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Background Brachyspira  ( B. )  hyodysenteriae  is a fastidious anaerobe spirochete that can cause swine dysentery, a severe mucohaemorragic colitis that affects pig production and animal welfare worldwide. In Switzerland, the population of  B. hyodysenteriae  is characterized by the predominance of macrolide-lincosamide-resistant  B. hyodysenteriae  isolates of sequence type (ST) ST196, prompting us to obtain deeper insights into the genomic structure and variability of ST196 using pangenome and whole genome variant analyses. Results The draft genome of 14  B. hyodysenteriae  isolates of ST196, sampled during a 7-year period from geographically distant pig herds, was obtained by whole-genome sequencing (WGS) and compared to the complete genome of the  B. hyodysenteriae  isolate Bh743-7 of ST196 used as reference. Variability results revealed the existence of 30 to 52 single nucleotide polymorphisms (SNPs), resulting in eight sublineages of ST196. The pangenome analysis led to the identification of a novel prophage,  pphBh CH20, of the  Siphoviridae  family in a single isolate of ST196, which suggests that horizontal gene transfer events may drive changes in genomic structure. Conclusions This study contributes to the catalogue of publicly available genomes and provides relevant bioinformatic tools and information for further comparative genomic analyses for  B. hyodysenteriae . It reveals that Swiss  B. hyodysenteriae  isolates of the same ST may have evolved independently over time by point mutations and acquisition of larger genetic elements. In line with this, the third type of mobile genetic element described so far in  B. hyodysenteriae , the novel prophage  pphBh CH20, has been identified in a single isolate of  B. hyodysenteriae  of ST196.

Whole-genome analyses reveal a novel prophage and cgSNPs-derived sublineages of Brachyspira hyodysenteriae ST196