Guidance

Specialist Microbiology Network: Public Health Delivery Laboratory North East of England

Updated 22 October 2024

Role of UKHSA specialist microbiology laboratories

Specialist microbiology laboratories provide specialist and reference microbiology laboratory testing and expert advice. It offers a comprehensive range of clinical diagnostic and public health microbiology tests and services in support of the NHS, other public health colleagues, local authorities and allied healthcare providers.​

UK Health Security Agency  (UKHSA) has a network of 5 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 (up to 500 specimens per day) 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 (for example flu pandemics)
• testing for look back exercises for health protection teams (HPTs), acute NHS trusts, clinical commissioning groups (CCGs), 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 CCGs)
• 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 UKHSA (including HPTs) and externally, for example local authorities and primary care groups or clusters involved in communicable disease control
• microbiology support for the investigation, management and control of incidents of infection and outbreaks of communicable disease both during and out of normal working hours
• assistance during field investigations by processing clinical samples
• 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 North East region

All UKHSA laboratories delivering specialist and reference testing either have UKHSA accreditation or are working towards it. The Food, Water and Environment (FW&E) laboratories are all recognised as Official Testing Laboratories and are accredited by UKAS.

Public health outcomes framework

In addition to its clinical diagnostic microbiology role, the UKHSA lead laboratory in the north east, Newcastle upon Tyne Hospitals NHS Foundation Trust, 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 be adopted
• advice on interpretation of test results and additional investigations that may be helpful
• support to incident or outbreak investigation teams
• prompt communication of results in agreement with published turnaround times
• follow up or clearance testing of patients or contacts of patients in whom organisms of public health importance are detected.
• support for trusts and 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
• clinical commissioning groups
• 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 (Microbiology Research services).

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

Please note that support and access to food, water and environmental microbiology services can be obtained from the UKHSA FW&E laboratory at York (refer to ‘Investigation of local outbreaks’).

Important contacts: Newcastle upon Tyne

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

Who to contact during normal working hours

In the event of a suspected outbreak or incident please use the following

contact numbers:

General and Clinical Virology enquiries – 0191 223 1019

GP enquiry line – 0191 223 1019

Out of Hours – 0191 233 6161

Medical advice

During working hours, our medical staff will be happy to help you with any 

enquiries that you may have. Our office will put you through to the most

appropriate person to answer your call: 0191 223 1019

General enquiries

For enquiries about laboratory results please phone the switchboard on 0191 233 6161 and ask for the Microbiology department

Important laboratory personnel and contact details

Consultant in Public Health Infection, Field Service North East Yorkshire and Humber

Field Service North East and Yorkshire and Humber Dr David Tate

Email:  david.tate@ukhsa.gov.uk

Contact number: 0300 303 8596 (opt 0, then opt 1)

Work Mobile: 0782 4836189

Duty microbiologist

Out of hours, please contact the Newcastle upon Tyne Hospitals NHS Foundation Trust switchboard 0191 233 6161 and ask to speak to the on call Consultant Microbiologist

Duty virologist

Out of Hours please contact the Newcastle upon Tyne Hospitals NHS Foundation Trust switchboard on 0191 233 6161 and ask to speak to the duty virologist

Within working hours please contact the duty virologist on: 0191 223 1019 option 2.

Email (non urgent queries only): nuth.newcastlevirology@nuth.nhs.uk  

Regional Head of Operations North East, Yorkshire and Humber

Anne Barrett

Email: anne.barrett@ukhsa.gov.uk

Contact number: 0191 222 3758

Mobile: 07983 408949

Laboratory manager

Jennifer Collins

Email: jennifer.collins24@nhs.net

Contact number: 0191 213 7292

For details of access to the food, water and environmental testing

service please contact UKHSA FW&E Laboratory, York Laboratory

Manager:

Laboratory manager

Amy Johnson

Email: amy.johnson@ukhsa.gov.uk

Contact number: 020 849 53 313

Or

Unit head

Dr Heather Aird

Email: heather.aird@phe.gov.uk

Contact number: 01904 468 948

Out of hours service

The FreemanLaboratory provides an emergency out of hours service for urgent advice (out of hours: 5pm to 9am on weekdays, and anytime at weekends and on bank holidays):

On call Microbiologist: Call 0191 233 6161 and ask to speak to the on call Consultant Microbiologist.

On call Virologist: Call 0191 233 6161 and ask to speak to the on call Consultant Virologist.

To submit microbiology samples to the Newcastle laboratory out of hours please call the switchboard on 0191 233 6161 and ask to speak to the on call Microbiology Biomedical Scientist.

To submit virology samples to the Freeman laboratory out of hours please call the switchboard on 0191 233 6161 and ask to speak to the on call Virologist.

To submit FW&E samples to the York laboratory out of hours call 01904 469 948 and speak to the on call FW&E Microbiologist.

