Novel, host-restricted genotypes of Bordetella bronchiseptica associated with phocine respiratory tract isolates

Abstract

During a succession of phocine morbillivirus outbreaks spanning the past 25 years, Bordetella bronchiseptica was identified as a frequent secondary invader and cause of death. The goal of this study was to evaluate genetic diversity and the molecular basis for host specificity among seal isolates from these outbreaks. MLST and PvuII ribotyping of 54 isolates from Scottish, English or Danish coasts of the Atlantic or North Sea revealed a single, host-restricted genotype. A single, novel genotype, unique from that of the Atlantic and North Sea isolates, was found in isolates from an outbreak in the Caspian Sea. Phylogenetic analysis based either on MLST sequence, ribotype patterns or genome-wide SNPs consistently placed both seal-specific genotypes within the same major clade but indicates a distinct evolutionary history for each. An additional isolate from the intestinal tract of a seal on the south-west coast of England has a genotype otherwise found in rabbit, guinea pig and pig isolates. To investigate the molecular basis for host specificity, DNA and predicted protein sequences of virulence genes that mediate host interactions were used in comparisons between a North Sea isolate, a Caspian Sea isolate and each of their closest relatives as inferred from genome-wide SNP analysis. Despite their phylogenetic divergence, fewer nucleotide and amino acid substitutions were found in comparisons of the two seal isolates than in comparisons with closely related strains. These data indicate isolates of B. bronchiseptica associated with respiratory disease in seals comprise unique, host-adapted and highly clonal populations.

Comparative genomic analysis of the swine pathogen Bordetella bronchisepticastrain KM22

“…Seven SNPs were observed in bipA from strain KM22 compared to RB50 and are predicted to result in 4 amino acid replacements: S322G, V813A, E912G, and S1131P. These findings are similar to the results reported in a recent study evaluating virulence gene polymorphisms among B. bronchiseptica seal isolates, in which bipA was found to have the greatest sequence divergence of the genes examined (Register et al, 2015).…”

Comparison of ribotyping and sequence-based typing for discriminating among isolates of Bordetella bronchiseptica

“…Phylogenetic analyses were conducted using MEGA6 version 6.05 (Tamura et al 2013). STs for 61 isolates included in this study have been reported previously (Diavatopoulos et al;2005;Rath et al 2008;Register et al 2015a). Those for an additional 21 isolates were deduced from genome sequence data (Register et al 2015b; GenBank accession #NZ_JGWN01000000).…”

“…Novel patterns were assigned to newly defined RTs. RTs for 78 of the isolates included in this study have been reported previously (Register et al 1997;Register and Magyar 1999;Register et al 2000;Register 2004;Rath et al 2008;Register et al 2015a).…”

“…A total of 122 isolates of B. bronchiseptica was analyzed, selected to represent diverse host and geographic origins. Included among these isolates are representatives of the 22 PvuII ribotypes so far recognized (Register et al 1997;Register and Magyar 1999;Register et al 2000;Register et al 2015a) and 25 of the 61 MLST sequence types (STs) currently associated with B. bronchiseptica isolates in the Bordetella PubMLST database (http://pubmlst.org/bordetella). Isolates were sourced from the United States, Europe, Israel and Australia and include 24 from humans, 20 from seals, 17 from pigs, 13 from turkeys, 12 from rabbits, 10 from dogs, 8 from guinea pigs, 7 from horses, 6 from cats, 3 from koalas, 1 from a leopard and 1 of unknown origin.…”

“…Dendrograms were derived from a matrix of similarity values by UPGMA (unweighted pair group method with arithmetic mean). Ribotype (RT) 1-RT22 have been previously described (Register et al 1997;Register and Magyar 1999;Register et al 2000;Register et al 2015a). Novel patterns were assigned to newly defined RTs.…”