Comparative genomics of Brachyspira pilosicoli strains: genome rearrangements, reductions and correlation of genetic compliment with phenotypic diversity

Abstract

BackgroundThe anaerobic spirochaete Brachyspira pilosicoli causes enteric disease in avian, porcine and human hosts, amongst others. To date, the only available genome sequence of B. pilosicoli is that of strain 95/1000, a porcine isolate. In the first intra-species genome comparison within the Brachyspira genus, we report the whole genome sequence of B. pilosicoli B2904, an avian isolate, the incomplete genome sequence of B. pilosicoli WesB, a human isolate, and the comparisons with B. pilosicoli 95/1000. We also draw on incomplete genome sequences from three other Brachyspira species. Finally we report the first application of the high-throughput Biolog phenotype screening tool on the B. pilosicoli strains for detailed comparisons between genotype and phenotype.ResultsFeature and sequence genome comparisons revealed a high degree of similarity between the three B. pilosicoli strains, although the genomes of B2904 and WesB were larger than that of 95/1000 (~2,765, 2.890 and 2.596 Mb, respectively). Genome rearrangements were observed which correlated largely with the positions of mobile genetic elements. Through comparison of the B2904 and WesB genomes with the 95/1000 genome, features that we propose are non-essential due to their absence from 95/1000 include a peptidase, glycine reductase complex components and transposases. Novel bacteriophages were detected in the newly-sequenced genomes, which appeared to have involvement in intra- and inter-species horizontal gene transfer. Phenotypic differences predicted from genome analysis, such as the lack of genes for glucuronate catabolism in 95/1000, were confirmed by phenotyping.ConclusionsThe availability of multiple B. pilosicoli genome sequences has allowed us to demonstrate the substantial genomic variation that exists between these strains, and provides an insight into genetic events that are shaping the species. In addition, phenotype screening allowed determination of how genotypic differences translated to phenotype. Further application of such comparisons will improve understanding of the metabolic capabilities of Brachyspira species.

Genes encoding ten newly designated OXA-63 group class D β-lactamases identified in strains of the pathogenic intestinal spirochaete Brachyspira pilosicoli

“…Consistent with the report of extensive genomic rearrangements being present in sequenced strains of B. pilosicoli (Mappley et al, 2012), the position of the bla OXA-63 group genes varied in the genomes in three of the four strains where the whole genome had been sequenced, and was absent from the genome of the fourth strain (P43/6/ 78 T ). Furthermore, these strains varied in the number of transposases identified in their genomes (from 0 to 34), and in the case of B2904 there were two transposases adjacent to the bla OXA-63 group gene.…”

“…The spirochaete has a recombinant population structure (Trott et al, 1998;Neo et al, 2013), and genomic sequencing has revealed that strains show extensive genomic rearrangements and that their genome sizes vary (Wanchanthuek et al, 2010;Mappley et al, 2012;Lin et al, 2013). Infection with B. pilosicoli occurs commonly in intensively housed pigs and adult poultry, and also in human beings living in crowded conditions in developing countries (Trott et al, 1997;Mikosza & Hampson, 2001;Margawani et al, 2004).…”

The pathogenic intestinal spirochaete Brachyspira pilosicoli forms a diverse recombinant species demonstrating some local clustering of related strains and potential for zoonotic spread

“…In addition, in the case of B . pilosicoli , recent analysis of the genomes of three sequenced strains identified genome rearrangements that largely correlated with the positions of mobile genetic elements [24]. Novel bacteriophages also were detected in the newly sequenced genomes, and clearly such genetic elements may have the potential to transduce genetic information and contribute to the recombination that has been recorded here.…”

The Spirochete Brachyspira pilosicoli, Enteric Pathogen of Animals and Humans

“…More recently Mappley et al (47) reported a comparative analysis of the genomes of B. pilosicoli strains 95/1000, B2904, and WesB, which were isolated from a pig, a chicken, and a human, respectively. The study included an analysis of phenotypic properties of the strains using a Biolog phenotype microarray.…”

“…Despite the small genome size range, B. pilosicoli strains encode more proteins than other Brachyspira species, possibly because of having a greater number of gene duplications and greater homogeneity than other Brachyspira species (48). The three strains of B. pilosicoli shared 2,132 genes, with 112 to 256 genes being unique to each strain (47). Different pairs of strains shared another 236, 38, and 19 genes, respectively.…”