Guidance

Public health laboratory, East of England: user handbook

Updated 28 November 2024

Role of the UKHSA Specialist Microbiology Network

The 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
• 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 or legal requirements
• efficient and timely communications with public health organisations, both within the 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
• expert medical and scientific microbiological advice, including access to UKHSA experts locally and nationally as necessary
• 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 East of England

All UKHSA diagnostic laboratories delivering specialist and reference testing either have accreditation to ISO 15189 standards with United Kingdom Accreditation Service (UKAS) or are working towards it. 

The Food, Water and Environment (FW&E) laboratories are all recognised as EU Official Testing Laboratories and are accredited by UKAS.

Public Health Outcomes Framework

In addition to its clinical diagnostic microbiology role, the UKHSA East of England laboratory in Cambridge 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 or HPTs in the specialist investigation of healthcare associated infection

These public health microbiology services are available to:

• staff in health protection teams
• local authority staff and directors of public health
• Integrated Care Boards
• acute NHS trusts

The East of England 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) as part of the Specialist Microbiology Service.

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. A separate laboratory user manual is available that documents the clinical diagnostic and research services provided by the UKHSA Cambridge laboratory.

Please note that support and access to Food, Water and Environmental Microbiology Services can be obtained from UKHSA Food, Water and Environmental Microbiology Services

Food, Water and Environmental Microbiology Laboratory London

Food, Water and Environmental Microbiology Laboratory London
61 Colindale Avenue
London
NW9 5EQ

Email fwecolindale@ukhsa.gov.uk

Telephone 1 0208 327 6548 / 6549 / 6550

Key contacts

Hours of service

The laboratory at Addenbrooke’s Hospital provides a 24-hour service every day of the year for microbiology and virology advice and to receive and process specimens. Specimens can be delivered to the laboratory reception.

A reduced service is provided outside of normal core (8am to 6pm) working hours, at weekends and on bank holidays. During these times, specimens can be passed through the secure specimen hatch outside the laboratory doors on level 6 at any time. There is an emergency contact system for specimen processing and clinical advice.

In the event of an incident or outbreak, please contact the laboratory in advance of submission with details of the investigations required along with the log or outbreak identifier, if one has been assigned.

Who to contact

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

The laboratory requests that, whenever possible, urgent requests are phoned ahead of specimen transportation so that the specimens can be identified on receipt.

Key personnel and contact details

Microbiology pre-analytical reception at Addenbrooke’s Hospital: 01223 257034 (Ext 257034) or 01223 257037 (Ext 257037)

Addenbrooke’s Hospital switchboard: 01223 245151

In case of any difficulty, contact:

• Dr Derren Ready, Consultant in Public Health Infections, Field Services, Southwest (for interim consultant in public health infections cover)
  • 07920 081927
• Clinical Services Director, UKHSA Cambridge, Dr Jenifer Mason
  • 01223 348130 or via the hospital switchboard on 01223 245151
• Regional Head of Operations, Laura Ryall
  • 01223 257021 or 07765 483918
• Laboratory Manager, Martin Strickland
  • 01223 349796 or 07879 113831

Medical advice

During working hours any of the medical microbiology or virology staff will be happy to help you with any enquiries that you may have. Our office administrators will put you through to the most appropriate person to answer your call.

Outside normal hours the duty biomedical scientist (BMS) for sample examination can be contacted via the Addenbrooke’s Hospital switchboard on 01223 245151.

Note: Do not phone the on-call biomedical scientist until the specimen is ready.

Contact the on-call microbiologist or virologist for advice on bacteriology or virology clinical advice, diagnosis, antimicrobial treatment or infection control via the Addenbrooke’s Hospital switchboard on 01223 245151.

General enquiries

During working hours, any of the microbiology staff will be happy to help you with any enquiries that you may have. Our office administrators will put you through to the most appropriate person to answer your call.

