Whole genome sequencing for investigations of meningococcal outbreaks in the United States: a retrospective analysis

Abstract Although rare in the U.S., outbreaks due to Neisseria meningitidis do occur. Rapid, early outbreak detection is important for timely public health response. In this study, we characterized U.S. meningococcal isolates (N = 201) from 15 epidemiologically defined outbreaks (2009–2015) along wi...

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Autores principales:	Melissa J. Whaley, Sandeep J. Joseph, Adam C. Retchless, Cecilia B. Kretz, Amy Blain, Fang Hu, How-Yi Chang, Sarah A. Mbaeyi, Jessica R. MacNeil, Timothy D. Read, Xin Wang
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2018
Materias:	Meningococcal Outbreaks PFGE Patterns Sporadic Isolates Outbreak Isolates Pulsed-field Gel Electrophoresis (PFGE) Medicine R Science Q
Acceso en línea:	https://doaj.org/article/c3b749783a564bc492f5796aded7a51b
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spelling	oai:doaj.org-article:c3b749783a564bc492f5796aded7a51b2021-12-02T11:41:25ZWhole genome sequencing for investigations of meningococcal outbreaks in the United States: a retrospective analysis10.1038/s41598-018-33622-52045-2322https://doaj.org/article/c3b749783a564bc492f5796aded7a51b2018-10-01T00:00:00Zhttps://doi.org/10.1038/s41598-018-33622-5https://doaj.org/toc/2045-2322Abstract Although rare in the U.S., outbreaks due to Neisseria meningitidis do occur. Rapid, early outbreak detection is important for timely public health response. In this study, we characterized U.S. meningococcal isolates (N = 201) from 15 epidemiologically defined outbreaks (2009–2015) along with temporally and geographically matched sporadic isolates using multilocus sequence typing, pulsed-field gel electrophoresis (PFGE), and six whole genome sequencing (WGS) based methods. Recombination-corrected maximum likelihood (ML) and Bayesian phylogenies were reconstructed to identify genetically related outbreak isolates. All WGS analysis methods showed high degree of agreement and distinguished isolates with similar or indistinguishable PFGE patterns, or the same strain genotype. Ten outbreaks were caused by a single strain; 5 were due to multiple strains. Five sporadic isolates were phylogenetically related to 2 outbreaks. Analysis of 9 outbreaks using timed phylogenies identified the possible origin and estimated the approximate time that the most recent common ancestor emerged for outbreaks analyzed. U.S. meningococcal outbreaks were caused by single- or multiple-strain introduction, with organizational outbreaks mainly caused by a clonal strain and community outbreaks by divergent strains. WGS can infer linkage of meningococcal cases when epidemiological links are uncertain. Accurate identification of outbreak-associated cases requires both WGS typing and epidemiological data.Melissa J. WhaleySandeep J. JosephAdam C. RetchlessCecilia B. KretzAmy BlainFang HuHow-Yi ChangSarah A. MbaeyiJessica R. MacNeilTimothy D. ReadXin WangNature PortfolioarticleMeningococcal OutbreaksPFGE PatternsSporadic IsolatesOutbreak IsolatesPulsed-field Gel Electrophoresis (PFGE)MedicineRScienceQENScientific Reports, Vol 8, Iss 1, Pp 1-13 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	Meningococcal Outbreaks PFGE Patterns Sporadic Isolates Outbreak Isolates Pulsed-field Gel Electrophoresis (PFGE) Medicine R Science Q
spellingShingle	Meningococcal Outbreaks PFGE Patterns Sporadic Isolates Outbreak Isolates Pulsed-field Gel Electrophoresis (PFGE) Medicine R Science Q Melissa J. Whaley Sandeep J. Joseph Adam C. Retchless Cecilia B. Kretz Amy Blain Fang Hu How-Yi Chang Sarah A. Mbaeyi Jessica R. MacNeil Timothy D. Read Xin Wang Whole genome sequencing for investigations of meningococcal outbreaks in the United States: a retrospective analysis
description	Abstract Although rare in the U.S., outbreaks due to Neisseria meningitidis do occur. Rapid, early outbreak detection is important for timely public health response. In this study, we characterized U.S. meningococcal isolates (N = 201) from 15 epidemiologically defined outbreaks (2009–2015) along with temporally and geographically matched sporadic isolates using multilocus sequence typing, pulsed-field gel electrophoresis (PFGE), and six whole genome sequencing (WGS) based methods. Recombination-corrected maximum likelihood (ML) and Bayesian phylogenies were reconstructed to identify genetically related outbreak isolates. All WGS analysis methods showed high degree of agreement and distinguished isolates with similar or indistinguishable PFGE patterns, or the same strain genotype. Ten outbreaks were caused by a single strain; 5 were due to multiple strains. Five sporadic isolates were phylogenetically related to 2 outbreaks. Analysis of 9 outbreaks using timed phylogenies identified the possible origin and estimated the approximate time that the most recent common ancestor emerged for outbreaks analyzed. U.S. meningococcal outbreaks were caused by single- or multiple-strain introduction, with organizational outbreaks mainly caused by a clonal strain and community outbreaks by divergent strains. WGS can infer linkage of meningococcal cases when epidemiological links are uncertain. Accurate identification of outbreak-associated cases requires both WGS typing and epidemiological data.
format	article
author	Melissa J. Whaley Sandeep J. Joseph Adam C. Retchless Cecilia B. Kretz Amy Blain Fang Hu How-Yi Chang Sarah A. Mbaeyi Jessica R. MacNeil Timothy D. Read Xin Wang
author_facet	Melissa J. Whaley Sandeep J. Joseph Adam C. Retchless Cecilia B. Kretz Amy Blain Fang Hu How-Yi Chang Sarah A. Mbaeyi Jessica R. MacNeil Timothy D. Read Xin Wang
author_sort	Melissa J. Whaley
title	Whole genome sequencing for investigations of meningococcal outbreaks in the United States: a retrospective analysis
title_short	Whole genome sequencing for investigations of meningococcal outbreaks in the United States: a retrospective analysis
title_full	Whole genome sequencing for investigations of meningococcal outbreaks in the United States: a retrospective analysis
title_fullStr	Whole genome sequencing for investigations of meningococcal outbreaks in the United States: a retrospective analysis
title_full_unstemmed	Whole genome sequencing for investigations of meningococcal outbreaks in the United States: a retrospective analysis
title_sort	whole genome sequencing for investigations of meningococcal outbreaks in the united states: a retrospective analysis
publisher	Nature Portfolio
publishDate	2018
url	https://doaj.org/article/c3b749783a564bc492f5796aded7a51b
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Whole genome sequencing for investigations of meningococcal outbreaks in the United States: a retrospective analysis

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