Background: Antimicrobial resistance (AMR) is a critical public health threat in the Philippines, necessitating rapid diagnostic tools for effective stewardship. This study evaluates the concordance between multiplex PCR resistance gene detection and conventional phenotypic culture-based susceptibility testing.

Methods: A cross-sectional analytical study was conducted at San Lazaro Hospital (June 2023 – April 2025) involving 109 patients. Resistance markers identified via multiplex PCR (including NDM, IMP, VIM, KPC, and CTX-M) were compared against culture-based resistance profiles.

Results: Concordance between AMR gene detection and phenotypic resistance patterns was notably low at 31.57%. Despite this, PCR enabled the rapid identification of critical carbapenemase and ESBL genes. In the 90 days prior to admission, 3rd and 4th generation cephalosporins were the most frequently used antibiotics, a trend that continued during hospitalization (utilized in 69% of cases), alongside carbapenems (29.8%).

Conclusion: The identification of resistance genes like NDM and KPC through molecular methods is critical for AMR surveillance and antimicrobial stewardship. While multiplex PCR provides rapid genotypic data essential for surveillance, its limited concordance with phenotypic susceptibility indicates it should complement, not replace, conventional culture. PCR may detect resistance genes that are not phenotypically expressed, or vice-versa, necessitating careful clinical interpretation. These findings emphasize the need for integrated diagnostic approaches to optimize antimicrobial stewardship in resource-limited settings.