Pharmacogenetics of Between-Individual Variability in Plasma Clearance of Bedaquiline and Clofazimine in South Africa

David W. Haas, Mahmoud Tareq Abdelwahab, Stijn W. van Beek, Paxton Baker, Gary Maartens, Yuki Bradford, Marylyn D. Ritchie, Sean Wasserman, Graeme Meintjes, Karen Beeri, Neel R. Gandhi, Elin M. Svensson, Paolo Denti, James C.M. Brust

Research output: Contribution to journalArticlepeer-review

10 Scopus citations


Background. Plasma bedaquiline clearance is reportedly more rapid with African ancestry. Our objective was to determine whether genetic polymorphisms explained between-individual variability in plasma clearance of bedaquiline, its M2 metabolite, and clofazimine in a cohort of patients treated for drug-resistant tuberculosis in South Africa. Methods. Plasma clearance was estimated with nonlinear mixed-effects modeling. Associations between pharmacogenetic polymorphisms, genome-wide polymorphisms, and variability in clearance were examined using linear regression models. Results. Of 195 cohort participants, 140 were evaluable for genetic associations. Among 21 polymorphisms selected based on prior genome-wide significant associations with any drug, rs776746 (CYP3A5∗3) was associated with slower clearance of bedaquiline (P = .0017) but not M2 (P = .25). CYP3A5∗3 heterozygosity and homozygosity were associated with 15% and 30% slower bedaquiline clearance, respectively. The lowest P value for clofazimine clearance was with VKORC1 rs9923231 (P = .13). In genome-wide analyses, the lowest P values for clearance of bedaquiline and clofazimine were with RFX4 rs76345012 (P = 6.4 × 10−7) and CNTN5 rs75285763 (P = 2.9 × 10−8), respectively. Conclusions. Among South Africans treated for drug-resistant tuberculosis, CYP3A5∗3 was associated with slower bedaquiline clearance. Different CYP3A5∗3 frequencies among populations may help explain the more rapid bedaquiline clearance reported in Africans. Associations with RFX4 and CNTN5 are likely by chance alone.

Original languageEnglish (US)
Pages (from-to)147-156
Number of pages10
JournalJournal of Infectious Diseases
Issue number1
StatePublished - Jul 1 2022


  • bedaquiline
  • clofazimine
  • pharmacogenomics
  • pharmacokinetics
  • tuberculosis

ASJC Scopus subject areas

  • General Medicine


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