Whole-genome sequencing-based genetic diversity, transmission dynamics, and drug-resistant mutations in Mycobacterium tuberculosis isolated from extrapulmonary tuberculosis patients in western Ethiopia

Front Public Health. 2024 Aug 9:12:1399731. doi: 10.3389/fpubh.2024.1399731. eCollection 2024.

Abstract

Background: Extrapulmonary tuberculosis (EPTB) refers to a form of Tuberculosis (TB) where the infection occurs outside the lungs. Despite EPTB being a devastating disease of public health concern, it is frequently overlooked as a public health problem. This study aimed to investigate genetic diversity, identify drug-resistance mutations, and trace ongoing transmission chains.

Methods: A cross-sectional study was undertaken on individuals with EPTB in western Ethiopia. In this study, whole-genome sequencing (WGS) was employed to analyze Mycobacterium tuberculosis (MTB) samples obtained from EPTB patients. Out of the 96 genomes initially sequenced, 89 met the required quality standards for genetic diversity, and drug-resistant mutations analysis. The data were processed using robust bioinformatics tools.

Results: Our analysis reveals that the majority (87.64%) of the isolates can be attributed to Lineage-4 (L4), with L4.6.3 and L4.2.2.2 emerging as the predominant sub-lineages, constituting 34.62% and 26.92%, respectively. The overall clustering rate and recent transmission index (RTI) were 30 and 17.24%, respectively. Notably, 7.87% of the isolates demonstrated resistance to at least one anti-TB drug, although multi-drug resistance (MDR) was observed in only 1.12% of the isolates.

Conclusions: The genetic diversity of MTBC strains in western Ethiopia was found to have low inter-lineage diversity, with L4 predominating and exhibiting high intra-lineage diversity. The notably high clustering rate in the region implies a pressing need for enhanced TB infection control measures to effectively disrupt the transmission chain. It's noteworthy that 68.75% of resistance-conferring mutations went undetected by both GeneXpert MTB/RIF and the line probe assay (LPA) in western Ethiopia. The identification of resistance mutations undetected by both GeneXpert and LPA, along with the detection of mixed infections through WGS, emphasizes the value of adopting WGS as a high-resolution approach for TB diagnosis and molecular epidemiological surveillance.

Keywords: Extrapulmonary tuberculosis; Mycobacterium tuberculosis; drug resistance-conferring mutations; genetic diversity; transmission dynamics; whole-genome sequencing.

MeSH terms

  • Adolescent
  • Adult
  • Antitubercular Agents / pharmacology
  • Cross-Sectional Studies
  • Drug Resistance, Bacterial / genetics
  • Ethiopia / epidemiology
  • Female
  • Genetic Variation*
  • Humans
  • Male
  • Middle Aged
  • Mutation*
  • Mycobacterium tuberculosis* / drug effects
  • Mycobacterium tuberculosis* / genetics
  • Mycobacterium tuberculosis* / isolation & purification
  • Tuberculosis / microbiology
  • Tuberculosis / transmission
  • Tuberculosis, Extrapulmonary
  • Tuberculosis, Multidrug-Resistant / microbiology
  • Tuberculosis, Multidrug-Resistant / transmission
  • Whole Genome Sequencing*
  • Young Adult

Substances

  • Antitubercular Agents

Grants and funding

The author(s) declare that financial support was received for the research, authorship, and/or publication of this article. The study received financial support from the Office of Vice President for Research and Technology Transfer, Addis Ababa University (Ref No. RD/PY 6223/2018). Additionally, the research project received support in kind, including reagents and research supplies, from the J. Craig Venter Institute in the United States. The funding agency played a role in providing financial support for materials and personnel but did not have a direct influence on the project’s methods or outcomes beyond funding. The funders were not directly involved in the study design, data collection and analysis, the decision to publish, or the preparation of the manuscript.