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Oxford University Hospitals NHS Foundation Trust

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Making a request for sample processing

Listed here is the most frequently needed information. If you cannot find the information you need please refer to our Microbiology Laboratory Users Manual or contact us.

Requests from OUH staff using the EPR system

For OUH patients the electronic patient record (EPR) must be used to request Microbiology Laboratory tests.

There is information for OUH staff on the OUH intranet for EPR support and training, and for EPR downtime procedures.

Ensure you make the request for the correct patient, and select the correct patient episode. This provides the lab with patient identification (NHS number, hospital number, name and date of birth), patient location and consultant.

  • Select 'Requests and Prescribing' option from menu on left-hand side of screen.
  • Click on 'Add' to make a new request.
  • Use MCS to search for types of culture request, PCR to search for molecular assays etc.


  • type the type of sample or culture request into the 'Find' search box, e.g.
    • Blood culture MCS
    • Urine MCS
    • Wound swab
    • Pus / deep wound / fluid / abscess / aspirate MCS
    • Mycobacteria culture MCS
    • HCV Ab screen
    • CMV IgG
    • Surface swab MCS is the correct option for eye, ear, throat, ulcer and skin swabs.
  • Click on the appropriate option that appears in the box below, and select 'Done' to add the test.
  • Provide appropriate clinical details, including:
    • brief clinical history and date of onset
    • risk factors for infection (e.g. immunocompromise, drugs, intravenous drug use)
    • travel history, if relevant
    • any prior, present, or planned antimicrobial therapy.
  • Provide your bleep or contact number so that you can be contacted if there are any problems or significant positive results.
  • Confirm the request by clicking 'Sign'.
  • Label each sample with the label printed via EPR, but do not cover the bar code on blood culture bottles.

Requests from primary care

For patients in primary care in Oxfordshire, SunquestICE™ should be used to request Microbiology Laboratory tests electronically.

Request cards

Where electronic requesting is not available, there is a standard request card suitable for all specimens.

Filled in correctly, this helps reduce data entry errors, speed up turnaround times and ensure correct locations for reports and invoices. It is available to GPs from the OUH Haematology Laboratory:

Haematology Laboratory: 01865 220336

Microbiology request cards are blue. It is important to use the correct one, so that samples are directed to the correct laboratory. The NHS number and hospital number are used to link samples to patients' records, so it is essential that this information is recorded on all requests.

Patient collected samples

Patients should not be asked to deliver their own samples to the Microbiology Laboratory. Outpatient samples should generally be delivered via the GP.

In the event of a patient delivering their own sample, this should be received at the specimen reception hatch on Level 7.

Consent for testing

It is the responsibility of the requesting doctor to obtain appropriate informed consent for all investigations, including testing for blood-borne viruses.


Specimen containers should be clearly identifiable. Use a sticky label when available but do not cover any bar codes. Electronic requests will always generate a sticky label that must be used for these types of request.

When making multiple electronic requests, make sure to put the correct label on each sample. Otherwise, the patient's full name and date of birth, NHS and/or hospital number should be clearly written.

Factors known to influence the performance of laboratory tests

A number of factors can affect the accuracy of the results generated by the Microbiology Laboratory. Examples are included in the table below.

Factor adversely influencing outcome of test How to optimise the accuracy of data reported by the laboratory
Delayed transportation to the laboratory Transport samples as promptly as possible to the laboratory.
  Discuss urgent samples with the laboratory / on-call Microbiology Registrar to alert the lab to their arrival.
  For storage of samples prior to transportation, see section 3.2.
Contamination at source or during transportation Pay close attention to optimum sampling techniques, including aseptic technique.
  Ensure samples are sealed appropriately to avoid subsequent contamination.
Insufficient volume of sample Aim to fill blood bottles as far as possible
  Guidelines for taking blood cultures in adults and neonates: 8-10 mls of blood/bottle recommended for adults, 1 ml for neonates.
  For serological and blood molecular assays the EPR system will print the correct number of labels for the number of blood tubes required. Please ensure these are well-filled.
  Send multiple separate samples to confirm the presence of infection in deep-seated surgical sites (e.g. minimum five samples recommended for bone and joint infection).
Incorrect sample container Ensure blood samples are sent in appropriate tubes; check with the laboratory first if in doubt. Specimen labels produced by the EPR system specify the correct container.
  Never pour blood from one container to another.
Inappropriate sample or request Avoid sending samples for which clinical interpretation will be difficult, e.g. surface swabs from chronic ulcers, where results will reflect colonisation only.
  Provide correct and up-to-date information on the patient's clinical history, including consideration of travel / occupation / drug history / risk factors where relevant.
Inappropriate timing of sample Whenever possible, send samples to Microbiology prior to initiation or change of antibiotic therapy. When this is not possible, prioritise sample collection as soon as possible after the first dose of antibiotics.
  Septic shock is a clinical emergency and urgent antibiotic treatment should always be initiated; do not delay if it is difficult or unsafe to obtain cultures.

