Acquired antimicrobial resistance genes in Bordetella Species: a global genomic analysis

The genus Bordetella comprises Gram-negative pathogens, notably B. pertussis, which causes whooping cough, underscoring the need to characterize antimicrobial resistance (AMR) within this group. However, reports of acquired antimicrobial resistance genes (ARGs) in non-B. pertussis Bordetella species remain scarce.

Non-B. pertussis Bordetella genomes were retrieved from NCBI, adapters trimmed and low-quality reads filtered, then assembled for analysis. ARGs were identified with Abricate, ResFinder, and BLAST, and their genomic contexts visualized using Easyfig. Core-genome SNP phylogeny and Bayesian clustering delineated lineages, and SNP-based thresholds quantified transmission.

Across 746 genomes, 105 ARGs were identified in three non-B. pertussis species: B. bronchiseptica (96 ARGs), B. trematum (7 ARGs) and B. avium (2 ARGs). Ten distinct ARG types covering sulphonamide (sul1, sul2), tetracycline (tet(A), tet(G), tet(31)), aminoglycoside (aac(6')-IIa, aadA2, aph(3″)-Ib, aph(6)-Id) and β-lactam (blaOXA-2) resistance were observed. Core-genome SNP analysis of 238 B. bronchiseptica strains resolved three lineages, of which lineage 2 harboured the greatest diversity of multidrug-resistant isolates. Transmission-event quantification using SNP thresholds revealed frequent international and cross-host spread, notably human-dog/rabbit transfers and international dissemination between France and the United States.

These findings underscore the importance of monitoring AMR in Bordetella species to anticipate and mitigate the spread of resistant strains.