Integrated Whole-Genome Sequencing Infrastructure for Outbreak Detection and Source Tracing of Salmonella enterica Serotype Enteritidis

Abstract

As an important foodborne pathogen, Salmonella enterica serotype Enteritidis is recognized as one of the most common causes of human salmonellosis globally. Outbreak detection for this highly homogenous serotype, however, has remained challenging. Rapid advances in sequencing technologies have presented whole-genome sequencing (WGS) as a significant advancement for source tracing and molecular typing of foodborne pathogens. A retrospective analysis was conducted using Salmonella Enteritidis isolates (n = 65) from 11 epidemiologically confirmed outbreaks and a collection of contemporaneous sporadic isolates (n = 258) during 2007-2017 to evaluate the performance of WGS in delineating outbreak-associated isolates. Whole-genome single-nucleotide polymorphism (SNP)-based phylogenetic analysis revealed well-supported clades in concordance with epidemiological evidence and pairwise distances of £3 SNPs for all outbreaks. WGS-based framework of outbreak detection was thus proposed and applied prospectively to investigate isolates (n = 66) from nine outbreaks during 2018-2019. We further demonstrated the superior discriminatory power and accuracy of WGS to resolve and delineate outbreaks for pragmatic food source tracing. The proposed integrated WGS framework is the first in China for Salmonella Enteritidis and has the potential to serve as a paradigm for outbreak detection and source tracing of Salmonella throughout the stages of food production, as well as expanded to other foodborne pathogens.

Genomic Epidemiology and Multilevel Genome Typing of Australian Salmonella enterica Serovar Enteritidis

“…Using STs at different MGT levels, 54.8% of the MDR isolates belonged to previously identified MDR-associated MGT STs ( 17 ), with MGT4-ST54, MGT6-ST107, and MGT4-ST354 as the major MDR-associated STs. Interestingly, all these STs belonged to MGT3-ST8, which was one of the dominant types in Asian countries such as China ( 41 , 42 ), South Korea, and Thailand. These findings further confirmed that clade B S. Enteritidis strains isolated in Australia were likely to have originated from other countries, likely from Asia, as part of the global spread of these MDR clones.…”

Genomic epidemiology and multilevel genome typing of Australian Salmonella enterica serovar Enteritidis

“…Using STs at different MGT levels, 54.8% of the MDR isolates belonged to previously identified MDR associated MGT STs [17], with MGT4-ST54, MGT6-ST107 and MGT4-ST354 as the major MDR associated STs. Interestingly, all these STs belonged to MGT3-ST8, which was one of the dominant types in Asian countries such as China [51, 52], South Korea and Thailand. These findings further confirmed that clade B S .…”

“…as the major MDR associated STs. Interestingly, all these STs belonged to MGT3-ST8, which was one of the dominant types in Asian countries such as China [51,52],…”

Impacts of Microbial Food Safety in China and Beyond

“…Since 2013, the Chinese Foodborne Disease Surveillance Network has started to adopt the whole-genome sequencing (WGS) approach as the routine toolkit for outbreak investigation and source tracking (Li et al, 2021a). A few Chinese groups used a local integrated WGS infrastructure for foodborne outbreak investigation, including an outbreak caused by Salmonella Enteritidis in this issue (Deng et al, 2021) and by a few other well-recognized pathogens (Chen et al, 2020;Elbediwi et al 2021;Hua et al 2021;Jiang et al, 2020;Wang et al 2021;Wu et al 2021;Xu et al 2020;Yu et al, 2020).…”