First genomic report of epidemic super-lineage, clade 2.5.6 Acinetobacter baumannii from hospital environmental surfaces in Bangladesh

Abstract

Abstract The World Health Organization classifies Acinetobacter baumannii as a critical-priority carbapenem-resistant nosocomial pathogen. Hospitals are underrecognized reservoirs of multidrug-resistant (MDR) bacteria, yet Bangladesh has limited environmental genomic surveillance, especially of International Clone 2 (IC2). A. baumannii was isolated and genomically characterized from 95 environment samples collected at two district-level hospitals in Jashore, Bangladesh. Biochemical characterization identified 38 isolates as Acinetobacter spp. (40%), of which 86% were moderate-to-strong biofilm formers and universally carbapenem-resistant. International Clone 2 (IC2) was identified by multiplex PCR using three isolates. Whole-genome sequencing was performed on two representative isolates, 2GbA2_JUST (pneumonia ward bed, XDR) and A_38_JUST (toilet dam water, MDR) and MLST analysis grouped them as ST2. Capybara SNP barcode categorization positively identified both samples as Epidemic Super-Lineage Clade 2.5.6. Resistome profiling found 28 ARGs per isolate, including OXA-66, plasmid-borne OXA-23, armA , ADC-73, and three full RND efflux systems. Virulome analysis found 17 functional virulence categories. Analysis of 37 A. baumannii genomes revealed an open pangenome (γ = 0.301). To our knowledge, this study provides the first genomic characterization of Epidemic Super Lineage (ESL) Clade 2.5.6 Acinetobacter baumannii recovered from hospital environmental surfaces in Bangladesh.