Whole-Genome Sequencing Provides Insight Into Antimicrobial Resistance and Molecular Characteristics of Salmonella From Livestock Meat and Diarrhea Patient in Hanzhong, China

Abstract

<i>Salmonella</i> is a major zoonotic pathogen, which usually contaminates food resulting in salmonellosis in humans. Exploring the characteristics and origins of <i>Salmonella</i> is essential in formulating prevention and control measures for <i>Salmonella</i> infection. We used slide agglutination, antimicrobial susceptibility testing, and whole-genome sequencing to analyze and compare <i>Salmonella</i>'s phenotype, genotyping diversity, and genetic relatedness from livestock meat and diarrhea patients in Hanzhong, China, from 2018 to 2020. Totally 216 <i>Salmonella</i> enterica isolates were screened from frozen whole chicken carcasses (44.3%, 70/158), frozen raw ground pork (36.2%, 59/163), and diarrhea patients (4.4%, 87/1964). <i>Salmonella</i> Typhimurium was the dominant serotype. Notably, compared with other sources, isolates obtained from frozen whole chicken carcasses showed significant resistance to third-generation cephalosporin and fluoroquinolones (<i>p</i> < 0.05). All strains were assigned into 36 sequence types (STs) and two novel STs, and an excellent consistency was observed between ST and serotype. Genomic data revealed that extended-spectrum β-lactamase genes were responsible for third-generation cephalosporin resistance in 52 <i>Salmonella</i> strains, and the most predominant resistance determinant was <i>bla</i> _CTX-M. Furthermore, of the 60 ciprofloxacin-resistant isolates, five single-base mutations in quinolone resistance-determining regions were identified in <i>gyrA</i> or <i>parC</i>, and the plasmid-mediated quinolone resistance gene <i>aac(6')Ib-cr</i> was most often detected. The cgMLST clusters show that five clusters among four serotypes (including <i>S</i>. Typhimurium, <i>S</i>. London, <i>S</i>. Derby, and <i>S</i>. Agona) cover samples from diarrhea patients and livestock meat pathway isolate, indicating a possibility of cross-host transmission. In conclusion, the livestock meat isolates have a higher level of resistance than diarrhea patients' isolates and could be an essential source of human <i>Salmonella</i> infection.