Prospective genomic characterization of the German enterohemorrhagic Escherichia coli O104:H4 outbreak by rapid next generation sequencing technology.

An ongoing outbreak of exceptionally virulent Shiga toxin (Stx)-producing Escherichia coli O104:H4 centered in Germany, has caused over 830 cases of hemolytic uremic syndrome (HUS) and 46 deaths since May 2011. Serotype O104:H4, which has not been detected in animals, has rarely been associated with...

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Autores principales: Alexander Mellmann, Dag Harmsen, Craig A Cummings, Emily B Zentz, Shana R Leopold, Alain Rico, Karola Prior, Rafael Szczepanowski, Yongmei Ji, Wenlan Zhang, Stephen F McLaughlin, John K Henkhaus, Benjamin Leopold, Martina Bielaszewska, Rita Prager, Pius M Brzoska, Richard L Moore, Simone Guenther, Jonathan M Rothberg, Helge Karch
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Publicado: Public Library of Science (PLoS) 2011
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spelling oai:doaj.org-article:b9eea798d9cc4a66915690e322d6888e2021-11-18T06:49:50ZProspective genomic characterization of the German enterohemorrhagic Escherichia coli O104:H4 outbreak by rapid next generation sequencing technology.1932-620310.1371/journal.pone.0022751https://doaj.org/article/b9eea798d9cc4a66915690e322d6888e2011-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21799941/?tool=EBIhttps://doaj.org/toc/1932-6203An ongoing outbreak of exceptionally virulent Shiga toxin (Stx)-producing Escherichia coli O104:H4 centered in Germany, has caused over 830 cases of hemolytic uremic syndrome (HUS) and 46 deaths since May 2011. Serotype O104:H4, which has not been detected in animals, has rarely been associated with HUS in the past. To prospectively elucidate the unique characteristics of this strain in the early stages of this outbreak, we applied whole genome sequencing on the Life Technologies Ion Torrent PGM™ sequencer and Optical Mapping to characterize one outbreak isolate (LB226692) and a historic O104:H4 HUS isolate from 2001 (01-09591). Reference guided draft assemblies of both strains were completed with the newly introduced PGM™ within 62 hours. The HUS-associated strains both carried genes typically found in two types of pathogenic E. coli, enteroaggregative E. coli (EAEC) and enterohemorrhagic E. coli (EHEC). Phylogenetic analyses of 1,144 core E. coli genes indicate that the HUS-causing O104:H4 strains and the previously published sequence of the EAEC strain 55989 show a close relationship but are only distantly related to common EHEC serotypes. Though closely related, the outbreak strain differs from the 2001 strain in plasmid content and fimbrial genes. We propose a model in which EAEC 55989 and EHEC O104:H4 strains evolved from a common EHEC O104:H4 progenitor, and suggest that by stepwise gain and loss of chromosomal and plasmid-encoded virulence factors, a highly pathogenic hybrid of EAEC and EHEC emerged as the current outbreak clone. In conclusion, rapid next-generation technologies facilitated prospective whole genome characterization in the early stages of an outbreak.Alexander MellmannDag HarmsenCraig A CummingsEmily B ZentzShana R LeopoldAlain RicoKarola PriorRafael SzczepanowskiYongmei JiWenlan ZhangStephen F McLaughlinJohn K HenkhausBenjamin LeopoldMartina BielaszewskaRita PragerPius M BrzoskaRichard L MooreSimone GuentherJonathan M RothbergHelge KarchPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 7, p e22751 (2011)
institution DOAJ
collection DOAJ
language EN
topic Medicine
R
Science
Q
spellingShingle Medicine
R
Science
Q
Alexander Mellmann
Dag Harmsen
Craig A Cummings
Emily B Zentz
Shana R Leopold
Alain Rico
Karola Prior
Rafael Szczepanowski
Yongmei Ji
Wenlan Zhang
Stephen F McLaughlin
John K Henkhaus
Benjamin Leopold
Martina Bielaszewska
Rita Prager
Pius M Brzoska
Richard L Moore
Simone Guenther
Jonathan M Rothberg
Helge Karch
Prospective genomic characterization of the German enterohemorrhagic Escherichia coli O104:H4 outbreak by rapid next generation sequencing technology.
