SCOTTISH Salmonella, Shigella & C.difficile REFERENCE LABORATORY (SSSCDRL)

Title SCOTTISH Salmonella, Shigella & C.difficile REFERENCE LABORATORY (SSSCDRL) LABORATORY PROCEDURE NUMBER / VERSION User Manual DATE OF ISSUE 17/04/2014 REVIEW INTERVAL AUTHORISED BY AUTHOR 2 Years Prof. J. Coia Henry Mather COPY 1 of 1 Master file in Q-Pulse LOCATION OF COPY GG&C website www.nhsggc.org.uk/smrl DOCUMENT REVIEW HISTORY All review / revision details are available in Q-Pulse Date Amendment Initials SSSCDRL User Manual Controlled document Page 1 of 12

Scottish Salmonella, Shigella & C. difficile Reference Laboratory User Manual 2014 We aim to select our test repertoire for the benefit of our users and their patients. If you have any suggestions for improving our service please contact us. CONFIDENTIALITY POLICY NHSGG&C Standing Financial Instructions and Fraud Policy ensure that users confidential information is protected and that this department cannot undertake activity that would diminish confidence in its impartiality. Users confidential information is also governed by our procedure RL_MP_010 Management of data & information and by NHSGG&C I.T. Policy. Activity that would diminish confidence in impartiality or integrity is also prohibited by the Health & Care Professions Council code of conduct. Complaints procedure:- We will:- 1. Take all complaints seriously. 2. Deal with the client in a courteous manner. 3. Try to resolve the issue immediately at a local level. 4. Inform the client about the progress of the complaint. 5. Make corrective action as soon as possible. 6. Investigate root cause analysis to prevent recurrence. If you have a complaint, contact the laboratory manager (see page 5). SSSCDRL User Manual Controlled document Page 2 of 12

Section One: The Scottish Salmonella, Shigella & C.difficile Reference Laboratory Introduction 4 Laboratory hours 4 Contact details 4 Section Two: Services provided by the SSSCDRL (including turnaround times) Submission of samples 6 Specimen acceptance & rejection criteria 7 Transportation of specimens 7 Salmonella & Shigella 8 Clostridium difficile Reference Service 9 Reporting of results 12 Section Three: Interpretation of SSSCDRL Results 12 Interpretation of Salmonella, Shigella and Clostridium difficile testing results. 12 SSSCDRL User Manual Controlled document Page 3 of 12

Section One: The Scottish Salmonella, Shigella and Clostridium difficile Reference Laboratory (SSSCDRL) Located on Level 5 of the New Lister Building, Glasgow Royal Infirmary, 10-16 Alexandra Parade, Glasgow G31 2ER, SSSCDRL is the National Reference Centre for characterisation and typing of Salmonella and Shigella species. It is also responsible for the confirmation of other enteropathogens including Vibrio cholerae and Aeromonas species. The laboratory provides a full complement of techniques, including serotyping, phage typing and a range of biochemical and molecular methods, for identification and typing of these pathogenic enteric bacteria. In addition the laboratory is a source of information and advice for the Health Service and other agencies in Scotland. SSSCDRL actively participates in training, development and relevant externally-funded research. There is close collaboration with a number of other agencies including the Health Protection Scotland (HPS) the Laboratory of Gastro-intestinal Pathogens (LGIP), Centre for Infections, Colindale, London (now part of Public Health England) and other international reference centres. The laboratory is a participant in the EU-funded network for Food and Waterborne Diseases and Zoonoses programme for surveillance of gastrointestinal infections, run by the European Communicable Diseases Centre (ECDC) in Stockholm. LABORATORY HOURS: Monday to Friday: Saturday morning: Public holidays: Emergency situations: Director. 8.45am to 5.00pm Specimen reception only. Specimen reception only. As required after discussion with Director or Medical List of Contacts Name Designation Telephone E-mail address Number Prof. John E. Coia Director 0141 201 8633 john.coia@ggc.scot.nhs.uk or john.coia@nhs.net Dr. Nitish Khanna Deputy Director 0141 201 8574 0141 354 9138 nitish.khanna@ggc.scot.nhs.uk or nitish.khanna@nhs.net SSSCDRL User Manual Controlled document Page 4 of 12

