Whole-genome sequence analysis and comparisons between drug-resistance mutations and minimum inhibitory concentrations of Mycobacterium tuberculosis isolates causing M/XDR-TB

被引:27
作者
Nonghanphithak, Ditthawat [1 ,2 ]
Kaewprasert, Orawee [1 ,2 ]
Chaiyachat, Pratchakan [1 ,2 ]
Reechaipichitkul, Wipa [2 ,3 ]
Chaiprasert, Angkana [4 ]
Faksri, Kiatichai [1 ,2 ]
机构
[1] Khon Kaen Univ, Fac Med, Dept Microbiol, Khon Kaen, Thailand
[2] Khon Kaen Univ, Res & Diagnost Ctr Emerging Infect Dis RCEID, Khon Kaen, Thailand
[3] Khon Kaen Univ, Fac Med, Dept Med, Khon Kaen, Thailand
[4] Mahidol Univ, Siriraj Hosp, Fac Med, Drug Resistant TB Res Fund Lab,Res & Dev Affairs, Bangkok, Thailand
来源
PLOS ONE | 2020年 / 15卷 / 12期
关键词
ANTIBIOTIC-RESISTANCE; SUSCEPTIBILITY; EVOLUTION; RIFAMPIN;
D O I
10.1371/journal.pone.0244829
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
Drug resistance (DR) remains a major challenge for tuberculosis (TB) control. Whole-genome sequencing (WGS) provides the highest genetic resolution for genotypic drug-susceptibility tests (DST). We compared DST profiles of 60 Mycobacterium tuberculosis isolates which were drug resistant according to agar proportion tests (one poly DR-TB, 34 multidrug-resistant TB and 25 extensively drug-resistant TB). We additionally performed minimum inhibitory concentration (MIC) tests using Sensititre MYCOTBI plates (MYCOTB) and a WGS-based DST. Agreement between WGS-based DST and MYCOTB was high for all drugs except ethambutol (65%) and ethionamide (62%). Isolates harboring the -15 c/t inhA promoter mutation had a significantly lower MIC for isoniazid than did isolates with the katG Ser315Thr mutation (p < 0.001). Similar patterns were seen for ethambutol (embB Gly406Asp vs. embB Met306Ile), streptomycin (gid Gly73Ala vs. rpsL Lys43Arg), moxifloxacin (gyrA Ala90Val vs. gyrA Asp94Gly) and rifabutin (rpoB Asp435Phe/Tyr/Val vs. rpoB Ser450Leu). For genotypic heteroresistance, isolates with lower proportion of mapped read tended to has lower MIC of anti-TB drugs than those with higher proportion. These results emphasize the high applicability of WGS for determination of DR-TB and the association of particular mutations with MIC levels.
引用
收藏
页数:14
相关论文
共 43 条
[1]   Discordance across Several Methods for Drug Susceptibility Testing of Drug-Resistant Mycobacterium tuberculosis Isolates in a Single Laboratory [J].
Banu, Sayera ;
Rahman, S. M. Mazidur ;
Khan, M. Siddiqur Rahman ;
Ferdous, Sara Sabrina ;
Ahmed, Shahriar ;
Gratz, Jean ;
Stroup, Suzanne ;
Pholwat, Suporn ;
Heysell, Scott K. ;
Houpt, Eric R. .
JOURNAL OF CLINICAL MICROBIOLOGY, 2014, 52 (01) :156-163
[2]   The ins and outs of Mycobacterium tuberculosis drug susceptibility testing [J].
Boettger, E. C. .
CLINICAL MICROBIOLOGY AND INFECTION, 2011, 17 (08) :1128-1134
[3]   Revisiting susceptibility testing in MDR-TB by a standardized quantitative phenotypic assessment in a European multicentre study [J].
Cambau, E. ;
Viveiros, M. ;
Machado, D. ;
Raskine, L. ;
Ritter, C. ;
Tortoli, E. ;
Matthys, V. ;
Hoffner, S. ;
Richter, E. ;
Perez Del Molino, M. L. ;
Cirillo, D. M. ;
van Soolingen, D. ;
Boettger, E. C. .
JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY, 2015, 70 (03) :686-696
[4]  
CANETTI G, 1969, B WORLD HEALTH ORGAN, V41, P21
[5]   Mutations in gyrA and gyrB among Fluoroquinolone- and Multidrug-Resistant Mycobacterium tuberculosis Isolates [J].
Chien, Jung-Yien ;
Chiu, Wei-Yih ;
Chien, Shun-Tien ;
Chiang, Chia-Jung ;
Yu, Chong-Jen ;
Hsueh, Po-Ren .
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, 2016, 60 (04) :2090-2096
[6]   Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences [J].
Coll, Francesc ;
McNerney, Ruth ;
Preston, Mark D. ;
Guerra-Assuncao, Jose Afonso ;
Warry, Andrew ;
Hill-Cawthorne, Grant ;
Mallard, Kim ;
Nair, Mridul ;
Miranda, Anabela ;
Alves, Adriana ;
Perdigao, Joao ;
Viveiros, Miguel ;
Portugal, Isabel ;
Hasan, Zahra ;
Hasan, Rumina ;
Glynn, Judith R. ;
Martin, Nigel ;
Pain, Arnab ;
Clark, Taane G. .
GENOME MEDICINE, 2015, 7
[7]   Evolution of drug resistance in Mycobacterium tuberculosis: a review on the molecular determinants of resistance and implications for personalized care [J].
Dookie, Navisha ;
Rambaran, Santhuri ;
Padayatchi, Nesri ;
Mahomed, Sharana ;
Naidoo, Kogieleum .
JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY, 2018, 73 (05) :1138-1151
[8]   EthA, a common activator of thiocarbamide-containing drugs acting on different mycobacterial targets [J].
Dover, Lynn G. ;
Alahari, Anuradha ;
Gratraud, Paul ;
Gomes, Jessica M. ;
Bhowruth, Veemal ;
Reynolds, Robert C. ;
Besra, Gurdyal S. ;
Kremer, Laurent .
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, 2007, 51 (03) :1055-1063
[9]   The role of whole genome sequencing in antimicrobial susceptibility testing of bacteria: report from the EUCAST Subcommittee [J].
Ellington, M. J. ;
Ekelund, O. ;
Aarestrup, F. M. ;
Canton, R. ;
Doumith, M. ;
Giske, C. ;
Grundman, H. ;
Hasman, H. ;
Holden, M. T. G. ;
Hopkins, K. L. ;
Iredell, J. ;
Kahlmeter, G. ;
Koser, C. U. ;
MacGowan, A. ;
Mevius, D. ;
Mulvey, M. ;
Naas, T. ;
Peto, T. ;
Rolain, J. -M. ;
Samuelsen, O. ;
Woodford, N. .
CLINICAL MICROBIOLOGY AND INFECTION, 2017, 23 (01) :2-22
[10]   Comparisons of whole-genome sequencing and phenotypic drug susceptibility testing for Mycobacterium tuberculosis causing MDR-TB and XDR-TB in Thailand [J].
Faksri, Kiatichai ;
Kaewprasert, Orawee ;
Ong, Rick Twee-Hee ;
Suriyaphol, Prapat ;
Prammananan, Therdsak ;
Teo, Yik-Ying ;
Srilohasin, Prapaporn ;
Chaiprasert, Angkana .
INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS, 2019, 54 (02) :109-116