Développement d’une technique de métagénomique infectieuse semi-ciblée basée sur la capture d’acides nucléiques pour le suivi des patients atteints de mucoviscidose

Abstract : Exploration of the microbiota living within the cavities of the human body requires new tools that are to be developed in order to overcome the limitations of the traditional culture-based methods. Although PCR and other recently-developed approaches are commonly used for clinical diagnosis of lung infections in cystic fibrosis patients, the narrow spectrum of such techniques does not depict the full picture of the lung microbiota. Metagenomics however enable the microbiologist to assess the whole diversity held within our airways and lungs. In order to routinely benefit from this tool, and apply this approach in a clinical study of the lung dysbiosis, we set up and tested an analytical pipeline combining next-generation sequencing (NGS) with liquid-based probe-aided capture of the nucleic acids present in samples. The findings of the experiments performed are presented in this work as preliminary results for the full implementation of this approach. We first tested a commercial capture array on both artificial and clinical samples. Experience thus gained helped us develop a novel pan-microbial capture array that was finally used to perform advanced testing on artificial samples. We show that identification of bacteria and viruses is possible up to the species level. Our custom design of a capture array showed no inferiority compared to previously published work with separate bacterial or viral designs. While remaining testing is still to be performed on clinical samples and reproducibility to be assessed, this work brings promising results for the exploration of microbiota and large-scale clinical studies.
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Master Thesis
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https://dumas.ccsd.cnrs.fr/dumas-02092449
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Submitted on : Monday, April 8, 2019 - 10:40:01 AM
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Benjamin Némoz. Développement d’une technique de métagénomique infectieuse semi-ciblée basée sur la capture d’acides nucléiques pour le suivi des patients atteints de mucoviscidose. Médecine humaine et pathologie. 2019. ⟨dumas-02092449⟩

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