Les infections à mycobactéries du complexe Mycobacterium tuberculosis à Libreville : profil des résistances aux antibiotiques et diversité génétique

par Amel Kevin Alame Emane

Thèse de doctorat en Microbiologie procaryote et eucaryote

Soutenue le 15-11-2016

à Sorbonne Paris Cité , dans le cadre de École doctorale Bio Sorbonne Paris Cité (Paris) , en partenariat avec Génétique mycobactérienne (Paris) (laboratoire) et de Université Paris Diderot - Paris 7 (1970-2019) (établissement de préparation) .

Le président du jury était Olivier Dussurget.

Le jury était composé de Howard E. Takiff, Nathalie Grall, Mathieu Picardeau.

Les rapporteurs étaient Beate Heym, Anandi Martin.


  • Résumé

    Le phénomène émergent de la tuberculose multirésistante et ultrarésistante est un problème de santé publique à l’échelle mondiale. Dans les pays en développement, ce problème est accru du fait que les laboratoires de diagnostic de la tuberculose manquent d’équipement et d’outils de diagnostics pour identifier ces cas pour prescrire une chimiothérapie adaptée. La première partie de ce travail de doctorat a permis à travers le séquençage du locus pncA, de mettre en évidence que la résistance au Pyrazinamide survient généralement et de manière significative lorsque la souche est multirésistante, c’est-à-dire après l’acquisition de la résistance à la Rifampicine et à l’Isoniazide. Le pourcentage des souches résistantes au PZA est même plus élevé chez les souches MDR résistantes aux FQs. Dans la seconde partie de l’étude, nous proposons une méthode alternative à la culture de bacilles dans un environnement confiné de type P3. À partir d’échantillons cliniques non cultivés (expectoration) et grâce au GeneXpert MTB/RIF, au séquençage de gènes et au spoligotypage, nous avons pu identifier 19 souches multirésistantes, une transmission active de souches sensibles appartenant aux clades LAM10, T1, MANU, H3 et enfin une épidémie sous-jacente de 5 souches Beijing multirésistantes.

  • Titre traduit

    Mycobacterium infections of the Mycobacterium tuberculosis complex in Libreville : profile of resistance to antibiotics and genetic diversity


  • Résumé

    The emerging phenomenon of the MDR and XDR-TB is a worldwide public health issue. In developing countries, this problem is amplified due to the fact that TB diagnostic laboratories lack equipment and diagnostic tools to identify these cases and therefore prescribe appropriate chemotherapy. In the first part of this doctoral work, the sequencing of the pncA gene allowed us to show that the resistance to Pyrazinamide occurs significantly when the strain is MDR, corresponding to the acquisition of resistance to Rifampicin and Isoniazid; and that after the acquisition of Fluoroquinolones and to injectable antibiotics of second line (Amykacine, Kanamycine, Capreomycine) resistance by MDR strains, this rate increases even more. In the second part of the study, we propose an alternative method to the culture of bacilli in a BSL3 confined environment. From uncultivated clinical samples (sputum) and through GeneXpert MTB/RIF, sequencing of genes and spoligotyping, we identified 19 MDR strains, active transmission of sensitive strains belonging to clades LAM10, T1, MANU, H3 and finally as well as an underlying epidemic of 5 Beijing MDR strains.In the first study, 272 retrospective samples of Mycobacterium tuberculosis isolates were selected from two large cosmopolitan cities: Northern Paris (Bichat-Claude Bernard Hospital, 101 strains) and Southwest of Shanghai (Songjiang district, 171 Strains). These strains were selected according to their known phenotypic sensitivity to Rifampicin (RIF) and Isoniazid (INH). These phenotypic resistances were confirmed by the HAIN genotype analysis tools MTBDRplus and by the sequencing of the rpoB and katG/inhA genes. To determine the extensively drug resistance strains (XDR), we sequenced the gyrA/gyrB and rrs genes to identify genetic mutations associated with resistance to Fluoroquinolones (FQs) and second-line injectable antibiotics: Amikacin (AMK)-Kanamycin ( KAN)-Capreomycin (CAP), respectively. Finally, we sequenced the pncA gene of all isolates to identify the genetic mutations associated with resistance to Pyrazinamide (PZA). The strains were genotyped by spoligotyping and MIRU-VNTR.In the second study, from October 2014 to February 2015, 159 morning sputum samples with smear-positive smear after Ziehl-Neelsen staining were collected at the three main diagnostic laboratories for tuberculosis in Libreville, Gabon. These clinical samples were transported to the National Laboratory of Public Health in Libreville for analysis with the GeneXpert MTB/RIF automaton to confirm the microscopic diagnosis and to determine the resistance of bacilli to Rifampicin. Of the 159 samples, 29 samples had a sputum volume less than 1 ml, the minimum required according to the manufacturer's recommendations. For the 130 sputum samples analyzed by the GeneXpert automaton, 375 μl of the remaining GeneXpert solution not introduced into the cartridge was introduced into a 50 ml conical tube containing 25 ml of phosphate buffer (autoclaved solution) to neutralize the pH of the GeneXpert solution. The conical tube is centrifuged for 15 minutes at 4,500 rpm, the pellet is taken up in 100 μl of TE and then transferred to a 100 μl microtube which is subsequently heated for 30 minutes at 90°C. After a cycle of freezing (-40 ° C. for 1 h)-defrosting, the microtube is briefly centrifuged and the supernatant is transferred to a new microtube. From this new microtube we amplified by PCR and then sequenced the rpoB, katG/inhA, pncA, gyrA, rrs and rpsL genes to identify mutations associated with resistance to Rifampicin, Isoniazid, Pyrazinamide, Fluoroquinolones, Antibiotics in second lines: Amikacin-Kanamycin-Capreomycin and Streptomycin (SM), respectively. All the samples were genotyped by the multiplexed spoligotyping applied to the Luminex MagPix.

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