Is Staphylococcus epidermidis isolated from a urine specimen a contaminant or indicative of a true urinary tract infection?

Staphylococcus epidermidis in Urine: Contaminant vs. Pathogen

Staphylococcus epidermidis isolated from urine is almost always a contaminant, particularly when present at low colony counts (<1,000 CFU/mL) or as part of mixed flora, and should not be treated in the vast majority of cases. 1

When S. epidermidis is Contamination

Coagulase-negative staphylococci (including S. epidermidis) at low colony counts (<1,000 CFU/mL) are not clinically relevant urine isolates and represent skin flora contamination. 1 The following features strongly indicate contamination:

• Mixed growth with ≥2 organisms at any concentration suggests specimen contamination from periurethral, vaginal, or perineal skin flora rather than true infection 1, 2
• High epithelial cell counts on urinalysis indicate skin cells were shed during collection, rendering the culture unreliable 3
• Collection method matters critically: clean-catch specimens have 14-32% contamination rates, while bag-collected specimens have 44-68% contamination rates 1, 2

Rare Exceptions: When S. epidermidis May Be Pathogenic

S. epidermidis can occasionally cause true UTI in highly specific clinical contexts, though this remains uncommon:

High-Risk Populations

• Children with anatomic urinary tract abnormalities (e.g., severe vesicoureteral reflux grade III-V) may develop S. epidermidis UTI 4, 5
• Patients with indwelling urinary catheters or recent instrumentation are at risk for coagulase-negative staphylococcal UTI 4, 5
• Patients on continuous antibiotic prophylaxis may develop breakthrough S. epidermidis infections due to selective pressure 5

Supporting Evidence for True Infection

When S. epidermidis is a true pathogen (rare), you will see:

• Pure growth of S. epidermidis as a single organism (not mixed flora) at ≥50,000 CFU/mL 1, 3
• Pyuria (≥10 WBCs/mm³) with bacteriuria increases likelihood of true infection 1
• Positive leukocyte esterase or nitrites suggest infection despite the unusual organism 1
• Gram stain of properly collected urine showing gram-positive cocci in a symptomatic patient 5
• Symptoms of pyelonephritis (fever, flank pain) with no other pathogen identified 5, 6

Clinical Decision Algorithm

Step 1: Assess Collection Method and Specimen Quality

• If mixed flora or epithelial cells present: Contamination—do not treat 1, 2, 3
• If bag-collected specimen in children: 85% false positive rate—never use to confirm UTI 2

Step 2: Evaluate Colony Count and Organism Purity

• <1,000 CFU/mL: Contamination—do not treat 1, 3
• ≥50,000 CFU/mL of S. epidermidis as single organism: Proceed to Step 3 3

Step 3: Assess Clinical Context

• No urinary symptoms + no risk factors: Contamination—do not treat 2
• Symptomatic + anatomic abnormality or catheter/instrumentation: Consider true pathogen—obtain repeat specimen by catheterization or suprapubic aspiration 1, 2, 4
• Symptomatic + no risk factors + no pyuria: Contamination—recollect specimen 1

Step 4: Confirm Before Treating

Never treat based on a single contaminated culture. 2 If clinical suspicion remains high:

• Obtain catheterized specimen (≥50,000 CFU/mL threshold) or suprapubic aspiration (any growth significant) 2, 3
• Verify pyuria is present (absence suggests contamination or asymptomatic bacteriuria) 1

Critical Pitfalls to Avoid

• Do not automatically treat S. epidermidis in urine—it is contamination in >95% of cases 1, 4
• Do not treat asymptomatic patients based on S. epidermidis growth, as this leads to inappropriate antibiotic use 2
• Do not accept bag-collected specimens as diagnostic in children—contamination rate is 60-68% 2
• Do not ignore specimen processing delays—urine held at room temperature >1 hour yields falsely elevated counts 2, 3
• In children with gram-positive cocci on urine Gram stain, consider enterococci first, then S. saprophyticus (a true uropathogen), before attributing infection to S. epidermidis 5, 7, 8