Correction: Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis (Nature Genetics DOI: 10.1038/s41588-017-0029-0);Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis

Nature Genetics

Volumn 50, Issue 2, 2018, Pages 307-316

  Coll, Francesc ^a   Phelan, Jody ^a   Hill Cawthorne, Grant A ^b,c   Nair, Mridul B ^b   Mallard, Kim ^a   Ali, Shahjahan ^b   Abdallah, Abdallah M ^b   Alghamdi, Saad ^d   Alsomali, Mona ^b   Ahmed, Abdallah O ^d   Portelli, Stephanie ^a,e   Oppong, Yaa ^a   Alves, Adriana ^f   Bessa, Theolis Barbosa ^g   Campino, Susana ^a   Caws, Maxine ^h,i   Chatterjee, Anirvan ^j   Crampin, Amelia C ^a,k   Dheda, Keertan ^l   Furnham, Nicholas ^a   Glynn, Judith R ^a,k   Grandjean, Louis ^m   Minh Ha, Dang ⁱ   Hasan, Rumina ⁿ   Hasan, Zahra ⁿ   Hibberd, Martin L ^a   Joloba, Moses ^o   Jones López, Edward C ^p   Matsumoto, Tomoshige ^q   Miranda, Anabela ^f   Moore, David J ^a,m   Mocillo, Nora ^r   Panaiotov, Stefan ^s   Parkhill, Julian ^t   Penha, Carlos ^u   Perdigão, João ^v   Portugal, Isabel ^v   Rchiad, Zineb ^b   Robledo, Jaime ^w   Sheen, Patricia ^l   Shesha, Nashwa Talaat ^x   Sirgel, Frik A ^y   Sola, Christophe ^z   Oliveira Sousa, Erivelton ^g,aa   Streicher, Elizabeth M ^y   Helden, Paul Van ^y   Viveiros, Miguel ^ab   Warren, Robert M ^y   McNerney, Ruth ^a,l   Pain, Arnab ^b,ac   Clark, Taane G ^a   more..

^a LONDON SCHOOL OF HYGIENE AND TROPICAL MEDICINE   (United Kingdom)

^b KING ABDULLAH UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Saudi Arabia)

^c UNIVERSITY OF SYDNEY   (Australia)

^d UMM AL QURA UNIVERSITY   (Saudi Arabia)

^e UNIVERSITY OF MELBOURNE   (Australia)

^f National Mycobacterium Reference Laboratory   (Portugal)

^g INSTITUTO OSWALDO CRUZ   (Brazil)

^h LIVERPOOL SCHOOL OF TROPICAL MEDICINE   (United Kingdom)

ⁱ Pham Ngoc Thach Hospital for Tuberculosis and Lung Disease   (Viet Nam)

^j FOUNDATION FOR MEDICAL RESEARCH   (India)

^k KARONGA PREVENTION STUDY   (Malawi)

^l UNIVERSITY OF CAPE TOWN   (South Africa)

^m UNIVERSIDAD PERUANA CAYETANO HEREDIA   (Peru)

ⁿ AGA KHAN UNIVERSITY   (Pakistan)

^o MAKERERE UNIVERSITY COLLEGE OF HEALTH SCIENCES   (Uganda)

^p BOSTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^q Osaka Hospital   (Japan)

^r Reference Laboratory of Tuberculosis Control   (Argentina)

^s NATIONAL CENTER OF INFECTIOUS AND PARASITIC DISEASES   (Bulgaria)

^t WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^u INSTITUTO GULBENKIAN DE CIÊNCIA   (Portugal)

^v RESEARCH INSTITUTE FOR MEDICINES IMED ULISBOA   (Portugal)

^w UNIVERSIDAD PONTIFICIA BOLIVARIANA   (Colombia)

^x Regional Laboratory Direc of Health Affairs   (Saudi Arabia)

^y UNIVERSITY OF STELLENBOSCH   (South Africa)

^z UNIVERSITÉ PARIS SACLAY   (France)

^aa Laboratorio Central de Saúde Pública Prof Gonçalo Moniz   (Brazil)

^ab INSTITUTO DE HIGIENE E MEDICINA TROPICAL   (Portugal)

^ac HOKKAIDO UNIVERSITY   (Japan)

more..

