Genomic heterogeneity and lineage-specific beta-lactamases in recurrent Achromobacter bloodstream infection patients

Recurrent Achromobacter infections pose significant clinical challenges due to antimicrobial resistance and within-host evolution. This study investigates the genetic and phenotypic changes among Achromobacter isolates using next-generation sequencing. We retrospectively analyzed 65 Achromobacter infection cases at a tertiary hospital in Taiwan from 2016 to 2023. Whole-genome sequencing of 12 isolates from patients with recurrent bloodstream infections was performed using Oxford Nanopore Technology. Resistance genes and beta-lactamases were identified, and genome similarity was assessed using average nucleotide identity (ANI) for phylogenetic analysis. Recurrent infections were significantly associated with bloodstream and urinary tract infections (p Achromobacter species and the first identification of A. insuavis as a bacteraemia pathogen. Beta-lactamases grouped according to phylogenetic clades, indicating lineage-specific resistance patterns. Missense mutations in genes such as siaT, rapA, atzEa1, AL523_09115, and clpA correlated with changes in antimicrobial resistance profiles, suggesting in vivo evolution during recurrent infections. This study enhances understanding of Achromobacter genomic heterogeneity and underscores the importance of whole-genome sequencing for accurate species identification and resistance detection. The findings highlight the need for larger-scale studies to monitor emerging variants and assess their clinical impact.