High-risk specimens

A high-risk specimen is one from a patient known to have been infected with:

  • hepatitis B or C virus
  • human immunodeficiency virus (HIV)
  • HTLV-1
  • Creutzfeldt-Jacob disease (CJD)
  • viral haemorrhagic fever (e.g. Ebola)
  • other hazardous pathogens such as TB, typhoid or brucella.

Note: MRSA colonisation / infection is not high risk.

or a specimen from a patient suspected to have:

  • Creutzfeldt-Jacob disease (CJD)
  • viral haemorrhagic fever (e.g. Ebola)
  • blood-borne virus infection (Hepatitis B / Hepatitis C / HIV)
  • other hazardous pathogens such as TB, typhoid or brucella but not MRSA.

This includes all febrile travellers returning from areas high risk for typhoid and brucella.

For this reason, blood cultures received from the Infectious Diseases Ward are all processed as high-risk.

It is important to identify high-risk specimens because extra precautions are needed; these specimens may pose an additional risk to ward staff, porters and laboratory staff.

Each specimen must be labelled 'DANGER of INFECTION' and sealed in its own separate plastic bag.

The request card or tab at the top of the specimen bag should also state 'DANGER of INFECTION'. The request card should not be sealed in the same bag pocket as the specimen.

Adding an extra request to an existing sample

To request additional tests on samples already received in the laboratory, please telephone (01865 2)21918 or liaise with the microbiology lab registrar (bleep 4077).

The timeframe within which additional tests can be added depends on the nature of the sample.

  • Urine: 2 days
  • Stool: 7 days
  • Pus samples: 7 days
  • Respiratory samples: 7 days
  • CSF samples: stored for a minimum of 2 weeks
  • Serum samples: stored for a minimum of 2 months
  • Virology molecular assays: stored for a minimum of 2 months
  • Prosthetic device samples: 7 days
  • Significant blood culture isolates are frozen, and can be tested further if required

Specimen transport

The most efficient way to transport specimens including blood cultures is through the hospital pod system.

Samples are collected once or twice a day from GP surgeries, and delivered to central specimen reception on Level 4 of the John Radcliffe Hospital. They are sorted and delivered to various laboratories including Microbiology.

For referral requests from outside the Trust please send samples to the laboratory using Hayes DX code:

DX 6540700 (Oxford University Hospitals NHS Trust, HEADINGTON 93 OX)

Urgent samples

Monday to Friday 9.00am - 5.00pm

Urgent specimens should be transported as rapidly as possible to:

Microbiology Specimen Reception
Level 7, John Radcliffe Hospital

For transport instructions, see Microbiology Laboratory Users Manual (pdf, 684 KB)

Please call the Microbriology Laboratory to request urgent specimen processing:

Microbriology Laboratory: 01865 221918

or contact the Laboratory Registrar on bleep 4077 if clinical discussion is needed.

On-call service: weekdays before 9.00am / after 5.00pm; weekends and bank holidays

An emergency service for bacteriology and virology is available outside normal laboratory working hours. This service is for the processing of:

  • urgent cultures from sterile sites (e.g. CSF, joint aspirates, pus/tissue collected at operation)
  • virology investigations prior to organ transplantation.

Urgent advice is also available from the on-call Biomedical Scientist.

To arrange these tests, please call the Biomedical Scientist on-call (via JR switchboard):

JR switchboard: 0300 304 7777

after the sample has been collected. All calls to the Biomedical Scientist between 9.00pm and 9.00am will be screened by the Churchill Hospital at Night RMO.

Blood cultures are processed routinely outside normal laboratory opening hours and there is no need to ring the laboratory to notify us of their arrival.

On-call service (midnight until 8.00am)

The urgent service is restricted to examining CSF for the diagnosis of meningitis, and virology investigations prior to organ transplantation only.

Urgent CSF microscopy is not performed for 'septic screens' from SCBU unless specifically agreed with the Microbiology medical staff.

Tests not routinely performed in the laboratory

OUH Microbiology Department focuses on ensuring the correct tests are requested by the clinicians. As Microbiology is a demand-led specialty, guidelines to advise users covering high volume specimen types have been introduced.

Some of these guidelines are listed below.

In addition, the laboratory will not usually process the following samples:

  • leaking specimens
  • unlabeled specimens
  • sample not stable (long delay in reaching laboratory or received in inappropriate container).

Please note: when the sample is clinically critical or irreplaceable, the laboratory may choose to process the sample, and will issue a final report indicating the nature of the problem, and where applicable, that caution is required when interpreting the result.


Microbiology Laboratory Users Manual (pdf, 684 KB)