Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011

被引：195

作者：

Grad, Yonatan H. ^{[2
,3
]}

Lipsitch, Marc ^{[3
,4
]}

Feldgarden, Michael ^{[1
,5
]}

Arachchi, Harindra M. ^{[1
,5
]}

Cerqueira, Gustavo C. ^{[1
,5
]}

FitzGerald, Michael ^{[1
,5
]}

Godfrey, Paul ^{[1
,5
]}

Haas, Brian J. ^{[1
,5
]}

Murphy, Cheryl I. ^{[1
,5
]}

Russ, Carsten ^{[1
,5
]}

Sykes, Sean ^{[1
,5
]}

Walker, Bruce J. ^{[1
,5
]}

Wortman, Jennifer R. ^{[1
,5
]}

Young, Sarah ^{[1
,5
]}

Zeng, Qiandong ^{[1
,5
]}

Abouelleil, Amr ^{[1
,5
]}

Bochicchio, James ^{[1
,5
]}

Chauvin, Sara ^{[1
,5
]}

DeSmet, Timothy ^{[1
,5
]}

Gujja, Sharvari ^{[1
,5
]}

McCowan, Caryn ^{[1
,5
]}

Montmayeur, Anna ^{[1
,5
]}

Steelman, Scott ^{[1
,5
]}

Frimodt-Moller, Jakob ^{[6
,7
]}

Petersen, Andreas M. ^{[7
,8
]}

Struve, Carsten ^{[7
]}

Krogfelt, Karen A. ^{[7
]}

Bingen, Edouard ^{[9
,10
]}

Weill, Francois-Xavier ^{[11
]}

Lander, Eric S. ^{[1
,5
,12
,13
]}

Nusbaum, Chad ^{[1
,5
]}

Birren, Bruce W. ^{[1
,5
]}

Hung, Deborah T. ^{[1
,2
,5
,14
,15
]}

Hanage, William P. ^{[3
]}

机构：

[1] Broad Inst Harvard, Cambridge, MA 02142 USA

[2] Brigham & Womens Hosp, Dept Med, Boston, MA 02115 USA

[3] Harvard Univ, Sch Publ Hlth, Ctr Communicable Dis Dynam, Dept Epidemiol, Boston, MA 02115 USA

[4] Harvard Univ, Sch Publ Hlth, Dept Immunol & Infect Dis, Boston, MA 02115 USA

[5] MIT, Cambridge, MA 02142 USA

[6] Hillerod Sygehus, Dept Clin Microbiol, DK-3400 Hillerod, Denmark

[7] Statens Serum Inst, Dept Microbial Surveillance & Res, DK-2300 Copenhagen, Denmark

[8] Hvidovre Univ Hosp, Dept Gastroenterol, DK-2650 Hvidovre, Denmark

[9] Hop Robert Debre, AP HP, Microbiol Serv, Lab Associe,Ctr Natl Reference Escherichia Coli &, F-75019 Paris, France

[10] Univ Paris Diderot, EA3105, F-75505 Paris, France

[11] Inst Pasteur, Ctr Natl Reference Escherichia Coli & Shigella, Unite Bacteries Pathogenes Enter, F-75015 Paris, France

[12] MIT, Dept Biol, Cambridge, MA 02139 USA

[13] Harvard Univ, Sch Med, Dept Syst Biol, Boston, MA 02115 USA

[14] Harvard Univ, Sch Med, Dept Microbiol & Immunobiol, Boston, MA 02115 USA

[15] Massachusetts Gen Hosp, Dept Mol Biol, Boston, MA 02115 USA

来源：

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA | 2012年 / 109卷 / 08期

基金：

美国国家卫生研究院;

关键词：

food-borne outbreak; Shiga toxin; enteroaggregative E. coli; enterohemorrhagic E. coli; HEMOLYTIC-UREMIC SYNDROME; FRAMEWORK; FRANCE;

D O I：

10.1073/pnas.1121491109

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

The degree to which molecular epidemiology reveals information about the sources and transmission patterns of an outbreak depends on the resolution of the technology used and the samples studied. Isolates of Escherichia coli O104:H4 from the outbreak centered in Germany in May-July 2011, and the much smaller outbreak in southwest France in June 2011, were indistinguishable by standard tests. We report a molecular epidemiological analysis using multiplatform whole-genome sequencing and analysis of multiple isolates from the German and French outbreaks. Isolates from the German outbreak showed remarkably little diversity, with only two single nucleotide polymorphisms (SNPs) found in isolates from four individuals. Surprisingly, we found much greater diversity (19 SNPs) in isolates from seven individuals infected in the French outbreak. The German isolates form a clade within the more diverse French outbreak strains. Moreover, five isolates derived from a single infected individual from the French outbreak had extremely limited diversity. The striking difference in diversity between the German and French outbreak samples is consistent with several hypotheses, including a bottleneck that purged diversity in the German isolates, variation in mutation rates in the two E. coli outbreak populations, or uneven distribution of diversity in the seed populations that led to each outbreak.

