Microbiology

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Investigation

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*Microscopy results may be available on the day the specimen is received.

Cell count is determined by automated microscopy. When automated microscopy is not available an alternative method of measuring cellular components of urine is performed.

Urine samples should be sent for culture if there is a clinical assessment that suggests complicated urinary tract infection or sepsis related to the urinary tract.  In otherwise healthy non- pregnant patients with clinical features of uncomplicated urinary tract infection (cystitis), urine culture may be useful in some patients to support the diagnosis or guide selection of antibiotic treatment. However, urine culture is often not required and should not be sent as a routine. Uncomplicated urinary tract infection (cystitis) is common in otherwise heathy women. In typical cases the diagnosis can be made with a very high degree of confidence based on clinical features 
and without a requirement for laboratory culture. Culture of urine is appropriate in this context if there is reason to expect that empiric guidance is not sufficient to guide treatment. It is often useful in those with recurrent urinary tract infection. 

A request for culture of urine should state clearly that one of the following suspected conditions/indications is present:

•  Pregnant (to assess for asymptomatic bacteriuria)
• Complicated UTI
• Recurrent UTI
• Pyelopnephritis
• Sepsis
• Abnormal urinary tract
• Planned urological procedure
• Other specific indication

In severe or complicated UTI, a follow-up specimen should be taken 5 days post completion of antibiotic therapy.  Persistence of bacteriuria implies a structural abnormality. 

Send a mid-stream specimen of urine (MSU) where possible.  Specimens should be processed within 4 hours.  In General Practice if transport to the laboratory has to be delayed, the specimen can be stored at 4° C for up to 48 hours. 

People with indwelling urinary catheters almost always have white cells and high numbers of bacteria in their urine within weeks of insertion of the catheter. Culture of urine from people with indwelling urinary catheters is only likely to be useful if there are clinical features of upper urinary tract infection or sepsis or a planned urological procedure for which targeted prophylaxis may be required. Urine for culture from patients with a urinary catheter must be directly from the catheter, never from the bag.

Related links

For further information please consult https://www.stjames.ie/services/laboratorymedicinelabmed/microbiology/

https://www.hse.ie/eng/about/who/cspd/lsr/resources/routine-microbiological-laboratory-examination-of-urine-samples-in-adults.pdf

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Last updated

Tue, 13 Jan 2026 16:13:31 GMT