Guidance

Specialist microbiology network: public health laboratory Bristol user handbook

Updated 7 June 2024

Role of the UKHSA specialist microbiology network

UK Health Security Agency (UKHSA) has a network of specialist microbiology laboratories across England. Each lead laboratory provides:

• microbiology support for the investigation, management and control of infection and outbreaks of communicable disease both during and out of normal working hours
• expert medical and scientific microbiological advice, including access to UKHSA experts locally and nationally as necessary
• a wide range of diagnostic, specialist and reference tests
• national standard methods and UKHSA testing algorithms
• clear guidance for users
• surge capacity to deal with large unanticipated outbreaks at short notice; UKHSA can also provide additional capacity for larger testing numbers and access to specific typing if required to define the epidemiology of outbreaks
• support for both regional and national capacity to respond to specific events of potential public health importance
• testing for look-back exercises for health protection teams (HPTs), acute NHS trusts, integrated care boards (ICBs), and local authorities
• reporting of laboratory results within specified turnaround times for diagnostic specialist and reference tests; results will be communicated by electronic means wherever possible and may be supported by paper reports as required or appropriate – these services will be provided to all customers (HPTs, NHS trusts and ICBs)
• standard interpretive comments as a part of test reports
• senior clinical and scientific staff will add specific interpretation and further advice relevant to individual patient needs or for public health significance
• mechanisms for the proper handling, storage and security of all samples and documentation at all times; this will be carried out in accordance with UKHSA guidelines, national guidelines and regulatory/legal requirement
• efficient and timely communications with public health organisations, both within the UKHSA (including HPTs) and externally - for example local authorities and primary care groups/clusters involved in communicable disease control
• receipt, processing and reporting of laboratory results and epidemiological data in a timely and efficient manner
• assistance in maintaining an efficient communication network with all public health and NHS organisations involved in communicable disease control in the south-west of England

All UKHSA diagnostic laboratories are accredited to the relevant international standard: ISO 15189 for medical laboratories and ISO 17025 for food, water and environment (FW&E) laboratories.

Public health outcomes framework

In addition to its clinical diagnostic microbiology role, the UKHSA laboratory in Bristol provides a range of public health microbiology services. These include:

• a full range of tests to investigate any event or outbreak of possible public health significance in the community
• advice on the best diagnostic strategies to adopt
• advice on the interpretation of test results and additional investigations that may be helpful
• support to incident/outbreak investigation teams
• prompt communication of results in agreement with published turnaround times
• follow up/clearance testing of patients or contacts of patients in whom organisms of public health importance are detected.
• support for trusts/HPTs in the specialist investigation of health care associated infection

These public health microbiology services are available to:

• staff in health protection teams
• local authority staff and directors of public health
• ICBs
• acute trusts

The laboratory is linked to a network of specialised UKHSA laboratories across England (including laboratories testing food water and environmental samples) and to major reference units at UKHSA Colindale and UKHSA Porton.

This user manual describes the provision of and access to public health microbiology services and gives contact details for the laboratory and its main personnel.

A separate laboratory user manual is available which documents the clinical diagnostic services provided by the Bristol laboratory and is available on the Severn Pathology website using the link Infection Sciences (Microbiology and Virology), North Bristol NHS Trust (nbt.nhs.uk)

Please note that support and access to food, water and environmental microbiology services can be obtained from the UKHSA FW&E laboratory at Porton Down (refer to Section 9).

Main contacts

Lead Microbiologist for the South West

In the event of a suspected outbreak or incident please contact one of the following so that appropriate arrangements for investigation can be made:

Dr Matthew Donati, Consultant Medical Virologist and Clinical Head of Virology

Telephone: 0117 414 6222
Personal assistant: 0117 414 6266
Email: [email protected]

Dr Derren Ready, Consultant in Public Health Infection
Email: [email protected]

Medical advice duty microbiologist

Telephone: 0117 9505050

Duty Virologist

Telephone: 0117 9505050

General enquiries

For enquiries about laboratory results please phone the results enquiry telephone lines:

