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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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Split decomposition analysis of Sakai genes in 24 EHEC 2 strains. The network was generated based on the presence/absence of 4800 Sakai genes among 24 EHEC 2 strains. 144 genes were excluded because their probe intensities were below those of randomized negative controls in the various Sakai/EHEC 2 hybridizations. Node labels refer to strain names (listed in Table 1). Parallel edges represent phylogenetic incompatibilities in the data set, which are indicative of parallel gene gain/loss by multiple transduction events. The network was generated in Splitstree 4.3, using neighbor net with the uncorrected p distance. Scale bar represents number of gene differences (present or divergent/absent) per gene site.
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Figure 3: Split decomposition analysis of Sakai genes in 24 EHEC 2 strains. The network was generated based on the presence/absence of 4800 Sakai genes among 24 EHEC 2 strains. 144 genes were excluded because their probe intensities were below those of randomized negative controls in the various Sakai/EHEC 2 hybridizations. Node labels refer to strain names (listed in Table 1). Parallel edges represent phylogenetic incompatibilities in the data set, which are indicative of parallel gene gain/loss by multiple transduction events. The network was generated in Splitstree 4.3, using neighbor net with the uncorrected p distance. Scale bar represents number of gene differences (present or divergent/absent) per gene site.

Mentions: We used the split decomposition method to infer the strain relatedness based on gene content data. We first analyzed all the 4,800 genes whose probe intensities were higher than those for negative controls. As expected, the analysis showed a network like phylogeny (Figure 3), in which the parallel edges reflected incompatible signals in the data that were indicative of parallel gene gain/loss due to multiple transduction events or past recombination. All O111:H8 strains were clustered closely and branched away from the remaining EHEC 2 strains, which formed a loose cluster without any recognizable concordance to serotypes, hosts, or locations (Figure 3). The pairwise homoplasy index (PHI) [43], generated in Splitstree, confirmed that there was significant evidence of recombination (p-value = 0.0).


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)

Split decomposition analysis of Sakai genes in 24 EHEC 2 strains. The network was generated based on the presence/absence of 4800 Sakai genes among 24 EHEC 2 strains. 144 genes were excluded because their probe intensities were below those of randomized negative controls in the various Sakai/EHEC 2 hybridizations. Node labels refer to strain names (listed in Table 1). Parallel edges represent phylogenetic incompatibilities in the data set, which are indicative of parallel gene gain/loss by multiple transduction events. The network was generated in Splitstree 4.3, using neighbor net with the uncorrected p distance. Scale bar represents number of gene differences (present or divergent/absent) per gene site.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: Split decomposition analysis of Sakai genes in 24 EHEC 2 strains. The network was generated based on the presence/absence of 4800 Sakai genes among 24 EHEC 2 strains. 144 genes were excluded because their probe intensities were below those of randomized negative controls in the various Sakai/EHEC 2 hybridizations. Node labels refer to strain names (listed in Table 1). Parallel edges represent phylogenetic incompatibilities in the data set, which are indicative of parallel gene gain/loss by multiple transduction events. The network was generated in Splitstree 4.3, using neighbor net with the uncorrected p distance. Scale bar represents number of gene differences (present or divergent/absent) per gene site.
Mentions: We used the split decomposition method to infer the strain relatedness based on gene content data. We first analyzed all the 4,800 genes whose probe intensities were higher than those for negative controls. As expected, the analysis showed a network like phylogeny (Figure 3), in which the parallel edges reflected incompatible signals in the data that were indicative of parallel gene gain/loss due to multiple transduction events or past recombination. All O111:H8 strains were clustered closely and branched away from the remaining EHEC 2 strains, which formed a loose cluster without any recognizable concordance to serotypes, hosts, or locations (Figure 3). The pairwise homoplasy index (PHI) [43], generated in Splitstree, confirmed that there was significant evidence of recombination (p-value = 0.0).

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