Urine Culture and Sensitivity

Urine culture grows bacteria and yeasts from a measured volume of urine on non-selective and selective media, counts the colonies and identifies the organism. Antimicrobial susceptibility testing then gives the minimum inhibitory concentration or zone size for a panel of antibiotics. It is the definitive test for urinary tract infection (UTI) and is read together with symptoms and with the urinalysis, because the presence of bacteria in urine does not always mean infection.

The test is used to confirm UTI, to select an antibiotic when infection is complicated, recurrent or treatment has failed, and to screen for asymptomatic bacteriuria in pregnancy and before urological surgery. In uncomplicated cystitis in non-pregnant women, treatment is often started empirically without culture.

UTI is among the commonest bacterial infections, affecting about 150 million people a year worldwide. About half of women have at least one episode, and 20 to 30% of these have a recurrence within 6 months. Escherichia coli causes 75 to 85% of community infections, followed by Klebsiella, Proteus, Enterococcus and Staphylococcus saprophyticus (young women). Resistance to trimethoprim and fluoroquinolones now exceeds 20% in many regions, and extended spectrum beta lactamase producers are common.

Indications. Suspected pyelonephritis, UTI in pregnancy, men, children and infants, catheter associated infection with symptoms, recurrent UTI (3 or more a year), failure of empirical treatment, structural or functional urinary tract abnormality, immunosuppression, diabetes with symptoms, before urological procedures, and routine antenatal screening for asymptomatic bacteriuria.

Specimen. A midstream clean catch sample after cleansing the periurethral area, collected into a sterile container. Deliver to the laboratory within 2 hours, or refrigerate at 4 °C for up to 24 hours, or use boric acid preservative, since bacteria double every 20 to 30 minutes at room temperature.

Catheter specimens are taken from a newly placed catheter or the sampling port, never from the bag.

In infants, a suprapubic aspirate or urethral catheter sample is the most reliable, and bag samples are used only for exclusion of infection. A first void sample is used for urethritis.

Colony counts. Reported as colony forming units/mL (cfu/mL).

• 10^5 cfu/mL or more of a single organism in a midstream sample: significant bacteriuria in most patients, and a single organism at this level in an asymptomatic woman on two consecutive samples defines asymptomatic bacteriuria.
• 10^3 to 10^4 cfu/mL of a single uropathogen: significant in symptomatic women (up to 30 to 50% of cystitis has counts of 10^2 to 10^4), in men, and in catheter and suprapubic specimens (any growth, from 10^2 cfu/mL).
• Suprapubic aspirate: any growth of a uropathogen is significant.
• Mixed growth of 3 or more organisms: contamination, and a repeat sample is taken.
• No growth: UTI is unlikely, unless the patient had antibiotics before sampling, or the organism is fastidious (Mycobacterium tuberculosis, Chlamydia, Ureaplasma, Mycoplasma), and then special culture or PCR is needed.

Pyuria and culture. Pyuria with negative culture (sterile pyuria) suggests recent antibiotics, urethritis, tuberculosis, stones, interstitial nephritis, genitourinary tumour or catheter.

Susceptibility report. Each isolate is reported as susceptible, intermediate or resistant for first line urinary agents (nitrofurantoin, trimethoprim, pivmecillinam, fosfomycin, cefalexin or co-amoxiclav) and for second line agents in complicated infection (ciprofloxacin, gentamicin, ceftriaxone, piperacillin-tazobactam and carbapenems). Resistance markers (extended spectrum beta lactamase, carbapenemase, vancomycin resistant enterococci) are flagged.

Interpretation by clinical group.

• Asymptomatic bacteriuria: treated in pregnancy (risk of pyelonephritis in 20 to 30% untreated, preterm birth and low birth weight) and before endoscopic urological procedures that breach the mucosa. Not treated in older adults, catheterised patients, diabetes or kidney transplant, because treatment adds resistance and adverse effects without benefit.
• Catheter associated UTI: only in the presence of fever, suprapubic or flank pain, rigors or delirium, and the catheter is changed before sampling.
• Recurrent UTI: culture at each episode to separate relapse (same organism within 2 weeks) from reinfection.
• Men: UTI is complicated by default, and prostatitis is considered.

Critical values and findings needing immediate action.

• A positive culture with fever, rigors, hypotension or confusion (urosepsis): blood cultures, lactate and urgent broad spectrum antibiotics.
• Extended spectrum beta lactamase or carbapenemase producer: infection control alert and change in antibiotic choice.
• Growth in a pregnant woman, even asymptomatic: treat and repeat culture after treatment.
• Candida in an immunosuppressed or neutropenic patient, or in a neonate: possible invasive disease.
• Growth in an infant or child with fever: urgent treatment and imaging.
• Proteus with alkaline urine and stones: struvite stone risk.

Interferences and pitfalls.

• Delay in transport lets bacteria overgrow and falsely raises the count. Preservative tubes limit this.
• Contamination from the skin, perineum or vagina (mixed growth, many squamous cells) is the commonest cause of false positives.
• Antibiotics in the last 48 to 72 hours cause false negatives.
• Counts under 10^5 cfu/mL do not exclude infection in symptomatic patients, particularly with frequent voiding, diuresis or dilute urine.
• Dipstick negative samples may still grow organisms that do not reduce nitrate.
• Treating asymptomatic bacteriuria is the commonest source of unnecessary antibiotic use.
• Yeast in the urine of catheterised patients is mostly colonisation.
• Susceptibility in vitro does not always predict clinical response, especially with nitrofurantoin in pyelonephritis or in kidney impairment.
• Repeat cultures to prove cure are not needed in symptom free non-pregnant adults.

Special groups.

• Pregnancy: routine screening at the first antenatal visit, and treatment of any bacteriuria with agents safe in pregnancy.
• Children: sample must be reliable, and UTI in an infant requires imaging in selected cases (ultrasound; micturating cystourethrogram in recurrent or atypical infection).
• Older adults: asymptomatic bacteriuria affects up to 20 to 50% of care home residents, and delirium alone does not mean UTI.
• Men: investigate for prostatitis, obstruction and stones.
• Regions: schistosomiasis and tuberculosis are important in endemic areas, and resistance to oral agents is widespread, so culture directs treatment.

Follow up tests. Urinalysis with microscopy, full blood count, CRP, urea, creatinine and electrolytes, blood cultures in sepsis, renal and bladder ultrasound, CT in obstruction or non-response, post-void residual volume, urine for acid fast bacilli and PCR, Chlamydia and gonorrhoea testing in sterile pyuria, prostate specific antigen interpretation caution in prostatitis, and cystoscopy in recurrent infection with haematuria.