Prospective Genomic Characterization of the German Enterohemorrhagic Escherichia coli O104:H4 Outbreak by Rapid Next Generation Sequencing Technology
Alexander Mellmann,Dag Harmsen,Craig 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 Brzoska,Richard Moore,Simone Guenther,Jonathan M. Rothberg,Helge Karch +19 more
Reads0
Chats0
TLDR
It is suggested 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.Abstract:
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.read more
Citations
More filters
Journal ArticleDOI
Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria
Mette Voldby Larsen,Salvatore Cosentino,Simon Rasmussen,Carsten Friis,Henrik Hasman,Rasmus L. Marvig,Lars Jelsbak,Thomas Sicheritz-Pontén,David W. Ussery,Frank Møller Aarestrup,Ole Lund +10 more
TL;DR: A Web-based method for MLST of 66 bacterial species based on whole-genome sequencing data that enables investigators to determine the sequence types of their isolates on the basis of WGS data.
Journal ArticleDOI
Comparison of Next-Generation Sequencing Systems
TL;DR: Technologies of next-generation sequencing systems are reviewed, and first-hand data from extensive experience is summarized and analyzed to discuss the advantages and specifics associated with each sequencing system.
Journal ArticleDOI
Performance comparison of benchtop high-throughput sequencing platforms
Nicholas J. Loman,Raju Misra,Timothy J. Dallman,Chrystala Constantinidou,Saheer E. Gharbia,John Wain,John Wain,Mark J. Pallen +7 more
TL;DR: The performance of these instruments were compared by sequencing an isolate of Escherichia coli O104:H4, which caused an outbreak of food poisoning in Germany in 2011, and the MiSeq had the highest throughput per run and lowest error rates.
Journal ArticleDOI
Recent Advances in Understanding Enteric Pathogenic Escherichia coli
Matthew A. Croxen,Robyn J. Law,Roland Scholz,Kristie M. Keeney,Marta Wlodarska,B. Brett Finlay +5 more
TL;DR: A comprehensive review highlights recent advances in understanding of the intestinal pathotypes of E. coli, which carry an enormous potential to cause disease and continue to present challenges to human health.
Journal ArticleDOI
Epidemic Profile of Shiga-Toxin–Producing Escherichia coli O104:H4 Outbreak in Germany
Christina Frank,Dirk Werber,Jakob P. Cramer,Mona Askar,Mirko Faber,Matthias an der Heiden,Helen Bernard,Angelika Fruth,Rita Prager,Anke Spode,Maria Wadl,Alexander Zoufaly,Sabine Jordan,Markus J Kemper,Per Follin,Luise Müller,Lisa A King,Bettina Rosner,Udo Buchholz,Klaus Stark,Gérard Krause,Hus investigation team +21 more
TL;DR: In this outbreak, caused by an unusual E. coli strain, cases of the hemolytic-uremic syndrome occurred predominantly in adults, with a preponderance of cases occurring in women.
References
More filters
Journal ArticleDOI
The Sequence Alignment/Map format and SAMtools
Heng Li,Bob Handsaker,Alec Wysoker,T. J. Fennell,Jue Ruan,Nils Homer,Gabor T. Marth,Gonçalo R. Abecasis,Richard Durbin +8 more
TL;DR: SAMtools as discussed by the authors implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments.
Journal ArticleDOI
CAP3: A DNA Sequence Assembly Program
Xiaoqiu Huang,Anup Madan +1 more
TL;DR: The third generation of the CAP sequence assembly program is described, which has a capability to clip 5' and 3' low-quality regions of reads and uses forward-reverse constraints to correct assembly errors and link contigs.
Journal ArticleDOI
Rapid procedure for detection and isolation of large and small plasmids.
C I Kado,Shih-Tung Liu +1 more
TL;DR: The method utilized the molecular characteristics of covalently closed circular deoxyribonucleic acid (DNA) released from cells under conditions that denature chromosomal DNA by using alkaline sodium dodecyl sulfate (pH 12.6) at elevated temperatures.
