Guidance

Specialist Microbiology Network Public Health Laboratory: Manchester user handbook

Updated 10 June 2025

Role of the UKHSA Specialist Microbiology Regional Laboratories, Manchester

The UK Health Security Agency (UKHSA) incorporates epidemiologists, microbiologists, infection specialists, modelers, statisticians, and other disciplines required to deliver a world-class service. Working with partners in the UK and internationally, the collective aim is to protect the population from infectious disease and reduce the burden of infectious disease.

The Manchester regional laboratory is one of 4 lead UKHSA specialised microbiology laboratories in England that 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 UK 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 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 or clusters involved in communicable disease control.
• assistance in maintaining an efficient communication network with all public health and NHS organisations involved in communicable disease control in the North West of England

The North West regional public health laboratory is accredited to the relevant international standard: ISO 15189 for medical laboratories. The Food, Water and Environment (FW&E) laboratories are accredited to ISO 17025.

Public Health Outcomes Framework

In addition to its clinical diagnostic microbiology role, the UKHSA lead laboratory in Manchester 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 health care associated infection

These public health microbiology services are available to:

• environmental health officers
• staff in health protection teams
• consultants in communicable disease control
• local authority staff and directors of public health
• clinical commissioning groups
• NHS hospitals
• private hospitals
• hospital infection control teams
• acute trusts
• ICBs

The laboratory is linked to a network of specialised UKHSA laboratories across England. This network includes laboratories testing food water and environmental samples and the 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 key personnel. The user manual is also available on the UKHSA website.

A separate laboratory user manual is available. This manual documents the clinical diagnostic and research services provided by the Manchester laboratory.

Note that support and access to food, water and environmental microbiology services can be obtained from a designated UKHSA FW&E laboratory (see the Laboratory location, working hours and access details section).

Important contacts

Who to contact during normal working hours:

In the event of a suspected outbreak or incident, use the following contact numbers in the first instance so that the laboratory can make appropriate arrangements for investigation:

Laboratory outbreak co-ordinator
Telephone number: 0161 276 6734
If unavailable, contact: 0161 276 5686 / 5699

Dr Andrew Fox
Consultant in Public Health Infection: 077362 44920 or 07825 827147

Medical advice

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

Virology advice

Virology secretary: 0161 276 8788 (automatic telephone filtering system, select option 2 for medical advice).

Bacteriology advice

Bacteriology secretary: 0161 276 8788 (automatic telephone filtering system, select option 3 for medical advice).

Outbreak Advice

Dr Andrew Fox: 077362 44920 or 07825 827147.

General enquiries

For bacteriology enquiries about laboratory results, phone the results enquiry on 0161 276 8788. You’ll get through to an automatic telephone filtering system. Select option 3 for result enquiries.

For virology enquiries about results or notifying about urgent sample deliveries email mft.virology.helpdesk@nhs.net

For all other virology enquiries phone 0161 276 8788. You’ll get through to an automatic telephone filtering system. Select option 2, then option 2 again.

For the UKHSA FW&E Laboratory in York, call 01904 468948,

Important laboratory personnel and contact details

UKHSA Consultant in Public Health Infection
Dr Andrew Fox
Email: andrew.fox@ukhsa.gov.uk
Contact number: 077362 44920 or 07825 827147

Head of Service
Dr Nicholas Machin
Email: nicholas.machin@ukhsa.gov.uk
Contact number: 0161 276 8853

Duty Microbiologist
Contact number: 0161 276 5686

Duty Virologist
Contact number: 0161 276 8853

Interim Regional Head of Operations
Ben Kirkman
Email: ben.kirkman@ukhsa.gov.uk
Contact number: 0161 276 5747

Microbiology Laboratory Manager
Simon Eccles
Email: Simon.Eccles@mft.nhs.uk
Contact number: 0161 701 6959

Virology Laboratory Manager
Alan Lord
Email: alan.lord@ukhsa.gov.uk
Contact number: 0161 276 5687

UKHSA Food, Water and Environmental Microbiology Service
York laboratory
Block 10, The National Agri-Food Innovation Campus
Sand Hutton
York YO41 1LZ

Unit Head
Heather Aird
Email: heather.aird@ukhsa.gov.uk
Contact number: 01904 468 948

Head of Operations
Mark Swindlehurst
Email: mark.swindlehurst@ukhsa.gov.uk
Contact number: 01904 468948

Out-of-hours service

Manchester Public Health Laboratory

The Laboratory provides an emergency out-of-hours service (including weekends and bank holidays) for urgent medical advice and to discuss the need for the receipt and processing of urgent specimens.

