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: Abstract 1. The aim of this work was to compare a group of virulence-associated characteristics of Escherichia coli isolates from broiler chickens that had died with signs of colibacillosis against E. coli isolates from ready-to-market chicken meat in the West-Bank. 2. The isolates were investigated to determine the virulence factor profile, phylogenetic group and the presence of extended-spectrum beta-lactamase (ESBL). A total of 66 avian pathogenic E. coli (APEC) strains from different affected broiler farms and 21 E. coli isolates from ready-to-market chicken carcasses (hereinafter called meat strains) from 8 slaughter houses were analysed. 3. The overall content of virulence factors (VF) was significantly higher (P < 0.05) among APEC strains, with over 75% of APEC strains having ≥ 4 VF, while over 75% of the meat strains had less than 4 VF. The VF iss, tsh and iucD were frequently detected in APEC and meat strains, whereas cvi, papC, vat, tsh and irp2 occurred more significantly in meat strains. Phylogenetic typing showed that 67% of the meat strains belonged to group B2. Phylogroup D was predominant (50%) in the APEC strains. Using double disc diffusion and PCR, 10.6% of the APEC and 9.5% of the meat strains were determined to be ESBL positive. 4. Our findings show that the virulence factors papC, vat, irp2 and to a lesser extent tsh and cvi are significantly more prevalent in APEC strains. The results demonstrate that chicken meat can be contaminated with APEC strains (≥ 4 VF). A significant percentage of the meat strains fall in the B2 group, which is a phylogroup largely associated with human pathogenic ExPEC strains. The results of ESBL screening indicated that broiler chicken products in Palestine represent a potential reservoir of ESBL genes and therefore could be considered a possible public health risk.
    British Poultry Science 07/2014; 55(4). DOI:10.1080/00071668.2014.935998 · 0.78 Impact Factor
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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.
    PLoS ONE 08/2014; 9(8):e105395. DOI:10.1371/journal.pone.0105395 · 3.53 Impact Factor
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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.
    Environmental Microbiology Reports 02/2013; 5(1):58-65. DOI:10.1111/1758-2229.12019 · 3.26 Impact Factor

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