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Phylogenetic background and habitat drive the genetic diversification of Escherichia coli

View ORCID ProfileMarie Touchon, View ORCID ProfileAmandine Perrin, View ORCID ProfileJorge André Moura de Sousa, View ORCID ProfileBelinda Vangchhia, View ORCID ProfileSamantha Burn, View ORCID ProfileClaire L. O’Brien, View ORCID ProfileErick Denamur, View ORCID ProfileDavid Gordon, View ORCID ProfileEduardo PC Rocha
doi: https://doi.org/10.1101/2020.02.12.945709
Marie Touchon
1Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, 25-28 rue Dr Roux, Paris, 75015, France
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  • For correspondence: mtouchon@pasteur.fr
Amandine Perrin
1Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, 25-28 rue Dr Roux, Paris, 75015, France
7Sorbonne Université, Collège doctoral, F-75005 Paris, France
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Jorge André Moura de Sousa
1Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, 25-28 rue Dr Roux, Paris, 75015, France
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Belinda Vangchhia
2Ecology and Evolution, Research School of Biology, The Australian National University, 116 Daley Road, Acton, ACT, 2601, Australia
3Department of Veterinary Microbiology, College of Veterinary Sciences & Animal Husbandry, Central Agricultural University, Selesih, Aizawl, Mizoram, 796014, India
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Samantha Burn
2Ecology and Evolution, Research School of Biology, The Australian National University, 116 Daley Road, Acton, ACT, 2601, Australia
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Claire L. O’Brien
4School of Medicine, University of Wollongong, Northfields Ave Wollongong, NSW 2522, Australia
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Erick Denamur
5Université de Paris, IAME, UMR 1137, INSERM, 75018, Paris, France
6AP-HP, Laboratoire de Génétique Moléculaire, Hôpital Bichat, 75018, Paris, France
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David Gordon
2Ecology and Evolution, Research School of Biology, The Australian National University, 116 Daley Road, Acton, ACT, 2601, Australia
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Eduardo PC Rocha
1Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, 25-28 rue Dr Roux, Paris, 75015, France
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Abstract

Escherichia coli is a commensal of birds and mammals, including humans. It can act as an opportunistic pathogen and is also found in water and sediments. Since most population studies have focused on clinical isolates, we studied the phylogeny, genetic diversification, and habitat-association of 1,294 isolates representative of the phylogenetic diversity of more than 5,000, mostly non-clinical, isolates originating from humans, poultry, wild animals and water sampled from the Australian continent. These strains represent the species diversity and show large variations in gene repertoires within sequence types. Recent gene transfer is driven by mobile elements and determined by habitat sharing and by phylogroup membership, suggesting that gene flow reinforces the association of certain genetic backgrounds with specific habitats. The phylogroups with smallest genomes had the highest rates of gene repertoire diversification and fewer but more diverse mobile genetic elements, suggesting that smaller genomes are associated with higher, not lower, turnover of genetic information. Many of these small genomes were in freshwater isolates suggesting that some lineages are specifically adapted to this environment. Altogether, these data contribute to explain why epidemiological clones tend to emerge from specific phylogenetic groups in the presence of pervasive horizontal gene transfer across the species.

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Posted February 13, 2020.
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Phylogenetic background and habitat drive the genetic diversification of Escherichia coli
Marie Touchon, Amandine Perrin, Jorge André Moura de Sousa, Belinda Vangchhia, Samantha Burn, Claire L. O’Brien, Erick Denamur, David Gordon, Eduardo PC Rocha
bioRxiv 2020.02.12.945709; doi: https://doi.org/10.1101/2020.02.12.945709
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Phylogenetic background and habitat drive the genetic diversification of Escherichia coli
Marie Touchon, Amandine Perrin, Jorge André Moura de Sousa, Belinda Vangchhia, Samantha Burn, Claire L. O’Brien, Erick Denamur, David Gordon, Eduardo PC Rocha
bioRxiv 2020.02.12.945709; doi: https://doi.org/10.1101/2020.02.12.945709

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