Genetic basis of antimicrobial resistance, virulence features and phylogenomics of carbapenem-resistant Acinetobacter baumannii clinical isolates

The worldwide emergence and clonal spread of carbapenem-resistant Acinetobacter baumannii (CRAB) is of great concern. In the present study, we determined the mechanisms of antimicrobial resistance, virulence gene repertoire and genomic relatedness of CRAB isolates circulating in Serbian hospitals.

CRAB isolates were analyzed using whole-genome sequencing (WGS) for the presence of antimicrobial resistance-encoding genes, virulence factors-encoding genes, mobile genetic elements and genomic relatedness. Antimicrobial susceptibility testing was done by disk diffusion and broth microdilution methods.

Eleven isolates exhibited an MDR resistance phenotype, while four of them were XDR. MIC₉₀ for meropenem and imipenem were > 64 µg/mL and 32 µg/mL, respectively. While all CRABs harbored bla_OXA−66 variant of bla_OXA−51 gene, those assigned to ST^Pas2, ST^Pas636 and ST^Pas492 had bla_ADC−73,bla_ADC−74 and bla_ADC−30 variants, respectively. The following acquired carbapenemases-encoding genes were found: bla_OXA−72 (n = 12), bla_OXA−23 (n = 3), and bla_NDM−1(n = 5), and were mapped to defined mobile genetic elements. MLST analysis assigned the analyzed CRAB isolates to three Pasteur sequence types (STs): ST^Pas2, ST^Pas492, and ST^Pas636. The Majority of strains belonged to International Clone II (ICII) and carried tested virulence-related genes liable for adherence, biofilm formation, iron uptake, heme biosynthesis, zinc utilization, serum resistance, stress adaptation, intracellular survival and toxin activity.

WGS elucidated the resistance and virulence profiles of CRABs isolated from clinical samples in Serbian hospitals and genomic relatedness of CRAB isolates from Serbia and globally distributed CRABs.