Salmonella enterica serovar Abortusovis is an ovine restricted agricultural pathogen that causes abortions in sheep flocks, mostly in Europe. However, since 2009 this serovar has been detected in commercial poultry flocks in New South Wales. In this study we examined the genomes of 39 Abortusovis isolates from multiple farms in two regions within NSW from 2013 to 2019 along with four publicly available clinical isolate genomes and compared them to existing international isolates.
Phylogenetic analysis revealed that the NSW genomes (including all four clinical samples) are very genetically distant from international Abortusovis (>20,000 SNPs) and all fall within one closely related clade. Bayesian analysis estimated the common ancestor of the NSW clade at 2009 which agrees with surveillance carried out in the poultry industry. Within the NSW Abortusovis clade there were two larger subclades and one smaller subclade. While some region and source type specific clustering can be seen in the small subclade, the two large subclades contain isolates from both regions suggesting that the serovar has moved between regions multiple times across 10 years. Interestingly all isolates from layer hens (across 4 years) come from a single phylogenetic cluster suggesting that isolates in that setting may be derived from a single infection event.
Analysis of the accessory genomes of all Abortusovis isolates identifies differences between the NSW clade and international isolates. Notably the NSW clade contains the yersiniabactin gene cluster, the CS54 virulence island and the individual factors misL and cdtB, none of which are present in the international isolates. These and other differences may account for the change in host from sheep to chicken and may also explain the apparent ability of this clade to cause human disease. Further surveillance of this clade in both agricultural and clinical settings will be important to ensure the serovar is not a new source of significant human infection.