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Genomic diversity of pathogenic Escherichia coli of the EHEC 2 clonal complex.

Abu-Ali GS, Lacher DW, Wick LM, Qi W, Whittam TS - BMC Genomics (2009)

Bottom Line: Of the 979 parsimoniously informative genes, 15% were found to be compatible and their distribution in EHEC 2 clustered O111:H8 and O118:H16 strains by serotype.No correlation was found between gene contents and geographic locations of EHEC 2 strains.These results suggest that EHEC 2 is a multiform pathogenic clonal complex, characterized by substantial intra-serotype genetic variation.

View Article: PubMed Central - HTML - PubMed

Affiliation: Microbial Evolution Laboratory, National Food Safety & Toxicology Center, 165 Food Safety & Toxicology Building, Michigan State University, East Lansing, Michigan 48824, USA. abualiga@cvm.msu.edu

ABSTRACT

Background: Evolutionary analyses of enterohemorrhagic Escherichia coli (EHEC) have identified two distantly related clonal groups: EHEC 1, including serotype O157:H7 and its inferred ancestor O55:H7; and EHEC 2, comprised of several serogroups (O26, O111, O118, etc.). These two clonal groups differ in their virulence and global distribution. Although several fully annotated genomic sequences exist for strains of serotype O157:H7, much less is known about the genomic composition of EHEC 2. In this study, we analyzed a set of 24 clinical EHEC 2 strains representing serotypes O26:H11, O111:H8/H11, O118:H16, O153:H11 and O15:H11 from humans and animals by comparative genomic hybridization (CGH) on an oligoarray based on the O157:H7 Sakai genome.

Results: Backbone genes, defined as genes shared by Sakai and K-12, were highly conserved in EHEC 2. The proportion of Sakai phage genes in EHEC 2 was substantially greater than that of Sakai-specific bacterial (non-phage) genes. This proportion was inverted in O55:H7, reiterating that a subset of Sakai bacterial genes is specific to EHEC 1. Split decomposition analysis of gene content revealed that O111:H8 was more genetically uniform and distinct from other EHEC 2 strains, with respect to the Sakai O157:H7 gene distribution. Serotype O26:H11 was the most heterogeneous EHEC 2 subpopulation, comprised of strains with the highest as well as the lowest levels of Sakai gene content conservation. Of the 979 parsimoniously informative genes, 15% were found to be compatible and their distribution in EHEC 2 clustered O111:H8 and O118:H16 strains by serotype. CGH data suggested divergence of the LEE island from the LEE1 to the LEE4 operon, and also between animal and human isolates irrespective of serotype. No correlation was found between gene contents and geographic locations of EHEC 2 strains.

Conclusion: The gene content variation of phage-related genes in EHEC 2 strains supports the hypothesis that extensive modular shuffling of mobile DNA elements has occurred among EHEC strains. These results suggest that EHEC 2 is a multiform pathogenic clonal complex, characterized by substantial intra-serotype genetic variation. The heterogeneous distribution of mobile elements has impacted the diversification of O26:H11 more than other EHEC 2 serotypes.

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Phylogenetic relationships of EHEC and EPEC sequence types. The sequence types (STs) of EHEC 2 belong to a clonal group (CG 14), which is more closely related to EPEC 2 (CG 17), than EHEC 1 STs (CG 11). The phylogenetic tree was constructed using the Neighbor-joining algorithm based on the Kimura 2-parameter distance matrix of nucleotide substitution. Bootstrap confidence values were based on 1000 replicates. Only those higher than 70% are shown.
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Figure 1: Phylogenetic relationships of EHEC and EPEC sequence types. The sequence types (STs) of EHEC 2 belong to a clonal group (CG 14), which is more closely related to EPEC 2 (CG 17), than EHEC 1 STs (CG 11). The phylogenetic tree was constructed using the Neighbor-joining algorithm based on the Kimura 2-parameter distance matrix of nucleotide substitution. Bootstrap confidence values were based on 1000 replicates. Only those higher than 70% are shown.

Mentions: Phylogenetic analyses of multi locus sequence typing (MLST) data grouped the 24 EHEC 2 strains (Table 1) into four STs. The most common was ST 106, which was found in 20 strains, while the remaining three STs each differed from ST 106 by a single nucleotide polymorphism (SNP) in almost 4,000 bp of the concatenated MLST sequence. MLST data revealed a lack of nucleotide sequence diversity in house keeping genes among these EHEC 2 strains. The neighbor-joining phylogeny based on concatenated MLST allelic sequences grouped the EHEC 2 strains into a distinct cluster, with 100% bootstrap support, which was more closely related to the EPEC 2 group (100% bootstrap support) than to members of EHEC 1 (Figure 1). Most of these EHEC 2 strains (n = 17) were PCR positive for only stx1, whereas four strains had both stx1 and stx2, and three strains were negative for both stx genes (Table 1).


