Genomic and functional analyses of Mycobacterium tuberculosis strains implicate ald in D-cycloserine resistance

Christopher A. Desjardins, Keira A Cohen, Vanisha Munsamy, Thomas Abeel, Kashmeel Maharaj, Bruce J. Walker, Terrance P. Shea, Deepak V. Almeida, Abigail L. Manson, Alex Salazar, More Authors

Research output: Contribution to journalArticleScientificpeer-review

89 Citations (Scopus)


A more complete understanding of the genetic basis of drug resistance in Mycobacterium tuberculosis is critical for prompt diagnosis and optimal treatment, particularly for toxic second-line drugs such as D-cycloserine. Here we used the whole-genome sequences from 498 strains of M. tuberculosis to identify new resistance-conferring genotypes. By combining association and correlated evolution tests with strategies for amplifying signal from rare variants, we found that loss-of-function mutations in ald (Rv2780), encoding L-alanine dehydrogenase, were associated with unexplained drug resistance. Convergent evolution of this loss of function was observed exclusively among multidrug-resistant strains. Drug susceptibility testing established that ald loss of function conferred resistance to D-cycloserine, and susceptibility to the drug was partially restored by complementation of ald. Clinical strains with mutations in ald and alr exhibited increased resistance to D-cycloserine when cultured in vitro. Incorporation of D-cycloserine resistance in novel molecular diagnostics could allow for targeted use of this toxic drug among patients with susceptible infections.
Original languageEnglish
Pages (from-to)544-551
Number of pages8
JournalNature Genetics
Issue number5
Publication statusPublished - 2016


  • Bacterial transformation
  • Bacteriology
  • Genome informatics
  • Tuberculosis


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