Laboratory location and access details

The UKHSA Cambridge laboratory is located at Addenbrooke’s Hospital, Hills Road, Cambridge. Details of parking arrangements and opening hours are below.

Map of Addenbrooke’s Hospital on the hospital’s website

Addenbrooke’s Hospital on Google Maps

Figure 1. Map of Addenbrooke’s Hospital showing laboratory block

We are here

The laboratory is located on the sixth floor of the laboratory block.

The postal address is:

UK Health Security Agency
Clinical Microbiology and Public Health Laboratory
Box 236, Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 0QQ

NHS laboratories and access to public health testing in the East of England

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 or outbreak control team meetings
• advice on appropriate investigations, interpretation of results and so on
• 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 and the lead microbiologist or virologist or duty consultant microbiologist or virologist in the Cambridge 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 (but please contact us first to discuss laboratory requirements, transport and so on).

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.

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).

Some circumstances in which public health specimens may be submitted are:

• 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 or 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 healthcare worker
• TB contact tracing
• investigation of a cluster of cases, for example Legionnaires’ disease, which could have a common source

Such specimens are usually submitted at the request of:

• senior staff of an HPT
• an environmental health officer
• at the request of, or on behalf of, the director of public health or consultant in communicable disease control
• at the instigation of the lead microbiologist or virologist, for example for specialist typing in the investigation of episodes of healthcare 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.

Sample collection and submission

Please ensure that the request form is completed fully before it is given to the patient.

Ask the patient to complete all details on the specimen container before collecting the specimen. The specimen container must be labelled with:

• patient’s full name (first and surname)
• patient’s NHS number or other unique numerical identifier
• the date the sample was taken
• patient’s date of birth

The information 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.

Faeces samples

See appendices for sample collection and postal instructions.

The specimen size should be at least 5ml. When collecting  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 that 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
• shiga toxin-producing E. coli (STEC) including E. coli O157
• diarrhoeagenic E. coli (other than STEC)
• campylobacter
• Clostridium difficile
• vibrio
• plesiomonas
• Yersinia enterocolitica
• cryptosporidium, cylospora, entamoeba and giardia species
• adenovirus
• norovirus
• rotavirus
• sapovirus

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

• 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

Throat or pharyngeal swabs

For detection of:

• carriage of Neisseria meningitidis, the swab should be taken through the mouth (sweeping posterior pharynx behind the uvula) and submit for culture

• group A streptococcus, swab the tonsillar area and submit for culture

• of Corynebacterium diphtheriae, nose and throat swabs should be submitted for culture

• Bordetella pertussis, a pernasal swab should be collected and submitted for PCR

Note: 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

Outbreaks of respiratory virus infections (for example COVID-19, influenza, respiratory syncytial virus (RSV)) can occur in institutions. The HPT incident management team will advise when specimens from these outbreaks need to be submitted. The standard specimen type is combined nose and throat swab and use a viral transport medium tube (Appendix 6: Viral swab). Please take one viral swab for flu and other respiratory viruses including COVID-19. Please seek further advice of the virology laboratory if there is any query regarding specimens or testing pathways. Appendix 5: Flu kits can be obtained from the laboratory (these include instructions for collection).

Avian influenza

In the case of contacts of highly pathogenic avian influenza, please contact HPT immediately for risk assessment and follow their instructions if nose and throat viral swab sample collection and testing are advised. See the current UKHSA guidance for Management of contacts of highly pathogenic avian influenza H5N1 during the 2023 to 2024 avian influenza season.

In the case of suspected avian influenza, please contact HPT or duty virologist immediately for high consequence infectious disease (HCID) risk assessment, and follow their advice on sample collection, transport and testing. The current UKHSA guidance should be followed at Avian influenza: guidance, data and analysis.

Two samples should be taken:

• an upper respiratory tract sample (combined nose and throat viral swabs or nasopharyngeal aspirate)
• if obtainable, a lower respiratory tract sample (sputum or an endotracheal tube aspirate if intubated)

Measles

To investigate outbreaks of measles following discussion with HPT, a viral swab should be used for mouth salivary specimen and use a viral transport medium tube (Appendix 6) for measles PCR. 

