Scottish E. coli O157/Shiga toxin-producing E. coli Reference Laboratory

Transcription

1 Scottish E. coli O157/Shiga toxin-producing E. coli Reference Laboratory 1 Authors: SERL68:Version L. Allison 6 Issue date & M. 27/09/2017 Hanson This is an electronic document Authors: L. Allison which & M. is Hanson uncontrolled when printed.

2 Contents Contents Introduction 2 Postal address 3 Working hours 4 Advice and consultation 5 Services 6 Service requests, transport and communication of results 8-9 Molecular subtyping 10 Training and research 11 2

3 Introduction Introduction The Scottish E. coli O157/Shiga toxin-producing E. coli Reference Laboratory The Scottish E. coli O157/Shiga toxin-producing E. coli Reference Laboratory (SERL) is located within the Department of Laboratory Medicine, Royal Infirmary of Edinburgh and is funded by National Services Scotland (NSS), Scottish Government Health Directorates. The department is accredited by Clinical Pathology Accreditation (UK) Ltd. SERL provides identification and typing of E. coli O157 and other Shiga toxinproducing E. coli, in order to guide the clinical management of individual patients and to supply detailed epidemiological information for health protection purposes. Samples and isolates are referred from diagnostic laboratories throughout Scotland. The laboratory primarily receives clinical samples and isolates, although we will also examine isolates from animals, food or the environment known or thought to be associated with human cases of infection. The laboratory is a source of advice and information for the NHS and collaborates with NHS boards, Health Protection Scotland, Public Health England, universities and international agencies. 3

4 Postal address Postal address Scottish E. coli O157/STEC Reference Laboratory Department of Laboratory Medicine Royal Infirmary of Edinburgh 51 Little France Crescent Old Dalkeith Road Edinburgh EH16 4SA DX Exchange: Edinburgh 96EH DX Number: DX

5 Normal laboratory working hours Working hours Monday-Friday: 9am - 5pm Out of Hours/Emergency Contact: For advice outwith normal working hours, please contact the switchboard ( , or ) and ask for the on-call Consultant Microbiologist. 5

6 Advice and consultation Consultation The Director and Principal Scientist may be contacted at any time for advice. Complaints should be directed to Dr Allison in the first instance. Director Dr Mary Hanson Deputy Clinical Lead Dr Pota Kalima Deputy Director/ Dr Lesley Allison Principal Scientist or 6013 Advanced BMS Mrs Sheena Miller or 6013 Clinical Scientist Dr Anne Holmes or 6013 Clinical Scientist Dr Juliet Kenicer or 6013 Administrator If you are unable to make the appropriate contact, please leave a message on the SERL answer phone ( ) and your call will be returned as soon as possible. 6

7 Services provided Services provided SERL receives isolates of E. coli O157 for confirmation of identity and typing, culture negative faecal samples for detection of E. coli O157 and other STEC, and serum samples for detection of antibodies to certain STEC serotypes. In recent years, non-o157 and sorbitol-fermenting STEC have been implicated in gastro-intestinal disease in many European countries, including Scotland. As these organisms may not be detected using routine laboratory procedures, diagnostic laboratory staff should consider the possibility of a non-o157 or a sorbitol-fermenting STEC infection, particularly when suspicion of a STEC infection is high but the sample has tested negative for typical non-sorbitol fermenting E. coli O157. SUBMITTED SAMPLE LABORATORY TEST TURNAROUND 1 Isolates of E. coli O157 2 Confirmation of Identity 3 days PCR Detection of virulence genes 3 days Phage Typing 3 days Isolates of E. coli (not O157) PCR Detection of virulence genes 3 days Faecal Specimens* PCR Detection of virulence genes 3 days 3 Immunomagnetic Separation 4 4 days Sera Immunoblotting 10 days 5 1 Turnaround times are based on working days and refer to predetermined timescales for processing 95% of samples. 2 Assuming receipt of a pure culture 3 Although it is possible to determine the presence of verotoxin genes in a faecal sample within three working days, isolation and characterisation of the STEC will take longer 4 IMS testing is restricted to those faeces testing positive by real-time PCR (to aid in isolation of the organism), and all faeces submitted from patients with HUS and contacts of cases of E. coli O This is a referred test. 7

