4.3 Article

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

Journal

FOODBORNE PATHOGENS AND DISEASE
Volume 18, Issue 8, Pages 582-589

Publisher

MARY ANN LIEBERT, INC
DOI: 10.1089/fpd.2020.2856

Keywords

Salmonella enterica serotype Enteritidis; outbreak detection; source tracing; food safety; whole-genome sequencing; single-nucleotide polymorphism

Funding

  1. National Key Research and Development Project [2019YFE0103800, 2018YFC1603902]
  2. Sanming Project of Medicine in Shenzhen [SZSM201811071]
  3. China National Science and Technology Major Projects Foundation [2017ZX10303406, 2018ZX10714002]
  4. National Natural Science Foundation of China [81673174]
  5. Shenzhen Municipal Science Technology Program [JSGG20160429101631739, JCYJ20160428142519080]
  6. Shenzhen Health and Family Planning Commission [201602004]
  7. Sichuan International Cooperation Project [18GJHZ0137]

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This study utilized whole-genome sequencing (WGS) to conduct outbreak detection of Salmonella enterica serotype Enteritidis, demonstrating the superior discriminatory power and accuracy of WGS in pragmatic food source tracing. The proposed integrated WGS framework in China for Salmonella Enteritidis has the potential to serve as a paradigm for outbreak detection and source tracing of Salmonella and other foodborne pathogens.
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.

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