title: Genomic and functional analyses of Mycobacterium tuberculosis strains implicate ald in D-cycloserine resistance.
abstract: 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.
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
authors.forename: Christopher A
authors.initials: CA
authors.lastname: Desjardins
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.|Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.|KwaZulu-Natal Research Institute for TB and HIV (K-RITH), Durban, South Africa.
authors.forename: Keira A
authors.initials: KA
authors.lastname: Cohen
authors.affiliation: KwaZulu-Natal Research Institute for TB and HIV (K-RITH), Durban, South Africa.
authors.forename: Vanisha
authors.initials: V
authors.lastname: Munsamy
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.|Delft Bioinformatics Laboratory, Delft University of Technology, Delft, the Netherlands.
authors.forename: Thomas
authors.identifier: 0000-0002-7205-7431
authors.initials: T
authors.lastname: Abeel
authors.affiliation: KwaZulu-Natal Research Institute for TB and HIV (K-RITH), Durban, South Africa.
authors.forename: Kashmeel
authors.initials: K
authors.lastname: Maharaj
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
authors.forename: Bruce J
authors.initials: BJ
authors.lastname: Walker
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
authors.forename: Terrance P
authors.initials: TP
authors.lastname: Shea
authors.affiliation: KwaZulu-Natal Research Institute for TB and HIV (K-RITH), Durban, South Africa.|Center for Tuberculosis Research, Johns Hopkins School of Medicine, Baltimore, Maryland, USA.
authors.forename: Deepak V
authors.initials: DV
authors.lastname: Almeida
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
authors.forename: Abigail L
authors.initials: AL
authors.lastname: Manson
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.|Delft Bioinformatics Laboratory, Delft University of Technology, Delft, the Netherlands.
authors.forename: Alex
authors.initials: A
authors.lastname: Salazar
authors.affiliation: Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa.
authors.forename: Nesri
authors.initials: N
authors.lastname: Padayatchi
authors.affiliation: Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa.|Division of Pulmonary, Allergy, and Critical Care Medicine, Columbia University College of Physicians and Surgeons, New York, New York, USA.|Department of Epidemiology, Columbia Mailman School of Public Health, New York, New York, USA.
authors.forename: Max R
authors.initials: MR
authors.lastname: O'Donnell
authors.affiliation: School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.|National Health Laboratory Service, Durban, South Africa.
authors.forename: Koleka P
authors.initials: KP
authors.lastname: Mlisana
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
authors.forename: Jennifer
authors.initials: J
authors.lastname: Wortman
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
authors.forename: Bruce W
authors.initials: BW
authors.lastname: Birren
authors.affiliation: KwaZulu-Natal Research Institute for TB and HIV (K-RITH), Durban, South Africa.|Center for Tuberculosis Research, Johns Hopkins School of Medicine, Baltimore, Maryland, USA.
authors.forename: Jacques
authors.initials: J
authors.lastname: Grosset
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
authors.forename: Ashlee M
authors.initials: AM
authors.lastname: Earl
authors.affiliation: KwaZulu-Natal Research Institute for TB and HIV (K-RITH), Durban, South Africa.
authors.forename: Alexander S
authors.initials: AS
authors.lastname: Pym
mesh_terms: D050788:Alanine Dehydrogenase / Q000235:genetics / Q000378:metabolism; D000411:Alanine Racemase / Q000235:genetics; D000904:Antibiotics, Antitubercular / Q000494:pharmacology*; D000995:Antitubercular Agents; D003523:Cycloserine / Q000494:pharmacology*; D024881:Drug Resistance, Bacterial / Q000235:genetics; D055786:Gene Knockout Techniques; D016680:Genome, Bacterial; D008826:Microbial Sensitivity Tests; D009154:Mutation; D009169:Mycobacterium tuberculosis / Q000187:drug effects* / Q000201:enzymology / Q000235:genetics*
chemical_list: D000904:Antibiotics, Antitubercular; D000995:Antitubercular Agents; D003523:Cycloserine; D050788:Alanine Dehydrogenase; D000411:Alanine Racemase