Whole-transcriptome and -genome analysis of extensively drug-resistant Mycobacterium tuberculosis clinical isolates identifies downregulation of ethA as a mechanism of ethionamide resistance

Antimicrobial Agents and Chemotherapy

Volumn 61, Issue 12, 2017, Pages

  De Welzen, Lynne ^a   Eldholm, Vegard ^b   Maharaj, Kashmeel ^a,e   Manson, Abigail L ^c   Earl, Ashlee M ^c   Pym, Alexander S ^a,d  

^a UNIVERSITY OF KWAZULU NATAL   (South Africa)

^b NORWEGIAN INSTITUTE OF PUBLIC HEALTH   (Norway)

^c BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^d UNIVERSITY COLLEGE LONDON   (United Kingdom)

^e Alere Healthcare (Pty) Ltd   (South Africa)

Author keywords

Drug resistance; Drug susceptibility testing; Flow cytometry; Fluorescent reporter; mymA; Promoter; RNA sequencing; RNA seq; Tuberculosis

Indexed keywords

ETHIONAMIDE; TRANSCRIPTOME; TRANSFER RNA; UNSPECIFIC MONOOXYGENASE; BACTERIAL PROTEIN; BACTERIAL RNA; ETHA PROTEIN, MYCOBACTERIUM TUBERCULOSIS; ETHR PROTEIN, MYCOBACTERIUM TUBERCULOSIS; ISONIAZID; MAZF PROTEIN, MYCOBACTERIUM TUBERCULOSIS; OXIDOREDUCTASE; REPRESSOR PROTEIN; RIBONUCLEASE; TUBERCULOSTATIC AGENT;

AMINO ACID SUBSTITUTION; ANTIBIOTIC RESISTANCE; ARTICLE; BACTERIAL GENE; DOWN REGULATION; DRUG RESISTANT TUBERCULOSIS; ETHA BACTERIAL GENE; FLOW CYTOMETRY; GENE EXPRESSION; GENOME ANALYSIS; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; PHYLOGENETIC TREE; PRIORITY JOURNAL; PROMOTER REGION; RNA SEQUENCE; SINGLE NUCLEOTIDE POLYMORPHISM; START CODON; TRANSCRIPTOMICS; BACTERIAL GENOME; DRUG EFFECT; ENZYMOLOGY; GENE EXPRESSION REGULATION; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN; ISOLATION AND PURIFICATION; METABOLISM; MICROBIOLOGY; MULTIDRUG RESISTANCE; MULTIDRUG RESISTANT TUBERCULOSIS; MUTATION; NUCLEOTIDE SEQUENCE; PATHOLOGY;

ANTITUBERCULAR AGENTS; BACTERIAL PROTEINS; BASE SEQUENCE; DRUG RESISTANCE, MULTIPLE, BACTERIAL; ENDORIBONUCLEASES; ETHIONAMIDE; GENE EXPRESSION REGULATION, BACTERIAL; GENOME, BACTERIAL; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; ISONIAZID; MUTATION; MYCOBACTERIUM TUBERCULOSIS; OXIDOREDUCTASES; PROMOTER REGIONS, GENETIC; REPRESSOR PROTEINS; RNA, BACTERIAL; TRANSCRIPTOME; TUBERCULOSIS, MULTIDRUG-RESISTANT;

EID: 85035008667     PISSN: 00664804     EISSN: 10986596     Source Type: Journal    
DOI: 10.1128/AAC.01461-17     Document Type: Article

References (40)

