Next Generation Sequencing as Rapid Diagnosis of Multidrug Resistance Tuberculosis

Anse Diana Valentiene Messah, Jeanne Adiwinata Pawitan

Abstract


Multi-drug-resistant tuberculosis (MDR-TB) is a threat to global health. In 2018, TB related death was estimated to be more than 1.5 million cases worldwide. Conventional diagnostic method, which requires a long time to get a result, causes delays in new cases discoveries that lead to delayed therapy. Further, delayed and inadequate therapy causes an increase in the level of resistance to anti-TB drugs that may lead to death. Therefore, diagnostic tools, which can detect quickly and accurately, are highly needed. Early and timely detection is crucial for globally effective TB control, but this is not popular in developing countries, especially in Asia. Therefore, the objective of this review is to provide current information on the use of NGS as a rapid diagnostic tool for MDR-TB, especially in Asian populations, and to highlight the various MDR genes.

Keywords: Next Generation sequencing; Multi-Drug Resistance; Tuberculosis; Mycobacterium tuberculosis; Rapid diagnosis


Full Text:

PDF

References


Chakaya JM, Harries AD, Marks GB. Ending tuberculosis by 2030-Pipe dream or reality? International Journal of Infectious Diseases, (2020); 92S: S51-S54.

WHO. Global tuberculosis report 2017. WHO, 2018. https://www.who.int/tb/publications/global_report/gtbr2017_main_text.pdf. Accessed on 20 May 2020.

Walker T, Radcliffe J, Way H. Headington. DNA sequencing predicts 1st-line tuberculosis drug susceptibility. The New England Journal of Medicine, (2018); 379(15): 1403-1415.

Zong Z, Huo F, Shi J, Jing W, Ma Y, Liang Q, et al. Relapse versus reinfection of recurrent tuberculosis patients in a national tuberculosis specialized hospital in Beijing, China. Frontiers in Microbiology, (2018); 9:1858.

Gilpin C, Korobitsyn A, Weyer K. Current tools available for the diagnosis of drug-resistant tuberculosis. Therapeutic Advances in Infectious Diseases, (2016); 3(6):145-151.

Nguyen TNA, Anton-Le Berre V, Bañuls AL, Nguyen TVA. Molecular diagnosis of drug-resistant tuberculosis; A literature review. Frontiers in Microbiology, (2019); 10: 794.

Dlamini MT, Lessells R, Iketleng T, de Oliveira T. Whole genome sequencing for drug-resistant tuberculosis management in South Africa: What gaps would this address and what are the challenges to implementation?. Journal of Clinical Tuberculosis and Other Mycobacterial Diseases, (2019); 16: 100115.

Hunter RL. The pathogenesis of tuberculosis: The early infiltrate of post-primary (adult pulmonary) tuberculosis: A distinct disease entity. Frontiers in Immunology, (2018); 9: 2108.

McIvor A, Koornhof H, Kana BD. Relapse, re-infection and mixed infections in tuberculosis disease. Pathogens and Disease, (2017); 75: 3.

WHO. The use of next-generation sequencing technologies for the detection of mutations associated with drug resistance in Mycobacterium tuberculosis complex: technical guide. WHO, 2018. https://apps.who.int/iris/handle/10665/274443. Accessed on 20 May 2020.

WHO. Tuberculosis: Multidrug-resistant tuberculosis (MDR-TB). WHO, 2018. https://www.who.int/news-room/q-a-detail/what-is-multidrug-resistant-tuberculosis-(mdr-tb)-and-how-do-we-control-it. Accessed on 20 May 2020.

CDC. Chapter 2 Transmission and Pathogenesis of Tuberculosis. https://www.cdc.gov/TB/education/corecurr/pdf/chapter2.pdf. Accessed on 20 May 2020.

Nguyen L. Antibiotic resistance mechanisms in M. tuberculosis: An update. Archives of Toxicology, (2016); 90(7): 1585-1604.

Song H, Sandie R, Wang Y, Andrade-Navarro MA, Niederweis M. Identification of outer membrane proteins of Mycobacterium tuberculosis. Tuberculosis (Edinb), (2008); 88(6): 526-544.

