appropriately completed request form, or that are leaking may be discarded. Sample types N. gonorrhoeae culture Chocolate agar slope of the culture after a minimum of 6 hours incubation at 35-37ºC, 5% CO 2. or Overnight growth of organism transferred to an Amies charcoal agar transport swab Supplemental N. gonorrhoeae NAAT Any positive or equivocal GC NAAT specimen in any media as recommended by the NAAT manufacturer. Please indicate on supplemental GC NAAT request form which test has already been performed and the result. N. gonorrhoeae typing directly from a clinical specimen Any NAAT specimen which is GC positive by two different NAATs or two different targets within the same NAAT Page 7

8 LGV PCR Any NAAT specimen that is chlamydia positive meeting the following criteria: specimens from symptomatic patients, contacts of LGV and chlamydia-positive swabs from HIV-positive patients. M. genitalium resistance testing Any NAAT specimen that is M. genitalium positive. Please indicate which collection medium the sample has been transported in. Sample transportation Specimens should be appropriately packaged in accordance with current regulations. Please ensure N. gonorrhoeae cultures arrive Monday-Friday. Do not send on Fridays. Viability in transit cannot be guaranteed beyond 2 days. Page 8

9 Results and turn around times It is NHS Lothian Laboratory Medicine policy that results should be returned via a secure address such Paper copies of reports can be sent via Royal Mail by prior arrangement. For gonococcal cultures, a report of confirmation of identity and antimicrobial susceptibility is issued, followed by a final report including sequence type in those selected for typing. NAAT reports are issued as soon as possible. For NAAT-positive samples an updated report containing sequence typing data may be issued at a later date. LGV PCR reports are issued as soon as possible. M. genitalium reports are issued as soon as possible. Turnaround times Test Turnaround time (days) GC identification and antibiotic susceptibility testing 7 Supplemental GC NAAT 3 NG-MAST sequence typing 90 LGV PCR 7 M. genitalium resistance testing 14 Turnaround time excludes weekends and public holidays Quality aspects SBSTIRL is accredited by the Clinical Pathology Accreditation (UK) Ltd as part of Microbiology at the Royal Infirmary of Edinburgh. Any technical queries about the SBSTIRL assays can be made to Lothian.STIRefLab@nhs.net Complaints can be discussed with Kate Templeton or Jill Shepherd. The NHS Lothian Department of Laboratory Medicine Compliance Manager is Nadine Wilkinson Nadine.Wilkinson@nhslothian.scot.nhs.uk Page 9

10 SBSTIRL lab no Neisseria gonorrhoeae identification and antibiotic susceptibility Scottish Bacterial Sexually Transmitted Infections Reference Laboratory (SBSTIRL) Microbiology Department, Royal Infirmary of Edinburgh 51 Little France Crescent, Edinburgh EH16 4SA Hays DX: DX , Edinburgh 96EH FROM Consultant Referring lab Address Telephone number PATIENT DETAILS Surname: Clinic number / CHI: Forename: Date of Birth: Sex: M / F / U Category of patient: GUM GP Hospital Other SPECIMEN Your lab number: Date collected: Date sent to SBSTIRL: Sample type: Urethral Cervical Rectal Throat Additional Information Page 10

11 SBSTIRL lab no Supplemental Neisseria gonorrhoeae NAAT Scottish Bacterial Sexually Transmitted Infections Reference Laboratory (SBSTIRL) Microbiology Department, Royal Infirmary of Edinburgh 51 Little France Crescent, Edinburgh EH16 4SA Hays DX: DX , Edinburgh 96EH FROM Consultant Referring lab Address Telephone number PATIENT DETAILS Surname: Clinic number / CHI: Forename: Date of Birth: Sex: M / F / U Category of patient: GUM GP Hospital Other SPECIMEN Your lab number: Date collected: Date sent to SBSTIRL: Sample type: Urethral Cervical Urine Vulvo/vaginal Rectal Throat TESTING Confirmation of initial screen result NG-MAST sequence typing only (already confirmed by sender) Screening GC NAAT test used: Abbott Roche Cobas 4800 BD Probetec / Viper Hologic Aptima Combo Qiagen Ct/Cq/DC test value: Page 11

12 SBSTIRL lab no Lymphogranuloma Venereum (LGV) PCR Scottish Bacterial Sexually Transmitted Infections Reference Laboratory (SBSTIRL) Microbiology Department, Royal Infirmary of Edinburgh 51 Little France Crescent, Edinburgh EH16 4SA Hays DX: DX , Edinburgh 96EH FROM Consultant Referring lab Address Telephone number PATIENT DETAILS Surname: Clinic number / CHI: Forename: Date of Birth: Sex: M / F / U Category of patient: GUM GP Hospital Other SPECIMEN Your lab number: Date collected: Date sent to SBSTIRL: Sample type: Urethral Cervical Urine Vulvo/vaginal Rectal Throat TESTING REFERRED SAMPLES MUST BE CHLAMYDIA TRACHOMATIS POSITIVE Screening Chlamydia trachomatis NAAT test used: Abbott Roche Cobas 4800 BD Probetec / Viper Hologic Aptima Combo Qiagen REASON FOR REQUEST Symptomatic Proctitis Inguinal lymphadenopathy Contact of confirmed LGV case Chlamydia trachomatis positive sample from HIV positive MSM Page 12

13 SBSTIRL lab no Mycoplasma genitalium resistance testing Scottish Bacterial Sexually Transmitted Infections Reference Laboratory (SBSTIRL) Microbiology Department, Royal Infirmary of Edinburgh 51 Little France Crescent, Edinburgh EH16 4SA Hays DX: DX , Edinburgh 96EH FROM Consultant Referring lab Address Telephone number PATIENT DETAILS Surname: Clinic number / CHI: Forename: Date of Birth: Sex: M / F / U Category of patient: GUM GP Hospital Other SPECIMEN Your lab number: Date collected: Date sent to SBSTIRL: Sample type: Urethral Cervical Urine Vulvo/vaginal Rectal Throat TESTING Screening M. genitalium NAAT assay used: SpeeDx Hologic Aptima In-house PCR Ct/Cq/DC test value: TREATMENT HISTORY Azithromycin Moxifloxacin Doxycycline Page 13