description An ongoing outbreak of exceptionally virulent Shiga toxin (Stx)-producing Escherichia coli O104:H4 centered in Germany, has caused over 830 cases of hemolytic uremic syndrome (HUS) and 46 deaths since May 2011. Serotype O104:H4, which has not been detected in animals, has rarely been associated with HUS in the past. To prospectively elucidate the unique characteristics of this strain in the early stages of this outbreak, we applied whole genome sequencing on the Life Technologies Ion Torrent PGM™ sequencer and Optical Mapping to characterize one outbreak isolate (LB226692) and a historic O104:H4 HUS isolate from 2001 (01-09591). Reference guided draft assemblies of both strains were completed with the newly introduced PGM™ within 62 hours. The HUS-associated strains both carried genes typically found in two types of pathogenic E. coli, enteroaggregative E. coli (EAEC) and enterohemorrhagic E. coli (EHEC). Phylogenetic analyses of 1,144 core E. coli genes indicate that the HUS-causing O104:H4 strains and the previously published sequence of the EAEC strain 55989 show a close relationship but are only distantly related to common EHEC serotypes. Though closely related, the outbreak strain differs from the 2001 strain in plasmid content and fimbrial genes. We propose a model in which EAEC 55989 and EHEC O104:H4 strains evolved from a common EHEC O104:H4 progenitor, and suggest that by stepwise gain and loss of chromosomal and plasmid-encoded virulence factors, a highly pathogenic hybrid of EAEC and EHEC emerged as the current outbreak clone. In conclusion, rapid next-generation technologies facilitated prospective whole genome characterization in the early stages of an outbreak.
format article
author Alexander Mellmann
Dag Harmsen
Craig A Cummings
Emily B Zentz
Shana R Leopold
Alain Rico
Karola Prior
Rafael Szczepanowski
Yongmei Ji
Wenlan Zhang
Stephen F McLaughlin
John K Henkhaus
Benjamin Leopold
Martina Bielaszewska
Rita Prager
Pius M Brzoska
Richard L Moore
Simone Guenther
Jonathan M Rothberg
Helge Karch
author_facet Alexander Mellmann
Dag Harmsen
Craig A Cummings
Emily B Zentz
Shana R Leopold
Alain Rico
Karola Prior
Rafael Szczepanowski
Yongmei Ji
Wenlan Zhang
Stephen F McLaughlin
John K Henkhaus
Benjamin Leopold
Martina Bielaszewska
Rita Prager
Pius M Brzoska
Richard L Moore
Simone Guenther
Jonathan M Rothberg
Helge Karch
author_sort Alexander Mellmann
title Prospective genomic characterization of the German enterohemorrhagic Escherichia coli O104:H4 outbreak by rapid next generation sequencing technology.
title_short Prospective genomic characterization of the German enterohemorrhagic Escherichia coli O104:H4 outbreak by rapid next generation sequencing technology.
title_full Prospective genomic characterization of the German enterohemorrhagic Escherichia coli O104:H4 outbreak by rapid next generation sequencing technology.
title_fullStr Prospective genomic characterization of the German enterohemorrhagic Escherichia coli O104:H4 outbreak by rapid next generation sequencing technology.
title_full_unstemmed Prospective genomic characterization of the German enterohemorrhagic Escherichia coli O104:H4 outbreak by rapid next generation sequencing technology.
title_sort prospective genomic characterization of the german enterohemorrhagic escherichia coli o104:h4 outbreak by rapid next generation sequencing technology.
publisher Public Library of Science (PLoS)
publishDate 2011
url https://doaj.org/article/b9eea798d9cc4a66915690e322d6888e
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