Journal ArticleDOI
An integrated semiconductor device enabling non-optical genome sequencing
Jonathan M. Rothberg,Wolfgang Hinz,Todd Rearick,Jonathan Schultz,William J. Mileski,Melville Davey,John H. Leamon,Kim L. Johnson,Mark James Milgrew,Matthew D. Edwards,Jeremy Hoon,Jan Fredrik Simons,David Marran,Jason W. Myers,John F. Davidson,Annika Branting,John Nobile,Bernard P. Puc,David Light,Travis A. Clark,Martin Huber,Jeffrey T. Branciforte,Isaac B. Stoner,Simon Cawley,Michael R. Lyons,Yutao Fu,Nils Homer,Marina Sedova,Xin Miao,Brian Reed,Jeffrey Sabina,Erika Feierstein,Michelle Schorn,Mohammad Alanjary,Eileen T. Dimalanta,Devin Dressman,Rachel Kasinskas,Tanya Sokolsky,Jacqueline A. Fidanza,Eugeni Namsaraev,Kevin McKernan,Alan Williams,G. Thomas Roth,James Bustillo +43 more
TL;DR: A DNA sequencing technology in which scalable, low-cost semiconductor manufacturing techniques are used to make an integrated circuit able to directly perform non-optical DNA sequencing of genomes, showing its robustness and scalability by producing ion chips with up to 10 times as many sensors and sequencing a human genome.
Journal ArticleDOI
Genome sequence of enterohaemorrhagic Escherichia coli O157:H7
Nicole T. Perna,Guy Plunkett,Valerie Burland,Bob Mau,Jeremy D. Glasner,Debra J. Rose,George F. Mayhew,Peter Evans,Jason Gregor,Heather A. Kirkpatrick,György Pósfai,Jeremiah D. Hackett,Sara A. Klink,Adam T. Boutin,Ying Shao,Leslie Miller,Erik J. Grotbeck,N. Wayne Davis,Alex Lim,Eileen T. Dimalanta,Konstantinos Potamousis,Jennifer Apodaca,Thomas Anantharaman,Jieyi Lin,Galex Yen,David C. Schwartz,Rodney A. Welch,Frederick R. Blattner +27 more
TL;DR: It is found that lateral gene transfer is far more extensive than previously anticipated and 1,387 new genes encoded in strain-specific clusters of diverse sizes were found in O157:H7, including candidate virulence factors, alternative metabolic capacities, several prophages and other new functions—all of which could be targets for surveillance.
Related Papers (5)
Origins of the E. coli Strain Causing an Outbreak of Hemolytic–Uremic Syndrome in Germany
David A. Rasko,Dale R. Webster,Jason W. Sahl,Ali Bashir,Nadia Boisen,Flemming Scheutz,Ellen E. Paxinos,Robert Sebra,Chen-Shan Chin,Dimitris Iliopoulos,Aaron Klammer,Paul Peluso,Lawrence Lee,Andrey Kislyuk,James H. Bullard,Andrew Kasarskis,Susanna Wang,John Eid,David R. Rank,Julia C. Redman,Susan R. Steyert,Jakob Frimodt-Møller,Carsten Struve,Andreas Petersen,Karen A. Krogfelt,James P. Nataro,Eric E. Schadt,Matthew K. Waldor +27 more
Epidemic Profile of Shiga-Toxin–Producing Escherichia coli O104:H4 Outbreak in Germany
Christina Frank,Dirk Werber,Jakob P. Cramer,Mona Askar,Mirko Faber,Matthias an der Heiden,Helen Bernard,Angelika Fruth,Rita Prager,Anke Spode,Maria Wadl,Alexander Zoufaly,Sabine Jordan,Markus J Kemper,Per Follin,Luise Müller,Lisa A King,Bettina Rosner,Udo Buchholz,Klaus Stark,Gérard Krause,Hus investigation team +21 more