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Microbiology & Infection » Specimens and requests » Microbiology tests

Last update to this site: 2.9.2014
    

Lab Tests OnlineUK
Microbiology and InfectionMicrobiology and Infection Investigations

Quoted turnaround times are the time from receipt of specimen into the laboratory to 90% of reports leaving the laboratory. Stated times are based on normal working hours, Monday to Friday, excluding statutory bank and public holidays.

Antibiotic assays Now done in Biochemistry - use A to Z pad in right-hand panel to look for antibiotic by name.

Biopsy specimens

needle aspirate
needle biopsy
tissue

Microbiology and Infection

Indications:

  • Bacterial infection
  • Fungal infection
  • TB

In sterile universal container. Do not add fixative or formalin.

Turnaround: 9 days (negative results typically available 2 days earlier).

Turnaround for routine TB specimens: 60 days.

State anatomical site and suspected cause.

Blood culture

Microbiology and Infection 

Full instructions available - click here.

Blood for serology

(see Virology and Serology pages or use the A to Z pad in the right-hand panel)

Virology/serology

Indications:

  • Investigation of bacterial and viral infections for which serological diagnosis is available.
  • Screening to exclude infection or identify existing immunity from past infection or immunisation.

Gold cap tube (serum with separator gel)5 mL clotted blood (smaller tubes available for paediatric samples)

For diagnosis of acute infections, paired acute (at onset of symptoms) and convalescent (10-14 days later) sera are preferable to show a rising antibody titre. A single convalescent sample may be sent for retrospective diagnosis.

Turnaround: 2 days

State relevant symptoms, their duration and infection(s) suspected.

Date of onset is essential.

For screening tests supply previous infection / immunisation history.

Body fluids - from
sterile sites

e.g. Ascitic fluid, bile, synovial fluid

Microbiology and Infection

Indications:

  • Bacterial infection
  • Fungal infection
  • TB

In sterile universal container. Do not add fixative or formalin.

Turnaround: 9 days (negative results typically available 2 days earlier).

Turnaround for routine TB specimens: 60 days.

State anatomical site and suspected cause.
Body fluids - other

e.g. wound drainage, abscess fluid 

Microbiology and Infection

Indications:

  • Bacterial infection
  • Fungal infection
  • TB

In sterile universal container. Do not add fixative or formalin.

Turnaround: 9 days (negative results typically available 2 days earlier).

Turnaround for routine TB specimens: 60 days.

State anatomical site and suspected cause.

Cannulae and central lines tips

Microbiology and Infection

Test no longer available.

CSF

cell count
protein screen
Gram and special stains (e.g. AFB, India ink)
antigen tests (as applicable)
culture
PCR (sent away - after discussion)
Microbiology and Infection

Note protein, glucose, xanthochromia scan and oligoclonal bands are done in Biochemistry.

Click here for full details of CSF collection.

Cell count will not be done on samples that are over 12 hours old. This is because cells disintegrate over time and extended delays may produce a cell count that does not reflect the clinical situation of the patient.

 Indications:

  • Investigation of suspected CNS infection or subarachnoid haemorrhage.

5 mL specimen split between 3 sterile universal containers (clearly label specimens with number order collected).

If special tests required please supply full details.

If extra investigations e.g. AFB culture, PCR, a larger volume will be needed.

Turnaround: 2 days

All microscopy results will be phoned to clinician ordering test where infection is suspected.

Antigen tests and referral for PCR will be performed as appropriate.

All positive cultures are phoned.

Faeces

Microbiology and Infection 

Indications:

  • Investigation of diarrhoea.
  • Screening of food handlers or special risk groups (at discretion of CCDC).
  • Helicobacter pylori antigen testing.

In sterile faeces collection container (with spatula). Rectal swabs are not recommended.

Send 3 specimens from separate bowel motions (one specimen is sufficient for H. pylori testing).

Indicate if parasitology required.

Investigation for viruses will be performed if clinically indicated.

Turnaround: 3 days (parasitology 30 days)

Routine culture includes Salmonella, Shigella, Campylobacter, E.coli O157.

Other tests (parasites, C.difficile toxin) should be specifically requested.

Clinical information should include travel abroad, if food handler, recent antibiotics, suspected food poisoning or other food details.

Investigation for Norovirus only performed in the case of a hospital outbreak, or at the request of Environmental Health.

Salmonella, Shigella and suspected food poisoning (whatever cause) are all notifiable to the CCDC.

Pus

Microbiology and Infection

Indications:

  • Investigation of suspected infection.

Pus is always preferable to a swab where possible.

In a sterile universal 30 or 60 mL container.

Turnaround: 9 days (negative results typically available 2 days earlier)

State current/ intended antibiotic therapy.