1. Cohen KA, Abeel T, Manson McGuire A, Desjardins CA, Munsamy V, Shea TP, Walker BJ, Bantubani N, Almeida DV, Alvarado L, Chapman SB, Mvelase NR, Duffy EY, Fitzgerald MG, Govender P, Gujja S, Hamilton S, Howarth C, Larimer JD, Maharaj K, Pearson MD, Priest ME, Zeng Q, Padayatchi N, Grosset J, Young SK, Wortman J, Mlisana KP, O’Donnell MR, Birren BW, Bishai WR, Pym AS, Earl AM. 2015. 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. https://doi.org/10.1371/journal.pmed.1001880.
2. O’Donnell MR, Padayatchi N, Kvasnovsky C, Werner L, Master I, Horsburgh CR. 2013. Treatment outcomes for extensively drug-resistant tuberculosis and HIV co-infection. Emerg Infect Dis 19:416–424. https://doi.org/10.3201/eid1903.120998.
3. Pietersen E, Ignatius E, Streicher EM, Mastrapa B, Padanilam X, Pooran A, Badri M, Lesosky M, van Helden P, Sirgel FA, Warren R, Dheda K. 2014. Long-term outcomes of patients with extensively drug-resistant tuberculosis in South Africa: a cohort study. Lancet (London, England) 383: 1230–1239. https://doi.org/10.1016/S0140-6736(13)62675-6.
4. Boehme CC, Nicol MP, Nabeta P, Michael JS, Gotuzzo E, Tahirli R, Gler MT, Blakemore R, Worodria W, Gray C, Huang L, Caceres T, Mehdiyev R, Raymond L, Whitelaw A, Sagadevan K, Alexander H, Albert H, Cobelens F, Cox H, Alland D, Perkins MD. 2011. Feasibility, diagnostic accuracy, and effectiveness of decentralised use of the Xpert MTB/RIF test for diagnosis of tuberculosis and multidrug resistance: a multicentre implementation study. Lancet (London, England) 377:1495–1505. https://doi.org/10.1016/S0140-6736(11)60438-8.
5. Hillemann D, Rusch-Gerdes S, Richter E. 2007. Evaluation of the GenoType MTBDRplus assay for rifampin and isoniazid susceptibility testing of Mycobacterium tuberculosis strains and clinical specimens. J Clin Microbiol 45:2635–2640. https://doi.org/10.1128/JCM.00521-07.
6. Hillemann D, Rusch-Gerdes S, Richter E. 2009. Feasibility of the GenoType MTBDRsl assay for fluoroquinolone, amikacin-capreomycin, and ethambutol resistance testing of Mycobacterium tuberculosis strains and clinical specimens. J Clin Microbiol 47:1767–1772. https://doi.org/ 10.1128/JCM.00081-09.
7. Brown AC, Bryant JM, Einer-Jensen K, Holdstock J, Houniet DT, Chan JZM, Depledge DP, Nikolayevskyy V, Broda A, Stone MJ, Christiansen MT, Williams R, McAndrew MB, Tutill H, Brown J, Melzer M, Rosmarin C, McHugh TD, Shorten RJ, Drobniewski F, Speight G, Breuer J. 2015. Rapid whole-genome sequencing of Mycobacterium tuberculosis isolates directly from clinical samples. J Clin Microbiol 53:2230 –2237. https://doi.org/10.1128/JCM.00486-15.
8. Desjardins CA, Cohen KA, Munsamy V, Abeel T, Maharaj K, Walker BJ, Shea TP, Almeida DV, Manson AL, Salazar A, Padayatchi N, O’Donnell MR, Mlisana KP, Wortman J, Birren BW, Grosset J, Earl AM, Pym AS. 2016. Genomic and functional analyses of Mycobacterium tuberculosis strains implicate ald in D-cycloserine resistance. Nat Genet 48:544 –551. https://doi.org/10.1038/ng.3548.
9. Walker TM, Kohl TA, Omar SV, Hedge J, Del Ojo Elias C, Bradley P, Iqbal Z, Feuerriegel S, Niehaus KE, Wilson DJ, Clifton DA, Kapatai G, Ip CLC, Bowden R, Drobniewski FA, Allix-Béguec C, Gaudin C, Parkhill J, Diel R, Supply P, Crook DW, Smith EG, Walker AS, Ismail N, Niemann S, Peto TEA, Davies J, Crichton C, Acharya M, Madrid-Marquez L, Eyre D, Wyllie D, Golubchik T, Munang M. 2015. Whole-genome sequencing for prediction of Mycobacterium tuberculosis drug susceptibility and resistance: a retrospective cohort study. Lancet Infect Dis 15:1193–1202. https://doi.org/10.1016/S1473-3099(15)00062-6.
10. Coll F, McNerney R, Preston MD, Guerra-Assunção JA, Warry A, Hill-Cawthorne G, Mallard K, Nair M, Miranda A, Alves A, Perdigão J, Viveiros M, Portugal I, Hasan Z, Hasan R, Glynn JR, Martin N, Pain A, Clark TG. 2015. Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences. Genome Med 7:51. https://doi.org/10.1186/s13073-015-0164-0.
