A standardised method for interpreting the association between mutations and phenotypic drug resistance in Mycobacterium tuberculosis

被引:258
作者
Miotto, Paolo [1 ]
Tessema, Belay [2 ]
Tagliani, Elisa [1 ]
Chindelevitch, Leonid [3 ]
Starks, Angela M. [4 ]
Emerson, Claudia [5 ]
Hanna, Debra [6 ]
Kim, Peter S. [7 ]
Liwski, Richard [6 ]
Zignol, Matteo [8 ]
Gilpin, Christopher [8 ]
Niemann, Stefan [9 ,10 ]
Denkinger, Claudia M. [11 ]
Fleming, Joy [12 ]
Warren, Robin M. [13 ]
Crook, Derrick [14 ,15 ]
Posey, James [4 ]
Gagneux, Sebastien [16 ,17 ]
Hoffner, Sven [18 ,19 ]
Rodrigues, Camilla [20 ]
Comas, Inaki [21 ,22 ,23 ]
Engelthaler, David M. [24 ]
Murray, Megan [25 ]
Alland, David [26 ]
Rigouts, Leen [27 ]
Lange, Christoph [28 ,29 ,30 ,31 ,32 ]
Dheda, Keertan [33 ,34 ]
Hasan, Rumina [35 ]
Ranganathan, Uma Devi K. [36 ]
McNerney, Ruth [37 ]
Ezewudo, Matthew [6 ]
Cirillo, Daniela M. [1 ]
Schito, Marco [6 ]
Koser, Claudio U. [38 ]
Rodwell, Timothy C. [3 ,11 ]
机构
[1] IRCCS, San Raffaele Sci Inst, Emerging Bacterial Pathogens Unit, Milan, Italy
[2] Univ Gondar, Dept Med Microbiol, Gondar, Ethiopia
[3] Simon Fraser Univ, Sch Comp Sci, Burnaby, BC, Canada
[4] Natl Ctr HIV AIDS Viral Hepatitis STD & TB Preven, Ctr Dis Control & Prevent, Div TB Eliminat, Atlanta, GA USA
[5] McMaster Univ, Inst Eth & Policy Innovat, Dept Philosophy, Hamilton, ON, Canada
[6] Crit Path Inst, Tucson, AZ USA
[7] NIH, Off AIDS Res, Rockville, MD USA
[8] WHO, Global TB Programme, Geneva, Switzerland
[9] Res Ctr Borstel, Mol & Expt Mycobacteriol Prior Area Infect, Borstel, Germany
[10] German Ctr Infect Res, Borstel, Germany
[11] Fdn Innovat New Diagnost, Campus Biotech, Geneva, Switzerland
[12] Chinese Acad Sci, Inst Biophys, Key Lab RNA Biol, Beijing, Peoples R China
[13] Stellenbosch Univ, DST NRF Ctr Excellence Biomed TB Research, SAMRC Ctr TB Res, Div Mol Biol & Human Genet,Fac Med & Hlth Sci, Stellenbosch, South Africa
[14] Univ Oxford, John Radcliffe Hosp, Nuffield Dept Med, Oxford, England
[15] Publ Hlth England, Nat Infect Serv, London, England
[16] Swiss Trop & Publ Hlth Inst, Basel, Switzerland
[17] Univ Basel, Basel, Switzerland
[18] Karolinska Inst, Microbiol Tumour & Cell Biol, Stockholm, Sweden
[19] Publ Hlth Agcy Sweden, Solna, Sweden
[20] Hinduja Hosp, Veer Savarkar Marg, Mumbai, Maharashtra, India
[21] CSIC, IBV, Biomed Inst Valencia, TB Genom Unit, Valencia, Spain
[22] Fdn Promot Hlth & Biomed Res Valencian Community, Valencia, Spain
[23] CIBER Ctr Invest Biomed Red Epidemiol & Publ Hlth, Madrid, Spain
[24] Translat Genom Res Inst, Flagstaff, AZ USA
[25] Harvard Sch Publ Hlth, Dept Epidemiol, Boston, MA USA
[26] Rutgers New Jersey Med Sch, Ctr Emerging Pathogens, Newark, NJ USA
[27] Inst Trop Med, Dept Biomed Sci, Antwerp, Belgium
[28] Res Ctr Borstel, Div Clin Infect Dis, Borstel, Germany
[29] Res Ctr Borstel, German Ctr Infect Res, TB Unit, Borstel, Germany
[30] Univ Lubeck, Int Hlth Infect Dis, Lubeck, Germany
[31] Karolinska Inst, Dept Med, Stockholm, Sweden
[32] Univ Namibia, Sch Med, Dept Internal Med, Windhoek, Namibia
[33] Univ Cape Town, Groote Schuur Hosp, Dept Med, Div Pulmonol,Lung Infection & Immun Unit, Cape Town, South Africa
[34] Univ Cape Town, Groote Schuur Hosp, UCT Lung Inst, Cape Town, South Africa
[35] Aga Khan Univ, Dept Pathol & Lab Med, Karachi, Pakistan
[36] Nat Inst Res TB, ICMR, Chennai, Tamil Nadu, India
[37] Univ Cape Town, Groote Schuur Hosp, Dept Med, Div Pulmonol, Cape Town, South Africa
[38] Univ Cambridge, Dept Genet, Cambridge, England
基金
欧洲研究理事会;
关键词
ANTIBIOTIC-RESISTANCE; MULTIDRUG-RESISTANT; LIKELIHOOD RATIOS; DIAGNOSTIC-TEST; SUSCEPTIBILITY; EVOLUTION; COMPLEX; POLYMORPHISMS; SURVEILLANCE; MOXIFLOXACIN;
D O I
10.1183/13993003.01354-2017
中图分类号
R56 [呼吸系及胸部疾病];
学科分类号
摘要
A clear understanding of the genetic basis of antibiotic resistance in Mycobacterium tuberculosis is required to accelerate the development of rapid drug susceptibility testing methods based on genetic sequence. Raw genotype-phenotype correlation data were extracted as part of a comprehensive systematic review to develop a standardised analytical approach for interpreting resistance associated mutations for rifampicin, isoniazid, ofloxacin/levofloxacin, moxifloxacin, amikacin, kanamycin, capreomycin, streptomycin, ethionamide/prothionamide and pyrazinamide. Mutation frequencies in resistant and susceptible isolates were calculated, together with novel statistical measures to classify mutations as high, moderate, minimal or indeterminate confidence for predicting resistance. We identified 286 confidence-graded mutations associated with resistance. Compared to phenotypic methods, sensitivity (95% CI) for rifampicin was 90.3% (89.6-90.9%), while for isoniazid it was 78.2% (77.4-79.0%) and their specificities were 96.3% (95.7-96.8%) and 94.4% (93.1-95.5%), respectively. For second-line drugs, sensitivity varied from 67.4% (64.1-70.6%) for capreomycin to 88.2% (85.1-90.9%) for moxifloxacin, with specificity ranging from 90.0% (87.1-92.5%) for moxifloxacin to 99.5% (99.0-99.8%) for amikacin. This study provides a standardised and comprehensive approach for the interpretation of mutations as predictors of M. tuberculosis drug-resistant phenotypes. These data have implications for the clinical interpretation of molecular diagnostics and next-generation sequencing as well as efficient individualised therapy for patients with drug-resistant tuberculosis.
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页数:13
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