Genomic insights into the resistome, mobilome and functional adaptation of Achromobacter xylosoxidans across clinical and environmental contexts

Achromobacter xylosoxidans is an emerging opportunistic pathogen associated with a wide range of infections in humans. This species is widely distributed in the environment due to its high adaptability. Isolates of A. xylosoxidans have intrinsic resistance to several antibiotics and the potential to acquire genetic resistance determinants. Despite its growing frequency of isolation, little is known about the genomic characteristics of this pathogen. In this study, we conducted a comprehensive genomic analysis of assemblies from the NCBI RefSeq database, along with a newly sequenced respiratory isolate from a patient with cystic fibrosis. Through pangenome analysis, we identified genes and functions associated with specific isolation sources, suggesting niche-specific adaptation. Resistance-associated mutations in the AxyZ efflux pump regulator, along with bla AXC-1 , were exclusively detected in genomes of clinical origin. Furthermore, while the resistome is limited, non-core antimicrobial resistance genes were detected to be primarily associated with the mobilome, underscoring the potential for horizontal gene transfer to further shape resistance in this species.