Epidemiological typing of nosocomial carbapenem-resistant Acinetobacter baumannii isolates by molecular genetic methods and whole-genome sequencing-based techniques

Abstract

The present study aimed to perform epidemiological typing of nosocomial carbapenem-resistant Acinetobacter baumannii (CRAB) isolates from four university hospitals in Bulgaria using molecular genetic methods and whole-genome sequencing (WGS)-based techniques. A total of 80 CRAB (2014-2024) preliminary identified by automated systems were investigated. Methodology included antimicrobial susceptibility testing, polymerase chain reaction (PCR) to detect carbapenemase-encoding genes, WGS, multiplex PCR to identify sequence groups and international clones (ICs), multilocus sequence typing (MLST), KL (capsular polysaccharide locus), and OCL (outer core lipooligosaccharide locus) typing. CRAB studied were categorized as isolates with multidrug (8.8%), extensive drug (52.5%), and extensive drug + difficult-to-treat antimicrobial resistance (38.8%). Acquired class D carbapenemases were identified with the following prevalence rates: 92.5% OXA-23-like, 3.8% OXA-24/40-like, and 3.8% OXA-23-like + OXA-24/40-like. WGS proved OXA-23 and OXA-72 (OXA-24/40-like group). Multiplex PCR results showed a predominance of IC2 (76.7%), followed by sequence group G5 (15%). In WGS-based MLST analysis of 20 CRAB isolates, nineteen belonged to sequence type (ST) 2 (IC2) and one to ST636 (IC2). ST2 was associated with OCL1 and several KL types (KL9, KL77, KL2, and KL3), while ST636, with OCL2 and KL40, respectively. In conclusion, the conducted epidemiological typing of CRAB isolates revealed a clear dominance of IC2 (82.5% overall, as determined by both groups of methods) and the global high-risk ST2 clone (95%) in the monitored hospitals over the 10-year follow-up period. KL typing is a valuable tool with high discriminatory power to distinguish nosocomial A. baumannii isolates by chronology and site of isolation.