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

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

doi:10.1093/cid/ciw242

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

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

Food Science

Research output: Contribution to journal › Article › peer-review

247 Scopus citations

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.

Original language	English (US)
Pages (from-to)	380-386
Number of pages	7
Journal	Clinical Infectious Diseases
Volume	63
Issue number	3
DOIs	https://doi.org/10.1093/cid/ciw242
State	Published - Aug 1 2016

All Science Journal Classification (ASJC) codes

Microbiology (medical)
Infectious Diseases

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10.1093/cid/ciw242

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Jackson, B. R., Tarr, C., Strain, E., Jackson, K. A., Conrad, A., Carleton, H., Katz, L. S., Stroika, S., Gould, L. H., Mody, R. K., Silk, B. J., Beal, J., Chen, Y., Timme, R., Doyle, M., Fields, A., Wise, M., Tillman, G., Defibaugh-Chavez, S., ... Gerner-Smidt, P. (2016). Implementation of Nationwide Real-time Whole-genome Sequencing to Enhance Listeriosis Outbreak Detection and Investigation. Clinical Infectious Diseases, 63(3), 380-386. https://doi.org/10.1093/cid/ciw242

@article{3ecb3e16a6ef481b9af0edf4a193dba0,

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

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.",

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

note = "Funding Information: Financial support. This work was supported by CDC, including CDC's Advanced Molecular Detection Initiative and Cooperative Agreement number U60HM000803; FDA; USDA-FSIS; National Institute for Biotechnology Information; and the Intramural Research Program of the NIH, National Library of Medicine. H. P. is an employee of Applied Maths. Publisher Copyright: {\textcopyright} 2016 Published by Oxford University Press for the Infectious Diseases Society of America 2016.",

year = "2016",

month = aug,

day = "1",

doi = "10.1093/cid/ciw242",

language = "English (US)",

volume = "63",

pages = "380--386",

journal = "Clinical Infectious Diseases",

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Jackson, BR, Tarr, C, Strain, E, Jackson, KA, Conrad, A, Carleton, H, Katz, LS, Stroika, S, Gould, LH, Mody, RK, Silk, BJ, Beal, J, Chen, Y, Timme, R, Doyle, M, Fields, A, Wise, M, Tillman, G, Defibaugh-Chavez, S, Kucerova, Z, Sabol, A, Roache, K, Trees, E, Simmons, M, Wasilenko, J, Kubota, K, Pouseele, H, Klimke, W, Besser, J, Brown, E, Allard, M & Gerner-Smidt, P 2016, 'Implementation of Nationwide Real-time Whole-genome Sequencing to Enhance Listeriosis Outbreak Detection and Investigation', Clinical Infectious Diseases, vol. 63, no. 3, pp. 380-386. https://doi.org/10.1093/cid/ciw242

TY - JOUR

T1 - Implementation of Nationwide Real-time Whole-genome Sequencing to Enhance Listeriosis Outbreak Detection and Investigation

AU - Jackson, Brendan R.

AU - Tarr, Cheryl

AU - Strain, Errol

AU - Jackson, Kelly A.

AU - Conrad, Amanda

AU - Carleton, Heather

AU - Katz, Lee S.

AU - Stroika, Steven

AU - Gould, L. Hannah

AU - Mody, Rajal K.

AU - Silk, Benjamin J.

AU - Beal, Jennifer

AU - Chen, Yi

AU - Timme, Ruth

AU - Doyle, Matthew

AU - Fields, Angela

AU - Wise, Matthew

AU - Tillman, Glenn

AU - Defibaugh-Chavez, Stephanie

AU - Kucerova, Zuzana

AU - Sabol, Ashley

AU - Roache, Katie

AU - Trees, Eija

AU - Simmons, Mustafa

AU - Wasilenko, Jamie

AU - Kubota, Kristy

AU - Pouseele, Hannes

AU - Klimke, William

AU - Besser, John

AU - Brown, Eric

AU - Allard, Marc

AU - Gerner-Smidt, Peter

N1 - Funding Information: Financial support. This work was supported by CDC, including CDC's Advanced Molecular Detection Initiative and Cooperative Agreement number U60HM000803; FDA; USDA-FSIS; National Institute for Biotechnology Information; and the Intramural Research Program of the NIH, National Library of Medicine. H. P. is an employee of Applied Maths. Publisher Copyright: © 2016 Published by Oxford University Press for the Infectious Diseases Society of America 2016.

PY - 2016/8/1

Y1 - 2016/8/1

N2 - 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.

AB - 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.

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DO - 10.1093/cid/ciw242

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JO - Clinical Infectious Diseases

JF - Clinical Infectious Diseases

IS - 3

ER -

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

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