Urine Contamination Threshold: Squamous Epithelial Cells
A urine specimen is generally considered contaminated when it contains ≥10 squamous epithelial cells per low-power field (SEC/LPF), though this threshold has limited reliability for predicting culture contamination and should be interpreted alongside clinical context and other specimen quality indicators. 1
Evidence-Based Thresholds
Traditional Clinical Practice Threshold
≥10 SEC/mm³ (approximately ≥10 SEC/LPF) has been used as the conventional cutoff to define specimen contamination, based on the observation that specimens with ≥10 SEC/mm³ had significantly more mixed growth (53% versus 22% in specimens with <10 SEC/mm³). 2
Specimens with <10 SEC/mm³ yielded fewer isolates per culture (0.9 isolate) compared to specimens with ≥10 SEC/mm³ (2 isolates per culture), suggesting better specimen quality below this threshold. 2
Critical Limitations of the SEC Threshold
Squamous epithelial cells are a poor predictor of urine culture contamination overall, with an area under the ROC curve of only 0.680 (95% CI 0.671–0.689), indicating limited discriminatory ability. 3
In catheterized specimens from women, 94% contained squamous cells yet none showed bacterial contamination, demonstrating that SEC presence does not reliably indicate contamination in all collection methods. 4
Even in midstream clean-catch specimens, 96% contained squamous cells but only 21% showed bacterial contamination, yielding a positive predictive value of just 21% for contamination. 4
Impact on Urinalysis Performance
Diagnostic Accuracy Degradation
The presence of >8 SEC/LPF significantly reduces the predictive performance of traditional urinalysis markers for bacteriuria. 3
When SECs are absent, the positive likelihood ratio for predicting bacteriuria is 4.98 (95% CI 4.59–5.40), but this drops to 2.35 (95% CI 2.17–2.54) when >8 SEC/LPF are present. 3
Urinalysis specimens with <8 SEC/LPF predict bacteriuria with 75% sensitivity and 84% specificity (diagnostic odds ratio 17.5), compared to specimens with >8 SEC/LPF showing 86% sensitivity but only 70% specificity (diagnostic odds ratio 8.7). 3
Individual Marker Performance
Pyuria, bacteriuria, and leukocyte esterase all demonstrate reduced diagnostic accuracy (lower AUC) in the presence of squamous epithelial cells. 5
The area under the curve for individual urinalysis markers ranged from 0.557 to 0.796, with consistently higher AUC values in clean samples compared to contaminated samples. 5
Clinical Decision Algorithm
When to Reject a Specimen
High epithelial cell count (≥10 SEC/LPF) PLUS mixed flora on culture → Strongly suggests contamination; obtain a properly collected specimen before making treatment decisions. 1, 2
High epithelial cell count PLUS absence of pyuria (<10 WBC/HPF) → Contamination likely; bacterial presence represents peri-urethral flora rather than bladder infection. 1
High epithelial cell count PLUS negative urinalysis markers → Contamination probable; repeat collection using proper technique. 1
When to Proceed Despite Elevated SECs
If pyuria (≥10 WBC/HPF) AND acute urinary symptoms are both present, proceed with culture and treatment even if SECs are elevated, because true infection can coexist with suboptimal collection technique. 1
In catheterized specimens, disregard SEC count entirely, as squamous cells are nearly universal (94%) yet do not indicate contamination in this collection method. 4
Proper Specimen Collection to Minimize Contamination
Women
In-and-out catheterization is the preferred method when initial specimens show high epithelial cells (≥3 cells/HPF) or mixed flora, as this bypasses peri-urethral contamination. 1
For midstream clean-catch, thorough cleansing of the urethral meatus and labia is essential, though even optimal technique yields squamous cells in 96% of specimens. 4
Men
- Midstream clean-catch after thorough cleansing of the urethral meatus, or use of a freshly applied clean condom catheter with frequent bag monitoring. 1
Specimen Handling
- Process specimens within 1 hour at room temperature or refrigerate within 4 hours to prevent bacterial overgrowth that falsely elevates colony counts and obscures contamination patterns. 1, 6
Common Pitfalls to Avoid
Do not reject a specimen based solely on SEC count without considering the entire clinical picture (symptoms, pyuria, culture results), as SECs have poor predictive value for contamination. 3, 4
Do not assume that absence of SECs guarantees a clean specimen, as contamination can occur through other mechanisms (delayed processing, improper storage). 2
Do not use SEC count to guide antibiotic decisions; instead, base treatment on the combination of symptoms, pyuria (≥10 WBC/HPF), and culture results showing a single predominant pathogen. 1
Recognize that clinical laboratories may misidentify renal tubular epithelial cells as squamous cells, leading to false-positive contamination flags; nephrologist-performed urinalysis shows superior accuracy in distinguishing cell types. 7
Never treat based on a contaminated culture (mixed flora, high SECs, multiple organisms) without obtaining a properly collected repeat specimen, as this promotes unnecessary antibiotic exposure and resistance. 1
Key Takeaway for Clinical Practice
While ≥10 SEC/LPF is the traditional threshold for flagging potential contamination, this cutoff has limited reliability (PPV only 21% in clean-catch specimens). 2, 4 The presence of squamous cells primarily signals reduced diagnostic accuracy of urinalysis markers rather than definitive contamination. 3 Clinical decisions should integrate SEC count with pyuria, symptoms, culture growth pattern (single organism versus mixed flora), and collection method—not rely on SEC count alone. 1, 3, 2, 4