Resistance to Second-Line Anti-TB Drugs in Cambodia: A Phenotypic and Genetic Study

References

• WHO. World Health Organization Global Tuberculosis Report 2018. Geneva: Switzerland; 2018.
   Google Scholar
• WHO. Drug-resistant TB: totally drug-resistant TB FAQ; 2019. Available from: https://www.who.int/tb/areas-of-work/drug-resistant-tb/totally-drug-resistant-tb-faq/en/. Accessed 102, 2019.
   Google Scholar
• Velayati AA, Masjedi MR, Farnia P, et al. Emergence of new forms of totally drug-resistant tuberculosis bacilli: super extensively drug-resistant tuberculosis or totally drug-resistant strains in Iran. Chest. 2009;136(2):420–425. doi:10.1378/chest.08-242719349380
   PubMed Web of Science ®Google Scholar
• Udwadia ZF, Amale RA, Ajbani KK, Rodrigues C. Totally drug-resistant tuberculosis in India. Clin Infect Dis. 2012;54(4):579–581. doi:10.1093/cid/cir88922190562
   PubMed Web of Science ®Google Scholar
• Banerjee R, Allen J, Westenhouse J, et al. Extensively drug-resistant tuberculosis in california, 1993–2006. Clin Infect Dis. 2008;47(4):450–457. doi:10.1086/59000918616396
   PubMed Web of Science ®Google Scholar
• Pinto L, Menzies D. Treatment of drug-resistant tuberculosis. Infect Drug Resist. 2011;4:129–135. doi:10.2147/IDR.S1033221904458
   PubMedGoogle Scholar
• WHO. World Health Organization Technical Report on Critical Concentrations for Drug Susceptibility Testing of Medicines Used in the Treatment of Drug-Resistant Tuberculosis. Geneva: Switzerland; 2018.
   Google Scholar
• WHO. World Health Organization consolidated guidelines on drug-resistant tuberculosis treatment. Geneva: Switzerland; 2019.
   Google Scholar
• WHO. World Health Organization Guidelines for Treatment of Drug-Susceptible Tuberculosis and Patient Care, 2017 Update. Geneva: Switzerland; 2017.
   Google Scholar
• CENAT. Tuberculosis Standard Treatment Regimens. Phnom Penh, Cambodia: National Center for Tuberculosis and Leprosy Control, Ministry of Health; 2011.
   Google Scholar
• WHO. World Health Organization Treatment of Tuberculosis Guidelines. Fourth ed. Geneva: Switzerland; 2010.
   Google Scholar
• Migliori GB, De Iaco G, Besozzi G, Centis R, Cirillo DM. First tuberculosis cases in Italy resistant to all tested drugs. Euro Surveill. 2007;12(5):E070517.070511. doi:10.2807/esw.12.20.03194-en
   Google Scholar
• Sam S, Shapiro AE, Sok T, et al. Initiation, scale-up and outcomes of the Cambodian National MDR-TB programme 2006–2016: hospital and community-based treatment through an NGO-NTP partnership. BMJ Open Respir Res. 2018;5(1):e000256–e000256. doi:10.1136/bmjresp-2017-000256
   Web of Science ®Google Scholar
• CENAT. Guideline for Tuberculosis Control. National Center for Tuberculosis and Leprosy Control, Ministry of Health; 2016.
   Google Scholar
• WHO. World Health Organization Treatment Guidelines for Drug-Resistant Tuberculosis, 2016 Update. Geneva: Switzerland; 2016.
   Google Scholar
• Garrigo M, Aragon LM, Alcaide F, et al. Multicenter laboratory evaluation of the MB/BacT Mycobacterium detection system and the BACTEC MGIT 960 system in comparison with the BACTEC 460TB system for susceptibility testing of Mycobacterium tuberculosis J Clin Microbiol. 2007;45(6):1766–1770. doi:10.1128/JCM.02162-0617442793
   PubMed Web of Science ®Google Scholar
• WHO. World Health Organization Updated Interim Critical Concentrations for First-Line and Second-Line DST. Geneva: Switzerland; 2012.
   Google Scholar
• Miotto P, Tessema B, Tagliani E, et al. A standardised method for interpreting the association between mutations and phenotypic drug resistance in Mycobacterium tuberculosis. Eur Respir J. 2017;50:6.
   Web of Science ®Google Scholar
• Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. In Nucleic acids symposium series; 1999; 41: 95–98. [London]: Information Retrieval Ltd., c1979-c2000.
   Google Scholar
• WHO. World Health Organization the Use of Next-Generation Sequencing Technologies for the Detection of Mutations Associated with Drug Resistance in Mycobacterium tuberculosis Complex: Technical Guide. Geneva: Switzerland; 2018.
