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

Abstract

Salmonella enterica (<i>S. enterica</i>) is an important foodborne pathogen, causing food poisoning and human infection, and critically threatening food safety and public health. <i>Salmonella</i> typing is essential for bacterial identification, tracing, epidemiological investigation, and monitoring. Serotyping and multilocus sequence typing (MLST) analysis are standard bacterial typing methods despite the low resolution. Core genome MLST (cgMLST) is a high-resolution molecular typing method based on whole genomic sequencing for accurate bacterial tracing. We investigated 250 <i>S. enterica</i> isolates from poultry, livestock, food, and human sources in nine provinces of China from 2004 to 2019 using serotyping, MLST, and cgMLST analysis. All <i>S. enterica</i> isolates were divided into 36 serovars using slide agglutination. The major serovars in order were Enteritidis (31 isolates), Typhimurium (29 isolates), Mbandaka (23 isolates), and Indiana (22 isolates). All strains were assigned into 43 sequence types (STs) by MLST. Among them, ST11 (31 isolates) was the primary ST. Besides this, a novel ST, ST8016, was identified, and it was different from ST40 by position 317 C → T in <i>dnaN</i>. Furthermore, these 250 isolates were grouped into 185 cgMLST sequence types (cgSTs) by cgMLST. The major cgST was cgST235530 (11 isolates), and only three cgSTs contained isolates from human and other sources, indicating a possibility of cross-species infection. Phylogenetic analysis indicated that most of the same serovar strains were putatively homologous except Saintpaul and Derby due to their multilineage characteristics. In addition, serovar I 4,[5],12:i:- and Typhimurium isolates have similar genomic relatedness on the phylogenetic tree. In conclusion, we sorted out the phenotyping and genotyping diversity of <i>S. enterica</i> isolates in China during 2004-2019 and clarified the temporal and spatial distribution characteristics of <i>Salmonella</i> from different hosts in China in the recent 16 years. These results greatly supplement <i>Salmonella</i> strain resources, genetic information, and traceability typing data; facilitate the typing, traceability, identification, and genetic evolution analysis of <i>Salmonella</i>; and therefore, improve the level of analysis, monitoring, and controlling of foodborne microorganisms in China.