Author keywords

[No Author keywords available]

Indexed keywords

AMIKACIN; AMINOSALICYLIC ACID; CAPREOMYCIN; CIPROFLOXACIN; CYCLOSERINE; ETHAMBUTOL; ETHIONAMIDE; ISONIAZID; KANAMYCIN; MOXIFLOXACIN; OFLOXACIN; PYRAZINAMIDE; RIFAMPICIN; STREPTOMYCIN; BACTERIAL DNA; TUBERCULOSTATIC AGENT;

ARTICLE; BACTERIUM ISOLATE; BIOSYNTHESIS; EXTENSIVELY DRUG RESISTANT TUBERCULOSIS; FOLLOW UP; GENE MUTATION; GENETIC ASSOCIATION; GENETIC IDENTIFICATION; GENETIC VARIABILITY; GENOME-WIDE ASSOCIATION STUDY; HUMAN; INDEL MUTATION; MINIMUM INHIBITORY CONCENTRATION; MULTIDRUG RESISTANT TUBERCULOSIS; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; PHYLOGENETIC TREE; PHYLOGENY; PRIORITY JOURNAL; PROMOTER REGION; SECONDARY METABOLISM; BACTERIAL GENOME; CLASSIFICATION; DNA SEQUENCE; GENETIC VARIATION; GENETICS; GEOGRAPHY; ISOLATION AND PURIFICATION; MICROBIAL SENSITIVITY TEST; MICROBIOLOGY; MULTIDRUG RESISTANCE; MUTATION;

ANTITUBERCULAR AGENTS; DNA, BACTERIAL; DRUG RESISTANCE, MULTIPLE, BACTERIAL; EXTENSIVELY DRUG-RESISTANT TUBERCULOSIS; GENETIC VARIATION; GENOME, BACTERIAL; GENOME-WIDE ASSOCIATION STUDY; GEOGRAPHY; HUMANS; MICROBIAL SENSITIVITY TESTS; MUTATION; MYCOBACTERIUM TUBERCULOSIS; PHYLOGENY; SEQUENCE ANALYSIS, DNA; TUBERCULOSIS, MULTIDRUG-RESISTANT;

EID: 85040763196     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/s41588-018-0074-3     Document Type: Erratum

References (71)

