Genomic analysis of the multi-host pathogen Erysipelothrix rhusiopathiae reveals extensive recombination as well as the existence of three generalist clades with wide geographic distribution.
Knowledge about how bacterial populations are structured is an important prerequisite for studying their ecology and evolutionary history and facilitates inquiry into host specificity, pathogenicity, geographic dispersal and molecular epidemiology. Erysipelothrix rhusiopathiae is an opportunistic pathogen that is currently reemerging in both the swine and poultry industries globally. This bacterium sporadically causes mortalities in captive marine mammals, and has recently been implicated in large-scale wildlife die-offs. However, despite its economic relevance and broad geographic and host distribution, including zoonotic potential, the global diversity, recombination rates, and population structure of this bacterium remain poorly characterized. In this study, we conducted a broad-scale genomic comparison of E. rhusiopathiae based on a diverse collection of isolates in order to address these knowledge gaps.



Eighty-three E. rhusiopathiae isolates from a range of host species and geographic origins, isolated between 1958 and 2014, were sequenced and assembled using both reference-based mapping and de novo assembly. We found that a high proportion of the core genome (58 %) had undergone recombination. Therefore, we used three independent methods robust to the presence of recombination to define the population structure of this species: a phylogenetic tree based on a set of conserved protein sequences, in silico chromosome painting, and network analysis. All three methods were broadly concordant and supported the existence of three distinct clades within the species E. rhusiopathiae. Although we found some evidence of host and geographical clustering, each clade included isolates from diverse host species and from multiple continents.



Using whole genome sequence data, we confirm recent suggestions that E. rhusiopathiae is a weakly clonal species that has been shaped extensively by homologous recombination. Despite frequent recombination, we can reliably identify three distinct clades that do not clearly segregate by host species or geographic origin. Our results provide an essential baseline for future molecular epidemiological, ecological and evolutionary studies of E. rhusiopathiae and facilitate comparisons to other recombinogenic, multi-host bacteria.
Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada. Taya.Forde@glasgow.ac.uk.|Current address: Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, Scotland, UK. Taya.Forde@glasgow.ac.uk.
Taya
T
Forde
Current address: Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, Scotland, UK.
Roman
R
Biek
Current address: Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, Scotland, UK.
Ruth
R
Zadoks
Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada.
Matthew L
ML
Workentine
Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada.
Jeroen
J
De Buck
Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada.
Susan
S
Kutz
The Roslin Institute, University of Edinburgh, Midlothian, Scotland, UK.
Tanja
T
Opriessnig
Current address: Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, Scotland, UK.
Hannah
H
Trewby
Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada.
Frank
F
van der Meer
Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada.
Karin
K
Orsel
D000818:Animals; D001435:Bacteriophages / Q000502:physiology; D016000:Cluster Analysis; D004888:Erysipelothrix / Q000145:classification* / Q000235:genetics* / Q000821:virology; D005828:Genetics, Population; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D054884:Host-Pathogen Interactions; D010802:Phylogeny; D010957:Plasmids / Q000235:genetics; D011995:Recombination, Genetic; D013552:Swine
Erysipelothrix rhusiopathiae; Genomics; Gram positive bacteria; Homologous recombination; Host specificity; Multi-host pathogen; Population structure; Whole genome sequencing