Telephone: 0117 414 6222

Main laboratory personnel and contact details

Mr Jonathan Steer, Head of Operations
Telephone: 0117 414 6239
[email protected]

Mrs Deborah Williams, Quality Manager
Telephone: 0117 414 6251
[email protected]

Duty Laboratory contact during working hours

Bacteriology

Ms Nicola Childs
Assistant Infection Sciences Service Manager (Bacteriology Laboratory Manager)
Telephone: 0117 414 6218
[email protected]

Virology

Mr Richard Hopes
Biomedical Head of Virology
Telephone: 0117 414 6276
[email protected]

Laboratory Administrator

Ms Helen Thresher
Telephone: 0117 414 6266
[email protected]

Out of hours service

Out of hours 5pm to 8:30am hours, weekends and bank holidays:

On call microbiologist/virologist: please contact via switchboard (0117 950 5050) Contact on call staff for specific delivery arrangements out of hours.

Laboratory location, working hours and access details

The laboratory is located within Pathology on the North Bristol NHS Trust Southmead site.

Contact Severn Pathology, North Bristol NHS Trust

Laboratory working hours

Monday to Friday: 8:30am to 5pm.

Weekends and bank holidays: 8:30am to 5pm.

Outside of these hours the laboratory runs an on-call service for urgent work. This can be arranged by contacting the on-call staff via the hospital switchboard (telephone: 0117 950 5050).

Please contact the laboratory in advance of submission with details of the incident/outbreak and investigations required.

Please notify the laboratory of the log/outbreak identifier if one has been assigned.

All non-urgent specimens should arrive in the laboratory within the hours specified.

Contact on call staff for specific delivery arrangements out of hours.

NHS laboratories and access to public health testing in the South West

NHS laboratories that have provided local public health outbreak support as part of their NHS functions should continue to do so.

All NHS laboratories have responsibilities for health protection which include providing support for the investigation of local outbreaks in their catchment area, through:

• contributing to the formulation of local contingency plans and participation in exercises
• detecting local outbreaks through monitoring laboratory findings
• detecting and promptly reporting unusual occurrences of public health significance
• providing initial laboratory support for outbreaks, incidents and look-back exercises as appropriate
• appropriate staff attending local community control of infection meetings and incident/outbreak control team meetings
• advice on appropriate investigations, interpretation of results and similar tasks
• forwarding appropriate specimens to reference laboratories

If outbreak specimens are usually sent to the local NHS Laboratory, then this practice can continue.

Initially, diagnostic patient specimens are likely to be examined at the local NHS laboratory, however, once an outbreak has been recognised and declared by the HPT (Health Protection Team) or other appropriate authority there should be a discussion between the initial investigating (NHS) laboratory or HPT with the Consultant in Public Health Infection (CPHI)/Regional Head of Laboratory Operations or duty consultant microbiologist in the regional laboratory to decide on testing of additional specimens and the method of transport. If either the number of specimens expected is likely to exceed the capacity of the local NHS laboratory or requires specialist tests, then the specimens should be referred to the nearest UKHSA laboratory or UKHSA collaborating centre.

If a local NHS laboratory is unable to provide this support at any time, for whatever reason, UKHSA will make arrangements to ensure that these services continue to be provided. If any difficulties with existing or new arrangements are encountered, please contact the CPHI or Regional Head of Laboratory Operations who will make sure that arrangements are securely in place.

Definition of a public health microbiology specimen

The list below provides some of the circumstances in which public health specimens may be submitted (this list is not exhaustive):

• in the investigation of an outbreak (for example, diarrhoea and vomiting in a nursing home or other institution)
• suspected food poisoning in a group or community
• respiratory symptoms in an institution for example, suspected Influenza
• to check for clearance of certain pathogens (see above) in individuals working in high-risk situations (for example, food handlers, those working with children or other vulnerable groups)
• screening of contacts of index cases, for example diphtheria or poliomyelitis
• look-back exercises, for example, carriage of blood borne viruses in a health care worker
• tuberculosis contact tracing
• investigation of a cluster of cases of for example, Legionnaires’ disease, which could have a common source

Such specimens are usually submitted at the request of:

• senior staff of a health protection team (HPT)
• an environmental health officer
• at the request or on behalf of the director of public health or consultant in communicable disease control
• at the instigation of the CPHI for example, for specialist typing in the investigation of episodes of health care associated infection

Collection of specimens

In order to provide the best quality results, it is essential that specimens are collected properly and at the appropriate time. It is also important that they are transported to the laboratory safely and without undue delay (see Appendix 1 for safety considerations).

