Genomic insights into the population structure, antimicrobial resistance, and virulence of Brachyspira hyodysenteriae from diverse geographical regions

Abstract

Swine dysentery, caused by the anaerobic spirochete Brachyspira hyodysenteriae, leads to mucohemorrhagic diarrhea in grower-finisher pigs, impacting swine production. Knowledge regarding its genomic epidemiology is limited. We performed a whole-genome sequence analysis for 251 B. hyodysenteriae genomes from 10 countries, including 117 isolates sequenced in this study. Phylogenomic analysis based on core-genome single nucleotide polymorphisms (SNPs) revealed nine lineages, with L7 (72 isolates, 28.69%), L9 (67 isolates, 26.69%), and L2 (53 isolates, 21.12%) predominating. Geographical clustering was observed with distinct lineage distributions. Multilocus sequence typing identified 69 sequence types (STs), including 20 novel STs across 251 genomes. Association between specific lineages, STs, and geographical regions was evident, highlighting evolutionary and regional patterns. The pan-genome analysis identified 5,231 genes, categorized into core (1,648), accessory (2,619), and unique (964) components. Functional annotation linked core genes to essential cellular processes, while accessory and unique genes were enriched in genetic variability, defense mechanisms, and secondary metabolism. The pan-genome exhibited a high proportion of hypothetical genes, necessitating further functional characterization. Antimicrobial resistance (AMR) screening detected the tva(A) and lnu(C) genes associated with tiamulin and lincomycin resistance, respectively, in specific lineages and STs. Virulence factor analysis identified genes linked to hemolysin production, iron uptake, and survival in host environments in most isolates, with a subset of genes demonstrating lineage-specific associations that are further linked to pathogenic potential. This comprehensive genomic epidemiological analysis elucidates the genetic diversity, antimicrobial resistance, and virulence of B. hyodysenteriae globally, enhancing understanding of its epidemiology and guiding interventions to mitigate swine dysentery.

Importance: Brachyspira hyodysenteriae, the primary causative agent of swine dysentery, remains a less-studied pathogen than other bacterial species that impact animal health. This study uses whole-genome sequencing and advanced phylogenomic approaches to reveal the genetic diversity and geographical distribution of B. hyodysenteriae isolates, focusing on U.S. populations. The identification of nine distinct phylogenetic lineages and associated sublineages highlights the pathogen's complex population structure and regional variation. Importantly, the study detects AMR genes, including tva(A) and lnu(C), linked to tiamulin and lincomycin resistance, that may pose significant challenges to disease management. The analysis also identifies virulence-associated genes, shedding light on molecular mechanisms underlying pathogenicity. By combining core-genome SNP phylogenies with multilocus sequence typing and accessory genome insights, this work provides a robust framework for a better understanding of B. hyodysenteriae evolution. Overall, these findings underscore the importance of genomic surveillance in informing control strategies and improving swine health worldwide.

Keywords: AMR; Brachyspira hyodysenteriae; MLST; phylogenomic analysis; population structure; swine dysentery; virulence; whole genome sequencing.

Fig 1

Circular phylogenetic tree based on core-genome SNPs of 251 B. hyodysenteriae genomes. The tree was constructed using IQ-TREE v2.1.4 from a multiple alignment of core-genome SNPs generated by Panaroo. The inner ring displays nine distinct lineages defined by the fastbaps “baps” option, with each lineage represented by a unique color. The middle ring displays sequence types (STs), with predominant STs shown in distinct colors, while STs detected five or fewer times are labeled as “other.” The outermost ring shows the countries of origin, with distinct colors representing each country. The legends on the left side of the figure correspond to these rings, providing a visual guide for interpreting the lineages, STs, and countries of origin.

Fig 2

Features of the B. hyodysenteriae pan-genome across 251 genomes. (A) Pan-genome composition. The pie chart displays the distribution of the 5,231 genes, categorized into core genes (present in all genomes), accessory genes (shared by two or more genomes), and unique genes (specific to a single genome). (B) Pan-genome and core genome curves. The curves show the trends observed as more genomes are added to the analysis: a decrease in the number of core genes and an increase in the total number of genes in the pan-genome but closely seem to have reached a plateau. The error bars represent confidence intervals, which decrease as more genomes are included, reflecting reduced variability in estimates.

Fig 3

The distribution of Clusters of Orthologous Groups (COG) 21 functional categories in the B. hyodysenteriae pan-genome annotated by eggNOG-mapper. Each COG category is represented by a letter and depicted in different colors on the bar graph. The x-axis lists the COG functional categories, while the y-axis displays the number of genes assigned to each category.

Fig 4

Distribution of COG functional categories across core, accessory, and unique genes in the B. hyodysenteriae pan-genome. The x-axis shows the COG functional categories. The y-axis displays the percentage of genes assigned to each COG category within the core, accessory, and unique gene types.

Fig 5

Circular phylogenetic tree based on core-genome SNPs of 251 Brachyspira hyodysenteriae isolates. The inner ring displays the nine distinct lineages defined by the Fastbaps “baps” option. The second ring shows the sequence types (STs). The third ring indicates the geographical origin of the isolates. The next two rings highlight the presence of AMR genes tva(A) and lnu(C). The four outermost rings represent the presence of virulence-associated genes. The legends on the left side of the figure correspond to these rings, providing a visual guide for interpreting the lineages, STs, countries of origin, AMR genes, and virulence genes.