Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011
Research output: Contribution to journal › Journal article › Research › peer-review
Standard
Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011. / Grad, Yonatan H.; Lipsitch, Marc; Feldgarden, Michael; Arachchi, Harindra M.; Cerqueira, Gustavo C.; FitzGerald, Michael; Godfrey, Paul; Haas, Brian J.; Murphy, Cheryl I.; Russ, Carsten; Sykes, Sean; Walker, Bruce J.; Wortman, Jennifer R.; Young, Sarah; Zeng, Qiandong; Abouelleil, Amr; Bochicchio, James; Chauvin, Sara; DeSmet, Timothy; Gujja, Sharvari; McCowan, Caryn; Montmayeur, Anna; Steelman, Scott; Frimodt-Møller, Jakob; Petersen, Andreas M.; Struve, Carsten; Krogfelt, Karen A.; Bingen, Edouard; Weill, François Xavier; Lander, Eric S.; Nusbaum, Chad; Birren, Bruce W.; Hung, Deborah T.; Hanage, William P.
In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 109, No. 8, 2012, p. 3065-3070.Research output: Contribution to journal › Journal article › Research › peer-review
Harvard
APA
Vancouver
Author
Bibtex
}
RIS
TY - JOUR
T1 - Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011
AU - Grad, Yonatan H.
AU - Lipsitch, Marc
AU - Feldgarden, Michael
AU - Arachchi, Harindra M.
AU - Cerqueira, Gustavo C.
AU - FitzGerald, Michael
AU - Godfrey, Paul
AU - Haas, Brian J.
AU - Murphy, Cheryl I.
AU - Russ, Carsten
AU - Sykes, Sean
AU - Walker, Bruce J.
AU - Wortman, Jennifer R.
AU - Young, Sarah
AU - Zeng, Qiandong
AU - Abouelleil, Amr
AU - Bochicchio, James
AU - Chauvin, Sara
AU - DeSmet, Timothy
AU - Gujja, Sharvari
AU - McCowan, Caryn
AU - Montmayeur, Anna
AU - Steelman, Scott
AU - Frimodt-Møller, Jakob
AU - Petersen, Andreas M.
AU - Struve, Carsten
AU - Krogfelt, Karen A.
AU - Bingen, Edouard
AU - Weill, François Xavier
AU - Lander, Eric S.
AU - Nusbaum, Chad
AU - Birren, Bruce W.
AU - Hung, Deborah T.
AU - Hanage, William P.
N1 - Erratum: Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011 (Proceedings of the National Academy of Sciences of the United States of America (2012) 109, 8, (3065-3070) doi:10.1073/pnas.1203955109
PY - 2012
Y1 - 2012
N2 - 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.
AB - 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.
KW - Enteroaggregative E. Coli
KW - Enterohemorrhagic E. Coli
KW - Food-borne outbreak
KW - Shiga toxin
UR - https://doi.org/10.1073/pnas.1203955109
U2 - 10.1073/pnas.1121491109
DO - 10.1073/pnas.1121491109
M3 - Journal article
C2 - 22315421
AN - SCOPUS:84857411659
VL - 109
SP - 3065
EP - 3070
JO - Proceedings of the National Academy of Sciences of the United States of America
JF - Proceedings of the National Academy of Sciences of the United States of America
SN - 0027-8424
IS - 8
ER -
ID: 203886454