11. Zhang H, Li D, Zhao L, Fleming J, Lin N, Wang T, Liu Z, Li C, Galwey N, Deng J, Zhou Y, Zhu Y, Gao Y, Wang T, Wang S, Huang Y, Wang M, Zhong Q, Zhou L, Chen T, Zhou J, Yang R, Zhu G, Hang H, Zhang J, Li F, Wan K, Wang J, Zhang X-E, Bi L. 2013. Genome sequencing of 161 Mycobacterium tuberculosis isolates from China identifies genes and intergenic regions associated with drug resistance. Nat Genet 45:1255–1260. https://doi.org/10.1038/ng.2735.
12. Cohen KA, Bishai WR, Pym AS. 2014. Molecular basis of drug resistance in Mycobacterium tuberculosis. Microbiol Spectr 2(3):MGM2-0036-2013. https://doi.org/10.1128/microbiolspec.MGM2-0036-2013.
13. Siddiqi N, Das R, Pathak N, Banerjee S, Ahmed N, Katoch VM, Hasnain SE. 2004. Mycobacterium tuberculosis isolate with a distinct genomic identity overexpresses a tap-like efflux pump. Infection 32:109–111. https://doi.org/10.1007/s15010-004-3097-x.
14. Louw GE, Warren RM, van Pittius NC, Leon R, Jimenez A, Hernandez-Pando R, McEvoy CRE, Grobbelaar M, Murray M, van Helden PD, Victor TC. 2011. Rifampicin reduces susceptibility to ofloxacin in rifampicin-resistant Mycobacterium tuberculosis through efflux. Am J Respir Crit Care Med 184:269–276. https://doi.org/10.1164/rccm.201011-1924OC.
15. Mdluli K, Sherman DR, Hickey MJ, Kreiswirth BN, Morris S, Stover CK, Barry CE. 1996. Biochemical and genetic data suggest that InhA is not the primary target for activated isoniazid in Mycobacterium tuberculosis. J Infect Dis 174:1085–1090. https://doi.org/10.1093/infdis/174.5.1085.
16. Scorpio A, Lindholm-Levy P, Heifets L, Gilman R, Siddiqi S, Cynamon M, Zhang Y. 1997. Characterization of pncA mutations in pyrazinamide-resistant Mycobacterium tuberculosis. Antimicrob Agents Chemother 41:540–543.
17. Juréen P, Werngren J, Toro JC, Hoffner S. 2008. Pyrazinamide resistance and pncA gene mutations in Mycobacterium tuberculosis. Antimicrob Agents Chemother 52:1852–1854. https://doi.org/10.1128/AAC.00110-08.
18. Yüksel P, Tansel Ö. 2009. Characterization of pncA mutations of pyrazinamide-resistant Mycobacterium tuberculosis in Turkey. New Microbiol 32:153–158.
19. Reeves AZ, Campbell PJ, Sultana R, Malik S, Murray M, Plikaytis BB, Shinnick TM, Posey JE. 2013. Aminoglycoside cross-resistance in Mycobacterium tuberculosis due to mutations in the 5= untranslated region of whiB7. Antimicrob Agents Chemother 57:1857–1865. https://doi.org/10.1128/AAC.02191-12.
20. Hartkoorn RC, Uplekar S, Cole ST. 2014. Cross-resistance between clofazimine and bedaquiline through upregulation of mmpL5 in Mycobacterium tuberculosis. Antimicrob Agents Chemother 58:2979–2981. https://doi.org/10.1128/AAC.00037-14.
21. Andries K, Villellas C, Coeck N, Thys K, Gevers T, Vranckx L, Lounis N, De Jong BC, Koul A. 2014. Acquired resistance of Mycobacterium tuberculosis to bedaquiline. PLoS One 9:e102135. https://doi.org/10.1371/journal.pone.0102135.
22. Baulard AR, Betts JC, Engohang-Ndong J, Quan S, McAdam RA, Brennan PJ, Locht C, Besra GS. 2000. Activation of the pro-drug ethionamide is regulated in mycobacteria. J Biol Chem 275:28326–28331.
23. DeBarber AE, Mdluli K, Bosman M, Bekker LG, Barry CE. 2000. Ethionamide activation and sensitivity in multidrug-resistant Mycobacterium tuberculosis. Proc Natl Acad Sci U S A 97:9677–9682. https://doi.org/10.1073/pnas.97.17.9677.
24. Morlock GP, Metchock B, Sikes D, Crawford JT, Cooksey RC. 2003. ethA, inhA, and katG loci of ethionamide-resistant clinical Mycobacterium tuberculosis isolates. Antimicrob Agents Chemother 47:3799 –3805. https://doi.org/10.1128/AAC.47.12.3799-3805.2003.
25. Engohang-Ndong J, Baillat D, Aumercier M, Bellefontaine F, Besra GS, Locht C, Baulard AR. 2004. EthR, a repressor of the TetR/CamR family implicated in ethionamide resistance in mycobacteria, octamerizes cooperatively on its operator. Mol Microbiol 51:175–188.
26. Vilchèze C, Jacobs WR, Jr. 2014. Resistance to isoniazid and ethionamide in Mycobacterium tuberculosis: genes, mutations, and causalities. Microbiol Spectr 2(4):MGM2-0014-2013. https://doi.org/10.1128/microbiolspec.MGM2-0014-2013.
