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. (December 2016)

• Record Type: Journal Article
• Authors: Forde, Taya; Biek, Roman; Zadoks, Ruth; Workentine, Matthew; De Buck, Jeroen; Kutz, Susan; Opriessnig, Tanja; Trewby, Hannah; van der Meer, Frank; Orsel, Karin
• Is Part Of: BMC genomics. Volume 17:Number 1(2016)
• Page Start: 1
• Page End: 15
• Publication Date: 2016-12
• Subjects: Erysipelothrix rhusiopathiae -- Genomics -- Gram positive bacteria -- Homologous recombination -- Host specificity -- Multi-host pathogen -- Population structure -- Whole genome sequencing; Genomes -- Periodicals; Gene mapping -- Periodicals; Genomics -- Periodicals; Base Sequence -- Periodicals; Chromosome Mapping -- Periodicals; Genetic Techniques -- Periodicals; Sequence Analysis, DNA -- Periodicals; 572.8605
• DOI: 10.1186/s12864-016-2643-0
• Languages: English
• ISSNs: 1471-2164

Abstract

Abstract Background 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 ofE. rhusiopathiae based on a diverse collection of isolates in order to address these knowledge gaps. Results Eighty-threeE. 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 andde 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 speciesE. rhusiopathiae . Although we found some evidence of host and geographical clustering, each clade included isolates from diverse host species and from multiple continents. Conclusions Using whole genome sequence data, we confirm recent suggestions thatE. 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 ofE. rhusiopathiae and facilitate comparisons to other recombinogenic, multi-host bacteria.