Achromobacter & Pandoraea : diversité et évolution adaptative de populations persistantes au cours de la mucoviscidose et dans l'environnement

Abstract : Bacterial persistence involves adaptation to environmental conditions and constraints, sometimes associated with genotype and phenotype diversification of bacterial populations. In the context of chronic infections, Cystic Fibrosis (CF) is a human disease among the most studied in terms of persistence and adaptation of opportunistic pathogens. Some environmental opportunistic pathogens like Achromobacter and Pandoraea genera are considered as emerging in CF and are able to chronically colonize CF Respiratory Tract (CFRT). Adaptation mechanisms required for colonization and persistence were studied for P. aeruginosa but remain largely unknown for emerging bacteria. We studied Achromobacter spp. persistence in the CFRT of 13 patients and in a dental care unit water network, and Pandoraea pulmonicola persistence in the CFRT of one patient, during colonization periods up to 7 years. In parallel, we studied Achromobacter population genomic and phenotypic diversity in sputum samples from 9 patients. Finally, we made an environmental investigation to study the diversity and the ecology of Achromobacter spp. in household of 3 Achromobacter chronically colonized CF patients. During these studies, Achromobacter and Pandoraea species were identified by molecular methods and genome dynamic and phenotypic diversity were studied.Diversity of Achromobacter species colonizing the CFRT is described and included an undescribed species. Chronically colonized patients had a unique Achromobacter or Pandoraea clone in their CFRT, supporting the initial acquisition of one environmental clone which persists over time. A large genomic and phenotypic diversity has been observed over time and also at the intra-specimen level. A wide antibiotic susceptibility profile diversity was observed within samples and its clinical impact remains to be assessed. Finally, Achromobacter species diversity was observed in patient domestic environment but the Achromobacter clone adapted to the patient CFRT was not isolated. These results suggested that after initial colonization and specialisation the CFRT, colonizing clones might secondarily be unable to survive in the environment.A colonizing clone quickly adapts to the specific local conditions of the CFRT and undergoes intense genomic and phenotypic diversification with genotype specialization to the different ecological niches of the heterogeneous CFRT, resulting in a diversified clonal population. This diversity certainly insures the population persistence according to the “bet hedging” theory stating that regardless of the environmental pressures, a bacteria or a subgroup of bacteria will be able to persist.Key words : Achromobacter, adaptation, antibiotic susceptibility, chronic colonization, Cystic Fibrosis, diversity, ecology, environment, epidemiology, evolution, genomic, Pandoraea, persistence, phenotype, water network.
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Chloé Dupont. Achromobacter & Pandoraea : diversité et évolution adaptative de populations persistantes au cours de la mucoviscidose et dans l'environnement. Microbiologie et Parasitologie. Université Montpellier, 2016. Français. ⟨NNT : 2016MONTT105⟩. ⟨tel-01615036⟩

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