Racha Beyrouthy1,2, Carolina Sabença3,4,5, Frédéric Robin1,2, Patricia Poeta3,6, Giberto Igrejas4,5,6, Richard Bonnet1,2. 1. Institut National de la Santé et de la Recherche Médicale, (UMR1071), Institut National de la Recherche Agronomique (USC-2018), Université Clermont Auvergne, 63000 Clermont-Ferrand, France. 2. Centre National de Référence de la Résistance aux Antibiotiques, Centre Hospitalier Universitaire, 63000 Clermont-Ferrand, France. 3. MicroART-Antibiotic Resistance Team, Department of Veterinary Sciences, University of Trá-os-Montes and Alto Douro (UTAD), 5001-801 Vila Real, Portugal. 4. Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, 5001-801 Vila Real, Portugal. 5. Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro, 5001-801 Vila Real, Portugal. 6. Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisbon, 2825-168 Caparica, Portugal.
Abstract
BACKGROUND: The emergence of multidrug-resistant bacteria remains poorly understood in the wild ecosystem and at the interface of habitats. Here, we explored the spread of Escherichia coli containing IncI1-ST3 plasmid encoding resistance gene cefotaximase-Munich-1 (blaCTX-M-1) in human-influenced habitats and wild fauna using a genomic approach. METHODS: Multilocus sequence typing (MLST), single-nucleotide polymorphism comparison, synteny-based analysis and data mining approaches were used to analyse a dataset of genomes and circularised plasmids. RESULTS: CTX-M-1 E. coli sequence types (STs) were preferentially associated with ecosystems. Few STs were shared by distinct habitats. IncI1-ST3-blaCTX-M-1 plasmids are disseminated among all E. coli phylogroups. The main divergences in plasmids were located in a shuffling zone including blaCTX-M-1 inserted in a conserved site. This insertion hot spot exhibited diverse positions and orientations in a zone-modulating conjugation, and the resulting synteny was associated with geographic and biological sources. CONCLUSIONS: The ecological success of IncI1-ST3-blaCTX-M-1 appears less linked to the spread of their bacterial recipients than to their ability to transfer in a broad spectrum of bacterial lineages. This feature is associated with the diversity of their shuffling conjugation region that contain blaCTX-M-1. These might be involved in the resistance to antimicrobials, but also in their spread.
BACKGROUND: The emergence of multidrug-resistant bacteria remains poorly understood in the wild ecosystem and at the interface of habitats. Here, we explored the spread of Escherichia coli containing IncI1-ST3plasmid encoding resistance gene cefotaximase-Munich-1 (blaCTX-M-1) in human-influenced habitats and wild fauna using a genomic approach. METHODS: Multilocus sequence typing (MLST), single-nucleotide polymorphism comparison, synteny-based analysis and data mining approaches were used to analyse a dataset of genomes and circularised plasmids. RESULTS:CTX-M-1E. coli sequence types (STs) were preferentially associated with ecosystems. Few STs were shared by distinct habitats. IncI1-ST3-blaCTX-M-1 plasmids are disseminated among all E. coli phylogroups. The main divergences in plasmids were located in a shuffling zone including blaCTX-M-1 inserted in a conserved site. This insertion hot spot exhibited diverse positions and orientations in a zone-modulating conjugation, and the resulting synteny was associated with geographic and biological sources. CONCLUSIONS: The ecological success of IncI1-ST3-blaCTX-M-1 appears less linked to the spread of their bacterial recipients than to their ability to transfer in a broad spectrum of bacterial lineages. This feature is associated with the diversity of their shuffling conjugation region that contain blaCTX-M-1. These might be involved in the resistance to antimicrobials, but also in their spread.