Complementary detection of respiratory pathogens and antimicrobial-resistance markers by multiplex PCR alongside culture in a High-AMR Egyptian cohort

Abstract

AIM: Lower respiratory tract infections frequently involve polymicrobial disease and antimicrobial-resistant pathogens, yet conventional culture may provide an incomplete and delayed microbiological picture. This study evaluated the complementary contribution of multiplex molecular testing and conventional culture in a high-AMR cohort in Egypt. METHODS: This retrospective cross-sectional study included 133 specimens collected at Souad Kafafi University Hospital, Egypt, during 2022-2023: 98 sputum records tested using the BioFire FilmArray Pneumonia Plus Panel and conventional culture with VITEK 2 susceptibility testing, and 35 blood-culture records evaluated using routine culture and BCID2 Panel. Paired molecular and culture results, descriptive analyses and multivariable logistic regression were performed. RESULTS: Among 133 specimen records, at least one pathogen was recorded at 58.6% (single-organism detection, 26.3%; mixed detection, 32.3%). Gram-negative bacteria predominated among organism-category detections (47.1%), followed by viruses (27.5%) and Gram-positive bacteria (25.5%). At least one AMR marker was detected in 51 records (38.3%), with blaCTX-M and blaNDM being the most frequent (each 27.8%). Among 98 paired sputum specimens, BioFire detected at least one target in 71.4%, compared with 51.0% by culture; the specimen-level PPA for any-target detection was 84.0%. Any degree of organism-level bacterial agreement was observed in 41.8%, while 58.2% showed complete discordance. Among 72 AMR-marker-positive observations with a matched cultured isolate and relevant susceptibility result, 64 demonstrated expected resistant phenotype (88.9% positive agreement). Both carbapenemases and Gram-negative detection were independently associated with phenotypic resistance. CONCLUSIONS: Integration of multiplex PCR and conventional culture expanded pathogen detection and provided valuable AMR profiling in resource-limited, high-resistance settings.