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Laboratory Medicine

Microbiology and Serology

Click here to view Microbiology and Serology test information

Guidance for Test Requesting and Interpretation of Results: Click Here

Protocol for Clinical Microbiological Advice Out of Hours: Click Here

Use of the Laboratory

In these days of clinical budgeting everyone is encouraged to use the laboratory in a cost-effective manner.

The microbiology laboratory can help to:

  • provide or confirm a diagnosis
  • suggest appropriate antibiotics
  • monitor response to treatment

Inevitably judgements will have to be made about whether to treat blind or request an investigation which may cost more than a course of antibiotics. 

Failure to investigate may lead to:

  • An increased use of antibiotics causing possible harm to patients
  • An increasing reliance on expensive new broad spectrum agents
  • Increasing antibiotic resistance in the community (and concomitant lack of knowledge of this)
  • Difficulty in establishing a diagnosis when a patient has failed to respond to treatment

Laboratory Methods

Microbiology assesses the clinical relevance of investigations performed and the reliability of interpretative comments in consultation with its users through user surveys and general feedback.

New tests/services may be commissioned through discussions with the Clinical Microbiologists.

Methodology and testing is benchmarked against the Health Protection Agency (HPA) national standard operating procedures, whose web-site offers valuable information on microbiological disease processes and associated microbiological investigations.

Contacts for the Microbiology Service:

For general result and specimen enquiries, clinical advice and key contact details for the Microbiology service: Click Here

For Infection Prevention key contact details: Click Here

Test Repertoire:

Microbiology provide a comprehensive traditional bacteriology service.  Please access Microbiology and Serology test information using the blue box at the top of this page. 

Routine Requests

Specimens for routine investigations should be collected as early in the day as possible to ensure that they arrive in the laboratory during normal working hours.

Urgent Requests

Urgent Requests must be telephoned to alert the laboratory staff of their arrival. The request form must be clearly marked URGENT.

The Microbiology BMS on call MUST be contacted by the Switchboard Operator when ANY specimen requires urgent microbiological analysis out of normal working hours.   It is the responsibility of the doctor initiating the request to ensure that all urgent and important samples are expected by the relevant Laboratory.

Add on Tests (requesting further tests on samples already received in the laboratory)

For information: Click Here 

Frequency of assays

Turn Around Times

For information on expected turnaround time please access Microbiology and Serology test information using the blue box at the top of this page. 

Key Factors which are known to affect the performance of Microbiology tests or interpretation of results

In general all specimens should reach the laboratory as soon as possible after being taken. Micro-organisms may be susceptible to drying, heat or cold (particularly freezing). In specimens such as sputum and urine they can multiply to inappropriate levels. Genital pathogens and anaerobic organisms are particularly sensitive to delays before culturing All bacterial swabs should be placed in Amies transport medium (the clear jelly seen in may swab tubes) that prevents drying, maintains pH and excludes oxygen; and kept at room temperature until delivery to the laboratory. Urine for culture should always be taken into the borate containing red-topped 30ml bottles to prevent bacterial overgrowth. Refrigerate until delivery. Specimens of clotted blood (brown top “serum” tubes) are suitable for all serological tests. Refrigerate until delivery: do NOT freeze. Blood cultures - Keep at room temperature and send the broths to the laboratory. Do not place on radiators etc as they get too hot (many pathogens cannot tolerate temperatures over 37°C).

Web page 53 last updated: 6th December 2018


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Visiting cancelled

Due to the increasing number of cases of coronavirus across the UK, York Teaching Hospital NHS Foundation Trust has made the decision to cancel all visiting to all its hospital sites in order to ensure the safety of patients and staff.

There are three exemptions to the ruling which are for one parent of a sick child under 18, for the partner of a woman giving birth and end of life patients at the discretion of the ward sister.

We would ask people to respect this decision and to treat our staff, who will be enforcing the visiting restrictions, with courtesy and respect.  For more information visit our website.

Outpatient appointments

We know that NHS services will come under intense pressure as the coronavirus spreads, and as a Trust we need to redirect staff, free up staff for refresher training and carry out any works as necessary, so we are able to maximise capacity for patients for when the number of infections peak.  We also need to reduce the number of people coming into our hospitals to protect our patients, as well as keeping our staff safe, well and able to come into work.

To do this, with effect from Tuesday 24 March 2020, along with other trusts in the Humber Coast and Vale partnerships, we have made the collective decision to suspend all non-urgent routine outpatient appointments for at least three months.  Urgent and emergency cases and cancer appointments will be carrying on as normal.

These are unprecedented times and we thank you for your understanding.  We know many people waiting for treatment will be disappointed or worried but please not contact the hospital as we will be contacting everyone directly affected in the coming days and weeks.

If you do not receive a letter or a phone call from the hospital, please turn up for your scheduled appointment as normal unless you have symptoms of coronavirus, a cold, flu or norovirus in which case you should contact us to cancel your appointment by clicking here.

Coronavirus (COVID-19)

If you have symptoms associated with coronavirus including a new continuous cough and a high temperature, you are advised to stay at home for 7 days.

Please do not book a GP appointment or attend your GP practice.

If you live with other people, they should stay at home for at least 14 days, to avoid spreading the infection outside the home.  After 14 days, anyone you live with who does not have symptoms can return to their normal routine.

But, if anyone in your home gets symptoms, they should stay at home for 7 days from the day their symptoms start. Even if it means they're at home for longer than 14 days. The most up-to-date public guidance is always online at

If your symptoms are serious, or get worse, NHS 111 has an online coronavirus service that can tell you if you need further medical help and advise you what to do.  Only call 111 direct if you are advised to do so by the online service or you cannot go online.