Resistance phenotypes and whole genome sequencing analysis of Salmonella from yaks in Tibet, China

Abstract This study aimed to elucidate the antimicrobial resistance profiles, genetic characteristics, and phylogenetic relationships of Salmonella originating from yaks in Naqu, Tibet. A total of 18 Salmonella isolates from yaks in Naqu were subjected to antimicrobial susceptibility testing (AST) and whole genome sequencing (WGS) for the analysis of their antimicrobial resistance profiles, genetic characteristics, and phylogeny. Antimicrobial susceptibility testing revealed 100% resistance to β-lactams. Resistance rates to ciprofloxacin, trimethoprim-sulfamethoxazole, and kanamycin/streptomycin were 83.3%, 77.8%, and 83.3%, respectively. Whole-genome sequencing analysis showed a high concordance between phenotypic resistance and the carriage of corresponding resistance genes: bla TEM−1 (100%), sul2 (77.8%), floR (61.1%), and tet(A) (38.9%). Virulence factor profiles were serovar-specific: all S . Dublin isolates harbored the complete spv virulence plasmid gene cluster; the monophasic variants of S . Typhimurium isolates carried genes such as gogB and sodCI ; whereas S . Rissen isolates commonly lacked key virulence factors including the spv cluster and sodCI . Plasmid analysis indicated that S . Dublin isolates carried IncFII(S)_1 and IncX1_1 plasmids, while S . Rissen isolates carried Col440I_1 and ColRNAI_1 plasmids. Average nucleotide identity (ANI) analysis revealed that all 18 isolates belonged to Salmonella enterica , with ANI values ranging from 98.69% to 100% among isolates. Intra-serovar ANI values exceeded 99.93%, while inter-serovar values ranged from 98.69% to 99.00%, confirming the accuracy of conventional serotyping at the genomic level. Phylogenetic analysis demonstrated that Naqu S . Rissen isolates from yaks clustered closely with Tibetan pig-origin S . Rissen isolates and some human- and food-origin isolates from China within the same clade. Salmonella isolates from yaks in Naqu exhibit severe antimicrobial resistance (AMR), including widespread multidrug resistance, a pattern potentially linked to local antibiotic usage. Significant disparities in virulence potential and plasmid profiles were observed across serovars. Notably, the predominant serovar, S . Rissen, demonstrated close phylogenetic relatedness to isolates from other hosts and food sources, suggesting potential cross-host transmission that warrants further investigation. However, due to the limited sample size, these findings should be considered preliminary, and enhanced surveillance is needed to confirm the transmission risks. This underscores an urgent need for enhanced surveillance and comprehensive control measures.