The use of GeneXpert remnants for drug resistance profiling and molecular epidemiology of tuberculosis in Libreville, Gabon

Amel Kévin Alame-Emane (1, 2) , Catherine Pierre-Audigier (1) , Oriane Cordelia Aboumegone-Biyogo (2) , Amandine Nzoghe-Mveang (2) , Véronique Cadet-Daniel (1) , Christophe Sola (3, 4) , Joël Fleury Djoba-Siawaya (2) , Brigitte Gicquel (1, 5) , Howard E. Takiff (1, 6)

1 Génétique mycobactérienne - Mycobacterial genetics
2 Research and Specialised Diagnostics Unit
3 I2BC - Institut de Biologie Intégrative de la Cellule
4 IGEPE - Infection Génétique Evolution des Pathogènes Emergents
5 IPS-CAS - Institut Pasteur de Shanghai, Académie des Sciences de Chine - Chinese Academy of Sciences
6 IVIC - Instituto Venezolano de Investigaciones Cientificas = Venezuelan Institute for Scientific Research

Multidrug (MDR) and extensively drug resistant (XDR) Mycobacterium tuberculosis are major problems in global health. The GeneXpertMTB/RIF (Xpert) rapidly detects resistance to rifampicin (RIF-R), but detection of the additional resistance that defines MDR and XDR-TB, and for molecular epidemiology, specimen cultures and biosafe infrastructure are generally required. We sought to determine whether the remnants of sputa prepared for Xpert could be used directly to find mutations associated with drug resistance and for molecular epidemiology, and thus provide a precise characterization of MDR-TB cases in countries lacking BSL3 facilities for M. tuberculosis cultures. After sputa were processed and run on the Xpert instrument, the leftovers of the samples prepared for Xpert were used for PCR amplification and sequencing or line probe assay to detect mutations associated with resistance to additional drugs, and for molecular epidemiology with spoligotyping and selective MIRU-VNTR. Of 130 sputum samples from Gabon tested with Xpert, 124 yielded interpretable results, of which 21 were determined to be RIF-R (17%). Amplification and sequencing or line probe assay of the Xpert remnants confirmed 18/21 as MDR: 11/116 (9.5%) new and 7/8 (87%) previously treated TB patients. Spoligotyping and MIRU with hypervariable loci identified an MDR Beijing strain present in five samples. We conclude that the remnants of samples processed for Xpert in PCR reactions can be used to find mutations associated with the resistance to the additional drugs that define MDR and XDR-TB, and to study molecular epidemiology without the need for culturing or biosafe infrastructure.

Mots clés: multidrug resistance; drug sensitivity testing; drug resistance; Beijing family; sequencing; Libreville; Mycobacterium tuberculosis; Gabon; molecular epidemiology; MDR-TB; GeneXpert

Domaines: Bactériologie; Maladies infectieuses; Maladies émergentes; Santé publique et épidémiologie

Amel Kévin Alame-Emane, Catherine Pierre-Audigier, Oriane Cordelia Aboumegone-Biyogo, Amandine Nzoghe-Mveang, Véronique Cadet-Daniel, et al.. The use of GeneXpert remnants for drug resistance profiling and molecular epidemiology of tuberculosis in Libreville, Gabon. Journal of Clinical Microbiology, 2017, 55 (7), pp.2105-2115. ⟨10.1128/JCM.02257-16⟩. ⟨hal-02185221⟩