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      Escherichia coli phylogenetic group determination and its application in the identification of the major animal source of fecal contamination

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          Abstract

          Background

          Escherichia coli strains are commonly found in the gut microflora of warm-blooded animals. These strains can be assigned to one of the four main phylogenetic groups, A, B1, B2 and D, which can be divided into seven subgroups (A 0, A 1, B1, B2 2, B2 3, D 1 and D 2), according to the combination of the three genetic markers chuA, yjaA and DNA fragment TspE4.C2. Distinct studies have demonstrated that these phylo-groups differ in the presence of virulence factors, ecological niches and life-history. Therefore, the aim of this work was to analyze the distribution of these E. coli phylo-groups in 94 human strains, 13 chicken strains, 50 cow strains, 16 goat strains, 39 pig strains and 29 sheep strains and to verify the potential of this analysis to investigate the source of fecal contamination.

          Results

          The results indicated that the distribution of phylogenetic groups, subgroups and genetic markers is non-random in the hosts analyzed. Strains from group B1 were present in all hosts analyzed but were more prevalent in cow, goat and sheep samples. Subgroup B2 3 was only found in human samples. The diversity and the similarity indexes have indicated a similarity between the E. coli population structure of human and pig samples and among cow, goat and sheep samples. Correspondence analysis using contingence tables of subgroups, groups and genetic markers frequencies allowed the visualization of the differences among animal samples and the identification of the animal source of an external validation set. The classifier tools Binary logistic regression and Partial least square -- discriminant analysis, using the genetic markers profile of the strains, differentiated the herbivorous from the omnivorous strains, with an average error rate of 17%.

          Conclusions

          This is the first work, as far as we are aware, that identifies the major source of fecal contamination of a pool of strains instead of a unique strain. We concluded that the analysis of the E. coli population structure can be useful as a supplementary bacterial source tracking tool.

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          Most cited references 24

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            Standard reference strains of Escherichia coli from natural populations.

             R. Selander,  H Ochman (1984)
            A set of 72 reference strains of Escherichia coli isolated from a variety of hosts and geographical locations has been established for use in studies of variation and genetic structure in natural populations. The strains, which have been characterized by multilocus enzyme electrophoresis, are representative of the range of genotypic variation in the species as a whole.
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              Phylogenetic distribution of extraintestinal virulence-associated traits in Escherichia coli.

              The 72 member strains of the Escherichia coli Reference collection were assessed as to genotype for 31 putative extraintestinal virulence factor (VF) genes and DNA sequence for papA, the P fimbrial structural subunit gene. Although most VFs were concentrated in phylogenetic group B2 or jointly in groups B2 and D, others were concentrated primarily in group D, were broadly distributed (without group-specific associations), and/or occurred only outside of group B2. Statistical correlations among VFs suggested linkage on pathogenicity-associated islands or plasmids. Isolates from humans and nonhuman primates had more VFs than did isolates from other animals. Sequence diversity was minimal within each F type-specific papA allele group but was substantial among different papA allele groups. The distribution patterns of papA variants and other VFs suggested multiple horizontal transfer events. These findings provide new insights into the phylogenetic origins of extraintestinal VFs in E. coli.
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                Author and article information

                Journal
                BMC Microbiol
                BMC Microbiology
                BioMed Central
                1471-2180
                2010
                1 June 2010
                : 10
                : 161
                Affiliations
                [1 ]Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas - UNICAMP, C. P. 6010, 13083-875 Campinas, S. P., Brasil
                [2 ]Programa de Pós Graduação em Ecologia, Instituto de Biologia, Universidade Estadual de Campinas -- UNICAMP, 13083-970 Campinas, S. P., Brasil
                [3 ]Departamento de Análises Ambientais, Companhia Ambiental do Estado de São Paulo - CETESB, 05459-900 São Paulo, S. P., Brasil
                [4 ]Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo -- UNIFESP, 04023-062 São Paulo, S. P., Brasil
                [5 ]Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista -- UNESP, 14884-900 Jaboticabal, S. P., Brasil
                Article
                1471-2180-10-161
                10.1186/1471-2180-10-161
                2889953
                20515490
                b191896b-ef3c-472e-a397-b6d37fe226d8
                Copyright ©2010 Carlos et al; licensee BioMed Central Ltd.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                Categories
                Research article

                Microbiology & Virology

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