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

Abstract

Salmonella enterica remains one of the leading causes of foodborne bacterial disease. Retail meat is a major source of human salmonellosis. However, comparative genomic analyses of S. enterica isolates from retail meat from different sources in China are lacking. A total of 341 S. enterica 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 S. 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 Salmonella In Silico Typing Resource (SISTR) (96.5%). The pangenome of the 341 S. enterica isolates contained 13,931 genes, and the core genome contained 3,635 genes. Higher Salmonella phage 118970 sal3 (219/341, 64.2%) and Gifsy-2 (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, blaCTX–M–55 (n = 15), blaCTX–M–14 (n = 11), and blaCTX–M–65 (n = 11), were more prevalent in retail meats. The emergence of qnrE1 and blaCTX–M–123 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 mcr-1.1 and mcr-9, respectively. Thus, we explored the evolution and genomic features of S. enterica isolates from retail meats in Beijing, China. The diverse ARGs of these isolates compromise food security and are a clinical threat.

Genome-Based Assessment of Antimicrobial Resistance and Virulence Potential of Isolates of Non-Pullorum/Gallinarum Salmonella Serovars Recovered from Dead Poultry in China

“…Indiana, which was considered the most resistant serovar in this study, carries plasmid types IncX1_1, IncHI2_1, IncHI2A_1, and Col156_1; these plasmids have been associated with the acquisition of resistance to different classes of antimicrobials, including aminoglycosides, sulfonamides, tetracyclines, quinolones, polymyxins, and β-lactams ( 52 , 53 ). Furthermore, our findings demonstrated that the plasmid type IncX1, in addition to IncFII(S) and IncFIB(S), is the key carrier of antimicrobial resistance determinants in Salmonella , which is in agreement with previous findings from China and elsewhere ( 54 – 57 ). Hence, the presence of these plasmids in the studied isolates is of major concern and may mediate the horizontal transmission of antimicrobial resistance along the food chain.…”

Serotyping, MLST, and Core Genome MLST Analysis of Salmonella enterica From Different Sources in China During 2004–2019

“…We also validated the serotyping by agglutination assay using SISTR prediction based on genomic sequences. The two methods are highly consistent with a consistency rate of 98%, which is similar to recent reports Uelze et al, 2019;Lyu et al, 2021). However, SISTR has a low identification for Typhimurium and I 4,[5],12:i:-in our research.…”

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

“…This study used traditional and in silico serotyping based on WGS to determine the serotype. Results demonstrated 93.52% concordance between the two methods, close to Cooper et al (2020) (89.2%) and Lyu et al (2021) (96.5%). Several untypable and/or ambiguous serotypes were addressed by in silico serotyping.…”