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

Mellmann A, Harmsen D, Cummings CA, Zentz EB, Leopold SR, Rico A, Prior K, Szczepanowski R, Ji Y, Zhang W, McLaughlin SF, Henkhaus JK, Leopold B, Bielaszewska M, Prager R, Brzoska PM, Moore RL, Guenther S, Rothberg JM, Karch H - PLoS ONE (2011)

Bottom Line: Serotype O104:H4, which has not been detected in animals, has rarely been associated with HUS in the past.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).In conclusion, rapid next-generation technologies facilitated prospective whole genome characterization in the early stages of an outbreak.

View Article: PubMed Central - PubMed

Affiliation: Institute of Hygiene, University Münster, Münster, Germany.

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.

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Optical Map similarity cluster of German EHEC O104:H4 outbreak.De novo whole genome optical maps from EHEC O104:H4 outbreak strains (‘LB’ prefix) and historical O104:H4 and O104:H21 strains (01-09591 and 02-03885) were created using the Argus™ Optical Mapping System with the NcoI restriction enzyme. An in silico genomic map of the reference strain 55989 was created in MapSolver™ by importing genomic sequence data from NCBI (acc. no. NC_011478) and applying the NcoI restriction pattern. Optical maps and in silico maps were compared using the default MapSolver™ parameters and clustered using UPGMA based on the resulting pairwise distance metrics. Scale represents percent difference. Strain name, serotype, country, city, and year of isolation are indicated.
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pone-0022751-g002: Optical Map similarity cluster of German EHEC O104:H4 outbreak.De novo whole genome optical maps from EHEC O104:H4 outbreak strains (‘LB’ prefix) and historical O104:H4 and O104:H21 strains (01-09591 and 02-03885) were created using the Argus™ Optical Mapping System with the NcoI restriction enzyme. An in silico genomic map of the reference strain 55989 was created in MapSolver™ by importing genomic sequence data from NCBI (acc. no. NC_011478) and applying the NcoI restriction pattern. Optical maps and in silico maps were compared using the default MapSolver™ parameters and clustered using UPGMA based on the resulting pairwise distance metrics. Scale represents percent difference. Strain name, serotype, country, city, and year of isolation are indicated.

Mentions: Whole genome optical maps were created for four outbreak isolates (including LB226692) from four different German cities and two historical reference strains 02-03885 (HUSEC037) and 01-09591 (HUSEC041). Comparison of the optical maps demonstrated that all four outbreak strains are identical within the limits of Optical Mapping resolution, suggesting that the outbreak is likely to be clonal and single-sourced (Fig. 2). Moreover, alignments of optical maps to an in silico digest of EAEC 55989 showed strong similarity of this strain to the outbreak strains and 01-09591.


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

Mellmann A, Harmsen D, Cummings CA, Zentz EB, Leopold SR, Rico A, Prior K, Szczepanowski R, Ji Y, Zhang W, McLaughlin SF, Henkhaus JK, Leopold B, Bielaszewska M, Prager R, Brzoska PM, Moore RL, Guenther S, Rothberg JM, Karch H - PLoS ONE (2011)

Optical Map similarity cluster of German EHEC O104:H4 outbreak.De novo whole genome optical maps from EHEC O104:H4 outbreak strains (‘LB’ prefix) and historical O104:H4 and O104:H21 strains (01-09591 and 02-03885) were created using the Argus™ Optical Mapping System with the NcoI restriction enzyme. An in silico genomic map of the reference strain 55989 was created in MapSolver™ by importing genomic sequence data from NCBI (acc. no. NC_011478) and applying the NcoI restriction pattern. Optical maps and in silico maps were compared using the default MapSolver™ parameters and clustered using UPGMA based on the resulting pairwise distance metrics. Scale represents percent difference. Strain name, serotype, country, city, and year of isolation are indicated.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3140518&req=5

pone-0022751-g002: Optical Map similarity cluster of German EHEC O104:H4 outbreak.De novo whole genome optical maps from EHEC O104:H4 outbreak strains (‘LB’ prefix) and historical O104:H4 and O104:H21 strains (01-09591 and 02-03885) were created using the Argus™ Optical Mapping System with the NcoI restriction enzyme. An in silico genomic map of the reference strain 55989 was created in MapSolver™ by importing genomic sequence data from NCBI (acc. no. NC_011478) and applying the NcoI restriction pattern. Optical maps and in silico maps were compared using the default MapSolver™ parameters and clustered using UPGMA based on the resulting pairwise distance metrics. Scale represents percent difference. Strain name, serotype, country, city, and year of isolation are indicated.
Mentions: Whole genome optical maps were created for four outbreak isolates (including LB226692) from four different German cities and two historical reference strains 02-03885 (HUSEC037) and 01-09591 (HUSEC041). Comparison of the optical maps demonstrated that all four outbreak strains are identical within the limits of Optical Mapping resolution, suggesting that the outbreak is likely to be clonal and single-sourced (Fig. 2). Moreover, alignments of optical maps to an in silico digest of EAEC 55989 showed strong similarity of this strain to the outbreak strains and 01-09591.

Bottom Line: Serotype O104:H4, which has not been detected in animals, has rarely been associated with HUS in the past.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).In conclusion, rapid next-generation technologies facilitated prospective whole genome characterization in the early stages of an outbreak.

View Article: PubMed Central - PubMed

Affiliation: Institute of Hygiene, University Münster, Münster, Germany.

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.

Show MeSH
Related in: MedlinePlus