   Google Scholar
• Camus JC, Pryor MJ, Medigue C, Cole ST. Re-annotation of the genome sequence of Mycobacterium tuberculosis H37Rv. Microbiology. 2002;148(Pt 10):2967–2973. doi:10.1099/00221287-148-10-296712368430
   PubMed Web of Science ®Google Scholar
• Walker TM, Kohl TA, Omar SV, et al. Whole-genome sequencing for prediction of Mycobacterium tuberculosis drug susceptibility and resistance: a retrospective cohort study. Lancet Infect Dis. 2015;15(10):1193–1202. doi:10.1016/S1473-3099(15)00062-626116186
   PubMed Web of Science ®Google Scholar
• Allix-Beguec C, Arandjelovic I, Bi L, et al. Prediction of Susceptibility to First-Line Tuberculosis Drugs by DNA Sequencing. N Engl J Med. 2018;379(15):1403–1415.30280646
   PubMed Web of Science ®Google Scholar
• Ramirez-Busby SM, Valafar F. Systematic review of mutations in pyrazinamidase associated with pyrazinamide resistance in Mycobacterium tuberculosis clinical isolates. Antimicrob Agents Chemother. 2015;59(9):5267–5277. doi:10.1128/AAC.00204-1526077261
   PubMed Web of Science ®Google Scholar
• Kamerbeek J, Schouls L, Kolk A, et al. Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology. J Clin Microbiol. 1997;35(4):907–914. doi:10.1128/JCM.35.4.907-914.19979157152
   PubMed Web of Science ®Google Scholar
• Filliol I, Driscoll JR, van Soolingen D, et al. Snapshot of moving and expanding clones of Mycobacterium tuberculosis and their global distribution assessed by spoligotyping in an international study. J Clin Microbiol. 2003;41(5):1963–1970. doi:10.1128/JCM.41.5.1963-1970.200312734235
   PubMed Web of Science ®Google Scholar
• Couvin D, David A, Zozio T, Rastogi N. Macro-geographical specificities of the prevailing tuberculosis epidemic as seen through SITVIT2, an updated version of the Mycobacterium tuberculosis genotyping database. Infect Genet Evol. 2018.
   Web of Science ®Google Scholar
• Vitol I, Driscoll J, Kreiswirth B, Kurepina N, Bennett KP. Identifying Mycobacterium tuberculosis complex strain families using spoligotypes. Infect Genet Evol. 2006;6(6):491–504. doi:10.1016/j.meegid.2006.03.00316632413
   PubMed Web of Science ®Google Scholar
• Supply P, Allix C, Lesjean S, et al. Proposal for standardization of optimized mycobacterial interspersed repetitive unit-variable-number tandem repeat typing of Mycobacterium tuberculosis. J Clin Microbiol. 2006;44(12):4498–4510. doi:10.1128/JCM.01392-0617005759
   PubMed Web of Science ®Google Scholar
• Hunter PR. Reproducibility and indices of discriminatory power of microbial typing methods. J Clin Microbiol. 1990;28(9):1903–1905. doi:10.1128/JCM.28.9.1903-1905.19902229371
   PubMed Web of Science ®Google Scholar
• Mokrousov I. Revisiting the Hunter Gaston discriminatory index: note of caution and courses of change. Tuberculosis. 2017;104:20–23. doi:10.1016/j.tube.2017.02.00228454645
   PubMed Web of Science ®Google Scholar
• Nei M, Chesser RK. Estimation of fixation indices and gene diversities. Ann Hum Genet. 1983;47(3):253–259. doi:10.1111/j.1469-1809.1983.tb00993.x6614868
   PubMed Web of Science ®Google Scholar
• Cavalli-Sforza LL, Edwards AWF. Phylogenetic analysis: models and estimation procedures. Evolution. 1967;21(3):550–570. doi:10.1111/j.1558-5646.1967.tb03411.x28563688
   PubMed Web of Science ®Google Scholar
• Allix-Beguec C, Harmsen D, Weniger T, Supply P, Niemann S. Evaluation and strategy for use of MIRU-VNTRplus, a multifunctional database for online analysis of genotyping data and phylogenetic identification of Mycobacterium tuberculosis complex isolates. J Clin Microbiol. 2008;46(8):2692–2699. doi:10.1128/JCM.00540-0818550737
   PubMed Web of Science ®Google Scholar
• Ramaswamy SV, Reich R, Dou SJ, et al. Single nucleotide polymorphisms in genes associated with isoniazid resistance in Mycobacterium tuberculosis. Antimicrob Agents Chemother. 2003;47(4):1241–1250. doi:10.1128/AAC.47.4.1241-1250.200312654653
   PubMed Web of Science ®Google Scholar
