Comparative Evaluation of Multiplex Real-Time PCR, Standard Urine Culture, and Rapid Nephelometric Screening in Patients with Complicated Urinary Tract Infections

Background/Objectives: Microbiological confirmation of suspected complicated urinary tract infections (cUTIs) is challenging, particularly in patients previously exposed to antibiotics or when fastidious organisms are involved. Molecular assays detect microbial nucleic acids independently of bacterial viability and may therefore yield results that differ from conventional culture. This study compared microorganism detection patterns and inter-method agreement between multiplex real-time PCR (mPCR), standard urine culture SUC, and rapid nephelometric screening (Uroquattro HB&L). Methods: In a prospective single-centre study, urine samples from 72 hospitalized patients with clinical suspicion of cUTIs were analyzed using SUC, mPCR (Novaplex™ UTI panel), and the Uroquattro system. Detection rates were calculated for each method. Agreement between paired methods was evaluated using Cohen’s kappa, and paired differences in detection were assessed using McNemar’s and Cochran’s Q tests. Results: mPCR detected microorganisms in 83.3% of samples, compared with 47.2% for SUC and 42.6% for Uroquattro. Agreement between mPCR and SUC was fair (κ = 0.26), whereas SUC and Uroquattro demonstrated high concordance. mPCR identified a broader spectrum of organisms, including fastidious and polymicrobial findings that were not recovered by culture. Correlation between PCR cycle threshold values and colony counts was weak and not statistically significant. Conclusions: mPCR demonstrated a substantially higher microorganism detection frequency than culture-based methods; however, the assays target different biological characteristics, highlight bacterial nucleic acid versus viable growth, and should be interpreted as complementary rather than interchangeable. Conventional culture remains necessary for antimicrobial susceptibility testing and clinical decision-making. Further studies incorporating clinical outcome-based reference standards are required to determine the clinical relevance of molecular detection in cUTIs.