Abstract
The enteric, pathogenic spirochaete Brachyspira pilosicoli colonizes and infects a variety of birds and mammals, including humans. However, there is a paucity of genomic data available for this organism. This study introduces 12 newly sequenced draft genome assemblies, boosting the cohort of examined isolates by fourfold and cataloguing the intraspecific genomic diversity of the organism more comprehensively. We used several in silico techniques to define a core genome of 1751 genes and qualitatively and quantitatively examined the intraspecific species boundary using phylogenetic analysis and average nucleotide identity, before contextualizing this diversity against other members of the genus Brachyspira . Our study revealed that an additional isolate that was unable to be species typed against any other Brachyspira lacked putative virulence factors present in all other isolates. Finally, we quantified that homologous recombination has as great an effect on the evolution of the core genome of the B. pilosicoli as random mutation (r/m=1.02). Comparative genomics has informed Brachyspira diversity, population structure, host specificity and virulence. The data presented here can be used to contribute to developing advanced screening methods, diagnostic assays and prophylactic vaccines against this zoonotic pathogen.
Highlights
Brachyspira is the sole genus of the family Brachyspiraceae within the order Spirochaetales, phylum Spirochaetes [1]
Our study is important for several reasons: (1) we introduced 12 newly sequenced draft genome assemblies to the literature, a 4-fold increase in the number of examined isolates; (2) we catalogued the intraspecific genomic diversity of the organism(s) comprehensively; (3) we found 1 isolate that was unable to be species typed against any other Brachyspira, and lacked putative virulence factors present in all other isolates, potentially suggesting a new species; (4) we quantified that homologous recombination has as great an effect on the evolution of the core genome of B. pilosicoli as random mutation
The 12 B. pilosicoli isolates were clustered into 8 sequence types (STs), based on a combination of 7 housekeeping loci
Summary
Brachyspira (previously Treponema, Serpula and Serpulina) is the sole genus of the family Brachyspiraceae within the order Spirochaetales, phylum Spirochaetes [1]. The genus Brachyspira includes nine officially recognized species [2], several of which are pathogenic – primarily to pigs and poultry, they can infect other animals and humans. These species are flagellated, anaerobic, aero-tolerant Gram-negative spirochaetes that inhabit the large intestine, where they are intimately associated with the colonic or caecal mucosa. Infection with Brachyspira hyodysenteriae (classical agent), Brachyspira hampsonii or Brachyspira suanatina causes swine dysentery (SD), a severe. Brachyspira aalborgi was assumed to be the sole aetiological agent causing histologically identified intestinal spirochaetosis (IS) in humans (HIS) [10], but it was reported that human gut colonization by B. pilosicoli is common [11, 12]
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