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01-12-2022 | Tuberculosis | Research

Prediction of drug resistance profile of multidrug-resistant Mycobacterium tuberculosis (MDR-MTB) isolates from newly diagnosed case by whole genome sequencing (WGS): a study from a high tuberculosis burden country

Authors: Wenwen Sun, Xuwei Gui, Zheyuan Wu, Yangyi Zhang, Liping Yan

Published in: BMC Infectious Diseases | Issue 1/2022

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Abstract

Objectives

Our aim was to assess the ability of the Whole-genome sequencing (WGS) in predicting drug resistance profile of multidrug-resistant mycobacterium tuberculosis (MDR-MTB) from newly diagnosed cases in China.

Methods

We validated the Phenotypic drug Sensitivity Test (pDST) for 12 anti-tuberculosis drugs using the Bactec MGIT 960 system. We described the characteristics of the isolates enrolled and compared the pDST results with resistance profiles predicted by WGS.

Results

The pDST showed that of the 43 isolates enrolled, 25.6% were sensitive to rifabutin (RFB); 97.7%、97.7%、93.0% and 93.0% were sensitive to cycloserine (Cs), amikacin/kanamycin (Ak/Km), para-aminosalicylic acid (Pas) and ethionamide Eto), respectively; 18.6% were resistant to fluoroquinolones (FQs) or second-line injections. Genotype DST determined by WGS of Ak/Km、Eto and RFP reached high consistency to 97.7% compared with pDST, followed by moxifloxacin (Mfx) 95.3%, levofloxaci (Lfx) and Pas 93%, streptomycin (Sm) 90.3%. The genotype DST of RFB and EMB showed low consistency with the pDST of 67.2 and 79.1%. WGS also detected 27.9% isolates of pyrazinamide(PZA)-related drug-resistant mutation. No mutations associated with linezolid (Lzd), bedaquiline (Bdq) and clofazimine (Cfz) were detectd.

