Comparative genomic analysis identifies potential adaptive variation and virulence factors in Mycoplasma ovipneumoniae

Abstract

Mycoplasma ovipneumoniae is associated with respiratory disease in wild and domestic Caprinae globally, with wide variation in disease outcomes within and between host species. To gain insight into phylogenetic structure and mechanisms of pathogenicity for this bacterial species, we compared M. ovipneumoniae genomes for 99 samples from six countries (Australia, Bosnia and Herzegovina, Brazil, China, France, USA) and four host species (domestic sheep, domestic goats, bighorn sheep, caribou). Core genome sequences of M. ovipneumoniae assemblies from domestic sheep and goats fell into two well-supported phylogenetic clades that are divergent enough to be considered different bacterial species, consistent with each of these two clades having an evolutionary origin in separate host species. Genome assemblies from bighorn sheep and caribou also fell within these two clades, indicating multiple spillover events, most commonly from domestic sheep. Pangenome analysis indicated a high percentage (91.4%) of accessory genes (i.e., genes found only in a subset of assemblies) compared to core genes (i.e., genes found in all assemblies), potentially indicating a propensity for this pathogen to adapt to within-host conditions. In addition, many genes related to carbon metabolism, which is a virulence factor for Mycoplasmas, showed evidence for homologous recombination, a potential signature of adaptation. The presence or absence of annotated genes was very similar between sheep and goat clades, with only two annotated genes significantly clade-associated. However, three M. ovipneumoniae genome assemblies from asymptomatic caribou in Alaska formed a highly divergent subclade within the sheep clade that lacked 23 annotated genes compared to other assemblies, and many of these genes had functions related to carbon metabolism. Overall our results provide evidence that adaptation of M. ovipneumoniae has involved evolution of carbon metabolism pathways and virulence mechanisms related to those pathways. The genes involved in these pathways, along with other genes identified as potentially involved in virulence in this study, are potential targets for future investigation into a possible genomic basis for the high variation observed in disease outcomes within and between wild and domestic host species. Data SummaryRaw sequence data and genome assemblies generated for this study have been deposited with the National Center for Biotechnology Information (NCBI) under BioProject number PRJNA1070810. Assemblies are also currently available for download through Dryad with the following link: https://datadryad.org/stash/share/aNet7o-xag3PTjJ0_A_BDoOPUpHHshArGW1eJMfLYl4 NCBI accession numbers and associated metadata for each assembly are available in the Supplemental Materials. DNA sequences extracted from these assemblies for four genetic markers (gyrB, rpoB, 16S, IGS) are available in the Supplemental Materials. Analysis code is available at https://github.com/kimandrews/Movi and an interactive phylogeny is available at https://nextstrain.org/community/narratives/kimandrews/Movi Impact statementMycoplasma ovipneumoniae causes respiratory disease in wild and domestic sheep and goats around the world, resulting in economic losses for the domestic sheep industry and severe population declines for wild species. Disease outcomes vary widely within and between host species, and this variation could be influenced by genomic differences across bacterial strains. We compared M. ovipneumoniae genomes from six countries and four host species and found species-level divergence for strains from domestic goats versus domestic sheep, indicating separate evolutionary origins in these two host species. All wildlife strains fell within these two groups, providing evidence that these strains originated by transmission from domestic populations. We identified genes potentially involved in adaptation to hosts, which could be responsible for differences in disease outcomes across bacterial strains and host species. Many of these genes had functions related to carbon metabolism, a potential virulence factor for Mycoplasmas.