Actinobacillus suis isolated from diseased pigs are phylogenetically related but harbour different number of toxin gene copies in their genomes

OBJECTIVE: The Gram‐negative bacterium Actinobacillus suis is an agent of global importance to the swine industry and the cause of lethal respiratory or septicaemic disease in pigs of different ages. Between 2018 and 2019, seven commercial farms in western Canada experienced episodes of increased mortality due to A. suis infection in grower pigs. The goal of this work was to profile, with molecular methods, A. suis isolated from diseased pigs and to compare them to other isolates. DESIGN: This inferential observational study used nine western Canadian strains obtained from diseased lungs (n = 6), heart (n = 2) and brain (n = 1) and whole genome sequencing was performed. Comparative genomic analyses were performed to characterise the genetic variability, antimicrobial resistance and the virulence genes present. RESULTS: Compared to the reference strain (ATCC 33415), an increased number of RTX (repeats in the structural toxin) gene copies were identified in strains isolated from organs without a mucosal surface, thus theoretically harder to invade. Western Canadian strains did not harbour genes associated with resistance to antimicrobial agents used in swine production. Novel regions were also identified in the genomes of five of nine strains demonstrating recombination and emergence of novel strains. CONCLUSIONS: The results obtained in this study were associated with the emergence of new lineages. An increased number of RTX toxin gene copies is suggested to be associated with increased virulence. This study will contribute to improve our understanding regarding A. suis and may help guide vaccine development and agent control measures.