Title : Diagnostic concordance between multiplex PCR and conventional culture for pathogen identification and antimicrobial resistance detection: Implications for clinical decision-making in infectious disease management
Abstract:
Background: Conventional microbiologic culture has long been the gold standard in microbiological diagnostics, providing valuable information on pathogen viability and antimicrobial susceptibility. However, multiplex polymerase chain reaction (mPCR) has emerged as a powerful alternative, offering rapid detection with high sensitivity and specificity. This study examines the concordance between conventional microbiologic culture and mPCR in detecting pathogens and antimicrobial resistance (AMR) genes and phenotypes. Analysis is stratified across four diagnostic panels—Blood Culture Identification (BCID), Gastrointestinal Pathogen (GI), Meningitis-Encephalitis (ME), and Pneumonia— to evaluate agreement, and between AMR gene detection and culture-based resistance profiles.
Methodology: This is a cross-sectional, analytical study done in San Lazaro Hospital, Philippines with sample population of 109 patients admitted between 1 June 2023 – 30 April 2025. The concordance metrics is performed using standard percent agreement calculations – positive agreement (PA), positive percent agreement (PPA), negative percent agreement (NPA), and Cohen’s kappa (κ).
Results: While multiplex PCR demonstrated high positive percent agreement (100%) across all diagnostic panels, overall concordance was low (κ = 0.0261), with particularly limited agreement observed in the Pneumonia panel (NPA = 10.20%). Pathogen-level agreement was suboptimal (PA = 27.5%), and concordance between AMR gene detection and phenotypic resistance patterns was limited (16.20%).
Conclusion: Despite limitations, the rapid detection capabilities of multiplex PCR support its complementary role in clinical diagnostics. The identification of globally relevant resistance genes (e.g.,NDM, IMP, VIM, KPC, CTX-M) underscores the importance of molecular diagnostics in AMR surveillance and antimicrobial stewardship. Ultimately, despite the precision in AMR detection, clinical correlation is still paramount in patient management.