Mr. Henry Mather Mr. Derek Brown Site Manager & Section Manager Principal Clinical Scientist 0141 201 8669 henry.mather@ggc.scot.nhs.uk or henry.mather@nhs.net 0141 201 8668 derek.brown2@ggc.scot.nhs.uk or derek.brown@nhs.net Result enquiries 0141 201 8670 henry.mather@ggc.scot.nhs.uk or henry.mather@nhs.net General enquiries 0141 201 8663 Availability of Advice Normally 8.45arn - 5.00pm Monday to Friday. Clinical Prof. John E. Coia 0141 201 8633 Technical Mr. Henry Mather 0141 201 8669 In an emergency situation out with these hours please contact the on-call microbiologist at Glasgow Royal Infirmary on 0141 211 4000. If there is a problem What to do Whom to contact. Minor issue - Telephone/e-mail Major issue Write/e-mail Minor issue Site & Section Manager Mr. Henry Mather Major issue - Director Prof. John E. Coia Complaints If you have a complaint please telephone, write e-mail or fax the key member of staff who will initiate our laboratory complaints procedure. SSSCDRL User Manual Controlled document Page 5 of 12

Section Two: Services provided by the SSSCDRL Submission of Samples What information to send: Use SSSCDRL Request Forms, http://library.nhsggc.org.uk/mediaassets/smrl/smrl_ssscdrl_request_form_nlb.pdf - completed as fully accurately and legibly as possible. Isolates which are incorrectly labelled or which do not carry a patient identifier, laboratory address will incur needless delays. The clinical and epidemiological data, including patient s address and recent travel history, should be regarded as essential request details. Sample and request form information must be compatible. The minimum information that should be provided is as follows: ESSENTIAL DESIRABLE Sample Patient s Full Name * Date of Birth and/ or Hospital Unit Number CHI number, etc. Date and Time Destination of Report Request Form main symptoms diagnosis date of onset investigation (s) required Patients Full Name* Date of Birth and/or Hospital Unit Number, CHI number, etc Name of requesting microbiologist. * or Proper Coded Identifier Clinical Information Date and Time of sample Collection Patients Address Referring microbiologist s Contact Number These details are essential for sample processing, interpretation of test results and for enhanced epidemiological surveillance. On the request form please also indicate where reports should be sent. SSSCDRL User Manual Controlled document Page 6 of 12

Specimen acceptance & rejection criteria. Improperly Labelled specimens/ Request Forms Sample or request forms received without the minimum essential identification will be referred back to the requesting laboratory. Samples and forms that are mismatched The requesting microbiologist (or appropriate laboratory staff) will be informed that the form & sample did not match and had been discarded. Samples that arrive with no form If a sample arrives with no form, a blank request form will be filled out with the details taken from the specimen, booked in and stored for future testing. Forms that arrive with no sample The form will be booked in & a report issued stating that no sample was received. Samples that are inappropriately labelled Samples that arrive with no details on them may still be processed, however the report will state No name on specimen but received in the same bag as request form. Under the direction of a senior member of staff further action might be: Processing the specimen and withholding results Storage of the specimen Requesting a fresh specimen and request form. Contact the sending laboratory by telephone to confirm / clarify details. Damaged/ Leaking Samples The action taken will often depend on the preciousness of the sample. Some may be difficult to repeat and it may be necessary to try to save and use what has been received. What specimens to send: Culture (Salmonella, Pure culture on Dorset's egg or Agar slopes Shigella and other Enterobacteriaceae) Faecal sample Standard sealed container (Not less than 1 gram) All submissions should be sent by first class mail and must comply with UN3373 postal regulations. Alternatively use the DX courier service: - DX Number 6490200, Exchange Bishopbriggs 90G. SSSCDRL User Manual Controlled document Page 7 of 12