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 Microbiologists 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 Coxiella
• 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.

See Hours of service.

Submission to the laboratory via GP surgeries

It may be possible for local authorities to submit samples via GP surgeries. This is only possible where it has been clearly established that GP surgeries connect with transport services that deliver samples to the UKHSA Cambridge Laboratory at Addenbrooke’s Hospital. Results will be returned to the sender. The HPT arranging the test should confirm the requesting location for the delivery of reports (for example East of England HPT or Public Health London).

Submission to the laboratory via other hospital pathology departments

There are daily transport runs to the UKHSA Cambridge Laboratory from East and North Hertfordshire. Samples may be dropped off at this location for transportation to the UKHSA Cambridge Laboratory by prior arrangement.

Note: An agreement must be reached with the hospitals involved and specimens must be appropriately labelled.

Results will be returned to the sender. The HPT arranging the test should confirm the requesting location for the delivery of reports (for example East of England HPT or Public Health London).

Submission to the laboratory via the 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 or HPTs 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 (see Appendix 2: Request and Appendix 3: Postal).

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 UKHSA Cambridge Laboratory:

• Microbiology pre-analytical reception at Addenbrooke’s Hospital

  • 01223 257034 (Ext 257034) or 01223 257037 (Ext 257037)

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 (see Appendix 3: Postal).

Pre-paid postal kits are available to the HPTs for collection and submission of faeces samples for enteric outbreak investigations and are distributed to the HPT from the laboratory for allocation to outbreak sites (see Appendix 4: Patient).

Submission to the laboratory using an agreed UKHSA courier

In special circumstances, related to the nature or scale of the outbreak, the Regional Head of Laboratory Operations at the UKHSA Public Health Laboratory may, by agreement authorise 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 outbreaks 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, the specimens should be referred to the regional 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 or UKHSA laboratory or collaborating centre will assign an outbreak number or identifier (for example zone number), 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 HPT, the outbreak specimens should be referred to the UKHSA laboratory in Cambridge under an outbreak number or identifier, if one has been allocated by the EHD or HPT.

Note: Food, water or environmental samples should be sent to the UKHSA Food, Water and Environmental (FW&E) microbiology laboratory at Colindale, and you should continue to follow current protocols to maintain the integrity of the samples during transport unless notified otherwise. Not all should be refrigerated.

UKHSA Food, Water and Environmental Microbiology Services

Food, Water and Environmental Microbiology Laboratory London

Food, Water and Environmental Microbiology Laboratory London
61 Colindale Avenue
London
NW9 5EQ

Email fwecolindale@ukhsa.gov.uk

Telephone 1 0208 327 6548 / 6549 / 6550

For specimens other than faeces, please contact the laboratory manager to arrange the provision of appropriate collection kits.

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 senior clinical  or laboratory staff before taking and submitting specimens.

Test turnaround times

Information on tests performed and approximate turnaround times (TATs) can be found in our Clinical Laboratory Handbook, which is available at East of England public health laboratory: services (see Cambridge UKHSA Clinical Microbiology Service User Handbook).

Alternatively, information can be obtained direct from the laboratory on 01223 257037.

Reporting results

Results will be securely reported, electronically through networked links or through Net delivery to a designated nhs.net account to sender sites or as hard copy where links are not established. Urgent results will be telephoned by agreement.

Results will be returned to the sender. The HPT arranging the test should confirm the requesting location for the delivery of reports (for example East of England HPT or Public Health London).

Complaints procedure

A complaint relating to public health microbiology may be made via any normal means of communication, normally to the Consultant in Public Health Infection (CPHI), the Head of Laboratory Operations or Clinical Services Director.

All complaints will be dealt with according to UKHSA’s complaints procedures.

Further information can be found at Complaints procedure.