A genome-wide association study to identify the genetic loci underlying carbapenem resistance in Acinetobacter baumannii

Carbapenem-resistant Acinetobacter baumannii (CRAB) is a major public health threat and a key contributor to the global antimicrobial resistance (AMR) crisis. This study applied a bacterial genome-wide association study (bGWAS) framework to identify genetic factors beyond the canonical carbapenemase OXA-23, that may contribute to carbapenem resistance. A. baumannii isolates with publicly available whole-genome sequencing (WGS) data and carbapenem-specific antimicrobial susceptibility testing (AST) results were compiled (n = 1,601). Unitigs were extracted from de novo assemblies, and single-nucleotide polymorphisms (SNPs) were called from raw sequence reads mapped to seven selected reference genomes. The population was highly clonal and comprised ten lineages, including three predominantly resistant ST2 lineages. The known CRAB-associated loci, including OXA-23, the RND efflux pump regulator AdeL, and an OXA-66 substitution (Leu167Val), were readily identified. Novel resistance-associated mutations were detected in outer-membrane proteins, including porins (OprD, DcaP) and proteins (PqiB, LptD) involved in lipopolysaccharide (LPS) biogenesis. Notably, the detection of OprD and DcaP was reference-dependent, indicating that a multi-reference bGWAS framework improves identification of resistance-associated variants that may be missed in single-reference analyses. Structural mapping of the identified mutations suggested plausible effects on protein function.