Global Distribution and Co-occurrence of Antimicrobial, Biocide, and Metal Resistance Genes in 11,921 Acinetobacter baumannii Genomes.

Acinetobacter baumannii is a critical priority pathogen globally. While antimicrobial resistance genes (ARGs) are well characterized, the prevalence, distribution, and co-occurrence patterns of biocide and metal resistance genes (BMRGs) remain poorly defined at global scale. We performed genomic analysis of 11,921 non-redundant A. baumannii genomes retrieved from NCBI RefSeq, representing isolates from 93 countries collected between 1982 and 2025. ARGs and BMRGs were identified using AMRFinderPlus (v4.2.7; organism-specific mode). Multilocus sequence typing (Pasteur MLST) was performed, and BMRG-ARG co-occurrence was assessed using one-sided Fisher's exact tests for enrichment with Benjamini-Hochberg correction (q < 0.05). Every genome carried at least one AMR determinant, and 99.98% carried at least one biocide or metal resistance locus at initial annotation. AMRFinderPlus identified 687 resistance-associated loci (633 AMR determinants; 39 biocide and metal resistance loci, of which 38 BMRGs were retained for analysis after exclusion of the core-genome gene nreB; and 15 virulence-associated loci, which were excluded from resistance analyses). Sequence type 2 (ST2) accounted for 56.4% of genomes. The carbapenemase gene blaOXA-23 was detected in 62.6% of genomes, and fluoroquinolone resistance mutations were highly prevalent (gyrA S81L: 84.9%; parC S84L: 77.2%). Co-occurrence analysis identified 38 significant BMRG-ARG associations overall (q < 0.05, OR ≥ 10), with a prominent module linking the integron-associated marker qacEΔ1 to ARGs (e.g., sul1, aadA1); the population-level mercury resistance-tet(A) association was not supported in the phylogeny-based sensitivity analysis. This study provides quantitative evidence for structured BMRG-ARG co-occurrence patterns in A. baumannii, shaped by ST2 dominance. These patterns are consistent with possible linkage and co-selection, although the present data cannot establish physical linkage.