Implementation of Nationwide Real-Time Whole-Genome Sequencing to Enhance Listeriosis Outbreak Detection and Investigation.

Jackson BR1, Tarr C1, Strain E2, Jackson KA1, Conrad A1, Carleton H1, Katz LS1, Stroika S1, Gould LH1, Mody RK1, Silk BJ1, Beal J2, Chen Y2, Timme R2,Doyle M2, Fields A2, Wise M1, Tillman G3, Defibaugh-Chavez S4, Kucerova Z1, Sabol A1, Roache K1, Trees E1, Simmons M3, Wasilenko J3, Kubota K5,Pouseele H6, Klimke W7, Besser J1, Brown E2, Allard M2, Gerner-Smidt P1.

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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 U.S.Lmisolates 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.

Published by Oxford University Press for the Infectious Diseases Society of America 2016. This work is written by (a) US Government employee(s) and is in the public domain in the US.