• Rigouts L, Gumusboga M, de Rijk WB, et al. Rifampin resistance missed in automated liquid culture system for Mycobacterium tuberculosis isolates with specific rpoB mutations. J Clin Microbiol. 2013;51(8):2641–2645. doi:10.1128/JCM.02741-1223761146
   PubMed Web of Science ®Google Scholar
• Al-Mutairi NM, Ahmad S, Mokaddas E, Eldeen HS, Joseph S. Occurrence of disputed rpoB mutations among Mycobacterium tuberculosis isolates phenotypically susceptible to rifampicin in a country with a low incidence of multidrug-resistant tuberculosis. BMC Infect Dis. 2019;19(1):3. doi:10.1186/s12879-018-3638-z30606116
   PubMed Web of Science ®Google Scholar
• Surcouf C, Heng S, Pierre-Audigier C, et al. Molecular detection of fluoroquinolone-resistance in multi-drug resistant tuberculosis in Cambodia suggests low association with XDR phenotypes. BMC Infect Dis. 2011;11:255. doi:10.1186/1471-2334-11-25521955640
   PubMed Web of Science ®Google Scholar
• Reed TAN, Krang S, Miliya T, et al. Antimicrobial resistance in Cambodia: a review. Int J Infect Dis. 2019;85:98–107. doi:10.1016/j.ijid.2019.05.03631176035
   PubMed Web of Science ®Google Scholar
• Jabeen K, Shakoor S, Hasan R. Fluoroquinolone-resistant tuberculosis: implications in settings with weak healthcare systems. Int J Infect Dis. 2015;32:118–123. doi:10.1016/j.ijid.2015.01.00625809767
   PubMed Web of Science ®Google Scholar
• Avalos E, Catanzaro D, Catanzaro A, et al. Frequency and geographic distribution of gyrA and gyrB mutations associated with fluoroquinolone resistance in clinical Mycobacterium tuberculosis isolates: a systematic review. PLoS One. 2015;10(3):e0120470. doi:10.1371/journal.pone.012047025816236
   PubMed Web of Science ®Google Scholar
• Duong DA, Nguyen THD, Nguyen TNL, et al. Beijing genotype of Mycobacterium tuberculosis is significantly associated with high-level fluoroquinolone resistance in Vietnam. Antimicrob Agents Chemother. 2009;53(11):4835–4839. doi:10.1128/AAC.00541-0919721073
   PubMed Web of Science ®Google Scholar
• Mokrousov I, Otten T, Manicheva O, et al. Molecular characterization of ofloxacin-resistant Mycobacterium tuberculosis strains from Russia. Antimicrob Agents Chemother. 2008;52(8):2937–2939. doi:10.1128/AAC.00036-0818559646
   PubMed Web of Science ®Google Scholar
• Blanco D, Perez-Herran E, Cacho M, et al. Mycobacterium tuberculosis gyrase inhibitors as a new class of antitubercular drugs. Antimicrob Agents Chemother. 2015;59(4):1868–1875. doi:10.1128/AAC.03913-1425583730
   PubMed Web of Science ®Google Scholar
• Sowajassatakul A, Prammananan T, Chaiprasert A, Phunpruch S. Molecular characterization of amikacin, kanamycin and capreomycin resistance in M/XDR-TB strains isolated in Thailand. BMC Microbiol. 2014;14:165. doi:10.1186/1471-2180-14-16524953243
   PubMed Web of Science ®Google Scholar
• Ei PW, Aung WW, Nyunt WW, et al. Extensively drug-resistant tuberculosis in Myanmar: burden and mutations causing second-line drug resistance. Int J Tuberc Lung Dis. 2018;22(1):47–53. doi:10.5588/ijtld.17.032129297425
   PubMed Web of Science ®Google Scholar
• Oudghiri A, Karimi H, Chetioui F, et al. Molecular characterization of mutations associated with resistance to second-line tuberculosis drug among multidrug-resistant tuberculosis patients from high prevalence tuberculosis city in Morocco. BMC Infect Dis. 2018;18(1):98. doi:10.1186/s12879-018-3009-929486710
   PubMed Web of Science ®Google Scholar
• Günther G, van Leth F, Altet N, et al. Beyond multidrug-resistant tuberculosis in Europe: a TBNET study. Int J Tuberc Lung Dis. 2015;19(12):1524–1527. doi:10.5588/ijtld.15.027426614196
   PubMed Web of Science ®Google Scholar
• Nguyen QH, Contamin L, Nguyen TVA, Bañuls A-L. Insights into the processes that drive the evolution of drug resistance in Mycobacterium tuberculosis. Evol Appl. 2018;11(9):1498–1511. doi:10.1111/eva.1265430344622
   PubMed Web of Science ®Google Scholar
• Gygli SM, Borrell S, Trauner A, Gagneux S. Antimicrobial resistance in Mycobacterium tuberculosis: mechanistic and evolutionary perspectives. FEMS Microbiol Rev. 2017;41(3):354–373. doi:10.1093/femsre/fux01128369307
   PubMed Web of Science ®Google Scholar