All cultures of suspected Hazard Group 3 organisms must be packed and labelled in accordance with standard safety precautions, dispatched via a recognised courier and notified by phone in advance of dispatch. All isolations of Salmonella and Shigella will be reported to Health Protection Scotland (HPS). Salmonella & Shigella Identification and typing Biochemical identification of Salmonella and Shigella isolates Biochemical identification of other members of the Enterobacteriaceae (by arrangement) Serotyping for Salmonella and Shigella Phage typing for S. Typhimurium and S. Enteritidis DNA-based typing. A range of DNA-based typing and fingerprinting techniques for Salmonella are utilised. These include plasmid profiling, MLVA typing and pulsed-field gel electrophoresis (PFGE) of epidemiologically relevant isolates. Other specific requests for these services should be discussed directly with SSSCDRL staff. Antibiotic susceptibility testing. All isolates are screened for resistance to a wide range of clinically relevant and epidemiologically important antimicrobials. Teaching and Training Facilities are available within SSSCDRL to provide a comprehensive programme of instruction in both the theoretical and practical aspects of enteric infectious disease. The programme runs on an ad-hoc basis being tailored to the needs of the individual rather than having a formal structure. Further information is available on request. SSSCDRL User Manual Controlled document Page 8 of 12

Turnaround Times (from receipt of culture to despatch of report). Salmonella identification Salmonella serotyping Salmonella phage typing Shigella etc 5-7 working days 3-5 working days 1-3 working days 5 7 working days Contact the Laboratory Manager or Director to arrange processing at weekends or out of hours. Results will be telephoned by request and during outbreak situations; however, in line with the Department of Health guidelines faxed reports will only refer to a source laboratory identifier. Patient or client names will be omitted. Faxed results must be requested in writing and their receipt acknowledged. Exceptions The above times are based on the receipt of pure cultures. Cultures which require reisolation may increase turnaround time significantly. In addition Salmonellae belonging to serogroups other than subspecies I (subspecies enterica) require additional biochemical tests that significantly increase turnaround time. Clostridium difficile Reference Service The Clostridium difficile Reference Service for Scotland is provided by the Scottish Salmonella, Shigella and Clostridium difficile Reference Laboratory (SSSCDRL). SSSCDRL actively participates in training, development and relevant externally-funded research. There is close collaboration with a number of other agencies including the Health Protection Scotland (HPS), Public Health England (PHE), the C. difficile Ribotyping Network hub in Leeds, the ESCMID study Group for Clostridium difficile and other international reference centres. Services Available DNA-based typing All C. difficile isolates will be tested by PCR Ribotyping according to the methods developed by Dr. Jon Brazier at the Anaerobic Reference Laboratory in Cardiff. The laboratory participates in C. difficile Ribotyping Network (CDRN) EQA scheme that is organised by Professor Mark Wilcox and in an EQA scheme organised by the ESCMID Clostridium difficile Working Group. The laboratory can also perform MLVA typing on selected C. difficile isolates in the investigation of outbreaks or confirmation of Hospital Acquired Infections (HAI). Before MLVA typing is undertaken it has to have the approval of Health Protection Scotland. SSSCDRL User Manual Controlled document Page 9 of 12

