Analysis of Multiple Brachyspira hyodysenteriae Genomes Confirms That the Species Is Relatively Conserved but Has Potentially Important Strain Variation

Abstract

The intestinal spirochete Brachyspira hyodysenteriae is an important pathogen in swine, causing mucohemorrhagic colitis in a disease known as swine dysentery. Based on the detection of significant linkage disequilibrium in multilocus sequence data, the species is considered to be clonal. An analysis of the genome sequence of Western Australian B. hyodysenteriae strain WA1 has been published, and in the current study 19 further strains from countries around the world were sequenced with Illumina technology. The genomes were assembled and aligned to over 97.5% of the reference WA1 genome at a percentage sequence identity better than 80%. Strain regions not aligned to the reference ranged between 0.2 and 2.5%. Clustering of the strain genes found on average 2,354 (88%) core genes, 255 (8.6%) ancillary genes and 77 (2.9%) unique genes per strain. Depending on the strain the proportion of genes with 100% sequence identity to WA1 ranged from 85% to 20%. The result is a global comparative genomic analysis of B. hyodysenteriae genomes revealing potential differential phenotypic markers for numerous strains. Despite the differences found, the genomes were less varied than those of the related pathogenic species Brachyspira pilosicoli, and the analysis supports the clonal nature of the species. From this study, a public genome resource has been created that will serve as a repository for further genetic and phenotypic studies of these important porcine bacteria. This is the first intra-species B. hyodysenteriae comparative genomic analysis.

Variation in hemolytic activity of Brachyspira hyodysenteriae strains from pigs

“…The sequences for hlyA were identical to the whole genome sequences of WA1 and the 18 additional strains [ 47 ], except strain 3bIII and 4cI, which differed with regard to two nucleotides. However, these nucleotide differences were synonymous and did not translate into a different amino acid sequence.…”

“…Furthermore, all sequences were compared to the whole genome sequences of 18 additional B. hyodysenteriae strains, including type strain B78 and reference strains B204 and FM88.90. These whole genome sequences were recently described by Black et al [ 47 ].…”

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

“…They included the sequences of the 4 B. pilosicoli strains 95/1000, WesB, B2904 and P43/ 6/78 T (accession numbers NC_014330, NC_018604, NC_018607 and NC_019908, respectively), 20 Brachyspira hyodysenteriae strains (accession numbers NC_012225 for the chromosome and NC_012226 for the plasmid of WA1, and NZ_JXNA00000000 through NZ_JXNS00000000 for the other 19 strains: Black et al, 2015), 5 'Brachyspira hampsonii' strains (accession numbers NZ_ALNZ00000000 and NZ_AOMM00000000, and 3 unpublished), 2 Brachyspira intermedia strains (NC_017243 and 1 unpublished), 1 Brachyspira innocens strain (NZ_ARQI00000000), 1 Brachyspira murdochii strain (NC_014150), 1 Brachyspira alvinipulli strain (NZ_JADF00000000), 1 Brachyspira aalborgi strain (unpublished) and 1 'Brachyspira suanatina' strain (NZ_CVLB00000000).…”

Hiding in Plain Sight: Colonic Spirochetosis in Humans

“…A major contribution of the study by Thorell lack the 36-kb plasmid thought to be important in pathogenesis (20). The B. aalborgi genomes have the characteristic low GϩC content of Brachyspira (28.1 to 28.3%) and are otherwise similar to genomes of the 8 other Brachyspira species for which sequences are available (20,21).…”

“…Intraspecies comparisons of the B. aalborgi genomes revealed a heterogeneity greater than expected, although the organisms were clearly separated from other species. Black et al (20) found that the genomes of B. hyodysenteriae strains had undergone significant rearrangements, and the heterogeneity in B. aalborgi may also be related in part to rearrangements. Availability of the B. aalborgi sequences will extend the comparative genomics possibilities within the Brachyspira genus, perhaps helping to reveal key differences important in host interactions, such as pathogenesis or host range (21).…”