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Peer-reviewedCC BY 4.0Frontiers in Microbiology

Whole-genome sequencing analysis of phylogenetic relationships and lineage diversity of Mycobacterium tuberculosis in Western Kenya

  • Susan Musau1,2
  • Eleanor I. Lamont3
  • Victor Moses Musyoki1,2
  • Susan Odera1
  • Noel Onyango1,4
  • Steve Wandiga5
  • Inosters Wambua Nzuki6
  • Bob Morrison3
  • Reymond Mumo7
  • David Sherman3
  • Marianne W. Mureithi1,4
  • Videlis Nduba2,8
8 affiliations
  1. 1Department of Medical Microbiology and Immunology, University of Nairobi
  2. 2Tuberculosis and Human Immunodeficiency Virus (HIV) Co-infection Training Program
  3. 3Department of Microbiology, University of Washington
  4. 4KAVI-Institute of Clinical Research, University of Nairobi
  5. 5Kenya Medical Research Institute, Centre for Global Health Research
  6. 6Center for Biotechnology and Bioinformatics, University of Nairobi
  7. 7Institute of Human Virology (IHV), University of Maryland School of Medicine
  8. 8Kenya Medical Research Institute, Centre for Respiratory Diseases Research
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Abstract

Background: Western Kenya remains a high-burden tuberculosis (TB) region, yet genomic data describing the diversity and phylogenetic relationships of Mycobacterium tuberculosis complex (MTBC) strains are limited. Understanding sub-lineage patterns and the phylogenetic relationships is essential for effective TB surveillance and control strategies.

Methods: This was a cross-sectional whole genome sequencing (WGS) study using archived MTBC isolates from 12 counties in Western Kenya. Genomic DNA was extracted using a modified CTAB protocol and sequenced using the Element AVITI platform. Reads were processed using DuffyNGS/DuffyTools pipeline and aligned to the H37Rv reference genome. Lineages were assigned using TBProfiler v4.3.0 based on single nucleotide polymorphisms (SNP). Phylogenetic relationships were reconstructed using Nextstrain and interpreted using tree topology.

Results: Of 316 MTBC isolates processed, 290 met quality criteria for WGS. Lineage 4 (L4) (42%) and Lineage 3 (L3) (38%) predominated, with significant county-level heterogeneity observed in Kisii and Homa Bay (L4), and Siaya and Migori (L3) ( p < 0.0296). Sub-lineage analysis revealed widespread circulation of L2.2.1 and L3.1.1 strains, alongside substantial L4 diversity. Rare sub-lineages showed limited geographic distribution and one Mycobacterium bovis isolate was identified. Phylogenetic analysis revealed geographically structured relatedness, with a localized circulation in Kisii, broader regional distribution in Homa Bay, and additional clades showing intermediate regional patterns.

Conclusion: Western Kenya harbors genetically diverse and spatially MTBC population with distinct patterns of phylogenetic relatedness. These findings demonstrate the value of WGS for characterizing population structure and informing targeted TB control in high-burden settings.

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Cite

BibTeXRIS
BibTeX
@article{musau2026wholegenome,
  title = {{Whole-genome sequencing analysis of phylogenetic relationships and lineage diversity of Mycobacterium tuberculosis in Western Kenya}},
  author = {Susan Musau and Eleanor I. Lamont and Victor Moses Musyoki and Susan Odera and Noel Onyango and Steve Wandiga and Inosters Wambua Nzuki and Bob Morrison and Reymond Mumo and David Sherman and Marianne W. Mureithi and Videlis Nduba},
  journal = {Frontiers in Microbiology},
  year = {2026},
  month = oct,
  doi = {10.3389/fmicb.2026.1980516},
  url = {https://www.frontiersin.org/articles/10.3389/fmicb.2026.1980516/full},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - Whole-genome sequencing analysis of phylogenetic relationships and lineage diversity of Mycobacterium tuberculosis in Western Kenya
AU  - Susan Musau
AU  - Eleanor I. Lamont
AU  - Victor Moses Musyoki
AU  - Susan Odera
AU  - Noel Onyango
AU  - Steve Wandiga
AU  - Inosters Wambua Nzuki
AU  - Bob Morrison
AU  - Reymond Mumo
AU  - David Sherman
AU  - Marianne W. Mureithi
AU  - Videlis Nduba
PY  - 2026
DA  - 2026/10/09
JO  - Frontiers in Microbiology
DO  - 10.3389/fmicb.2026.1980516
UR  - https://www.frontiersin.org/articles/10.3389/fmicb.2026.1980516/full
AB  - Background: Western Kenya remains a high-burden tuberculosis (TB) region, yet genomic data describing the diversity and phylogenetic relationships of Mycobacterium tuberculosis complex (MTBC) strains are limited. Understanding sub-lineage patterns and the phylogenetic relationships is essential for effective TB surveillance and control strategies.  Methods: This was a cross-sectional whole genome sequencing (WGS) study using archived MTBC isolates from 12 counties in Western Kenya. Genomic DNA was extracted using a modified CTAB protocol and sequenced using the Element AVITI platform. Reads were processed using DuffyNGS/DuffyTools pipeline and aligned to the H37Rv reference genome. Lineages were assigned using TBProfiler v4.3.0 based on single nucleotide polymorphisms (SNP). Phylogenetic relationships were reconstructed using Nextstrain and interpreted using tree topology.  Results: Of 316 MTBC isolates processed, 290 met quality criteria for WGS. Lineage 4 (L4) (42%) and Lineage 3 (L3) (38%) predominated, with significant county-level heterogeneity observed in Kisii and Homa Bay (L4), and Siaya and Migori (L3) ( p < 0.0296). Sub-lineage analysis revealed widespread circulation of L2.2.1 and L3.1.1 strains, alongside substantial L4 diversity. Rare sub-lineages showed limited geographic distribution and one Mycobacterium bovis isolate was identified. Phylogenetic analysis revealed geographically structured relatedness, with a localized circulation in Kisii, broader regional distribution in Homa Bay, and additional clades showing intermediate regional patterns.  Conclusion: Western Kenya harbors genetically diverse and spatially MTBC population with distinct patterns of phylogenetic relatedness. These findings demonstrate the value of WGS for characterizing population structure and informing targeted TB control in high-burden settings.
SN  - 1664-302X
ER  -