Antibiotic susceptibility testing All isolates are screened for resistance to a wide range of clinically relevant and epidemiologically important antimicrobials by E-Test. The results of metronidazole and vancomycin sensitivities will be included in the final report to the sending laboratory. Teaching and Training Facilities are available within SSSCDRL to provide a comprehensive programme of instruction in both the theoretical and practical aspects of enteric infectious disease. The programme runs on an ad-hoc basis being tailored to the needs of the individual rather than having a formal structure. Further information is available on request. How to obtain services Isolates of C. difficile should be submitted to the Scottish Clostridium difficile Reference Service in the case of the following: - 1) Severe cases Admission to a healthcare facility for treatment of community associated CDI. Admission to ITU for treatment of CDI or its complications. Endoscopic diagnosis of pseudomembranous colitis (with or without toxin confirmation). Surgery for the complications of CDI (toxic megacolon, perforation or refractory colitis). Death within 30 days following a diagnosis of CDI where it is either the primary or a major contributory factor. Persisting CDI where the patient has remained symptomatic and toxin positive despite 2 courses of appropriate therapy. 2) Suspected outbreaks When an outbreak is suspected and stools are positive for Clostridium difficile toxin. An outbreak of CDAD occurs when more cases of CDAD than would normally be expected occur in a clinical unit, ward or hospital. SSSCDRL User Manual Controlled document Page 10 of 12

3) Suspected infections and/or outbreaks with ribotype 027 When infection with the hypervirulent strain 027 is suspected the C. difficile reference service must be contacted. This is required when: Isolates of ribotype 027 have been identified. Patients have been recently hospitalised in England or abroad. 4) Representative Surveillance Clostridium difficile Snapshot Programme Only isolates that meet these guidelines will be accepted. Full guidelines and the protocol for the Scottish Surveillance Program for Clostridium difficile Infections can be obtained on the HPS web-site: - The Clostridium difficile Snapshot Programme looks at less severe hospital cases and isolates that are possibly community acquired. The protocol for the programme is available at: http://www.documents.hps.scot.nhs.uk/hai/sshaip/guidelines/clostridium-difficile/cdadsnapshot-programme-1-0.pdf http://www.documents.hps.scot.nhs.uk/hai/sshaip/guidelines/clostridiumdifficile/protocol-scottish-surveillance-programme-cdad-2009-03.pdf What information to send: Use the C. difficile Request Form: - http://library.nhsggc.org.uk/mediaassets/smrl/smrl_ssscdrl_cdiff_request_form_nlb.pd f completed as fully accurately and legibly as possible. Isolates which are incorrectly labelled or which do not carry a patient identifier, laboratory address will incur needless delays. The clinical and epidemiological data, including any contact with healthcare establishments, should be regarded as essential request details. What specimens to send: Culture Pure culture in Robertson s cooked meat medium All submissions should be sent by first class mail and must comply with postal regulations. Alternatively use the DX courier service: - DX Number 64902000, Exchange Bishopbriggs 90G. All isolations of C. difficile will be reported to Health Protection Scotland (HPS). SSSCDRL User Manual Controlled document Page 11 of 12

Turnaround Times (from receipt of culture to despatch of report). C. difficile PCR Ribotyping 7 days Contact the laboratory manager or director to arrange processing at weekends or out of hours. Results will be telephoned by request and during outbreak situations; however, in line with the Department of Health guidelines faxed reports will only refer to a source laboratory identifier. Patient or client names will be omitted. Faxed results must be requested in writing and their receipt acknowledged. Exceptions The above times are based on the receipt of pure cultures. Cultures which require reisolation may increase turnaround time significantly. Reporting of SSSCDRL results All results of diagnostic importance or epidemiological value are telephoned directly to the Consultant Microbiologist and/or senior BMS staff at the submitting laboratory. We routinely inform CPHMs and HPS of results that may have public health significance, including clusters of cases and possible outbreaks. Section Three: Interpretation of SSSCDRL results This guidance is provided to assist in the interpretation of SSSCDRL results regarding the laboratory confirmation of isolates. Although all of our tests have been evaluated and validated, a small number of cases will require individual interpretation. Clinical information should be taken into account where necessary when interpreting SSSCDRL results, particularly the patients current symptoms should be considered in potential cases of CDI. SSSCDRL User Manual Controlled document Page 12 of 12