In the latter part of 2008 and early 2009, strongly beta-hemolytic Brachyspira spp. not identified as B. hyodysenteriae by published polymerase chain reaction assays were recovered with increasing frequency from North American pigs with clinical swine dysentery (SD). Biochemical and molecular characterization of these atypical and untypable Brachyspira isolates revealed the emergence of a putatively novel species with two distinct phylogenetic clades (clade I and clade II) and the name “Brachyspira hampsonii” has been proposed. The ultimate goal of this study was to genetically characterize a representative isolate of each clade and compare these isolates with other known pathogenic and poorly or non-pathogenic Brachyspira in efforts to determine potential virulence genes that could be used as a target for a virulence gene PCR assay. This study addressed the overall goal in two ways: 1) whole genome sequencing of strains of both clades of “B. hampsonii” along with a strain of the pathogenic B. hyodysenteriae and the non-pathogenic B. innocens by the PacBio platform and 2) whole genome sequencing of these same 2 strains of “B. hampsonii” as well as an additional strain of “B. hampsonii” clade I and strains of the weakly beta-hemolytic B. pilosicoli, B. intermedia, and B. murdochii using the Ion Torrent platform. Using two separate platforms for whole genome sequencing of the proposed novel “B. hampsonii” provides greater confidence in the resultant sequences prior to comparison and analysis with other strains. Sequences of B. hyodysenteriae, B. pilosicoli, B. intermedia and B. murdochii are available in GenBank for comparison and validation of the sequences obtained in this project.
The isolation of adequate DNA and whole genome sequencing of these spirochetes proved highly challenging and took much longer than expected. As a result, sequence analysis remains ongoing and the development of a virulence gene PCR was not completed within the timeframe of this project. However, the ultimate result of this project was the completion of whole genome sequencing on more than double the number of isolates as originally planned and the obtained sequences will be extremely valuable as many of these isolates have been used in our prior animal inoculation experiments and have a known pathotype. Having a well-characterized virulence phenotype will be key in properly categorizing these genetic sequences as originating from either pathogenic or poorly/non-pathogenic spirochetes in future efforts to identify putative virulence genes and target sequences for a swine dysentery-specific PCR that would detect the presence of pathogens rather than specific Brachyspira spp.
Contact information:
Dr. Pat Halbur, Department Chair
Veterinary Diagnostic and Production Animal Medicine
Iowa State University
1600 South 16th St
Ames, IA 50011
