Integrating genomic and transcriptomic analyses reveals virulence factors and bloodstream infection mechanisms of Acinetobacter junii

Acinetobacter junii , an emerging pathogen of the Acinetobacter genus, exhibits concerning environmental persistence and clinical virulence potential. Despite its growing significance in bloodstream infections (BSIs), the genetic determinants distinguishing pathogenic from environmental strains remain poorly characterized, limiting our understanding of its transmission dynamics and host adaptation mechanisms. We explored the diversity and population structure of A. junii using a comprehensive genome dataset, including four strains isolated from China, one of which (acj0210) was derived from BSIs. We analysed the pangenome of A. junii and characterized its virulence and antibiotic resistance profile. Bacterial genome-wide association studies (bGWAS) were performed to identify the virulence potential. The virulence potential for BSIs was further investigated through RNA-seq analysis under different conditions. Additionally, transmission dynamics of bla NDM -carrying plasmids in carbapenem-resistant A. junii were inferred from plasmid network analysis. We identified seven lineages within A. junii , with BAPS1 as the dominant group. Discrepancies in accessory genes were observed between lineages, along with unique genes, particularly one novel capsular polysaccharide variant in acj0210. Using bGWAS, we uncovered key genetic differences, including transporter-encoding genes ( tauA , urtD ), regulatory mutations and exopolysaccharide-encoding genes that distinguish human and environmental strains. Transcriptomic analysis revealed potential virulence factors in BSIs, with distinct gene expression patterns between blood and immune cells, despite shared fatty acid metabolism profiles. As critical resistance determinants, bla NDM genes may have been acquired from A. baumannii. A. junii has adapted to diverse geographical and ecological niches, particularly in BSIs, with lineage-specific virulence factors aligned with antibiotic resistance genes, especially those carried by bla NDM harbouring plasmids.