AUTHOR=Lyu Na , Feng Yuqing , Pan Yuanlong , Huang Hua , Liu Yan , Xue Chenyu , Zhu Baoli , Hu Yongfei 

TITLE=Genomic Characterization of Salmonella enterica Isolates From Retail Meat in Beijing, China

JOURNAL=Frontiers in Microbiology

VOLUME=12

YEAR=2021

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2021.636332

DOI=10.3389/fmicb.2021.636332

ISSN=1664-302X

ABSTRACT=<p><italic>Salmonella enterica</italic> remains one of the leading causes of foodborne bacterial disease. Retail meat is a major source of human salmonellosis. However, comparative genomic analyses of <italic>S. enterica</italic> isolates from retail meat from different sources in China are lacking. A total of 341 <italic>S. enterica</italic> strains were isolated from retail meat in sixteen districts of Beijing, China, at three different time points (January 1st, May 1st, and October 1st) in 2017. Comparative genomics was performed to investigate the genetic diversity, virulence and antimicrobial resistance gene (ARG) profiles of these isolates. The most common serotype was <italic>S.</italic> Enteritidis (203/341, 59.5%), which dominated among isolates from three different time points during the year. Laboratory retesting confirmed the accuracy of the serotyping results predicted by the <italic>Salmonella In Silico</italic> Typing Resource (SISTR) (96.5%). The pangenome of the 341 <italic>S. enterica</italic> isolates contained 13,931 genes, and the core genome contained 3,635 genes. Higher <italic>Salmonella phage 118970 sal3</italic> (219/341, 64.2%) and <italic>Gifsy-2</italic> (206/341, 60.4%) prevalence contributed to the diversity of the accessory genes, especially those with unknown functions. IncFII(S), IncX1, and IncFIB(S) plasmid replicons were more common in these isolates and were major sources of horizontally acquired foreign genes. The virulence gene profile showed fewer virulence genes associated with type III secretion systems in certain isolates from chicken. A total of 88 different ARGs were found in the 341 isolates. Three beta-lactamases, namely, <italic>bla</italic><sub><italic>CTX</italic></sub><sub>–</sub><sub><italic>M</italic></sub><sub>–</sub><sub>55</sub> (<italic>n</italic> = 15), <italic>bla</italic><sub><italic>CTX</italic></sub><sub>–</sub><sub><italic>M</italic></sub><sub>–</sub><sub>14</sub> (<italic>n</italic> = 11), <italic>and bla</italic><sub><italic>CTX</italic></sub><sub>–</sub><sub><italic>M</italic></sub><sub>–</sub><sub>65</sub> (<italic>n</italic> = 11), were more prevalent in retail meats. The emergence of <italic>qnrE1</italic> and <italic>bla</italic><sub><italic>CTX</italic></sub><sub>–</sub><sub><italic>M</italic></sub><sub>–</sub><sub>123</sub> indicated a potential increase in the prevalence of retail meats. After the prohibition of colistin in China, three and four isolates were positive for the colistin resistance genes <italic>mcr-1.1</italic> and <italic>mcr-9</italic>, respectively. Thus, we explored the evolution and genomic features of <italic>S. enterica</italic> isolates from retail meats in Beijing, China. The diverse ARGs of these isolates compromise food security and are a clinical threat.</p>