Conclusions

WGS has the potential to infer resistance profiles without time-consuming phenotypic methods, which could be provide a basis to formulate reasonable treatment in high TB burden areas.
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Literature
1.
go back to reference World Health Organization. Global tuberculosis report 2020 in Geneva. Geneva: World Health Organization; 2020. World Health Organization. Global tuberculosis report 2020 in Geneva. Geneva: World Health Organization; 2020.
2.
go back to reference Coll F, Phelan J, Hill-Cawthorne GA, Nair MB, Mallard K, Ali S, et al. Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis. Nat Genet. 2018;50:307–16.CrossRef Coll F, Phelan J, Hill-Cawthorne GA, Nair MB, Mallard K, Ali S, et al. Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis. Nat Genet. 2018;50:307–16.CrossRef
3.
go back to reference Kaniga K, Cirillo DM, Hoffner S, Ismail NA, Kaur D, Lounis N, Metchock B, Pfyffer GE, Venter A. A multilaboratory, multicountry study to determine MIC quality control ranges for phenotypic drug susceptibility testing of selected first-line antituberculosis drugs, second-line injectables, fluoroquinolones, clofazimine, and linezolid. J Clin Microbiol. 2016;54:2963–8.CrossRef Kaniga K, Cirillo DM, Hoffner S, Ismail NA, Kaur D, Lounis N, Metchock B, Pfyffer GE, Venter A. A multilaboratory, multicountry study to determine MIC quality control ranges for phenotypic drug susceptibility testing of selected first-line antituberculosis drugs, second-line injectables, fluoroquinolones, clofazimine, and linezolid. J Clin Microbiol. 2016;54:2963–8.CrossRef
4.
go back to reference Angeby K, Jureen P, Kahlmeter G, Hoffner SE, Schon T. Challenging a dogma: antimicrobial susceptibility testing breakpoints for Mycobacterium tuberculosis. Bull World Health Organ. 2012;90(9):693–8.CrossRef Angeby K, Jureen P, Kahlmeter G, Hoffner SE, Schon T. Challenging a dogma: antimicrobial susceptibility testing breakpoints for Mycobacterium tuberculosis. Bull World Health Organ. 2012;90(9):693–8.CrossRef
5.
go back to reference Zignol M, Dean AS, Alikhanova N, et al. Population-based resistance of Mycobacterium tuberculosis isolates to pyrazinamide and fluoroquinolones: results from a multicountry surveillance project. Lancet Infect Dis. 2016;16:1185–92.CrossRef Zignol M, Dean AS, Alikhanova N, et al. Population-based resistance of Mycobacterium tuberculosis isolates to pyrazinamide and fluoroquinolones: results from a multicountry surveillance project. Lancet Infect Dis. 2016;16:1185–92.CrossRef
6.
go back to reference Coll F, McNerney R, Preston MD, et al. Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences. Genome Med. 2015;7:51.CrossRef Coll F, McNerney R, Preston MD, et al. Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences. Genome Med. 2015;7:51.CrossRef
7.
go back to reference Nebenzahl-Guimaraes H, Jacobson KR, Farhat MR, Murray MB. Systematic review of allelic exchange experiments aimed at identifying mutations that confer drug resistance in Mycobacterium tuberculosis. J Antimicrob Chemother. 2014;69:331–42.CrossRef Nebenzahl-Guimaraes H, Jacobson KR, Farhat MR, Murray MB. Systematic review of allelic exchange experiments aimed at identifying mutations that confer drug resistance in Mycobacterium tuberculosis. J Antimicrob Chemother. 2014;69:331–42.CrossRef
8.
go back to reference Tagliani E, Cabibbe AM, Miotto P, et al. Diagnostic performance of the new version (v2.0) of GenoType MTBDRsl assay for detection of resistance to fluoroquinolones and second-line injectable drugs: a multicenter study. J Clin Microbiol. 2015;53:2961.CrossRef Tagliani E, Cabibbe AM, Miotto P, et al. Diagnostic performance of the new version (v2.0) of GenoType MTBDRsl assay for detection of resistance to fluoroquinolones and second-line injectable drugs: a multicenter study. J Clin Microbiol. 2015;53:2961.CrossRef
9.
go back to reference Van Beek J, Haanperä M, Smit PW, et al. Evaluation of whole genome sequencing and software tools for drug susceptibility testing of Mycobacterium tuberculosis. Clin Microbiol Infect. 2019;25:82–6.CrossRef Van Beek J, Haanperä M, Smit PW, et al. Evaluation of whole genome sequencing and software tools for drug susceptibility testing of Mycobacterium tuberculosis. Clin Microbiol Infect. 2019;25:82–6.CrossRef
10.
12.
