Comparative genomic analysis of Bordetella bronchiseptica isolates from the lungs of pigs with porcine respiratory disease complex (PRDC)

Background: Bordetella bronchiseptica (B. bronchiseptica), as an opportunistic pathogen, can cause respiratory diseases in a variety of animals, including humans. In additional to being involved in porcine atrophic rhinitis through coinfection with Pasteurella multocida, B. bronchiseptica is associated with porcine respiratory disease complex (PRDC). While there are genomic data available from different host species, little is known about B. bronchiseptica isolates from pig lungs, especially from lungs characterized as having PRDC. Results: A total of five B. bronchiseptica isolates were identified from pig lungs characterized as PRDC. The draft genomes of these strains were generated. In comparison with the other reported genomes, these five isolates showed the similar general characteristic including G+C content, rRNAs/tRNA, and clusters of orthologous groups of proteins (COGs). Phylogenetic analysis of all B. Bronchiseptica isolates of different species available at GenBank based on core genome multilocus sequence typing (cgMLST) classified them into two genogroups. All five isolates from this study, with the other isolates from pigs, were placed into a subclade of genogroup I consisting of only mammalian isolates. By contrast, genogroup II contained the isolates from an avian species (turkey) and some mammals (human and dog). Moreover, genome annotation revealed the presence of antibiotic resistance genes and virulence genes among these five genomes, consistent with the similarity and variety in genomic traits. Finally, comparative analysis of insertion sequence (IS) and prophages in five genomes further showed the similarity and variety in genomic characteristic. Conclusions: This is the first study to provide comparative genomics of B. bronchiseptica strains from pig lungs characterized as having PRDC. Importantly, the findings presented in this study reveal novel genomic characteristic of B. bronchiseptica, which should provide insightful information on genome evolution.