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Milieux urbains et exposition aux Actinobactéries pathogènes : cas particulier des bassins d’infiltration

Abstract : In cities, runoff waters are collected and directed toward infiltration basins. They collect during flooding and soils or roofs leaching diverse pollutants: hydrocarbons, organic matter, heavy metals. These accumulated particles on the infiltration basins surface constitute a layer of urban sediments rich in pollutants that constitute a new ecological niche for opportunistic pathogens. Pathogenic Actinobacteria whose Nocardia cyriacigeorgica are found here. For the moment, physiopathological studies performed on this species were done only on clinical strains and don’t take into consideration environmental isolates. Main objectives of this thesis were to assess the spatial-temporal biodiversity of Actinobacteria present in the sediments of the infiltration basin with a more specific focus on Nocardia pathogenic species, and to establish phylogenetic links between strains from an urban environment and the ones arising from French patients affected by nocardiosis and so determine the hazardousness of these environmental clones. Three sampling campaigns were performed in the infiltration basin of the Lyon east area (Django-Reinhardt) during spring, summer and autumn. The actinobacterial biodiversity was described for the first time by next generation sequencing (NGS) tools with the hsp65 marker. The infraspecific diversity of the environmental isolates of N. cyriacigeorgica arising from the infiltration basin et clinical strains provided by the French Observatory of Nocardiosis was quantified by a multilocus analysis (rrs-hsp65-sodA-secA1). The virulence of the two model strains urban EML446 and clinical GUH-2 of N. cyriacigeorgica was assessed by comparative genomics on the virulence genes of the two genomes, then by animal testing on a murine model of transient immunoparalysis CLP 30 %. Results highlight the variability of the spatial-temporal diversity of the pathogenic and indigenous Actinobacteria species dominated by around 80 % of the genus Mycobacterium and Nocardia present too in the sediments of the Django-Reinhardt infiltration basin. Mercury, copper and humidity seem to favor the development of pathogenic species. The urban strain EML446, that doesn’t be part of the highly pathogenic GUH-2 phylogroup, harbors an important pathogenicity on the murine model of transient immunoparalysis at a dose of 1,0x106 CFU/mice, as well as a similar virulence genes content. To conclude, this thesis highlights the microbial risk due to the presence of the N. cyriacigeorgica pathogenic species in a polluted urban environment linked to the runoff water management. It also opens new perspectives on the N. cyriacigeorgica taxonomic reorganization and a potential split in three distinct species that could impact the virulence and antibiotic resistance, as well as the use of new tools for the fine identification of clinic or environmental isolates of Nocardia bacterial communities by hsp65 metabarcoding or by MALDI-ToF MS
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Florian Vautrin. Milieux urbains et exposition aux Actinobactéries pathogènes : cas particulier des bassins d’infiltration. Ecologie, Environnement. Université de Lyon, 2019. Français. ⟨NNT : 2019LYSE1300⟩. ⟨tel-02546498⟩

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