Genomic diversity of pathogenic Escherichia coli of the EHEC 2 clonal complex.

Abu-Ali GS, Lacher DW, Wick LM, Qi W, Whittam TS - BMC Genomics (2009)

Phylogenetic relationships of EHEC and EPEC sequence types. The sequence types (STs) of EHEC 2 belong to a clonal group (CG 14), which is more closely related to EPEC 2 (CG 17), than EHEC 1 STs (CG 11). The phylogenetic tree was constructed using the Neighbor-joining algorithm based on the Kimura 2-parameter distance matrix of nucleotide substitution. Bootstrap confidence values were based on 1000 replicates. Only those higher than 70% are shown.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2713265&req=5

Figure 1: Phylogenetic relationships of EHEC and EPEC sequence types. The sequence types (STs) of EHEC 2 belong to a clonal group (CG 14), which is more closely related to EPEC 2 (CG 17), than EHEC 1 STs (CG 11). The phylogenetic tree was constructed using the Neighbor-joining algorithm based on the Kimura 2-parameter distance matrix of nucleotide substitution. Bootstrap confidence values were based on 1000 replicates. Only those higher than 70% are shown.
Mentions: Phylogenetic analyses of multi locus sequence typing (MLST) data grouped the 24 EHEC 2 strains (Table 1) into four STs. The most common was ST 106, which was found in 20 strains, while the remaining three STs each differed from ST 106 by a single nucleotide polymorphism (SNP) in almost 4,000 bp of the concatenated MLST sequence. MLST data revealed a lack of nucleotide sequence diversity in house keeping genes among these EHEC 2 strains. The neighbor-joining phylogeny based on concatenated MLST allelic sequences grouped the EHEC 2 strains into a distinct cluster, with 100% bootstrap support, which was more closely related to the EPEC 2 group (100% bootstrap support) than to members of EHEC 1 (Figure 1). Most of these EHEC 2 strains (n = 17) were PCR positive for only stx1, whereas four strains had both stx1 and stx2, and three strains were negative for both stx genes (Table 1).

Bottom Line: Of the 979 parsimoniously informative genes, 15% were found to be compatible and their distribution in EHEC 2 clustered O111:H8 and O118:H16 strains by serotype.No correlation was found between gene contents and geographic locations of EHEC 2 strains.These results suggest that EHEC 2 is a multiform pathogenic clonal complex, characterized by substantial intra-serotype genetic variation.

View Article: PubMed Central - HTML - PubMed

Affiliation: Microbial Evolution Laboratory, National Food Safety & Toxicology Center, 165 Food Safety & Toxicology Building, Michigan State University, East Lansing, Michigan 48824, USA. abualiga@cvm.msu.edu

ABSTRACT

Background: Evolutionary analyses of enterohemorrhagic Escherichia coli (EHEC) have identified two distantly related clonal groups: EHEC 1, including serotype O157:H7 and its inferred ancestor O55:H7; and EHEC 2, comprised of several serogroups (O26, O111, O118, etc.). These two clonal groups differ in their virulence and global distribution. Although several fully annotated genomic sequences exist for strains of serotype O157:H7, much less is known about the genomic composition of EHEC 2. In this study, we analyzed a set of 24 clinical EHEC 2 strains representing serotypes O26:H11, O111:H8/H11, O118:H16, O153:H11 and O15:H11 from humans and animals by comparative genomic hybridization (CGH) on an oligoarray based on the O157:H7 Sakai genome.

Results: Backbone genes, defined as genes shared by Sakai and K-12, were highly conserved in EHEC 2. The proportion of Sakai phage genes in EHEC 2 was substantially greater than that of Sakai-specific bacterial (non-phage) genes. This proportion was inverted in O55:H7, reiterating that a subset of Sakai bacterial genes is specific to EHEC 1. Split decomposition analysis of gene content revealed that O111:H8 was more genetically uniform and distinct from other EHEC 2 strains, with respect to the Sakai O157:H7 gene distribution. Serotype O26:H11 was the most heterogeneous EHEC 2 subpopulation, comprised of strains with the highest as well as the lowest levels of Sakai gene content conservation. Of the 979 parsimoniously informative genes, 15% were found to be compatible and their distribution in EHEC 2 clustered O111:H8 and O118:H16 strains by serotype. CGH data suggested divergence of the LEE island from the LEE1 to the LEE4 operon, and also between animal and human isolates irrespective of serotype. No correlation was found between gene contents and geographic locations of EHEC 2 strains.

Conclusion: The gene content variation of phage-related genes in EHEC 2 strains supports the hypothesis that extensive modular shuffling of mobile DNA elements has occurred among EHEC strains. These results suggest that EHEC 2 is a multiform pathogenic clonal complex, characterized by substantial intra-serotype genetic variation. The heterogeneous distribution of mobile elements has impacted the diversification of O26:H11 more than other EHEC 2 serotypes.

Show MeSH
Related in: MedlinePlus