Concordance Between Molecular Techniques (like Multiplex PCR/BioFire) and Traditional Cultures – A Review

Abstract Background Advances in molecular diagnostics have significantly changed the landscape of clinical microbiology. Techniques such as multiplex polymerase chain reaction (mPCR) and automated systems like the BioFire FilmArray enable rapid detection of multiple pathogens directly from clinical specimens. Traditional culture methods remain the diagnostic gold standard; however, they are time-consuming and may fail to detect fastidious or non-culturable organisms. Evaluating the concordance between molecular techniques and conventional cultures is therefore essential to understand their diagnostic reliability and clinical utility. Methods A comprehensive literature search was conducted across PubMed, Scopus, Web of Science, Embase, and Google Scholar for studies published between 2000 and 2025. Studies comparing molecular diagnostic methods, particularly multiplex PCR and BioFire FilmArray systems, with traditional culture techniques in human clinical samples were included. Data regarding concordance rates, sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were extracted and synthesized. Results Eighteen studies met the inclusion criteria and evaluated concordance across various sample types including respiratory, bloodstream, cerebrospinal fluid, stool, and tissue specimens. Overall concordance between molecular techniques and traditional cultures ranged from approximately 85% to 95% in respiratory and bloodstream infections, while cerebrospinal fluid and gastrointestinal samples showed concordance rates exceeding 90%. Molecular assays frequently detected additional pathogens missed by culture, particularly in patients receiving prior antibiotic therapy. Furthermore, these platforms significantly reduced diagnostic turnaround time from 24–72 hours with culture to approximately one hour. Conclusion Molecular diagnostic techniques such as multiplex PCR and BioFire panels demonstrate high concordance with traditional culture methods while providing substantially faster pathogen detection. Although limitations such as higher costs and potential detection of non-viable organisms exist, integrating molecular diagnostics with conventional culture methods can enhance diagnostic accuracy, support antimicrobial stewardship, and improve clinical decision-making in infectious disease management.