Emergence of multi-drug-resistant Mycobacterium tuberculosis in Niger: A snapshot based on whole-genome sequencing

PLoS Negl Trop Dis. 2022 May 25;16(5):e0010443. doi: 10.1371/journal.pntd.0010443. eCollection 2022 May.

Abstract

Background: Among other West African countries experiencing the high endemicity of deadly tuberculosis, the situation in Niger is poorly evidenced by microbiological investigations.

Methodology/principal findings: The study of 42 isolates of Mycobacterium tuberculosis from Niger by whole genome sequencing using Illumina iSeq technology yielded four M. tuberculosis lineages: Indo-Oceanic L1 (n = 1) (2.3%), East-Asian (n = 1) (2.3%), East-African Indian L3 (n = 2) (4.7%) and Euro-American L4 (n = 38) (90.4%). The sub-lineage L4.1.3 comprising 18 isolates (47.3%) was predominant, followed by the L4.6.2.2 sub-lineage (Cameroon genotype, n = 13 isolates) (34.2%). Investigating drug resistance profile for 12 antibiotics found 8/42 (19%) pan-susceptible isolates and 34/42 (81%) resistant isolates; with 40/42 (95.2%) isolates being susceptible to clofazimine-bedaquiline.

Conclusions/significance: These unprecedented data from Niger highlight the dynamics of tuberculosis transmission and drug resistance in Niger and may assist tuberculosis control in this country which continues to support a high burden of tuberculosis.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Antitubercular Agents / pharmacology
  • Antitubercular Agents / therapeutic use
  • Asteraceae*
  • Genotype
  • Humans
  • Mycobacterium tuberculosis* / genetics
  • Niger / epidemiology
  • Phylogeny
  • Tuberculosis, Lymph Node*
  • Tuberculosis, Multidrug-Resistant* / epidemiology
  • Whole Genome Sequencing

Substances

  • Antitubercular Agents

Grants and funding

This work was supported by Agence Nationale de la Recherche (ANR-17-CE35-0006-01 PRIME, http://www.agencenationale-recherche.fr/) and by the French Government under the «Investissements d’Avenir » (Investments for the Future) program managed by the ANR (reference: Méditerranée Infection 10-IAHU-03). This work was also supported by Region Provence Alpes Côte d’Azur and European funding FEDER IHUBIOTK by funding to ZHH. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.