Diagnostic Performance and Clinical Utility of PCR-Based Molecular Detection for Bloodstream Infections: A Prospective Comparative Study with Conventional Blood Culture in a Tertiary Care Hospital

Abstract

Background: Early accurate identification of bloodstream pathogens is critical for initiating appropriate antimicrobial therapy. This study evaluated the diagnostic performance of PCR-based molecular detection as a complementary modality to conventional blood culture.

Methods: Prospective observational cohort study of 120 patients with clinically suspected bloodstream infections. Blood samples were simultaneously processed for conventional blood culture (BacT/ALERT) and PCR-based molecular diagnostics targeting 16S rRNA genes. Sensitivity, specificity, PPV, NPV, diagnostic accuracy, turnaround time, and concordance (Cohen's kappa) were calculated. ROC curve analysis and impact of prior antimicrobial exposure were assessed.

Results: PCR positivity rate (52.5%, 95% CI: 43.3-61.4%) significantly exceeded blood culture (35.0%, 95% CI: 26.7-43.3%). PCR demonstrated excellent sensitivity (95.2%, 95% CI: 88.6-99.1%), moderate specificity (70.5%, 95% CI: 62.3-78.7%), with NPV of 96.5% (95% CI: 91.2-99.3%) and diagnostic accuracy of 79.2% (95% CI: 71.0-87.4%). Mean turnaround time for PCR (6.3±1.4 hours) was significantly faster than blood culture (72.4±11.8 hours), representing 11-fold improvement (t=-34.2, p<.001). Cohen's kappa coefficient of 0.64 (95% CI: 0.52-0.76) indicated substantial concordance. Prior antimicrobial therapy significantly reduced blood culture positivity (23.3% vs. 46.7%, χ²=6.12, p=.013) but did not substantially affect PCR detection (55.0% vs. 50.0%, p=.601). ROC analysis revealed AUC of 0.88 (95% CI: 0.80-0.95, p<.001) with optimal Ct cut-off value of ≤32 cycles.

Conclusion: PCR-based molecular diagnostics demonstrated superior sensitivity, markedly reduced turnaround time, and stable diagnostic performance in antibiotic-exposed patients. An integrated diagnostic approach combining PCR and conventional culture optimizes diagnostic accuracy and clinical outcomes while supporting antimicrobial stewardship.