Unusual genotype of a Uropathogenic Escherichia coli strain assigned to the B2 phylogenetic group.

Center of Pharmaceutical Sciences, Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal.
Journal of clinical microbiology (Impact Factor: 4.23). 06/2011; 49(8):3105-6. DOI: 10.1128/JCM.00585-11
Source: PubMed

ABSTRACT Extraintestinal pathogenic Escherichia coli (ExPEC) cause infections such as urinary tract infections, septicemia and meningitis.…

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    ABSTRACT: There is extensive genetic substructure within the species Escherichia coli. In 2000 a simple triplex PCR method was described by Clermont and colleagues that enables an E. coli isolate to be assigned to one of the phylo-groups A, B1, B2 or D. The growing body of multi-locus sequence data and genome data for E. coli has refined our understanding of E. coli's phylo-group structure and eight phylo-groups are now recognized: seven (A, B1, B2, C, D, E, F) belong to E. coli sensu stricto, whereas the eighth is the Escherichia cryptic clade I. Here a new PCR-based method is developed that enables an E. coli isolate to be assigned to one of the eight phylo-groups and which allows isolates that are members of the other cryptic clades (II to V) of Escherichia to be identified. The development of the method is described and the method is validated. Over 95% of E. coli isolates can be correctly assigned to a phylo-group. Two collections of human faecal isolates were screened using the new phylo-group assignment method demonstrating that about 13% of E. coli isolates belong to the newly described phylo-groups C, E, F and clade I.
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    ABSTRACT: The characterization of population structures plays a main role for understanding outbreaks and the dynamics of bacterial spreading. In Escherichia coli, the widely used combination of multiplex-PCR scheme together with goeBURST has some limitations. The purpose of this study is to show that the combination of different phylogenetic approaches based on concatenated sequences of MLST genes results in a more precise assignment of E. coli phylogenetic groups, complete understanding of population structure and reconstruction of ancestral clones. A collection of 80 Escherichia coli strains of different origins was analyzed following the Clermont and Doumith's multiplex-PCR schemes. Doumith's multiplex-PCR showed only 1.7% of misassignment, whereas Clermont's-2000 protocol reached 14.0%, although the discrepancies reached 30% and 38.7% respectively when recombinant C, F and E phylogroups were considered. Therefore, correct phylogroup attribution is highly variable and depends on the clonal composition of the sample. As far as population structure of these E. coli strains, including 48 E. coli genomes from GenBank, goeBURST provides a quite dispersed population structure; whereas NeighborNet approach reveals a complex population structure. MLST-based eBURST can infer different founder genotypes, for instance ST23/ST88 could be detected as the founder genotypes for STC23; however, phylogenetic reconstructions might suggest ST410 as the ancestor clone and several evolutionary trajectories with different founders. To improve our routine understanding of E. coli molecular epidemiology, we propose a strategy based on three successive steps; first, to discriminate three main groups A/B1/C, D/F/E and B2 following Doumith's protocol; second, visualization of population structure based on MLST genes according to goeBURST, using NeighborNet to establish more complex relationships among STs; and third, to perform, a cost-free characterization of evolutionary trajectories in variants emerging along the clonal expansion using parsimony methods of phylogenetic analysis.
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    ABSTRACT: The four major phylogenetic groups of Escherichia coli (A, B1, B2, D) can be determined using a multiplex PCR targeting three DNA fragments (ChuA, YjaA, TspE4.C2) published by Clermont et al. (AEM 2000, 66:4555). Isolates are assigned to one of the phylogroups based on the presence or absence of these three fragments, i.e. B1 isolates are defined by the absence of ChuA and the presence of TspE4.C2. Recently, Mendonca et al. (JCM 2011, 49:3105) proposed that an extraintestinal pathogenic E. coli positive for YjaA and TspE4.C2 was a new pathogenic genotype that should be assigned to phylogroup B2. We investigated the occurrence of this genotype among 1355 E. coli collected in Denmark from animals, meat, healthy humans, and patients. A total of four isolates were identified from pig, broiler chicken meat and patients. Investigations of multilocus sequence types, virulence genes and in vivo virulence indicated pathogenicity. Although B2 isolates are often pathogenic, some remain non-pathogenic. Until further investigations of larger collections of this genotype we do not find the evidence compelling to assign the YjaA/TspE4.C2 genotype to the B2 phylogroup.
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