Whole genome sequencing of clinical samples reveals extensively drug resistant tuberculosis (XDR TB) strains from the Beijing lineage in Nigeria, West Africa

Sci Rep. 2021 Aug 30;11(1):17387. doi: 10.1038/s41598-021-96956-7.

Abstract

Multi-drug (MDR) and extensively drug-resistant (XDR) tuberculosis (TB) continues to be a global public health problem especially in high TB burden countries like Nigeria. Many of these cases are undetected and go on to infect high risk individuals. Clinical samples from positive rifampicin resistant Xpert®MTB/Rif assay were subjected to direct whole genome sequencing and bioinformatics analysis to identify the full antibiotics resistance and lineage profile. We report two (2) XDR TB samples also belonging to the East-Asian/Beijing family of lineage 2 Mycobacterium tuberculosis complex from clinical samples in Nigeria. Our findings further reveal the presence of mutations that confer resistance to first-line drugs (rifampicin, isoniazid, ethambutol and pyrazanimide), second-line injectables (capreomycin, streptomycin, kanamycin and/or amikacin) and at least one of the fluoroquinolones (ofloxacin, moxifloxacin, levofloxacin and/or ciprofloxacin) in both samples. The genomic sequence data from this study not only provide the first evidence of XDR TB in Nigeria and West Africa, but also emphasize the importance of WGS in accurately detecting MDR and XDR TB, to ensure adequate and proper management treatment regimens for affected individuals. This will greatly aid in preventing the spread of drug resistance TB in high burden countries.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Antitubercular Agents / pharmacology
  • Antitubercular Agents / therapeutic use
  • Capreomycin / pharmacology
  • Capreomycin / therapeutic use
  • DNA, Bacterial / chemistry
  • DNA, Bacterial / metabolism
  • Extensively Drug-Resistant Tuberculosis / complications
  • Extensively Drug-Resistant Tuberculosis / diagnosis*
  • Extensively Drug-Resistant Tuberculosis / drug therapy
  • Extensively Drug-Resistant Tuberculosis / microbiology
  • Female
  • Fluoroquinolones / pharmacology
  • Fluoroquinolones / therapeutic use
  • HIV Infections / complications
  • HIV Infections / diagnosis
  • Humans
  • Male
  • Microbial Sensitivity Tests
  • Middle Aged
  • Mycobacterium tuberculosis / classification
  • Mycobacterium tuberculosis / drug effects
  • Mycobacterium tuberculosis / genetics*
  • Mycobacterium tuberculosis / isolation & purification
  • Nigeria
  • Phylogeny
  • Rifampin / pharmacology
  • Rifampin / therapeutic use
  • Whole Genome Sequencing
  • Young Adult

Substances

  • Antitubercular Agents
  • DNA, Bacterial
  • Fluoroquinolones
  • Capreomycin
  • Rifampin