Whole-genome sequencing of Salmonella serovars isolated from diarrheic and non-diarrheic foals.

Salmonella spp. are important pathogens of foals, causing clinical enterocolitis and sepsis. We characterized the resistance, virulence, and stress response genes in Salmonella isolates from foals with or without diarrhea. Salmonella isolates (n = 23) recovered from fecal samples of 16 diarrheic and 7 non-diarrheic <1-y-old foals were subjected to whole-genome sequencing. The most common serovars detected in diarrheic foals were S. enterica subsp. enterica serovars Infantis and Minnesota. Multidrug resistance was observed in 9 of 23 isolates, with 8 of the 9 from diarrheic foals. All of the isolates contained at least 2 resistance genes, with most of the genes related to the multidrug efflux pump complex. Among the 9 isolates shown to be resistant to β-lactam antimicrobials, at least one antimicrobial resistance gene (ARG) related to the inactivation of these antimicrobials was observed (blaTEM-1, blaCMY-2, blaCTX-M-8). Among the 7 isolates resistant to the quinolone class, 3 contained ARGs (qnrB19, qnrB6). The occurrence of multidrug-resistant isolates, particularly among foals with diarrhea, and the zoonotic potential of Salmonella species, highlight the importance of implementing biosecurity measures on the studied farms.