Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis.

Methods and any associated references are available in the online\ud
version of the paper.\ud
Accession codes. All sequences have been rendered publically available\ud
through NCBI. The Haarlem, C, 98_r168 and w-148 genome\ud
assemblies are available under GenBank accessions AASN00000000,\ud
AAKR00000000, ABVM00000000 and ACSX00000000, respectively.\ud
Raw sequences for the 35 isolates from Vancouver are available\ud
at the NCBI Sequence Read Archive (SRA) under accession\ud
SRA020129. KZN-DS (KZN-4207), KZN_MDR (KZN-1435) and\ud
KZN_XDR (KZN-605) raw sequence reads are available under accession\ud
SRA009637. Raw sequence data for the isolates corresponding to\ud
our study identification numbers 51–73 are available under accession\ud
SRA009341. Read sequences for the rest of our isolates are available\ud
under accession SRA009458 with the project name XDR comparative.\ud
Publicly available partial or complete genome sequences for MTB210,\ud
H37Ra, HN878, R1207 and X122 were accessed from GenBank\ud
accessions ADAB00000000, AAYK01000000, ADNF01000000,\ud
ADNH01000000 and ADNG01000000, respectively.\ud
Note: Any Supplementary Information and Source Data files are available in the\ud
online version of the paper.M. tuberculosis is evolving antibiotic resistance, threatening attempts at tuberculosis epidemic control. Mechanisms of resistance, including genetic changes favored by selection in resistant isolates, are incompletely understood. Using 116 newly sequenced and 7 previously sequenced M. tuberculosis whole genomes, we identified genome-wide signatures of positive selection specific to the 47 drug-resistant strains. By searching for convergent evolution--the independent fixation of mutations in the same nucleotide position or gene--we recovered 100% of a set of known resistance markers. We also found evidence of positive selection in an additional 39 genomic regions in resistant isolates. These regions encode components in cell wall biosynthesis, transcriptional regulation and DNA repair pathways. Mutations in these regions could directly confer resistance or compensate for fitness costs associated with resistance. Functional genetic analysis of mutations in one gene, ponA1, demonstrated an in vitro growth advantage in the presence of the drug rifampicin.We thank the technical staff of the British Columbia Centre for Disease Control Public Health Microbiology and Reference Mycobacteriology Laboratory in Vancouver, M. Bosman from the National Health Laboratory Service in Cape Town and L. Fattorini from the Istituto Superiore di Sanita in Rome. This work was funded by a Senior Ellison Foundation Award (M.M.) and in part by a contact from the National Institute of Allergy and Infectious Diseases (HHSN266200400001C to B.B.), the Department of Pulmonary and Critical Care at Massachusetts General Hospital (M.R.F.), a postdoctoral fellowship from the Harvard MIDAS Center for Communicable Disease Dynamics (B.J.S.) and a Packard Foundation Fellowship (P.C.S.). S.G. was supported by the Swiss National Science Foundation (PP0033_119205).Peer-reviewedPost-prin