8 * This is in line with the Health Protection Network guidance on laboratory diagnosis of VTEC (revised, 2013) which advises the immediate referral to SERL of faecal samples from: Any suspected case of Haemolytic Uraemic Syndrome (HUS) or Thrombotic Thrombocytopenic Purpura (TTP) or bloody diarrhoea in whom conventional culture has failed to yield a pathogen All symptomatic contacts of cases of STEC infection (NSF STEC O157, SF STEC O157 or non-o157 STEC) or any STEC outbreak-associated case in whom conventional culture has failed to yield a pathogen All asymptomatic contacts of a case of infection with SF STEC O157. HPN guidance also advises the immediate referral to SERL of serum samples from likely cases of E. coli O157 infection who have: Haemolytic Uraemic Syndrome (HUS) or Thrombotic Thrombocytopenic Purpura (TTP) AND Negative faecal samples by direct culture and specialised laboratory techniques OR Who have failed to provide a faecal sample 8

9 Sample submission, transport Samples,transport Samples must be appropriately packaged and transported in accordance with current regulations. If unsure of the current transport regulations or packaging requirements, please contact SERL for advice. Please ensure that packages containing faecal specimens contain sufficient absorbent material to contain ALL liquid and please ensure request forms are placed between the plastic container and cardboard outer, not with the faeces. A completed SERL request form carrying all relevant clinical and epidemiological information must accompany each sample and SERL must be NOTIFIED IN ADVANCE by telephone ( ) prior to dispatch of isolates. This procedure ensures compliance with the postal regulations and any loss of isolates in transit can be detected. SERL will confirm receipt of all E. coli O157/STEC isolates by telephone. If known, please ensure that the Clinical Details and Type of Incident fields are completed as this will inform which tests will be performed. SERL Request forms can be downloaded from the HPS website ( reflab/reflablist.aspx) and must carry the following information: 1. Patient Identifier No (CHI) 2. Surname 3. Forename 4. Date of Birth 5. Address 6. Gender 7. Location of sender 8. Specimen type being sent for analysis (faeces, isolate or sera) 9. Sample date and time 10. Sender s laboratory sample number 11. Associated clinical and epidemiological information. Minimum data are also required on the sample container: 1. Surname 2. Forename 3. Date of birth 4. Sender s laboratory sample number 9

10 and communication of results Results On small culture vials, patient s name and the sender s laboratory number are required as a minimum. Samples or request forms not carrying this information may be rejected or processing may be delayed. If in doubt as to the appropriate specimen or container, please contact SERL for advice. Isolate Pure culture on an agar slope Faeces At least 1g in a suitably sealed container Sera 500 μl Blood or clotted blood will no longer be accepted Urgent specimens will be processed out of hours following discussion with the Director or her deputy, the Principal Scientist. Please telephone in advance to arrange or, if calling out of hours, contact the on-call consultant microbiologist through the switchboard. Reports are dispatched within five working days of receipt of the isolate although all positive test results are notified in advance by telephone to the sending laboratories. If an STEC is identified in a submitted faecal sample, this finding will be immediately communicated to the duty microbiologist at the diagnostic laboratory. Results are reported to Health Protection Scotland (HPS) on a daily basis. The majority of users receive SERL reports by electronic transfer of the PDF files and these will be received the same day the results are authorised. If you would like to participate in electronic reporting, please contact us to discuss. 10

11 Molecular subtyping Subtyping The SERL introduced whole genome sequence-based typing of all Shiga toxinproducing E coli (STEC) in August This allows us to characterise strains and assess relatedness at the bacterial genome level with very high discriminatory power, and will be used in conjunction with phage typing. Routine MLVA typing was discontinued at the time of introduction of WGS. This enables us to report extra typing information such as the presence of other genes in addition to Shiga toxin genes (eae, stx subtype), the serotype of non-o157 E coli, and a multilocus sequence type (ST) and SNP address. The SNP address is a way of reporting variation between strains that allows easy comparison of strains isolated throughout the UK. Matched isolates identified by WGS at SERL will be immediately communicated to the local Health Protection Teams and to Health Protection Scotland. 11

12 Training and research Training+research SERL is actively involved in the training of B Sc Honours students, healthcare scientists, health protection and infection control nurses, and postgraduate medical trainees in Microbiology, Infectious Diseases and Public Health. This is carried out on an ad hoc basis and interested parties are invited to contact the Director to arrange training attachments. SERL also participates in and collaborates on externally funded research projects. 12

13 Notes Notes 13

14 The Scottish E. coli O157 Reference Laboratory is funded by National Services Scotland, Scottish Government Health Directorate. Escherichia coli photograph provided by the Department of Medical Microbiology, University of Aberdeen. Royal Infirmary of Edinburgh photograph used with permission from NHS Communcations Department. Design: Graphic Design Service, LTW, ISG, The University of Edinburgh 14 SERL68:Version Authors: L. Allison 6 Issue & date M. Hanson 27/09/2017