Genomic characterization of carbapenem-resistant Acinetobacter baumannii isolates from the National Clinical Bacteriology Reference Laboratory, Ethiopia

Abstract

Acinetobacter baumannii is a major cause of healthcare-associated infections, and carbapenem-resistant strains pose a critical public health threat owing to limited treatment options and the dissemination of AMR determinants. However, genomic data on carbapenem-resistant A baumannii(CRAB) in Ethiopia are limited. This study characterized 30 A. baumannii isolates from the National Clinical Bacteriology Reference Laboratory (NRL) using phenotypic and whole-genome sequencing (WGS). All 30 A. baumannii isolates exhibited multidrug-resistant (MDR) phenotypes, and 29/30 (96.7%) were phenotypically resistant to carbapenems. WGS identified acquired carbapenemase genes in 28/29 (96.6%) carbapenem-resistant isolates, predominantly bla NDM−1 (20/29) and bla OXA−23 (17/29), together with diverse AMR determinants. Population structure analysis using the Pasteur multilocus sequence typing (MLST) scheme identified ST2 (International Clone 2) as the predominant lineage (14/30, 46.7%), followed by ST85 (5/30, 16.7%) and ST1 (3/30, 10.0%). The Oxford MLST scheme further resolved the isolates into ST1697 (9/30, 30.0%), ST1089 (5/30, 16.7%), ST451 (5/30, 16.7%), and ST405 (3/30, 10.0%), while three isolates had unassigned MLST profiles that were not matched to existing sequence types in the MLST database. The core-genome SNP phylogeny showed that isolates generally clustered according to their MLST sequence types, while also revealing genetic diversity within individual sequence types. Closely related clusters were consistent with clonal relatedness, whereas genetically distinct isolates within the same sequence type suggested diversification among isolates. Capsular typing identified nine KL types, with KL152 predominating (14/30, 46.7%), and three major Outer Core Locus (OCL) types, OCL1 (15/30, 50.0%), OCL16 (6/30, 20.0%), and OCL15 (5/30, 16.7%). All isolates carried conserved virulence determinants associated with biofilm formation, quorum sensing, iron acquisition, secretion systems, and type IV pili, and harbored Rep_3 superfamily plasmids representing 14 distinct plasmid types. Genomic characterization of MDR clinical isolates A. baumannii revealed the predominance of international high-risk lineages carrying clinically relevant carbapenemase genes, diverse virulence determinants and plasmid replicons. WGS provides high-resolution insights into population structure and genetic diversity, highlighting its value for strengthening antimicrobial resistance surveillance and informing infection prevention and control strategies.