Rapid identification of microbial pathogens in intra-abdominal infections using multiplex PCR

Intra-abdominal infections (IAI) resulting from the perforation of hollow viscera are associated with high morbidity and mortality. In addition to timely surgical source control, rapid and accurate pathogen identification is crucial to guide targeted antimicrobial therapy, particularly in polymicrobial infections involving potentially virulent pathogens. In this prospective study (ClinicalTrials.gov NCT07562204), we compared real-time multiplex PCR Unyvero A50 (Curetis^®) as a point-of-care (POC) tool with conventional microbiological culture (cMB). 50 patients with suspected hollow organ perforation or peritonitis were included. 2 intraoperative samples were collected per patient: one for immediate PCR testing and one for standard culture-based diagnostics. Turnaround times, pathogen detection rates, resistance marker detections and microbial distribution according to anatomical sampling site were assessed descriptively. PCR results were available on the same day or the next day in all cases (n=41), whereas cMB results required ≥2 days in all cases (n=50). 9 samples (18%) yielded invalid PCR results according to the manufacturer's system output and were excluded from concordance analyses. Among the 41 evaluable sample pairs, complete concordance between PCR and cMB was observed in 29% (12/41), while non-concordant results occurred in 71% (29/41). PCR detected at least one additional pathogen not identified by cMB in 49% (20/41) of cases. Pathogen detection rates and pathogen group distributions were analyzed per protocol in samples with valid PCR results (n=41) and compared with cMB results from the total cohort (n=50). Gram-positive bacteria were detected in 58% (29/50) of cMB and 56% (23/41) of PCR samples. Aerobic/facultative Gram-negative bacteria were detected in 46% (23/50) of cMB samples and in 59% (24/41) of PCR samples. Enterobacteriaceae represented the predominant subgroup and were detected in 34% (17/50) of cMB and 37% (15/41) of PCR samples. Anaerobic bacteria were detected more frequently by PCR than by cMB (cMB 24%, 12/50 vs. PCR 44%, 18/41). In conclusion, multiplex PCR cannot replace conventional culture, but may serve as a complementary tool, providing rapid detection of selected pathogens, including anaerobes. Its implementation may support earlier antimicrobial decision-making in IAIs. Further multicenter studies are needed to evaluate its clinical utility in routine diagnostic workflows.