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. 2016 Aug 1;63(3):380-6.
doi: 10.1093/cid/ciw242. Epub 2016 Apr 18.

Implementation of Nationwide Real-time Whole-genome Sequencing to Enhance Listeriosis Outbreak Detection and Investigation

Brendan R Jackson  1 , Cheryl Tarr  1 , Errol Strain  2 , Kelly A Jackson  1 , Amanda Conrad  1 , Heather Carleton  1 , Lee S Katz  1 , Steven Stroika  1 , L Hannah Gould  1 , Rajal K Mody  1 , Benjamin J Silk  1 , Jennifer Beal  2 , Yi Chen  2 , Ruth Timme  2 , Matthew Doyle  2 , Angela Fields  2 , Matthew Wise  1 , Glenn Tillman  3 , Stephanie Defibaugh-Chavez  4 , Zuzana Kucerova  1 , Ashley Sabol  1 , Katie Roache  1 , Eija Trees  1 , Mustafa Simmons  3 , Jamie Wasilenko  3 , Kristy Kubota  5 , Hannes Pouseele  6 , William Klimke  7 , John Besser  1 , Eric Brown  2 , Marc Allard  2 , Peter Gerner-Smidt  1
Affiliations

Implementation of Nationwide Real-time Whole-genome Sequencing to Enhance Listeriosis Outbreak Detection and Investigation

Brendan R Jackson et al. Clin Infect Dis. .

Abstract

Listeria monocytogenes (Lm) causes severe foodborne illness (listeriosis). Previous molecular subtyping methods, such as pulsed-field gel electrophoresis (PFGE), were critical in detecting outbreaks that led to food safety improvements and declining incidence, but PFGE provides limited genetic resolution. A multiagency collaboration began performing real-time, whole-genome sequencing (WGS) on all US Lm isolates from patients, food, and the environment in September 2013, posting sequencing data into a public repository. Compared with the year before the project began, WGS, combined with epidemiologic and product trace-back data, detected more listeriosis clusters and solved more outbreaks (2 outbreaks in pre-WGS year, 5 in WGS year 1, and 9 in year 2). Whole-genome multilocus sequence typing and single nucleotide polymorphism analyses provided equivalent phylogenetic relationships relevant to investigations; results were most useful when interpreted in context of epidemiological data. WGS has transformed listeriosis outbreak surveillance and is being implemented for other foodborne pathogens.

Keywords: DNA sequencing; Listeria monocytogenes; foodborne diseases; outbreaks.

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Figures

Figure 1.
Figure 1.
Listeriosis clusters detected and outbreaks solved before and after implementation of real-time whole-genome sequencing (WGS) of Listeria monocytogenes isolates from patients, food, and the environment, United States, September 2012–August 2015. *Cluster detection sooner or only by WGS, as compared with pulsed-field gel electrophoresis.
Figure 2.
Figure 2.
Phylogenetic tree showing whole-genome multilocus sequence typing (wgMLST) allele differences among Listeria monocytogenes isolates from patients and food that were indistinguishable by pulsed-field gel electrophoresis (PFGE) and were identified as a disease cluster for investigation, United States, 2013 (N = 24). Most isolates were not highly related, with >30 allele differences between them, indicating this PFGE-defined cluster was a “pseudo-cluster” by whole-genome sequencing.
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References

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