1. Dheda, K. et al. Global control of tuberculosis: from extensively drugresistant to untreatable tuberculosis. Lancet Respir. Med. 2, 321-338 (2014).
2. Bastos, M. L. et al. Treatment outcomes of patients with multidrug-resistant and extensively drug-resistant tuberculosis according to drug susceptibility testing to first-and second-line drugs: an individual patient data metaanalysis. Clin. Infect. Dis. 59, 1364-1374 (2014).
3. Shean, K. et al. Drug-associated adverse events and their relationship with outcomes in patients receiving treatment for extensively drug-resistant tuberculosis in South Africa. PLoS One 8, e63057 (2013).
4. Clark, T. G. et al. Elucidating emergence and transmission of multidrugresistant tuberculosis in treatment experienced patients by whole genome sequencing. PLoS One 8, e83012 (2013).
5. Coll, F. et al. A robust SNP barcode for typing Mycobacterium tuberculosis complex strains. Nat. Commun. 5, 4812 (2014).
6. Black, P. A. et al. Energy metabolism and drug efflux in Mycobacterium tuberculosis. Antimicrob. Agents Chemother. 58, 2491-2503 (2014).
7. de Vos, M. et al. Putative compensatory mutations in the rpoC gene of rifampin-resistant Mycobacterium tuberculosis are associated with ongoing transmission. Antimicrob. Agents Chemother. 57, 827-832 (2013).
8. Coll, F. et al. Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences. Genome Med. 7, 51 (2015).
9. Farhat, M. R. et al. Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis. Nat. Genet. 45, 1183-1189 (2013).
10. Zhang, H. et al. Genome sequencing of 161 Mycobacterium tuberculosis isolates from China identifies genes and intergenic regions associated with drug resistance. Nat. Genet. 45, 1255-1260 (2013).
11. Desjardins, C. A. et al. Genomic and functional analyses of Mycobacterium tuberculosis strains implicate ald in d-cycloserine resistance. Nat. Genet. 48, 544-551 (2016).
12. Earle, S. G. et al. Identifying lineage effects when controlling for population structure improves power in bacterial association studies. Nat. Microbiol. 1, 16041 (2016).
13. Chewapreecha, C. et al. Comprehensive identification of single nucleotide polymorphisms associated with β-lactam resistance within pneumococcal mosaic genes. PLoS Genet. 10, e1004547 (2014).
14. Manson, A. L. et al. Genomic analysis of globally diverse Mycobacterium tuberculosis strains provides insights into the emergence and spread of multidrug resistance. Nat. Genet. 49, 395-402 (2017).
15. Cohen, K. A. et al. Evolution of extensively drug-resistant tuberculosis over four decades: whole genome sequencing and dating analysis of Mycobacterium tuberculosis isolates from KwaZulu-Natal. PLoS Med. 12, e1001880 (2015).
16. Perdigão, J. et al. Unraveling Mycobacterium tuberculosis genomic diversity and evolution in Lisbon, Portugal, a highly drug resistant setting. BMC Genomics 15, 991 (2014).
17. Phelan, J. et al. The variability and reproducibility of whole genome sequencing technology for detecting resistance to anti-tuberculous drugs. Genome Med. 8, 132 (2016).
18. Meier, A., Sander, P., Schaper, K. J., Scholz, M. &Böttger, E. C. Correlation of molecular resistance mechanisms and phenotypic resistance levels in streptomycin-resistant Mycobacterium tuberculosis. Antimicrob. Agents Chemother. 40, 2452-2454 (1996).
19. Zhang, X. et al. Genetic determinants involved in p-aminosalicylic acid resistance in clinical isolates from tuberculosis patients in northern China from 2006 to 2012. Antimicrob. Agents Chemother. 59, 1320-1324 (2015).
20. Bisson, G. P. et al. Upregulation of the phthiocerol dimycocerosate biosynthetic pathway by rifampin-resistant, rpoB mutant Mycobacterium tuberculosis. J. Bacteriol. 194, 6441-6452 (2012).
21. Chatterjee, A., Saranath, D., Bhatter, P. &Mistry, N. Global transcriptional profiling of longitudinal clinical isolates of Mycobacterium tuberculosis exhibiting rapid accumulation of drug resistance. PLoS One 8, e54717 (2013).
22. Comas, I. et al. Whole-genome sequencing of rifampicin-resistant Mycobacterium tuberculosis strains identifies compensatory mutations in RNA polymerase genes. Nat. Genet. 44, 106-110 (2011).
