Isolation and Whole-Genome Sequencing of a Less Prevalent Indian A. baumannii Strain Reveals Unique Uncharacterized Hypothetical Proteins and AMR-Linked ncRNAs.

Acinetobacter baumannii is a high-priority pathogen due to its extensive antimicrobial resistance and persistence in clinical environments. This study describes the genomic features of AB_Varanasi, a carbapenem-resistant clinical isolate from India belonging to ST149 (Pasteur)/ST1506 (Oxford), a lineage not linked to major international clones. The isolate was resistant to almost all tested antibiotics, retaining susceptibility only to tigecycline and showing intermediate susceptibility to colistin. Whole-genome sequencing produced a 4.19 Mb circular chromosome encoding 4,039 predicted genes, with metabolism-associated functions forming the largest subsystem category.The genome carried multiple resistance determinants, including carbapenem-hydrolysing β-lactamases (OXA-23, OXA-104), extended-spectrum β-lactamases (ADC-26, PER-7), aminoglycoside-modifying enzymes, fluoroquinolone resistance–associated mutations, and several multidrug efflux systems (AdeABC, AdeIJK, AcrAB-TolC, and MFS transporters). Several of these genes were embedded within mobile genetic element–rich regions, suggesting a high potential for horizontal gene transfer. Virulence profiling identified the complete acinetobactin iron acquisition system, a functional Type VI secretion system, Type IV pilus components, and biofilm-associated operons.Variant analysis detected 30,385 high-confidence mutations with a transition-to-transversion ratio of 3.05. High-impact variants affected ribosomal protein L22 and the RNA polymerase β-subunit, while moderate-impact mutations involved metabolic and recombination-related genes. The regulatory landscape comprised 113 non-coding RNAs, including riboswitches and antisense RNAs. A total of 294 hypothetical proteins were identified, representing 192 DUF families, many predicted to encode membrane-associated or transport-related functions. Several of these uncharacterized proteins may serve as promising therapeutic or vaccine targets, given their potential surface exposure and species-specific conservation.