Da Silva PEA, Palomin JC. Molecular basis and mechanisms of drug resistance in Mycobacterium tuberculosis: classical and new drugs. Journal of Antimicrobial Chemotherapy, (2011); 66: 1417-1430.

Zhang Y, Yew WW. Mechanisms of drug resistance in Mycobacterium tuberculosis: Update 2015. The International Journal of Tuberculosis and Lung Disease, (2015); 11: 1276-1289.

Daum LT, Konstantynovska OS, Solodiankin OS, Liashenko OO, Poteiko PI, Bolotin VI, et al. Next-generation sequencing for characterizing drug resistance-conferring Mycobacterium tuberculosis genes from clinical isolates in the Ukraine. Journal of Clinical Microbiology, (2018); 56(6): e00009.

Miotto P, Zhang Y, Cirillo DM, Yam WC. Drug resistance mechanisms and drug susceptibility testing for tuberculosis. Respirology, (2018); 23: 1098–1113.

Palomino JC, Martin A. Drug resistance mechanisms in Mycobacterium tuberculosis. Antibiotics (Basel), (2014); 3(3): 317-340.

Ando H, Akiyama TM, Watanabe S, Kirikae T. A silent mutation in mabA confers isoniazid resistant in Mycobacterium tuberculosis. Molecular Microbiology, (2014); 91 (3) : 538–547.

Maningi NE, Daum L, Rodriguez J, Mphahlele M, Peters R, Fischer G, et al. Improved detection by next-generation sequencing of pyrazinamide resistance in Mycobacterium tuberculosis isolates. Journal of Clinical Microbiology (2015) ; 53(12): 3779-3783.

Lin SYG, Desmond EP. Molecular diagnosis of tuberculosis and drug resistance. Clinics in Laboratory Medicine, (2014); 34: 297–314.

Falzon D, Gandhi N, Migliori GB, Sotgiu G, Cox HS, Holtz TH, et al. Resistance to fluoroquinolones and second-line injectable drugs: Impact on multidrug-resistant TB outcomes. European Respiratory Journal, (2013); 42(1):156-168.

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 Microbiology, (2014) ;14:165 .

Jeanes C, O’Grady J. Diagnosing tuberculosis in the 21st century – Dawn of a genomics revolution? International Journal of Mycobacteriology, (2016); 5(4): 384-391.

Dlamini MT, Lessells R, Iketleng T, de Oliveira T. Whole genome sequencing for drug-resistant tuberculosis management in South Africa: What gaps would this address and what are the challenges to implementation? Journal of Clinical Tuberculosis and Other Mycobacterial Diseases, (2019); 16: 100115.

Cohen KA, Manson AL, Desjardins CA, Abeel T, Earl AE. Deciphering drug resistance in Mycobacterium tuberculosis using wholegenome sequencing: progress, promise, and challenges. Genome Medicine, (2019); 11: 45.

McNerney R., Zignol M., Clark TG. Use of whole genome sequencing in surveillance of drug resistant tuberculosis. Expert Review of Anti-infective Therapy, (2018); 16(5):433-442.

Dewey FE, Megan E, Grove MS, Pan C, Goldstein BA, Bernstein JA, et al. Clinical interpretation and implications of whole-genome sequencing. JAMA, (2014); 311(10): 1035-1045.

Cirilo D, Blnaco M, Armaos A, Buness A, Avner P, Guttman M, et al. Quantitative predictions of protein interaction with long noncoding RNAs. Corespondence. Nature Methods, (2016); 14(1) : 5-6.

Roetzer A, Roland Diel R, Kohl TA, Ru¨ckert C, Nu¨bel U, Blom J, et al. Whole genome sequencing versus traditional genotyping for investigation of a Mycobacterium tuberculosis outbreak: A longitudinal molecular epidemiological study. PLOS Medicine, (2013); 10(2): e1001387 .

Nikolayevskyy V, Trovato A, Broda A, Borroni E, Cirillo D, Drobniewski F. MIRU-VNTR genotyping of Mycobacterium tuberculosis strains using QIAxcel technology: A multicentre evaluation study. PLoS One, (2016);11(3): e0149435.

