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Peer-reviewedCC BYInternational Journal of Infectious Diseases

Whole-genome sequencing of

  • Marianne Antar Soutou
  • Hiam Yaacoub1
  • Zeina Awad2
  • Laurice Tabet3
  • Sirine Abou Ismail3
  • Danielle Chaaya3
  • Camille Allam4
  • Clément Lecarpentier5
  • Kevin La6
  • Nicolas Godron6
  • Sukaina Basma1
  • Laurent Raskine7
4 more authors
  • Marianne Abifadel3
  • Josette Najjar-Pellet8
  • Emmanuelle Cambau4
  • Christophe Sola9
9 affiliations
  1. 1National TB Program, Ministry of Public Health, Beirut, Lebanon
  2. 2Service de Mycobactériologie Spécialisée et de Référence, Laboratoire Associé du Centre National de Référence des Mycobactéries et Résistance des Mycobactéries aux Antituberculeux, APHP GHU Nord Université Paris Cité, Paris, France
  3. 3Laboratoire Rodolphe Mérieux Liban, Faculté de Pharmacie, Université Saint-Joseph de Beyrouth, Beyrouth, Liban
  4. 4INSERM, IAME, UMR1137, Université Paris Cité-Université Sorbonne-Paris Nord, Paris, France; Service de Mycobactériologie Spécialisée et de Référence, Laboratoire Associé du Centre National de Référence des Mycobactéries et Résistance des Mycobactéries aux Antituberculeux, APHP GHU Nord Université Paris Cité, Paris, France
  5. 5Université Marie et Louis Pasteur, Besançon, France
  6. 6INSERM, IAME, UMR1137, Université Paris Cité-Université Sorbonne-Paris Nord, Paris, France
  7. 7Direction médicale et scientifique, Fondation Mérieux, Lyon, France
  8. 8Direction régionale MENA, Fondation Mérieux, Beyrouth, Liban
  9. 9INSERM, IAME, UMR1137, Université Paris Cité-Université Sorbonne-Paris Nord, Paris, France; Université Paris-Saclay, Gif-sur-Yvette, France; Corresponding author: Marianne Antar Soutou and Christophe Sola, INSERM, IAME, UMR1137, Université Paris Cité-Université Sorbonne-Paris Nord, 16 rue Henri Huchard, Paris, 75018, France.
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Abstract

Objectives: Lebanon is a low-burden tuberculosis (TB) country with a complex demographic context shaped by migration, socioeconomic instability, and recent healthcare disruptions. We aimed to characterize the population structure, drug resistance, and transmission dynamics of Mycobacterium tuberculosis using whole-genome sequencing (WGS). Methods: WGS was performed on 218 M. tuberculosis isolates collected in Lebanon between 2018 and 2024, of which 196 passed quality control. TB-Profiler identified lineages and resistance-associated mutations, with results compared against available phenotypic drug susceptibility testing (DST) and line-probe assays (LPA). TB-Annotator provided high-resolution sub-lineage classification, phylogenomic contextualization within a global MTB dataset, and identification of genomic clusters. Results: Lineage 4 predominated (71.4%), followed by Lineage 3 (15.3%), Lineage 2 (6.6%), and Lineage 1 (6.1%), with a single rare Lineage 7 isolate. Resistance-associated mutations were identified in 41.3% of isolates, including MDR-TB (7.1%) and pre-XDR-TB (2.6%). WGS-based resistance prediction showed high concordance (91.8-100%) with phenotypic DST and LPA. Fourteen genomic clusters included 29/195 isolates (14.9%); incorporation of publicly available Lebanese genomes identified additional Lineage 4-associated clusters, supporting ongoing local transmission. Conclusion: This nationwide WGS study revealed a highly diverse MTB population in Lebanon and supports the integration of WGS into routine TB surveillance and control activities.

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Cite

BibTeXRIS
BibTeX
@article{soutou2026wholegenome,
  title = {{Whole-genome sequencing of}},
  author = {Marianne Antar Soutou and Hiam Yaacoub and Zeina Awad and Laurice Tabet and Sirine Abou Ismail and Danielle Chaaya and Camille Allam and Clément Lecarpentier and Kevin La and Nicolas Godron and Sukaina Basma and Laurent Raskine and Marianne Abifadel and Josette Najjar-Pellet and Emmanuelle Cambau and Christophe Sola},
  journal = {International Journal of Infectious Diseases},
  year = {2026},
  month = oct,
  doi = {10.1016/j.ijid.2026.109155},
  url = {https://doi.org/10.1016/j.ijid.2026.109155},
  note = {CC BY},
}
RIS
TY  - JOUR
TI  - Whole-genome sequencing of
AU  - Marianne Antar Soutou
AU  - Hiam Yaacoub
AU  - Zeina Awad
AU  - Laurice Tabet
AU  - Sirine Abou Ismail
AU  - Danielle Chaaya
AU  - Camille Allam
AU  - Clément Lecarpentier
AU  - Kevin La
AU  - Nicolas Godron
AU  - Sukaina Basma
AU  - Laurent Raskine
AU  - Marianne Abifadel
AU  - Josette Najjar-Pellet
AU  - Emmanuelle Cambau
AU  - Christophe Sola
PY  - 2026
DA  - 2026/10/30
JO  - International Journal of Infectious Diseases
DO  - 10.1016/j.ijid.2026.109155
UR  - https://doi.org/10.1016/j.ijid.2026.109155
AB  - Objectives: Lebanon is a low-burden tuberculosis (TB) country with a complex demographic context shaped by migration, socioeconomic instability, and recent healthcare disruptions. We aimed to characterize the population structure, drug resistance, and transmission dynamics of Mycobacterium tuberculosis using whole-genome sequencing (WGS). Methods: WGS was performed on 218 M. tuberculosis isolates collected in Lebanon between 2018 and 2024, of which 196 passed quality control. TB-Profiler identified lineages and resistance-associated mutations, with results compared against available phenotypic drug susceptibility testing (DST) and line-probe assays (LPA). TB-Annotator provided high-resolution sub-lineage classification, phylogenomic contextualization within a global MTB dataset, and identification of genomic clusters. Results: Lineage 4 predominated (71.4%), followed by Lineage 3 (15.3%), Lineage 2 (6.6%), and Lineage 1 (6.1%), with a single rare Lineage 7 isolate. Resistance-associated mutations were identified in 41.3% of isolates, including MDR-TB (7.1%) and pre-XDR-TB (2.6%). WGS-based resistance prediction showed high concordance (91.8-100%) with phenotypic DST and LPA. Fourteen genomic clusters included 29/195 isolates (14.9%); incorporation of publicly available Lebanese genomes identified additional Lineage 4-associated clusters, supporting ongoing local transmission. Conclusion: This nationwide WGS study revealed a highly diverse MTB population in Lebanon and supports the integration of WGS into routine TB surveillance and control activities.
SN  - 1201-9712
SN  - 1878-3511
ER  -