23. Sherman, D. R. et al. Compensatory ahpC gene expression in isoniazidresistant Mycobacterium tuberculosis. Science 272, 1641-1643 (1996).
24. Safi, H. et al. Evolution of high-level ethambutol-resistant tuberculosis through interacting mutations in decaprenylphosphoryl-β-d-arabinose biosynthetic and utilization pathway genes. Nat. Genet. 45, 1190-1197 (2013).
25. Mori, G. et al. Thiophenecarboxamide derivatives activated by EthA kill Mycobacterium tuberculosis by inhibiting the CTP synthetase PyrG. Chem. Biol. 22, 917-927 (2015).
26. Merker, M. et al. Whole genome sequencing reveals complex evolution patterns of multidrug-resistant Mycobacterium tuberculosis Beijing strains in patients. PLoS One 8, e82551 (2013).
27. Casali, N. et al. Evolution and transmission of drug-resistant tuberculosis in a Russian population. Nat. Genet. 46, 279-286 (2014).
28. Zhang, Y., Heym, B., Allen, B., Young, D. &Cole, S. The catalase-peroxidase gene and isoniazid resistance of Mycobacterium tuberculosis. Nature 358, 591-593 (1992).
29. Larsen, M. H. et al. Overexpression of inhA, but not kasA, confers resistance to isoniazid and ethionamide in Mycobacterium smegmatis, M. bovis BCG and M. tuberculosis. Mol. Microbiol. 46, 453-466 (2002).
30. Banerjee, A. et al. inhA, a gene encoding a target for isoniazid and ethionamide in Mycobacterium tuberculosis. Science 263, 227-230 (1994).
31. DeBarber, A. E., Mdluli, K., Bosman, M., Bekker, L. G. &Barry, C. E. III Ethionamide activation and sensitivity in multidrug-resistant Mycobacterium tuberculosis. Proc. Natl. Acad. Sci. USA 97, 9677-9682 (2000).
32. Telenti, A. et al. The emb operon, a gene cluster of Mycobacterium tuberculosis involved in resistance to ethambutol. Nat. Med. 3, 567-570 (1997).
33. Scorpio, A. &Zhang, Y. Mutations in pncA, a gene encoding pyrazinamidase/ nicotinamidase, cause resistance to the antituberculous drug pyrazinamide in tubercle bacillus. Nat. Med. 2, 662-667 (1996).
34. Shi, W. et al. Pyrazinamide inhibits trans-translation in Mycobacterium tuberculosis. Science 333, 1630-1632 (2011).
35. Shi, W. et al. Aspartate decarboxylase (PanD) as a new target of pyrazinamide in Mycobacterium tuberculosis. Emerg. Microbes Infect. 3, e58 (2014).
36. Perdigão, J. et al. GidB mutation as a phylogenetic marker for Q1 cluster Mycobacterium tuberculosis isolates and intermediate-level streptomycin resistance determinant in Lisbon, Portugal. Clin. Microbiol. Infect. 20, O278-O284 (2014).
37. Takiff, H. E. et al. Cloning and nucleotide sequence of Mycobacterium tuberculosis gyrA and gyrB genes and detection of quinolone resistance mutations. Antimicrob. Agents Chemother. 38, 773-780 (1994).
38. Kocagöz, T. et al. Gyrase mutations in laboratory-selected, fluoroquinoloneresistant mutants of Mycobacterium tuberculosis H37Ra. Antimicrob. Agents Chemother. 40, 1768-1774 (1996).
39. Pasca, M. R. et al. Rv2686c-Rv2687c-Rv2688c, an ABC fluoroquinolone efflux pump in Mycobacterium tuberculosis. Antimicrob. Agents Chemother. 48, 3175-3178 (2004).
40. Zaunbrecher, M. A., Sikes, R. D. Jr., Metchock, B., Shinnick, T. M. &Posey, J. E. Overexpression of the chromosomally encoded aminoglycoside acetyltransferase eis confers kanamycin resistance in Mycobacterium tuberculosis. Proc. Natl. Acad. Sci. USA 106, 20004-20009 (2009).
41. Awasthy, D., Bharath, S., Subbulakshmi, V. &Sharma, U. Alanine racemase mutants of Mycobacterium tuberculosis require d-alanine for growth and are defective for survival in macrophages and mice. Microbiology 158, 319-327 (2012).
42. Köser, C. U. et al. Whole-genome sequencing for rapid susceptibility testing of M. tuberculosis. N. Engl. J. Med. 369, 290-292 (2013).
43. Schön, T. et al. Mycobacterium tuberculosis drug-resistance testing: challenges, recent developments and perspectives. Clin. Microbiol. Infect. 23, 154-160 (2017).
44. Smith, T., Wolff, K. A. &Nguyen, L. Molecular biology of drug resistance in Mycobacterium tuberculosis. Curr. Top. Microbiol. Immunol. 374, 53-80 (2013).
45. McNerney, R. et al. Removing the bottleneck in whole genome sequencing of Mycobacterium tuberculosis for rapid drug resistance analysis: a call to action. Int. J. Infect. Dis. 56, 130-135 (2017).