go back to reference Shea J, Halse TA, Lapierre P, Shudt M, Kohlerschmidt D, Van Roey P, et al. Comprehensive whole-genome sequencing and reporting of drug resistance profiles on clinical cases of Mycobacterium tuberculosis in New York state. J Clin Microbiol. 2017;55(6):1871–82.CrossRef Shea J, Halse TA, Lapierre P, Shudt M, Kohlerschmidt D, Van Roey P, et al. Comprehensive whole-genome sequencing and reporting of drug resistance profiles on clinical cases of Mycobacterium tuberculosis in New York state. J Clin Microbiol. 2017;55(6):1871–82.CrossRef
13.
go back to reference Charlotte G, Elisabeth H, Jean-Luc B, et al. Whole-genome sequencing in drug susceptibility testing of Mycobacterium tuberculosis in routine practice in Lyon. France Int J Antimicrob Agents. 2020;55: 105912.CrossRef Charlotte G, Elisabeth H, Jean-Luc B, et al. Whole-genome sequencing in drug susceptibility testing of Mycobacterium tuberculosis in routine practice in Lyon. France Int J Antimicrob Agents. 2020;55: 105912.CrossRef
14.
go back to reference Ranzani O, Rodrigues L, Bombarda S, Minto C, Waldman E, Carvalho C. Long-term survival and cause-specific mortality of patients newly diagnosed with tuberculosis in São Paulo state, Brazil, 2010–15: a population-based, longitudinal study. Lancet Infect Dis. 2020;20(1):123–32.CrossRef Ranzani O, Rodrigues L, Bombarda S, Minto C, Waldman E, Carvalho C. Long-term survival and cause-specific mortality of patients newly diagnosed with tuberculosis in São Paulo state, Brazil, 2010–15: a population-based, longitudinal study. Lancet Infect Dis. 2020;20(1):123–32.CrossRef
15.
go back to reference Lee J, Armstrong DT, Ssengooba W, Park JA, Yu Y, Mumbowa F, et al. Sensititre MYCOTB MIC plate for testing Mycobacterium tuberculosis susceptibility to first- and second-line drugs. Antimicrob Agents Chemother. 2014;58(1):11–8.CrossRef Lee J, Armstrong DT, Ssengooba W, Park JA, Yu Y, Mumbowa F, et al. Sensititre MYCOTB MIC plate for testing Mycobacterium tuberculosis susceptibility to first- and second-line drugs. Antimicrob Agents Chemother. 2014;58(1):11–8.CrossRef
16.
go back to reference Luna-Herrera J, Martinez-Cabrera G, Parra-Maldonado R, Enciso-Moreno JA, Torres-Lopez J, Quesada-Pascual F, et al. Use of receiver operating characteristic curves to assess the performance of a microdilution assay for determination of drug susceptibility of clinical isolates of Mycobacterium tuberculosis. Eur J Clin Microbiol Infect Dis. 2003;22(1):21–7.CrossRef Luna-Herrera J, Martinez-Cabrera G, Parra-Maldonado R, Enciso-Moreno JA, Torres-Lopez J, Quesada-Pascual F, et al. Use of receiver operating characteristic curves to assess the performance of a microdilution assay for determination of drug susceptibility of clinical isolates of Mycobacterium tuberculosis. Eur J Clin Microbiol Infect Dis. 2003;22(1):21–7.CrossRef
17.
go back to reference World Health Organization. Global TB Programme. Updated interim critical concentrations for first-line and second-line DST. Geneva: World Health Organization; 2012. World Health Organization. Global TB Programme. Updated interim critical concentrations for first-line and second-line DST. Geneva: World Health Organization; 2012.
18.
go back to reference Aldous WK, Pounder JI, Cloud JL, Woods GL. Comparison of six methods of extracting Mycobacterium tuberculosis DNA from processed sputum for testing by quantitative real-time PCR. J Clin Microbiol. 2005;43(5):2471–3.CrossRef Aldous WK, Pounder JI, Cloud JL, Woods GL. Comparison of six methods of extracting Mycobacterium tuberculosis DNA from processed sputum for testing by quantitative real-time PCR. J Clin Microbiol. 2005;43(5):2471–3.CrossRef
19.
go back to reference Yang C, Lu L, Warren JL, et al. Internal migration and transmission dynamics of tuberculosis in Shanghai, China: an epidemiological, spatial, genomic analysis. Lancet Infect Dis. 2018;18(7):788–95.CrossRef Yang C, Lu L, Warren JL, et al. Internal migration and transmission dynamics of tuberculosis in Shanghai, China: an epidemiological, spatial, genomic analysis. Lancet Infect Dis. 2018;18(7):788–95.CrossRef
20.
go back to reference Liu Q, Ma A, Wei L, Pang Y, Wu B, Luo T, Zhou Y, Zheng HX, Jiang Q, Gan M, Zuo T, Liu M, Yang C, Jin L, Comas I, Gagneux S, Zhao Y, Pepperell CS, Gao Q. China’s tuberculosis epidemic stems from historical expansion of four strains of Mycobacterium tuberculosis. Nat Ecol Evol. 2018;2:1982–92.CrossRef Liu Q, Ma A, Wei L, Pang Y, Wu B, Luo T, Zhou Y, Zheng HX, Jiang Q, Gan M, Zuo T, Liu M, Yang C, Jin L, Comas I, Gagneux S, Zhao Y, Pepperell CS, Gao Q. China’s tuberculosis epidemic stems from historical expansion of four strains of Mycobacterium tuberculosis. Nat Ecol Evol. 2018;2:1982–92.CrossRef