Desikan S, Narayanan S. Genetic markers, genotyping methods & next generation sequencing in Mycobacterium tuberculosis. Indian Journal of Medical Research, (2015); 141(6): 761-774.

Petersen LM, Martin IW, Moschetti WE, Kershaw CM, Tsongalis GJ. Third-generation sequencing in the clinical laboratory: Exploring the advantages and challenges of nanopore sequencing. Journal of Clinical Microbiology, (2019); 58(1): e01315-19.

Mertes F, Elsharawy A, Sauer S, van Helvoort JMLM, van der Zaag PJ, Franke A, et al. Targeted enrichment of genomic DNA regions for next-generation sequencing. Briefings in Functional Genomics, (2011); 10(6): 374-386.

Integrated DNA technologies. Targeted sequencing guide. https://go.idtdna.com/rs/400-UEU-432/images/IDT%20Targeted%20sequencing%20guide%20%281%29.pdf. Accessed on 20 May 2020.

Clark DP, Pazdernik NJ. Genomic and system biology: Molecular biology. 2013; 2nd edition: e110-e117. Academic Cell.

Yin R, Kwoh CK, Zheng J. Whole genome sequencing analysis: Encyclopedia of bioinformatics and computational biology. 2019; 3: 176-183. Elsevier.

Zignol M, Cabibbe AM, Dean AS, Glaziou P, Alikhanova N, Ama C, et al. Genetic sequencing for surveillance of drug resistance in tuberculosis in highly endemic countries: A multi-country population-based surveillance study. The Lancet Infectious Diseases, (2018); 18(6): 675-683.

Mbelele P, Mohamed S, Sauli E, Mpolya EA, Mfinanga SG, Addo K, et al. Meta narrative review of molecular methods for diagnosis and monitoring of multidrug resistant tuberculosis treatment in adults. International Journal of Mycobacteriology, (2018); 7(4): 299-309.

Huang H, Zhang Y, Li S, Wang J, Chen J, Pan Z, et al. Rifampicin resistance and multidrug resistant tuberculosis detection using Xpert MTB/RIF in Wuhan, China: A retrospective study. Microb Microbial Drug Resistance, (2018); 24: 675 679.

Dorman SE, Schumacher SG, Alland D, Nabeta P, Armstrong DT, King B. Xpert MTB/RIF ultra for detection of Mycobacterium tuberculosis and rifampicin resistance: A prospective multicentre diagnostic accuracy study. The Lancet Infectious Diseases, (2018); 18: 76 84.

Lin HC, Perng CL, Lai YW, Lin FG, Chiang CJ, Lin HA, et al. Molecular screening of multidrug-resistance tuberculosis by a designated public health laboratory in Taiwan. European journal of clinical microbiology & infectious diseases, (2017) ; 36(12): 2431–2439.

Chaidir L, Ruesen C, Dutilh BE, Ganiem AR, Andryani A, Apriani L, et al. Use of whole-genome sequencing to predict Mycobacterium tuberculosis drug resistance in Indonesia. Journal of Global Antimicrobial Resistance, (2019); 16: 170-177.

Banu S, Pholwat S, Foongladda S, Chinli R, Boonlert D, Ferdous S, et al Performance of TaqMan array card to detect TB drug resistance on direct specimens. PloS one, (2017); 12(5), e0177167.

San LL, Saw Aye K, Aye Thida N, Shwe MM, Fukushima Y, Gordom S, et al. Insight into multidrug Beijing Genotype Mycobacterium tuberculosis isolates in Myanmmar. International Journal Infection Diseases, (2018); 76: 109-119.

Ko DH, Lee EJ, Lee EJ, Lee SK, Kim HS, Shin SY, et al. Application of next-generation sequencing to detect variants of drug-resistant Mycobacterium tuberculosis: Genotype-phenotype correlation. Annals of Clinical Microbiology and Antimicrobials, (2019); 18(1): 2.




DOI: http://dx.doi.org/10.62940/als.v8i1.1031

Refbacks

  • There are currently no refbacks.