27. Grant SS, Wellington S, Kawate T, Desjardins CA, Silvis MR, Wivagg C, Thompson M, Gordon K, Kazyanskaya E, Nietupski R, Haseley N, Iwase N, Earl AM, Fitzgerald M, Hung DT. 2016. Baeyer-Villiger monooxygenases EthA and MymA are required for activation of replicating and non-replicating Mycobacterium tuberculosis inhibitors. Cell Chem Biol 23: 666–677. https://doi.org/10.1016/j.chembiol.2016.05.011.
28. Manson AL, Cohen KA, Abeel T, Desjardins CA, Armstrong DT, Barry CE, III, Brand J, Chapman SB, Cho S-N, Gabrielian A, Gomez J, Jodals AM, Joloba M, Jureen P, Lee JS, Malinga L, Maiga M, Nordenberg D, Noroc E, Romancenco E, Salazar A, Ssengooba W, Velayati AA, Winglee K, Zalutskaya A, Via LE, Cassell GH, Dorman SE, Ellner J, Farnia P, Galagan JE, Rosenthal A, Crudu V, Homorodean D, Hsueh P-R, Narayanan S, Pym AS, Skrahina A, Swaminathan S, Van der Walt M, Alland D, Bishai WR, Cohen T, Hoffner S, Birren BW, Earl AM. 2017. Genomic analysis of globally diverse Mycobacterium tuberculosis strains provides insights into the emergence and spread of multidrug resistance. Nat Genet 49:395–402. https://doi.org/10.1038/ng.3767.
29. Swofford D. 1991. PAUP: phylogenetic analysis using parsimony, version 3.1. Sinauer Associates, Sunderland, MA.
30. Farhat MR, Sultana R, Iartchouk O, Bozeman S, Galagan J, Sisk P, Stolte C, Nebenzahl-Guimaraes H, Jacobson K, Sloutsky A, Kaur D, Posey J, Kreiswirth BN, Kurepina N, Rigouts L, Streicher EM, Victor TC, Warren RM, van Soolingen D, Murray M. 2016. Genetic determinants of drug resistance in Mycobacterium tuberculosis and their diagnostic value. Am J Respir Crit Care Med 194:621–630. https://doi.org/10.1164/rccm.201510-2091OC.
31. Casali N, Nikolayevskyy V, Balabanova Y, Harris SR, Ignatyeva O, Kontsevaya I, Corander J, Bryant J, Parkhill J, Nejentsev S, Horstmann RD, Brown T, Drobniewski F. 2014. Evolution and transmission of drug-resistant tuberculosis in a Russian population. Nat Genet 46:279–286. https://doi.org/10.1038/ng.2878.
32. Rueda J, Realpe T, Mejia GI, Zapata E, Rozo JC, Ferro BE, Robledo J. 2015. 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. https://doi.org/10.1128/AAC.01028-15.
33. Vilcheze C, Weisbrod TR, Chen B, Kremer L, Hazbon MH, Wang F, Alland D, Sacchettini JC, Jacobs WRJ. 2005. Altered NADH/NAD ratio mediates coresistance to isoniazid and ethionamide in mycobacteria. Antimicrob Agents Chemother 49:708–720. https://doi.org/10.1128/AAC.49.2.708-720.2005.
34. Tiwari P, Arora G, Singh M, Kidwai S, Narayan OP, Singh R. 2015. MazF ribonucleases promote Mycobacterium tuberculosis drug tolerance and virulence in guinea pigs. Nat Commun 6:6059. https://doi.org/10.1038/ncomms7059.
35. Kirchner S, Ignatova Z. 2015. Emerging roles of tRNA in adaptive translation, signalling dynamics and disease. Nat Rev Genet 16:98–112. https://doi.org/10.1038/nrg3861.
36. World Health Organization. 2016. WHO treatment guidelines for drug-resistant tuberculosis 2016. World Health Organization, Geneva, Switzerland.
37. Kaniga K, Cirillo DM, Hoffner S, Ismail NA, Kaur D, Lounis N, Metchock B, Pfyffer GE, Venter A. 2016. A multilaboratory, multicountry study to determine MIC quality control ranges for phenotypic drug susceptibility testing of selected first-line antituberculosis drugs, second-line inject-ables, fluoroquinolones, clofazimine, and linezolid. J Clin Microbiol 54: 2963–2968. https://doi.org/10.1128/JCM.01138-16.
38. Alli OAT, Mangan, Butcher JA, Alli O. 2009. Optimization of RNA extraction in Mycobacterium tuberculosis for studying intracellular gene expression. Afr J Clin Exp Microbiol 10:64–79.
39. Eldholm V, Pettersson JH-O, Brynildsrud OB, Kitchen A, Rasmussen EM, Lillebaek T, Rønning JO, Crudu V, Mengshoel AT, Debech N, Alfsnes K, Bohlin J, Pepperell CS, Balloux F. 2016. Armed conflict and population displacement as drivers of the evolution and dispersal of Mycobacterium tuberculosis. Proc Natl Acad Sci U S A 113:13881–13886. https://doi.org/10.1073/pnas.1611283113.
40. van Kessel JC, Hatfull GF. 2007. Recombineering in Mycobacterium tuberculosis. Nat Methods 4:147–152. https://doi.org/10.1038/nmeth996.