This can be arranged by contacting the on-call microbiologist or virologist through the hospital switchboard 0161 2761234.

Or:

UKHSA Consultant in Public Health Infection

Dr Andrew Fox: 077362 44920 or 07825 827147

UKHSA FW&E Laboratory, York

Out-of-hours, please contact 01904 468948

Laboratory location, working hours and access details

Manchester Public Health Laboratory

The laboratory specimen reception is at:

Microbiology Specimen Reception Postal Address:

Second floor PO Box 209
Clinical Sciences Building 2
Manchester Royal Infirmary
Manchester
Oxford Road
Manchester
M13 9WZ

Virology Specimen Reception Postal Address:

Third floor PO Box 209
Clinical Sciences Building 2
Manchester Royal Infirmary
Manchester
Oxford Road
Manchester
M13 9WZ

Laboratory working hours:

• Monday to Friday 8:30am to 5pm
• weekends and bank holidays 8:30am to 12:30pm

UKHSA FW&E Laboratory, York
Block 10, The National Agri-Food Innovation Campus
Sand Hutton
York, YO41 1LZ

Laboratory working hours:

• Monday to Friday 8:30am to 6pm
• 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 through the hospital switchboard.

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

Please notify the laboratory of the ILog or 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 North 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 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 (health protection team) or other appropriate authority there should be a discussion between the initial investigating (NHS) laboratory or with the Consultant in Public Health Infection (CPHI) or 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 regional UKHSA laboratory.

If a local NHS laboratory is unable to provide this support at any time, for whatever reason, UKHSA will plan to ensure that these services are provided. If any difficulties with existing or new arrangements are encountered, please contact the Consultant in Public Health Infection (CPHI) on (077362 44920 or 07825 827147) or Head of Operations (0161 276 5747) who will make sure that arrangements are securely in place.

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 or 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
• tuberculosis (TB) 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 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 the sample submission safety considerations 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
• the date the sample was taken
• patient’s date of birth
• patient’s postcode (request form only)

The above will assist us in the surveillance of communicable diseases. Provide full details of where to send the result and who to contact if we need to report an urgent, significant result. Provide an outbreak number if available.

Sample collection and submission

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 and second name
• date of birth

Faeces

The specimen size should be at least 5ml or 5 grams. 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
• contamination with urine should be avoided
• a portion of faeces can then be collected with the spoon provided in the specimen pot and transferred to the specimen container
• the specimen pot should then be placed inside the plastic screw top container, and sealed into the plastic pre-paid postal envelope along with the outbreak request form (see appendix 2)
• all materials used to collect the specimen should be discarded via the biological waste route relevant to sending department and as per local risk assessment

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.

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 public health scientist 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

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

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.

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).

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 (without waiting for confirmation by culture). A 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. 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, 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 or incident or outbreak management team

Sample submission safety considerations

Health and safety

The specimen containers and mail transport systems provided by the laboratory should be used. The individual requesting or taking specimens from patients known to be infectious must ensure that the form, sample, and specimen bag are appropriately labelled.

It is essential, where the requester knows or strongly suspects that the patient is infected with a dangerous pathogen that this specific information is provided with every specimen or request form.

Packaging of specimens

This is guidance only. Each submitter location will need to carry out their own suitable and sufficient risk assessment and COSHH assessments.

Specimens must be placed in the appropriate specimen container, which must be securely closed, and any accidental spillage cleaned immediately, with an appropriate disinfectant. The specimen container must be packaged to contain leakages should they occur in transit, as described in appendices 1 to 4.

Each specimen should be placed in a clear plastic double (marsupial) self-sealing bag with one compartment containing the request form and the other the specimen. One specimen per specimen bag.

Where a needle has been used to obtain the specimen, the needle should be disposed of safely into an approved sharps container at the point of use,

The needle must not be included in the packet transported to the laboratory.

Packaging of ‘high risk’ specimens

Specimens from patients in the ‘infection risk from blood’ category should be placed in the appropriate specimen container, which must be securely fastened, and any accidental spillage cleaned immediately with an appropriate disinfectant. The specimen container must be wrapped in absorbent material to contain leakages should they occur in transit.

This should be placed and sealed in a clear plastic double (marsupial) self-sealing bag. One specimen per specimen bag. This must then be placed and sealed in a second clear plastic double (marsupial) self-sealing bag with one compartment containing the request form and the other the specimen.