Inappropriate specimens or those that are inadequately labelled (see request form), damaged or leaking are liable to be discarded. Should this occur, every attempt will be made to inform the sender so that a second specimen can be collected.

Both the request form and specimen container must be labelled with:

• patient’s full name
• hospital/clinic number or NHS number
• date the sample was taken
• patient’s date of birth
• patient’s postcode

The above will assist us in the surveillance of communicable diseases. Please provide full details of where to send the result and who to contact if we need to report an urgent, significant result. Please provide an Outbreak Number (HPZ) if available.

Sample collection and submission

Please ensure that all details are completed on the request form before it is given to the patient. Ask the patient to complete all details on the specimen container before collecting the specimen.

These must include:

• first name
• second name

Faeces

The specimen size should be at least 5ml. The following methods can be used to collect a specimen:

• the patient or carer should wear disposable gloves
• toilet paper can be crumpled into the toilet bowl or suspended across the toilet bowl in a cross to make a sling.
• a clean plastic container can be positioned in the toilet bowl
• cling film can be stretched across the top of the toilet bowl
• contamination with urine should be avoided
• a portion of faeces can then be collected with a wooden tongue depressor or the spoon provided in the specimen pot and transferred to the specimen container
• the specimen pot should then be sealed into the specimen bag and the form included in the pocket provided
• all materials should be placed in a plastic bag which is sealed before disposal in the refuse bin

Please ensure that all details on both the specimen and accompanying request form are completed. Failure to do so may lead to rejection of the specimen.

Please give full clinical details and brief details of the outbreak on the request form. In outbreak situations or when unusual pathogens may be implicated, it is essential to discuss the request with one of our consultant microbiologists before submission of specimens.

Faecal samples will be examined for the presence of:

• salmonella
• shigella
• E. coli O157
• campylobacter
• cryptosporidium and giardia species if clinically appropriate
• C. difficile in all patients over the age of 65 years and where clinically indicated, for example in nursing home or care home outbreaks

Please discuss with a member of the laboratory staff should you suspect any of the following pathogens:

• Vibrio cholerae
• diarrhoeagenic E. Coli (other than E. coli O157)
• Yersinia enterocolitica
• enteric parasites

Please also discuss with a member of laboratory staff if you suspect food poisoning due to:

• Staphylococcus aureus
• Clostridium perfringens
• Bacillus cereus

Should the clinical history suggest infection with viral pathogens, this too should be clearly indicated on the request form.

When a viral aetiology is suspected faeces for Virology will be routinely investigated for norovirus/rotavirus.

Additional viral pathogens can be sought (adenovirus, astrovirus, sapovirus); please discuss with the duty virologist.

Throat/Pharyngeal swabs

For detection of carriage of Neisseria meningitides, the swab should be taken through the mouth (sweeping posterior pharynx behind the uvula).

For detection of group A streptococcus, swab the tonsillar area.

For detection of Corynebacterium diphtheriae, nose and throat swabs should be submitted. If infection with C. diphtheriae is suspected on clinical grounds, a microbiologist should be contacted without delay (that is, without waiting for confirmation by culture). One suspected case of diphtheria requires urgent public health action.

Viral respiratory specimens

Occasionally outbreaks of influenza occur in institutions. The incident management team will advise when specimens from these outbreaks need to be submitted. Please seek the advice of the virology laboratory on what specimens are required and how these should be submitted.

‘Flu’ kits can be obtained from the laboratory (these include instructions for collection).

