Genome-wide characterization and comparative phylogenomics of three Salmonella Abortusequi strains isolated from equine abortions in Kazakhstan.

Abstract

Background and aim: Salmonella Abortusequi is a significant etiological agent of equine abortions, yet limited genomic data exist, particularly in Central Asia. This study aimed to perform the first genome-wide characterization and phylogenetic analysis of three S. Abortusequi strains isolated from equine abortions in different regions of Kazakhstan.

Materials and methods: Whole-genome sequencing was conducted on three isolates using the Illumina MiSeq platform. Genomic assemblies were annotated using SPAdes and Prokka, while phenotypic traits were predicted through BioNumerics. Antimicrobial resistance genes, virulence factors, and prophage elements were identified using established databases. Phylogenetic relationships were examined through whole-genome single-nucleotide polymorphism (wgSNP) analysis against a global panel of S. Abortusequi and related serovars.

Results: All isolates displayed high genomic similarity and were classified as Salmonella enterica subsp. enterica serovar Abortusequi with an antigenic profile of 4:a:e,n,x. Twelve Salmonella pathogenicity islands and three prophages were identified, with ST64B present in all isolates. The ac(6')-Iaa gene, which confers resistance to aminoglycosides, was detected in all strains. Each genome encoded 101-109 virulence factors, with 94 conserved across isolates. wgSNP analysis confirmed close phylogenetic clustering of the Kazakh strains, with regional variation between northern and southern isolates. Prophage-associated virulence elements, particularly virulence factor protein (SseK), were also documented.

Conclusion: This study reveals the genetic uniformity and virulence potential of S. Abortusequi strains circulating in Kazakhstan. The presence of conserved resistance and virulence genes, including prophage-encoded elements, underscores the pathogenic risk posed by these isolates. These findings contribute valuable genomic data for surveillance, diagnosis, and control of salmonellosis in equine populations. Despite the limited sample size, the study establishes a foundation for future genomic epidemiological studies and targeted disease mitigation strategies.