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Evolution of enterohemorrhagic escherichia coli O26 based on single-nucleotide polymorphisms.

Bletz S, Bielaszewska M, Leopold SR, Köck R, Witten A, Schuldes J, Zhang W, Karch H, Mellmann A - Genome Biol Evol (2013)

Bottom Line: Within approximately 1 Mb of core genes, WGS resulted in 476 high-quality bi-allelic SNP localizations.SNP-CC2 was significantly associated with the development of HUS.WGS and subsequent SNP typing enabled us to gain new insights into the evolution of EHEC O26 suggesting a common theme in this EHEC group with analogies to EHEC O157.

View Article: PubMed Central - PubMed

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

ABSTRACT
Enterohemorrhagic Escherichia coli (EHEC) O26:H11/H⁻ is the predominant non-O157 EHEC serotype among patients with diarrhea, bloody diarrhea, and hemolytic uremic syndrome (HUS) worldwide. To elucidate their phylogeny and association between their phylogenetic background and clinical outcome of the infection, we investigated 120 EHEC O26:H11/H⁻ strains isolated between 1965 and 2012 from asymptomatic carriers and patients with diarrhea or HUS. Whole-genome shotgun sequencing (WGS) was applied to ten representative EHEC O26 isolates to determine single nucleotide polymorphism (SNP) localizations within a predefined set of core genes. A multiplex SNP assay, comprising a randomly distributed subset of 48 SNPs, was established to detect SNPs in 110 additional EHEC O26 strains. Within approximately 1 Mb of core genes, WGS resulted in 476 high-quality bi-allelic SNP localizations. Forty-eight of these were subsequently investigated in 110 EHEC O26 and four different SNP clonal complexes (SNP-CC) were identified. SNP-CC2 was significantly associated with the development of HUS. Within the subsequently established evolutionary model of EHEC O26, we dated the emergence of human EHEC O26 to approximately 19,700 years ago and demonstrated a recent evolution within humans into the 4 SNP-CCs over the past 1,650 years. WGS and subsequent SNP typing enabled us to gain new insights into the evolution of EHEC O26 suggesting a common theme in this EHEC group with analogies to EHEC O157. In addition, the SNP-CC analysis may help to assess a risk in infected individuals for the progression to HUS and to implement more specific infection control measures.

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Distribution of the investigated 1,130 core genome ORFs (in green), of the discovered 476 SNPs (in blue), and the 48 SNPs of the multiplex assay (in red) illustrated in a circular map of reference genome of O26:H11 strain 11368.
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evt136-F1: Distribution of the investigated 1,130 core genome ORFs (in green), of the discovered 476 SNPs (in blue), and the 48 SNPs of the multiplex assay (in red) illustrated in a circular map of reference genome of O26:H11 strain 11368.

Mentions: The SNP discovery was performed using WGS of ten EHEC O26 isolates listed in supplementary table S1, Supplementary Material online. After assembly, we queried the assemblies for the 1,144 ORF sequences of previously published E. coli core ORF definition (Mellmann et al. 2011). In total, 1,130 of these 1,144 ORFs were present in all O26 isolates and extracted for further analysis (supplementary table S2, Supplementary Material online). Within these 1,130 ORFs representing 952,632 bp of the chromosome, we identified 476 SNPs (in 298 ORFs) (supplementary table S3, Supplementary Material online). Of these, we selected in total 48 SNP localizations manually at random, 12 per quarter of the chromosome (fig. 1), to develop a multiplex SNP assay. All 48 SNPs were bi-allelic, synaptomorphic polymorphisms; of these 30 were nonsynonymous (ns) and 18 were synonymous (s), when compared with the reference sequence (table 1).Fig. 1.—


Evolution of enterohemorrhagic escherichia coli O26 based on single-nucleotide polymorphisms.

Bletz S, Bielaszewska M, Leopold SR, Köck R, Witten A, Schuldes J, Zhang W, Karch H, Mellmann A - Genome Biol Evol (2013)

Distribution of the investigated 1,130 core genome ORFs (in green), of the discovered 476 SNPs (in blue), and the 48 SNPs of the multiplex assay (in red) illustrated in a circular map of reference genome of O26:H11 strain 11368.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3814194&req=5

evt136-F1: Distribution of the investigated 1,130 core genome ORFs (in green), of the discovered 476 SNPs (in blue), and the 48 SNPs of the multiplex assay (in red) illustrated in a circular map of reference genome of O26:H11 strain 11368.
Mentions: The SNP discovery was performed using WGS of ten EHEC O26 isolates listed in supplementary table S1, Supplementary Material online. After assembly, we queried the assemblies for the 1,144 ORF sequences of previously published E. coli core ORF definition (Mellmann et al. 2011). In total, 1,130 of these 1,144 ORFs were present in all O26 isolates and extracted for further analysis (supplementary table S2, Supplementary Material online). Within these 1,130 ORFs representing 952,632 bp of the chromosome, we identified 476 SNPs (in 298 ORFs) (supplementary table S3, Supplementary Material online). Of these, we selected in total 48 SNP localizations manually at random, 12 per quarter of the chromosome (fig. 1), to develop a multiplex SNP assay. All 48 SNPs were bi-allelic, synaptomorphic polymorphisms; of these 30 were nonsynonymous (ns) and 18 were synonymous (s), when compared with the reference sequence (table 1).Fig. 1.—

Bottom Line: Within approximately 1 Mb of core genes, WGS resulted in 476 high-quality bi-allelic SNP localizations.SNP-CC2 was significantly associated with the development of HUS.WGS and subsequent SNP typing enabled us to gain new insights into the evolution of EHEC O26 suggesting a common theme in this EHEC group with analogies to EHEC O157.

View Article: PubMed Central - PubMed

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

ABSTRACT
Enterohemorrhagic Escherichia coli (EHEC) O26:H11/H⁻ is the predominant non-O157 EHEC serotype among patients with diarrhea, bloody diarrhea, and hemolytic uremic syndrome (HUS) worldwide. To elucidate their phylogeny and association between their phylogenetic background and clinical outcome of the infection, we investigated 120 EHEC O26:H11/H⁻ strains isolated between 1965 and 2012 from asymptomatic carriers and patients with diarrhea or HUS. Whole-genome shotgun sequencing (WGS) was applied to ten representative EHEC O26 isolates to determine single nucleotide polymorphism (SNP) localizations within a predefined set of core genes. A multiplex SNP assay, comprising a randomly distributed subset of 48 SNPs, was established to detect SNPs in 110 additional EHEC O26 strains. Within approximately 1 Mb of core genes, WGS resulted in 476 high-quality bi-allelic SNP localizations. Forty-eight of these were subsequently investigated in 110 EHEC O26 and four different SNP clonal complexes (SNP-CC) were identified. SNP-CC2 was significantly associated with the development of HUS. Within the subsequently established evolutionary model of EHEC O26, we dated the emergence of human EHEC O26 to approximately 19,700 years ago and demonstrated a recent evolution within humans into the 4 SNP-CCs over the past 1,650 years. WGS and subsequent SNP typing enabled us to gain new insights into the evolution of EHEC O26 suggesting a common theme in this EHEC group with analogies to EHEC O157. In addition, the SNP-CC analysis may help to assess a risk in infected individuals for the progression to HUS and to implement more specific infection control measures.

Show MeSH
Related in: MedlinePlus