引用

页码：3065 / 3070

页数：6

共 23 条

[1] Emerging foodborne pathogens: Escherichia coli O157:H7 as a model of entry of a new pathogen into the food supply of the developed world [J].

Armstrong, GL ;

Hollingsworth, J ;

Morris, JG .

EPIDEMIOLOGIC REVIEWS, 1996, 18 (01) :29-51

[2] Characterisation of the Escherichia coli strain associated with an outbreak of haemolytic uraemic syndrome in Germany, 2011: a microbiological study [J].

Bielaszewska, Martina ;

Mellmann, Alexander ;

Zhang, Wenlan ;

Koeck, Robin ;

Fruth, Angelika ;

Bauwens, Andreas ;

Peters, Georg ;

Karch, Helge .

LANCET INFECTIOUS DISEASES, 2011, 11 (09) :671-676

[3] Genome sequence analyses of two isolates from the recent Escherichia coli outbreak in Germany reveal the emergence of a new pathotype: Entero-Aggregative-Haemorrhagic Escherichia coli (EAHEC) [J].

Brzuszkiewicz, Elzbieta ;

Thuermer, Andrea ;

Schuldes, Joerg ;

Leimbach, Andreas ;

Liesegang, Heiko ;

Meyer, Frauke-Dorothee ;

Boelter, Juergen ;

Petersen, Heiko ;

Gottschalk, Gerhard ;

Daniel, Rolf .

ARCHIVES OF MICROBIOLOGY, 2011, 193 (12) :883-891

[4] progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement [J].

Darling, Aaron E. ;

Mau, Bob ;

Perna, Nicole T. .

PLOS ONE, 2010, 5 (06)

[5] A framework for variation discovery and genotyping using next-generation DNA sequencing data [J].

DePristo, Mark A. ;

Banks, Eric ;

Poplin, Ryan ;

Garimella, Kiran V. ;

Maguire, Jared R. ;

Hartl, Christopher ;

Philippakis, Anthony A. ;

del Angel, Guillermo ;

Rivas, Manuel A. ;

Hanna, Matt ;

McKenna, Aaron ;

Fennell, Tim J. ;

Kernytsky, Andrew M. ;

Sivachenko, Andrey Y. ;

Cibulskis, Kristian ;

Gabriel, Stacey B. ;

Altshuler, David ;

Daly, Mark J. .

NATURE GENETICS, 2011, 43 (05) :491-+

[6]

European Food Safety Authority, 2011, TRAC SEEDS PART FEN

[7]

Frank C., 2011, EURO SURVEILL, V16

[8] Epidemic Profile of Shiga-Toxin-Producing Escherichia coli O104:H4 Outbreak in Germany [J].

Frank, Christina ;

Werber, Dirk ;

Cramer, Jakob P. ;

Askar, Mona ;

Faber, Mirko ;

an der Heiden, Matthias ;

Bernard, Helen ;

Fruth, Angelika ;

Prager, Rita ;

Spode, Anke ;

Wadl, Maria ;

Zoufaly, Alexander ;

Jordan, Sabine ;

Kemper, Markus J. ;

Follin, Per ;

Muller, Luise ;

King, Lisa A. ;

Rosner, Bettina ;

Buchholz, Udo ;

Stark, Klaus ;

Krause, Gerard .

NEW ENGLAND JOURNAL OF MEDICINE, 2011, 365 (19) :1771-1780

[9] Whole-Genome Sequencing and Social-Network Analysis of a Tuberculosis Outbreak [J].

Gardy, Jennifer L. ;

Johnston, James C. ;

Sui, Shannan J. Ho ;

Cook, Victoria J. ;

Shah, Lena ;

Brodkin, Elizabeth ;

Rempel, Shirley ;

Moore, Richard ;

Zhao, Yongjun ;

Holt, Robert ;

Varhol, Richard ;

Birol, Inanc ;

Lem, Marcus ;

Sharma, Meenu K. ;

Elwood, Kevin ;

Jones, Steven J. M. ;

Brinkman, Fiona S. L. ;

Brunham, Robert C. ;

Tang, Patrick .

NEW ENGLAND JOURNAL OF MEDICINE, 2011, 364 (08) :730-739

[10]

Gault G, 2011, EUROSURVEILLANCE, V16, P5

← 1 2 3 →