Please contact the laboratory in advance of submission, with details of the incident or outbreak and investigations required. Please notify the laboratory of the i-Iog/outbreak identifier if one has been assigned.

Laboratory location, working hours and access details

Regional laboratory Newcastle

Microbiology and Virology Department
The Newcastle upon Tyne Hospitals NHS Foundation Trust
Freeman Hospital, Freeman Road
High Heaton
Newcastle upon Tyne
NE7 7DN

The Freeman Hospital Laboratory is open 8.30am to 5pm (excluding bank holidays). For access at weekends and bank holidays please contact the on call Microbiology Biomedical Scientist via the Switchboard on 0191 233 6161

Please see a map of the Freeman site below

FW&E Laboratory York

The laboratory is located as follows:

UKHSA FW&E Microbiology Laboratory, York
Block 10 Food and Environmental Research Agency
Sand Hutton
York
YO41 1LZ

NHS laboratories and access to public health testing in the North East region

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

All NHS laboratories (including former collaborating laboratories) have responsibilities for health protection which includes 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
• detection of local outbreaks through monitoring laboratory findings
• detection and prompt reporting of unusual occurrences of public health significance
• providing initial laboratory support for outbreaks, incidents and look back exercises as appropriate
• attendance of appropriate staff at local community control of infection meetings and
• Incident outbreak control team meetings
• advice on appropriate investigations, interpretation of results, among others
• forwarding of appropriate specimens to reference laboratories

If outbreak specimens are normally 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 or other appropriate authority there should be a discussion between the initial investigating (NHS) laboratory or HPT with the regional microbiologist or duty consultant microbiologist in the lead 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 Regional Head of Operations 0191 222 3758 or 07983 408949 or Freeman Microbiology Laboratory Manager 0191 213 7292 who will make sure that arrangements are securely in place.

Few NHS laboratories have a Food, Water and Environmental testing capability. In the event of anoutbreak or incident where a possible link to food or water has been made arrangements can be made for samples to be tested by the York FW&E Laboratory.

Definition of a public health microbiology specimen

A public health microbiology specimen is usually submitted to determine the cause and extent of an outbreak in a community (institution, family group or the wider community) or to see whether an observed cluster of cases is related and constitutes an outbreak.

Specimens may also be submitted to detect spread and contain and or prevent an outbreak (for example, diphtheria, group A streptococcus).

Patient specimens may also be submitted for clearance purposes (for example, faeces for Escherichia coli O157) or to detect carriage of pathogens in asymptomatic individuals (for example Salmonella typhi)

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, poliomyelitis
• look back exercises for example carriage of blood borne viruses in a health care worker
• 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 regional microbiologist, 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 good 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
• the 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 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 5 mililitres. 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 or virologists 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, adenovirus, sapovirus and astrovirus

Throat Pharyngeal swabs

For detection of carriage of Neisseria meningitidis, 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.

Please note: All swabs specimens must be Transwab or similar type swabs. Supplies can be obtained from Freeman Microbiology laboratory upon request.

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 Health Protection Team on 0300 303 8596 in the first instance who will liaise with the virology laboratory on what specimens are required and how these should be collected and submitted.

 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 submitting samples to the laboratory.

Newcastle: Please direct to the Department of Microbiology at Freeman Hospital . Directions are outlined in ‘Laboratory location, working hours and access details’ above.

Submission to the laboratory via Post

Specimens can be submitted to the laboratory by post provided they are packaged according to current postal regulations. Details of postal packs are given in Appendix 3.

Details of how more postal packs can be obtained. Environmental health departments will be provided with an initial small supply of postal transport packs for these purposes. These packs contain the appropriate packaging materials, instructions for use and a request form to accompany the specimen (example, in Appendix 3).

Any specimens sent by post must comply with infectious substances transport regulations.

Further supplies of sample packs, request forms and specimen containers are available by contacting the FW&E laboratory in York.

Postage costs

A separate pack should be used for each specimen. Local authorities are expected to provide postage and it is not expected that patients should pay. Specimens must be sent by First Class post. In special circumstances for example the nature or scale of the outbreak, the Head of Operations or Laboratory Manager at the lead UKHSA laboratory may, by agreement, organise courier transport, additional specimen containers and any other materials

DX tracked specimens

If sending samples by DX courier services please use the following address:

DX6361207
Newcastle 95NE

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 Lead UKHSA Public Health laboratory or collaborating laboratory, 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 Lead UKHSA laboratory or collaborating centre 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 Freeman Laboratory under an outbreak number/identifier if one has been allocated by the EHD or HPT.

If a food or water source is implicated then advice on sampling and sample submission should be sought from the UKHSA Food Water and Environmental Laboratory located in York.

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 direct from the laboratory, please call: 0191 223 1019 .

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 via established routes.

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 at this time.