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

## TL;DR

This study analyzes antimicrobial resistance genes in non-B. pertussis Bordetella species using global genomic data to understand resistance patterns and transmission.

## Contribution

The study provides the first comprehensive global genomic analysis of acquired antimicrobial resistance genes in non-B. pertussis Bordetella species.

## Key findings

- 105 antimicrobial resistance genes were identified across 746 genomes of three non-B. pertussis Bordetella species.
- B. bronchiseptica showed the highest diversity of resistance genes and multidrug-resistant isolates in lineage 2.
- International and cross-host transmission events were detected, including human-dog/rabbit transfers and spread between France and the US.

## Abstract

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.