Effects of abortion on the vaginal microbiota of mares and isolation and identification of a new strain of Salmonella abortus in horses of equine origin, and whole genome sequencing and analyses

Equine abortus salmonellosis, caused by Salmonella abortus equi (S. abortus equi), is a contagious disease primarily characterized by abortion in pregnant equine animals. Due to its high pathogenicity and increasing incidence, this disease has attracted significant scientific attention. While the causes of abortion in mares are multifactorial and may involve numerous pathogenic factors, the specific impact of S. abortus equi on the vaginal microecological environment and its pivotal role as the primary causative agent of abortion remain poorly understood. This study endeavors to address this gap by establishing a control group comprising aborted mares (20 mares) and a healthy mare group (20 mares). High-throughput sequencing technology was employed to analyze the bacterial community structure of vaginal samples from both groups, with the goal of comparing and elucidating the differences in their vaginal microbiota. The findings indicated that the microbial community richness in the abortion group was markedly higher than that in the healthy group. However, notable disparities were also observed in the structural composition and evolutionary trajectories of the microbiota between the two groups. Further analysis led to the successful isolation and identification of S. abortus equi from vaginal samples of aborted mares. A highly pathogenic isolate, designated as XJ2032, was selected for further analysis. To gain a more profound understanding of the functional genomic composition and genetic traits of this strain, whole-genome sequencing was conducted, and sophisticated bioinformatics techniques were employed to predict and annotate its gene sequences. Furthermore, in vitro vaginal microbiota simulation, animal model experiments, and PCR-based molecular biological detection methods were utilized to assess the virulence and drug resistance genes of the isolated strain XJ2032, further confirming its pathogenic potential. The comparison between the abortion group and the healthy group exhibited a rising trend in both the richness and diversity of the vaginal microbiota in the aborted mares. Significant differences were also noted in terms of microbiota similarity, dispersion, and community structure. In the abortion group, bacterial orders such as Bifidobacteriales and Micrococcales demonstrated significant specificity, whereas in the healthy group, bacterial families such as Enterococcaceae and Lachnospiraceae were more prevalent. Variations in the abundance of these bacterial taxa were intimately linked to the onset and progression of abortion. Functional prediction results further underscored a close correlation between the vaginal bacteria and metabolic pathways, suggesting that these microbial communities influence the functional state of the microbiota. Whole-genome sequencing analysis confirmed that strain XJ2032 is indeed S. abortus equi. Although its genome structure is largely conserved, some rearrangements and inversions were identified. The strain harbors multiple virulence genes and drug resistance genes, including horizontally transferable genes and mobile genetic elements. These findings suggest that genomic islands and bacteriophages play a vital role in the pathogenicity and genetic diversity of S. abortus equi.