21.
go back to reference Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9(4):357–9.CrossRef Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9(4):357–9.CrossRef
22.
go back to reference Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup. The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25(16):2078–9.CrossRef Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup. The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25(16):2078–9.CrossRef
23.
go back to reference Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, Lin L, Miller CA, Mardis ER, Ding L, Wilson RK. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res. 2012;22(3):568–76.CrossRef Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, Lin L, Miller CA, Mardis ER, Ding L, Wilson RK. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res. 2012;22(3):568–76.CrossRef
24.
go back to reference Luo T, Comas I, Luo D, et al. Southern East Asian origin and coexpansion of Mycobacterium tuberculosis Beijing family with Han Chinese. Proc Natl Acad Sci U S A. 2015;112(26):8136–41.CrossRef Luo T, Comas I, Luo D, et al. Southern East Asian origin and coexpansion of Mycobacterium tuberculosis Beijing family with Han Chinese. Proc Natl Acad Sci U S A. 2015;112(26):8136–41.CrossRef
25.
go back to reference Merker M, Blin C, Mona S, et al. Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage. Nat Genet. 2015;47(3):242–9.CrossRef Merker M, Blin C, Mona S, et al. Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage. Nat Genet. 2015;47(3):242–9.CrossRef
27.
go back to reference World Health Organization. WHO consolidated guidelines on drug-resistant tuberculosis treatment. Geneva: World Health Organization; 2019. World Health Organization. WHO consolidated guidelines on drug-resistant tuberculosis treatment. Geneva: World Health Organization; 2019.
28.
go back to reference Leandro AC, Rocha MA, Lamoglia-Souza A, et al. No association of IFNG+874T/A SNP and NOS2A-954G/C SNP variants with nitric oxide radical serum levels or susceptibility to tuberculosis in a Brazilian population subset. Biomed Res Int. 2013;2013:901740.CrossRef Leandro AC, Rocha MA, Lamoglia-Souza A, et al. No association of IFNG+874T/A SNP and NOS2A-954G/C SNP variants with nitric oxide radical serum levels or susceptibility to tuberculosis in a Brazilian population subset. Biomed Res Int. 2013;2013:901740.CrossRef
29.
go back to reference Marsili L, Pasqualucci CR, Vigevani A, Gioia B, Schioppacassi G, Oronzo G. New rifamycins modified at positions 3 and 4. Synthesis, structure and biological evaluation. J Antibiot. 1981;34:1033–8.CrossRef Marsili L, Pasqualucci CR, Vigevani A, Gioia B, Schioppacassi G, Oronzo G. New rifamycins modified at positions 3 and 4. Synthesis, structure and biological evaluation. J Antibiot. 1981;34:1033–8.CrossRef
30.
go back to reference Sirgel FA, Warren RM, Böttger EC, Klopper M, Victor TC, van Helden PD. The rationale for using rifabutin in the treatment of MDR and XDR tuberculosis outbreaks. PLoS ONE. 2013;8: e59414.CrossRef Sirgel FA, Warren RM, Böttger EC, Klopper M, Victor TC, van Helden PD. The rationale for using rifabutin in the treatment of MDR and XDR tuberculosis outbreaks. PLoS ONE. 2013;8: e59414.CrossRef
31.
go back to reference Jamieson FB, Guthrie JL, Neemuchwala A, Lastovetska O, Melano RG, Mehaffy C. Profiling of rpoB mutations and MICs for rifampin and rifabutin in Mycobacterium tuberculosis. J Clin Microbiol. 2014;52(6):2157–62.CrossRef Jamieson FB, Guthrie JL, Neemuchwala A, Lastovetska O, Melano RG, Mehaffy C. Profiling of rpoB mutations and MICs for rifampin and rifabutin in Mycobacterium tuberculosis. J Clin Microbiol. 2014;52(6):2157–62.CrossRef
32.
go back to reference Vilchèze C, Jacobs J, William R. The mechanism of isoniazid killing: clarity through the scope of genetics. Annu Rev Microbio. 2007;61:35–50.CrossRef Vilchèze C, Jacobs J, William R. The mechanism of isoniazid killing: clarity through the scope of genetics. Annu Rev Microbio. 2007;61:35–50.CrossRef
33.
