Characterization of Foodborne Outbreaks of Salmonella enterica Serovar Enteritidis with Whole-Genome Sequencing Single Nucleotide Polymorphism-Based Analysis for Surveillance and Outbreak Detection - PubMed (original) (raw)

Characterization of Foodborne Outbreaks of Salmonella enterica Serovar Enteritidis with Whole-Genome Sequencing Single Nucleotide Polymorphism-Based Analysis for Surveillance and Outbreak Detection

Angela J Taylor et al. J Clin Microbiol. 2015 Oct.

Abstract

Salmonella enterica serovar Enteritidis is a significant cause of gastrointestinal illness in the United States; however, current molecular subtyping methods lack resolution for this highly clonal serovar. Advances in next-generation sequencing technologies have made it possible to examine whole-genome sequencing (WGS) as a potential molecular subtyping tool for outbreak detection and source trace back. Here, we conducted a retrospective analysis of S. Enteritidis isolates from seven epidemiologically confirmed foodborne outbreaks and sporadic isolates (not epidemiologically linked) to determine the utility of WGS to identify outbreaks. A collection of 55 epidemiologically characterized clinical and environmental S. Enteritidis isolates were sequenced. Single nucleotide polymorphism (SNP)-based cluster analysis of the S. Enteritidis genomes revealed well supported clades, with less than four-SNP pairwise diversity, that were concordant with epidemiologically defined outbreaks. Sporadic isolates were an average of 42.5 SNPs distant from the outbreak clusters. Isolates collected from the same patient over several weeks differed by only two SNPs. Our findings show that WGS provided greater resolution between outbreak, sporadic, and suspect isolates than the current gold standard subtyping method, pulsed-field gel electrophoresis (PFGE). Furthermore, results could be obtained in a time frame suitable for surveillance activities, supporting the use of WGS as an outbreak detection and characterization method for S. Enteritidis.

Copyright © 2015, American Society for Microbiology. All Rights Reserved.

PubMed Disclaimer

Figures

FIG 1

FIG 1

Maximum-likelihood tree of S. Enteritidis isolates produced by SNP analysis, showing outbreak clusters and PFGE pattern distribution. Outbreak isolates are indicated by brackets and descriptions giving the outbreak time frame (month[s] and year) and state. Sporadic and suspect isolates constitute all isolates not indicated as belonging to an outbreak (except for MDH-2014-00208, which was a suspect isolate that clusters with outbreak isolates). Isolates with CDC PulseNet PFGE pattern JEGX01.0004 are colored red, and isolates with pattern JEGX01.0002 are colored green. Purple values at the bases of the nodes are approximate likelihood-ratio test values displayed as percentages. The scale bar indicates the average number of substitutions per site. The letters in parentheses at the end of some isolate labels indicate the following: (A) suspect isolate in same time frame and PFGE pattern as outbreak 1; (B) all isolates are from the same patient; (C) suspect isolate in the same time frame and PFGE pattern as outbreak 5; (D) environmental isolate from outbreak 5.

References

    1. Witt-Kushner J, Astles JR, Ridderhof JC, Martin RA, Wilcke B Jr, Downes FP, Inhorn SL, Kelley HP, Kimsey PB, Mills DE, Salfinger M, Shult PA, Verma MP, Becker SJ, Drabkowski DJ. 2002. Core functions and capabilities of state public health laboratories: a report of the Association of Public Health Laboratories. MMWR Recommend Rep 51:1–8. -PubMed
    1. Foley SL, Zhao SH, Walker RD. 2007. Comparison of molecular typing methods for the differentiation of Salmonella foodborne pathogens. Foodborne Pathog Dis 4:253–276. doi: 10.1089/fpd.2007.0085. -DOI -PubMed
    1. Scallan E, Hoekstra RM, Angulo FJ, Tauxe RV, Widdowson MA, Roy SL, Jones JL, Griffin PM. 2011. Foodborne illness acquired in the United States—major pathogens. Emerg Infect Dis 17:7–15. doi: 10.3201/eid1701.P11101. -DOI -PMC -PubMed
    1. Guard-Petter J. 2001. The chicken, the egg and Salmonella enteritidis. Environ Microbiol 3:421–430. doi: 10.1046/j.1462-2920.2001.00213.x. -DOI -PubMed
    1. Centers for Disease Control and Prevention. 2013. Surveillance for foodborne disease outbreaks—United States, 1998-2008. MMWR Surveill Summ 62:1–34. -PubMed

Publication types

MeSH terms

LinkOut - more resources