State anatomical site of lesion.

State whether collected at operative procedure.

Scrapings/ clippings for mycological investigation

Microbiology and Infection

Indications:

  • Investigation of suspected dermatophyte infection.

Collect in clean folded black paper and place in a sealed envelope labelled with patient’s name.

Turnaround: 21 days

State specimen site, type and brief description of lesion.

Sputum

routine culture
Pneumocystis antigen detection
RSV antigen detection
Legionella

Microbiology and Infection 

Indications:

  • Investigation of suspected bacterial infection.
  • Suspected Pneumocystis pneumonia (PCP).
  • Suspected RSV infection.
  • Suspected Legionella infection.

Collect in sterile universal container.

Ensure specimen comprises sputum (not saliva or food). A specimen collected at physiotherapy is preferable.

Induced sputum or bronchial washings are needed for PCP.

Nasopharyngeal aspirate is required for RSV.

Turnaround times:
Routine culture: 3 days
Legionella culture: 10 days
PCP: 1 day

State recent antibiotic therapy.

State any underlying chest disease, especially if chronic: cystic fibrosis, bronchiectasis, COAD.

State duration of current symptoms.

Send paired sera for serology for mycoplasma, chlamydia, viral causes and Legionella as indicated by clinical picture.

PCR for TB on respiratory samples must be arranged via the Microbiology Consultants. Test referred to HPA Mycobacterium Reference Laboratory, Institute of Cell and Molecular Sciences, 4 Newark Street, London E1 2AT.

Swabs

conjunctival
ear, nose, throat
vaginal, genital
wound/ulcer

Microbiology and Infection 

Indications:

  • Investigation of suspected infection.

Swab in Stuart’s transport medium.

Collect specimen after wound has been thoroughly cleaned to avoid colonising flora.

Superficial swabs are poor predictors of deep/invasive infection.

Turnaround:
Wound swabs: 4 days (negative results typically available 2 days earlier)
Genital swabs: 2 days

State site of wound/swab and type and date of recent surgery/injury and antibiotics.

When interpreting results remember common pathogens (e.g. Staph. aureus) may also be found in normal flora.

Chronic wounds/ulcers will often be colonised with faecal flora and Pseudomonas which do not require systemic antibiotics.

Pertussis

Microbiology and Infection

Indications:

  • Suspected whooping cough.

Pernasal swab for Pertussis.

Use blue top wire swab, not orange top wire swab.

Turnaround: 7 days
 

MRSA screening swabs

Microbiology and Infection 

Indications:

  • Exclusion of MRSA carriage.
  • Investigation of extent of colonisation in known MRSA positive patients (as directed by Infection Control Team).

Nose, throat, axillae, groins/perineum, hairline, wounds and other lesions (as directed by Infection Control).

Turnaround: 2 days (negative results typically available in 1 day)

State if patient known to be MRSA positive in the past, whether decolonised or treated and reason for screening.

Advice on MRSA screening and indications for decolonisation are available from the Infection Control Team on RSCH ext. 4367/4595

Meningococcal and diphtheria screening swabs

Microbiology and Infection

Indications:

  • Investigation of possible outbreaks.

Nose/throat swabs.

Turnaround: 2 days

As directed by the Consultant in Communicable Disease Control (CCDC) only.

TB culture

sputum
urine
bronchial washings etc.
tissue/biopsy specimens
other specimens as relevant (CSF, bone marrow, fluids etc.)
blood for AFB culture
Microbiology and Infection

Indications:

  • Investigation of suspected mycobacterial infection.

3 separate sputum specimens.

3 early morning urines.

Other specimens in sterile universal container.

Blood for mycobacterial culture in special culture bottles only.

Turnaround: 60 days

Microscopy for AFB can be performed on the same day if urgent (please indicate clearly on request form reason for urgent request).

Culture for AFB takes 4-8 weeks and antibiotic sensitivities a further 2-4 weeks after initial isolation.

All positive results are notified by telephone and a preliminary report sent.

Please state relevant details e.g. contact history, ethnicity, other risk factors e.g. HIV, IVDU.

Urine

Microbiology and Infection 

Indications:

  • Investigation of suspected urinary tract infection.

Mid stream urine collected using the green urine collection kit supplied, containing boric acid.

Catheter specimen collected using sterile technique with needle and syringe from catheter tubing.

Bag urine in infants/children.

Turnaround: 2 days (negative results typically available 1 day earlier)

Always state type of specimen and how collected.

State current/intended antibiotic therapy.

Urine dip strips with leukocyte and nitrite are available for rapid screening for suspected UTI (and remove the need for urgent microscopy of urines on call).


    

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