Genomic characterization of Salmonella enterica serotype Saintpaul isolates from horses

Salmonellosis is a highly contagious, zoonotic disease affecting both animal and human health. Early characterization of emerging Salmonella serotypes and associated antimicrobial resistance patterns are essential for outbreak controls in animals and humans. Between 2018 and 2025, 245 Salmonella enterica subsp. enterica were isolated from both ante-mortem and post-mortem equine cases. The predominant Salmonella serotypes were Typhimurium (83), Newport (28), 1,4,[5],12:i:- (26), Saintpaul (25), Hartford (15), and Mbandaka (12). S. Saintpaul, previously rare in horses, was detected in 21 cases in 2025, all originating from Central Kentucky, and was associated with enterocolitis, bronchopneumonia, omphalitis, and septicemia, primarily in young foals. Sixteen S. Saintpaul isolates were subjected to whole genome sequencing and exhibited a White-Kauffmann-Le Minor scheme antigenic profile of 1,4,[5],12:e,h:1,2, consistent with previously reported S. Saintpaul strains. Multi-locus sequence typing assigned all isolates to sequence type ST50. Core genome MLST revealed low genetic diversity among the isolates, suggesting closely related strain cluster. Antimicrobial susceptibility testing revealed widespread multi-drug resistance, particularly to aminoglycosides, beta-lactams, tetracyclines and sulfonamides. Genotypic analysis confirmed the presence of antimicrobial resistance genes, including bla_CTX-M-32 (not previously reported in Salmonella from horses), bla_CMY-2, sul1, dfrA34, and rmtE1, aligning with phenotypic findings. S. Saintpaul isolates harbored multiple plasmids, primarily of the IncI-gamma/K1 and, to a lesser extent, ColRNAI family. IncI-gamma/K1 plasmids were consistently associated with the MOB_P relaxase and MPF_I mating pair formation system. The emergence of multi-drug-resistant S. Saintpaul in horses underscores the importance of continued surveillance and antimicrobial resistance monitoring to mitigate animal and zoonotic risks.