Clinical Relevance of PCR Versus Culture in Urinary Tract Infections Diagnosis: Quantification Cycle as a Predictor of Bacterial Load

Abstract

Background: Unambiguous clinical interpretation of PCR results for urinary tract infections (UTIs) remains a challenge. Here we compare and correlate multiplex qPCR results (quantification cycle values) with traditional microbial culture results (colony forming units) for clinical samples. Methods: Serial dilutions [108 to 100 colony forming units (CFU)/mL] were performed on five Gram-negative and two Gram-positive UTI-causing bacterial pathogens. For each dilution, quantitative cultures on solid media to confirm CFU/mL values and a real-time PCR UTI panel employing a nanofluidic Open ArrayTM platform producing quantification cycle (Cq) values were performed. Cq values were correlated with CFU/mL values, generating a semi-quantitative interpretive scale for clinical samples. The clinical utility of the scale was then assessed using PCR and culture data from 168 clinical urine samples. Results: For Gram-negative bacteria, Cq values of <23, 23 to 28, and >28 corresponded with ≥105 CFU/mL, <105 CFU/mL and negative cultures, respectively. For Gram-positive bacteria, Cq values of <26, 26 to 30, and >30 corresponded with ≥105 CFU/mL, <105 CFU/mL and negative cultures, respectively. Among 168 urine specimens (including 138 Gram-negative and 30 Gram-positive bacteria), there was 83.3% agreement (n = 140/168) and 16.6% non-agreement (n = 28/168) between culture CFU/mL and qPCR Cq. Gram-negative bacteria had higher agreement (87.6%, 121/138) than Gram-positive bacteria (63.3%, 19/30). Conclusions: This study demonstrates that qPCR Cq results can be directly correlated with traditional urine quantitative culture results and reliably identify the clinically relevant cutoff of 105 CFU/mL for detected uropathogens.