46. Li, H. Toward better understanding of artifacts in variant calling from high-coverage samples. Bioinformatics 30, 2843-2851 (2014).
47. Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079 (2009).
48. DePristo, M. A. et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 43, 491-498 (2011).
49. Phelan, J. et al. Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance. BMC Med. 14, 31 (2016).
50. Rausch, T. et al. DELLY: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics 28, i333-i339 (2012).
51. World Health Organization. Guidelines for Surveillance of Drug Resistance in Tuberculosis (World Health Organization, Geneva, 2009).
52. Kubica, G. &Kent, K. Public Health Mycobacteriology: A Guide for the Level III Laboratory (Centers for Disease Control, US Department of Health and Human Services, Atlanta, 1985).
53. Canetti, G. et al. Mycobacteria: laboratory methods for testing drug sensitivity and resistance. Bull. World Health Organ. 29, 565-578 (1963).
54. Minion, J., Leung, E., Menzies, D. &Pai, M. Microscopic-observation drug susceptibility and thin layer agar assays for the detection of drug resistant tuberculosis: a systematic review and meta-analysis. Lancet Infect. Dis. 10, 688-698 (2010).
55. Wayne, L. G. Simple pyrazinamidase and urease tests for routine identification of mycobacteria. Am. Rev. Respir. Dis. 109, 147-151 (1974).
56. Pfyffer, G.E., Palicova, F. &Rüsch-Gerdes, S. Testing of susceptibility of Mycobacterium tuberculosis to pyrazinamide with the nonradiometric BACTEC MGIT 960 system. J. Clin. Microbiol. 40, 1670-1674 (2002).
57. Stamatakis, A., Hoover, P. &Rougemont, J. A rapid bootstrap algorithm for the RAxML Web servers. Syst. Biol. 57, 758-771 (2008).
58. Coll, F. et al. SpolPred: rapid and accurate prediction of Mycobacterium tuberculosis spoligotypes from short genomic sequences. Bioinformatics 28, 2991-2993 (2012).
59. Zhou, X. &Stephens, M. Genome-wide efficient mixed-model analysis for association studies. Nat. Genet. 44, 821-824 (2012).
60. Alam, M. T. et al. Dissecting vancomycin-intermediate resistance in Staphylococcus aureus using genome-wide association. Genome Biol. Evol. 6, 1174-1185 (2014).
61. Velankar, S. et al. PDBe: improved accessibility of macromolecular structure data from PDB and EMDB. Nucleic Acids Res. 44 (D1), D385-D395 (2016).
62. Pires, D. E. V., Ascher, D. B. &Blundell, T. L. mCSM: predicting the effects of mutations in proteins using graph-based signatures. Bioinformatics 30, 335-342 (2014).
63. Pires, D. E. V., Blundell, T. L. &Ascher, D. B. mCSM-lig: quantifying the effects of mutations on protein-small molecule affinity in genetic disease and emergence of drug resistance. Sci. Rep. 6, 29575 (2016).
64. Pires, D. E. V., Ascher, D. B. &Blundell, T. L. DUET: a server for predicting effects of mutations on protein stability using an integrated computational approach. Nucleic Acids Res. 42, W314-W319 (2014).
65. Pettersen, E. F. et al. UCSF Chimera-A visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605-1612 (2004).
66. Asojo, O. A. et al. Structural and biochemical analyses of alanine racemase from the multidrug-resistant Clostridium difficile strain 630. Acta Crystallogr. D, Biol. Crystallogr. 70, 1922-1933 (2014).
67. Wong, S. Y. et al. Mutations in gidB confer low-level streptomycin resistance in Mycobacterium tuberculosis. Antimicrob. Agents Chemother. 55, 2515-2522 (2011).
68. Rueda, J. et al. Genotypic analysis of genes associated with independent resistance and cross-resistance to isoniazid and ethionamide in Mycobacterium tuberculosis clinical isolates. Antimicrob. Agents Chemother. 59, 7805-7810 (2015).
69. Kambli, P. et al. Correlating rrs and eis promoter mutations in clinical isolates of Mycobacterium tuberculosis with phenotypic susceptibility levels to the second-line injectables. Int. J. Mycobacteriol. 5, 1-6 (2016).
70. Domínguez, J. et al. Clinical implications of molecular drug resistance testing for Mycobacterium tuberculosis: a TBNET/RESIST-TB consensus statement. Int. J. Tuberc. Lung Dis. 20, 24-42 (2016).
71. Cambau, E. et al. Revisiting susceptibility testing in MDR-TB by a standardized quantitative phenotypic assessment in a European multicentre study. J. Antimicrob. Chemother. 70, 686-696 (2015).