Transport of specimens

It is a legal requirement that all diagnostic samples carried on the public road must be packaged and transported in compliance with The Carriage of Dangerous Goods and Use of Transportable Pressure Equipment Regulations 2011. Under these regulations, it is the sender’s responsibility to ensure that they are complied with. See Guidance on regulations for the transport of infectious substances 2021 to 2022.

High risk incidents and safety

This is guidance only. Each submitter location will need to carry out their own suitable and sufficient risk assessment.

Universal precautions must be observed, and appropriate personal protective equipment worn when specimens are collected (sterile gloves to take blood, masks, protective eyewear and a plastic apron if splashing of blood or other body fluids is likely to occur). Any inoculation incidents (needlesticks or contamination of conjunctiva, mucous membranes, or broken skin, with blood or body fluids), must be reported as soon as possible – within 2 hours – to your occupational health service so that any required action can be instituted promptly.

This procedure must be followed whether or not the patient is perceived to be high risk.

Methods of specimen submission

Direct submission to the laboratory

For specimens other than faeces, contact the Virology Laboratory on
0161 276 8788 (select option 2).

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

Submission to the laboratory via GP surgeries

It may be possible for local authorities to submit samples via local GP surgeries. This is only possible where it has been clearly established that local GP surgeries submit samples to the Manchester 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. The packs include first class pre-paid postage to the regional laboratory (see appendices). They will be supplied with Tracked 24 Royal Mail labels, but the package does not need to be taken to the post office, it can be placed in a post box if required.

Details of how more postal packs can be obtained

Environmental health departments and health protection teams will be provided with postal transport packs for these purposes. These packs contain the appropriate packaging materials, outbreak request form, and instructions for use. Any specimens sent by post must comply with infectious substances transport regulations:

• Transportation of infectious substances: Blood borne viruses (BBV)
• Packaging and transport requirements for patient samples – UN3373

Further supplies of faeces postal sample packs, outbreak request forms and specimen containers are available on request from donna.johnson@ukhsa.gov.uk or alan.lord@mft.nhs.uk

Submission to the laboratory using an agreed UKHSA courier

In special circumstances (for example, the nature or scale of the outbreak) please contact the laboratory to discuss and organise courier transport, additional specimen containers and any other materials.

UKHSA Consultant in Public Health Infection:

Dr Andrew Fox
Email: Andrew.fox@ukhsa.gov.uk
Contact number: 077362 44920 or 07825 827147

Head of Service:

Dr Nicholas Machin
Email: nicholas.machin@ukhsa.gov.uk
Contact number: 0161 276 8853

Interim Regional Laboratory Head of Operations:

Ben Kirkman
Email: ben.kirkman@ukhsa.gov.uk
Contact number: 0161 276 5747

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 regional UKHSA public health 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 regional UKHSA laboratory will assign an outbreak number or 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 or health protection team the outbreak specimens should be referred to the Regional UKHSA Public Health laboratory in Manchester under an outbreak number or identifier if one has been allocated by the EHD or HPT.

For ILog numbers:

• Bacteriology - contact 0161 276 6734
• Virology - contact 0161 276 8843

If a food or water source is implicated then seek advice on sampling and sample submission from a Food Examiner at a UKHSA FW&E Laboratory. UKHSA operates a courier system for the collection and transport of FW&E samples to the laboratory.

The contact details of the York laboratory are:

UKHSA FW&E Laboratory, York
Block 10, The National Agri-Food Innovation Campus
Sand Hutton
York YO41 1LZ
01904 468948

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. (See important contacts).

Test turnaround times

Information on tests carried out and approximate turn-around-times can be found in our laboratory handbook.

Alternatively, information can be obtained direct from the laboratory. Call
0161 276 5686.

For communication on high priority specimens or any concerns during regular working hours, call 0161 276 5686 or 0161 276 5699.

For UKHSA FW&E Laboratory, call 01904 468948.

Reporting results

Results will be reported as hard copy printouts or electronically via elab and FW&E, and distributed by established routes. Urgent results will be telephoned by agreement.

Should results be required urgently, notify the laboratory prior to sending the sample. If results need to be phoned through this must also be requested prior to submitting the samples. Please provide a contact name and telephone number.

Appendices

For further information, see the appendices on the main landing page.

• Appendix 1: Outbreak request form
• Appendix 2: Postal packaging instructions for faecal samples
• Appendix 3: Postal packaging instructions for Flu Kit samples
• Appendix 4: Additional specimen types that may be submitted to laboratory