Sputum

Please contact the laboratory to discuss the submission of specimens. Should you need to submit sputum specimens to examine for the presence of mycobacteria, for example in cases of suspected tuberculosis, please contact laboratory consultant medical staff for advice and discussion before submitting any specimens.

Urine

Fresh urine specimens (in a clean universal container) may be required for the diagnosis of Legionnaires’ disease

Serum

Specimens of clotted blood may be required for:

• investigation of clusters of atypical pneumonia
• look back exercises to detect the transmission of blood borne viruses, by arrangement with laboratory/incident or outbreak management team

Methods of specimen submission

Direct submission to the laboratory

This method of submission is available to all local authorities (LAs) submitting samples to the laboratory.

For ease of access, for samples being submitted to the laboratory from the community please deliver to the site at North Bristol NHS Trust. There are regular deliveries between this site and the bacteriology dept within the hospital.

Samples which require testing from the Bath region can either be delivered directly to the North Bristol NHS Trust Southmead site as above or be submitted via the Royal United Hospitals Bath (RUH) pathology department and they will then be transported from the RUH hospital via the routine transport method.

Submission to the laboratory via GP surgeries

It may be possible for local authorities to submit samples via local GP surgeries.

Submission to the laboratory via other hospital pathology departments

Many hospitals have daily transport to the Bristol Laboratory.

Submission to the laboratory via post

Specimens should be submitted to the laboratory by post provided they are packaged according to current postal regulations. Packaging instructions are included with each kit.

Details of how more postal packs can be obtained

Postal packs are available from the Bristol public health laboratory and can be requested [email protected]

Postage costs

A separate pack should be used for each specimen. The Tracked24 Royal Mail service is utilised for sending samples which includes covering the cost of postage. LAs and patients are not expected to pay for the submission of samples for testing.

Submission to the laboratory using an agreed UKHSA courier

In special circumstances the Health Protection Team may, by agreement, organise courier transport, additional specimen containers and any other materials.

Investigation of local outbreaks

Environmental Health Officers, Health Protection Teams and General Practitioners can continue to refer specimens for investigation of individual cases of infection and small community out- breaks using their local NHS laboratories if this has been their practice.

If an outbreak control team is convened by the Health Protection Team and specimen numbers exceed or are likely to exceed the capacity of the NHS laboratory then the specimens should be referred to the South West Public Health laboratory based at Bristol, after discussion with a senior member of the UKHSA laboratory staff. Mechanisms for the continued investigation of the outbreak will then be agreed by the outbreak control team.

As soon as an outbreak is recognised (of whatever size) the HPT will assign an outbreak number/identifier and this should be used to identify specimens associated with the outbreak or incident.

If an outbreak is identified initially by an Environmental Health Department (EHD) or Health Protection Team, the outbreak specimens should be referred to the South West Public Health laboratory in Bristol under an outbreak number/identifier assigned by the HPT.

If a food or water source is implicated, advice on sampling and sample submission should be sought from a Food Examiner at the UKHSA Food Water and Environmental Laboratory located at Porton Down in Wiltshire. The UKHSA operates a courier system for the collection and transport of FW&E samples to the laboratory at Porton.

The contact details of the Porton laboratory are:

Food Water and Environmental Microbiology Laboratory Porton
UKHSA Porton Down, Wiltshire SP4 0JG
Telephone: 01980 616766
Email: [email protected]

Other communicable diseases

Less common infections may require different specimen types or have less distinct storage and transport needs. In such circumstances, please consult with laboratory staff before taking and submitting specimens.

Test turnaround times

Information on tests performed and approximate turn-around times (TATs) can be obtained directly from the laboratory or via the laboratory user manual available on the Severn Pathology website using the link Infection Sciences (Microbiology & Virology), North Bristol NHS Trust (nbt.nhs.uk)

For communication on high priority specimens or any concerns during regular working hours, please call a member of the clinical staff:

Reporting results

Results will be reported as hard copy printouts and distributed via established routes. Results are available via electronic look up on Open ICE.

Should results be required urgently please notify the laboratory prior to sending the sample. If results need to be phoned through this must also be requested at this time and to facilitate this please supply a contact name and phone number.