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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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Related in: MedlinePlus

The minimum spanning tree (MST) shows the molecular phylogeny of 120 EHEC O26 isolates. The different colors represent the symptoms of the infected patients. Each node represents a unique SNP profile. SNP clonal clusters (SNP-CCs) are numbered (SNP-CC1 to SNP-CC4). The node size reflects the number of isolates. Small numbers on connecting lines display the distance (number of differing SNPs) between two nodes.
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evt136-F2: The minimum spanning tree (MST) shows the molecular phylogeny of 120 EHEC O26 isolates. The different colors represent the symptoms of the infected patients. Each node represents a unique SNP profile. SNP clonal clusters (SNP-CCs) are numbered (SNP-CC1 to SNP-CC4). The node size reflects the number of isolates. Small numbers on connecting lines display the distance (number of differing SNPs) between two nodes.

Mentions: Overall, SNP genotyping of the 120 EHEC O26 isolates resulted in ten unique SNP profiles. Their phylogenetic relationships are displayed in a minimum spanning tree (MST) in figure 2. Clustering of SNP genotypes enabled us to assign SNP clonal complexes (SNP-CCs) as phylogenetically conserved groups, which is analogous to MLST, where MLST clonal complexes are phylogenetically informative groups (Feil and Spratt 2001). Isolates sharing ≥90% of the 48 SNPs (i.e., ≥44 SNPs) were grouped, resulting in four different SNP-CCs (SNP-CC1 to SNP-CC4) (fig. 2). Further details of the 48 investigated SNP localizations, for example, their ability to serve as a canonical SNP for a certain SNP-CC, are given in table 1. Of the determined SNP-CCs, SNP-CC2 and SNP-CC3 encompassed most isolates (60 [50.0%] and 39 [32.5%] isolates, respectively). The remaining SNP-CCs contained 13 (10.1%, SNP-CC4) and 8 (6.7%, SNP-CC1) isolates. Comparison of SNP data with MLST corroborated this separation as all isolates of SNP-CC2 and SNP-CC4 were exclusively MLST ST29 and ST21, respectively. Moreover, nearly all (36 of 39) SNP-CC3 isolates were ST21 and the majority of SNP-CC1 (6 of 8 isolates) were ST29 with few single locus variants (slv) of either ST21 (ST591, ST1565, and ST1705 in SNP-CC3) or ST29 (ST396 and ST1566 in SNP-CC1). Taken together, SNP genotyping subdivided the EHEC O26 population into four different SNP-CCs, one of which (SNP-CC2) was the recently described highly pathogenic “new clone” that separated from the remaining O26 population (Bielaszewska et al. 2013) and three further SNP-CCs.Fig. 2.—


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)

The minimum spanning tree (MST) shows the molecular phylogeny of 120 EHEC O26 isolates. The different colors represent the symptoms of the infected patients. Each node represents a unique SNP profile. SNP clonal clusters (SNP-CCs) are numbered (SNP-CC1 to SNP-CC4). The node size reflects the number of isolates. Small numbers on connecting lines display the distance (number of differing SNPs) between two nodes.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

evt136-F2: The minimum spanning tree (MST) shows the molecular phylogeny of 120 EHEC O26 isolates. The different colors represent the symptoms of the infected patients. Each node represents a unique SNP profile. SNP clonal clusters (SNP-CCs) are numbered (SNP-CC1 to SNP-CC4). The node size reflects the number of isolates. Small numbers on connecting lines display the distance (number of differing SNPs) between two nodes.
Mentions: Overall, SNP genotyping of the 120 EHEC O26 isolates resulted in ten unique SNP profiles. Their phylogenetic relationships are displayed in a minimum spanning tree (MST) in figure 2. Clustering of SNP genotypes enabled us to assign SNP clonal complexes (SNP-CCs) as phylogenetically conserved groups, which is analogous to MLST, where MLST clonal complexes are phylogenetically informative groups (Feil and Spratt 2001). Isolates sharing ≥90% of the 48 SNPs (i.e., ≥44 SNPs) were grouped, resulting in four different SNP-CCs (SNP-CC1 to SNP-CC4) (fig. 2). Further details of the 48 investigated SNP localizations, for example, their ability to serve as a canonical SNP for a certain SNP-CC, are given in table 1. Of the determined SNP-CCs, SNP-CC2 and SNP-CC3 encompassed most isolates (60 [50.0%] and 39 [32.5%] isolates, respectively). The remaining SNP-CCs contained 13 (10.1%, SNP-CC4) and 8 (6.7%, SNP-CC1) isolates. Comparison of SNP data with MLST corroborated this separation as all isolates of SNP-CC2 and SNP-CC4 were exclusively MLST ST29 and ST21, respectively. Moreover, nearly all (36 of 39) SNP-CC3 isolates were ST21 and the majority of SNP-CC1 (6 of 8 isolates) were ST29 with few single locus variants (slv) of either ST21 (ST591, ST1565, and ST1705 in SNP-CC3) or ST29 (ST396 and ST1566 in SNP-CC1). Taken together, SNP genotyping subdivided the EHEC O26 population into four different SNP-CCs, one of which (SNP-CC2) was the recently described highly pathogenic “new clone” that separated from the remaining O26 population (Bielaszewska et al. 2013) and three further SNP-CCs.Fig. 2.—

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