go back to reference Machado D, Perdigão J, Ramos J, et al. High-level resistance to isoniazid and ethionamide in multidrug-resistant Mycobacterium tuberculosis of the Lisboa family is associated with inhA double mutations. J Antimicrob Chemother. 2013;68:1728–32.CrossRef Machado D, Perdigão J, Ramos J, et al. High-level resistance to isoniazid and ethionamide in multidrug-resistant Mycobacterium tuberculosis of the Lisboa family is associated with inhA double mutations. J Antimicrob Chemother. 2013;68:1728–32.CrossRef
34.
go back to reference World Health Organization. Policy guidance on drug-susceptibility testing (DST) of second-line antituberculosis drugs. Geneva: WHO; 2008. World Health Organization. Policy guidance on drug-susceptibility testing (DST) of second-line antituberculosis drugs. Geneva: WHO; 2008.
35.
go back to reference Mikusová K, Slayden RA, Besra GS, et al. Biogenesis of the mycobacterial cell wall and the site of action of ethambutol. Antimicrob Agents Chemother. 1995;39:2484–9.CrossRef Mikusová K, Slayden RA, Besra GS, et al. Biogenesis of the mycobacterial cell wall and the site of action of ethambutol. Antimicrob Agents Chemother. 1995;39:2484–9.CrossRef
36.
go back to reference Palomino JC, Martin A. Drug resistance mechanisms in Mycobacterium tuberculosis. Antibiotics (Basel). 2014;3:317–40.CrossRef Palomino JC, Martin A. Drug resistance mechanisms in Mycobacterium tuberculosis. Antibiotics (Basel). 2014;3:317–40.CrossRef
37.
go back to reference Gillespie SH. Evolution of drug resistance in Mycobacterium tuberculosis: clinical and molecular perspective. Antimicrob Agents Chemother. 2002;46:267–74.CrossRef Gillespie SH. Evolution of drug resistance in Mycobacterium tuberculosis: clinical and molecular perspective. Antimicrob Agents Chemother. 2002;46:267–74.CrossRef
38.
go back to reference Georghiou SB, Magana M, Garfein RS, et al. Evaluation of genetic mutations associated with Mycobacterium tuberculosis resistance to amikacin, kanamycin and capreomycin: a systematic review. PLoS ONE. 2012;7: e33275.CrossRef Georghiou SB, Magana M, Garfein RS, et al. Evaluation of genetic mutations associated with Mycobacterium tuberculosis resistance to amikacin, kanamycin and capreomycin: a systematic review. PLoS ONE. 2012;7: e33275.CrossRef
39.
go back to reference Almeida Da Silva PE, Palomino JC. Molecular basis and mechanisms of drug resistance in Mycobacterium tuberculosis: classical and new drugs. J Antimicrob Chemother 2011; 66: 1417–30 Almeida Da Silva PE, Palomino JC. Molecular basis and mechanisms of drug resistance in Mycobacterium tuberculosis: classical and new drugs. J Antimicrob Chemother 2011; 66: 1417–30
40.
go back to reference Mathys V, Wintjens R, Lefevre P, et al. Molecular genetics of para-aminosalicylic acid resistance in clinical isolates and spontaneous mutants of Mycobacterium tuberculosis. Antimicrob Agents Chemother. 2009;53:2100–9.CrossRef Mathys V, Wintjens R, Lefevre P, et al. Molecular genetics of para-aminosalicylic acid resistance in clinical isolates and spontaneous mutants of Mycobacterium tuberculosis. Antimicrob Agents Chemother. 2009;53:2100–9.CrossRef
41.
go back to reference Jalil K-Y, Hossein K, Simone B, et al. Mycobacterium tuberculosis whole genome sequencing results associated with minimum inhibitory concentrations of 14 anti-tuberculosis drugs among rifampicin-resistant isolates of from Iran. J Clin Med. 2020;9:465.CrossRef Jalil K-Y, Hossein K, Simone B, et al. Mycobacterium tuberculosis whole genome sequencing results associated with minimum inhibitory concentrations of 14 anti-tuberculosis drugs among rifampicin-resistant isolates of from Iran. J Clin Med. 2020;9:465.CrossRef
42.
go back to reference Pankhurst LJ, del Ojo EC, Votintseva AA, et al. Rapid, comprehensive, and affordable mycobacterial diagnosis with whole-genome sequencing: a prospective study. Lancet Respir Med. 2016;4:49–58.CrossRef Pankhurst LJ, del Ojo EC, Votintseva AA, et al. Rapid, comprehensive, and affordable mycobacterial diagnosis with whole-genome sequencing: a prospective study. Lancet Respir Med. 2016;4:49–58.CrossRef
Metadata
Title
Prediction of drug resistance profile of multidrug-resistant Mycobacterium tuberculosis (MDR-MTB) isolates from newly diagnosed case by whole genome sequencing (WGS): a study from a high tuberculosis burden country
Authors
Wenwen Sun
Xuwei Gui
Zheyuan Wu
Yangyi Zhang
Liping Yan
Publication date
01-12-2022
Publisher
BioMed Central
Published in
BMC Infectious Diseases / Issue 1/2022
Electronic ISSN: 1471-2334
DOI
https://doi.org/10.1186/s12879-022-07482-4

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