Genetic Identification and Drug-Resistance Characterization of Using a Portable Sequencing Device. A Pilot Study

Overview

Journal Antibiotics (Basel)

Specialty Pharmacology

Date 2020 Sep 2

PMID 32867304

Citations 7

Authors

Jorge Cervantes

Noemi Yokobori

Bo-Young Hong

Affiliations

Soon will be listed here.

Abstract

Clinical management of tuberculosis (TB) in endemic areas is often challenged by a lack of resources including laboratories for (Mtb) culture. Traditional phenotypic drug susceptibility testing for Mtb is costly and time consuming, while PCR-based methods are limited to selected target loci. We herein utilized a portable, USB-powered, long-read sequencing instrument (MinION), to investigate Mtb genomic DNA from clinical isolates to determine the presence of anti-TB drug-resistance conferring mutations. Data analysis platform EPI2ME and antibiotic-resistance analysis using the real time ARMA workflow, identified Mtb species as well as extensive resistance gene profiles. The approach was highly sensitive, being able to detect almost all described drug resistance conferring mutations based on previous whole genome sequencing analysis. Our findings are supportive of the practical use of this system as a suitable method for the detection of antimicrobial resistance genes, and effective in providing Mtb genomic information. Future improvements in the error rate through statistical analysis, drug resistance prediction algorithms and reference databases would make this a platform suited for the clinical setting. The small size, relatively inexpensive cost of the device, as well as its rapid and simple library preparation protocol and analysis, make it an attractive option for settings with limited laboratory infrastructure.

Citing Articles

A pragmatic pipeline for drug resistance and lineage identification in Mycobacterium tuberculosis using whole genome sequencing.

Elton L, Aydin A, Stoker N, Rofael S, Wildner L, Abdul J PLOS Glob Public Health. 2025; 5(2):e0004099.

PMID: 39928651 PMC: 11809915. DOI: 10.1371/journal.pgph.0004099.

Diagnostic value of nanopore sequencing technology in nontuberculous mycobacterial pulmonary disease.

Lin W, Tang F, Liu S Am J Transl Res. 2024; 16(8):4208-4215.

PMID: 39262756 PMC: 11384362. DOI: 10.62347/HHRH8076.

High-throughput nanopore targeted sequencing for efficient drug resistance assay of .

Tang C, Wu L, Li M, Dai J, Shi Y, Wang Q Front Microbiol. 2024; 15:1331656.

PMID: 38841074 PMC: 11152171. DOI: 10.3389/fmicb.2024.1331656.

Accuracy of Nanopore Sequencing as a Diagnostic Assay for Pulmonary Tuberculosis versus Smear, Culture and Xpert MTB/RIF: A Head-to-Head Comparison.

Yang J, Ye W, Zhang C, Lin W, Mei L, Liu S Trop Med Infect Dis. 2023; 8(9).

PMID: 37755902 PMC: 10535524. DOI: 10.3390/tropicalmed8090441.

Differential Impact of the Mutant on Rifampin and Rifabutin Resistance Signatures of Is Revealed Using a Whole-Genome Sequencing Assay.

Yu M, Hung C, Huang C, Wang C, Liang Y, Lin J Microbiol Spectr. 2022; 10(4):e0075422.

PMID: 35924839 PMC: 9430608. DOI: 10.1128/spectrum.00754-22.

References

Balcells M, Garcia P, Meza P, Pena C, Cifuentes M, Couvin D . A first insight on the population structure of Mycobacterium tuberculosis complex as studied by spoligotyping and MIRU-VNTRs in Santiago, Chile. PLoS One. 2015; 10(2):e0118007. PMC: 4324903. DOI: 10.1371/journal.pone.0118007. View

Meza P, Elvira Balcells M, Miranda C, Cifuentes M, Wozniak A, Garcia P . [Presence of Bejing genotype among Mycobacterium tuberculosis strains in two centres of the Region Metropolitana of Chile]. Rev Chilena Infectol. 2014; 31(1):21-7. DOI: 10.4067/S0716-10182014000100003. View

Ritacco V, Iglesias M, Ferrazoli L, Monteserin J, Dalla Costa E, Cebollada A . Conspicuous multidrug-resistant Mycobacterium tuberculosis cluster strains do not trespass country borders in Latin America and Spain. Infect Genet Evol. 2011; 12(4):711-7. DOI: 10.1016/j.meegid.2011.06.006. View

Votintseva A, Bradley P, Pankhurst L, Del Ojo Elias C, Loose M, Nilgiriwala K . Same-Day Diagnostic and Surveillance Data for Tuberculosis via Whole-Genome Sequencing of Direct Respiratory Samples. J Clin Microbiol. 2017; 55(5):1285-1298. PMC: 5405248. DOI: 10.1128/JCM.02483-16. View

Laver T, Harrison J, ONeill P, Moore K, Farbos A, Paszkiewicz K . Assessing the performance of the Oxford Nanopore Technologies MinION. Biomol Detect Quantif. 2016; 3:1-8. PMC: 4691839. DOI: 10.1016/j.bdq.2015.02.001. View

Ocheretina O, Escuyer V, Mabou M, Royal-Mardi G, Collins S, Vilbrun S . Correlation between genotypic and phenotypic testing for resistance to rifampin in Mycobacterium tuberculosis clinical isolates in Haiti: investigation of cases with discrepant susceptibility results. PLoS One. 2014; 9(3):e90569. PMC: 3944071. DOI: 10.1371/journal.pone.0090569. View

Runtuwene L, Tuda J, Mongan A, Suzuki Y . On-Site MinION Sequencing. Adv Exp Med Biol. 2019; 1129:143-150. DOI: 10.1007/978-981-13-6037-4_10. View

Daley C . The Global Fight Against Tuberculosis. Thorac Surg Clin. 2018; 29(1):19-25. DOI: 10.1016/j.thorsurg.2018.09.010. View

Harel N, Meir M, Gophna U, Stern A . Direct sequencing of RNA with MinION Nanopore: detecting mutations based on associations. Nucleic Acids Res. 2019; 47(22):e148. PMC: 7107797. DOI: 10.1093/nar/gkz907. View

10.

Gagneux S . Ecology and evolution of Mycobacterium tuberculosis. Nat Rev Microbiol. 2018; 16(4):202-213. DOI: 10.1038/nrmicro.2018.8. View

11.

Koch A, Cox H, Mizrahi V . Drug-resistant tuberculosis: challenges and opportunities for diagnosis and treatment. Curr Opin Pharmacol. 2018; 42:7-15. PMC: 6219890. DOI: 10.1016/j.coph.2018.05.013. View

12.

Monteserin J, Perez-Lago L, Yokobori N, Paul R, Rodriguez Maus S, Simboli N . Trends of Two Epidemic Multidrug-Resistant Strains of in Argentina Disclosed by Tailored Molecular Strategy. Am J Trop Med Hyg. 2019; 101(6):1308-1311. PMC: 6896870. DOI: 10.4269/ajtmh.19-0397. View

13.

Henry V, Bandrowski A, Pepin A, Gonzalez B, Desfeux A . OMICtools: an informative directory for multi-omic data analysis. Database (Oxford). 2014; 2014. PMC: 4095679. DOI: 10.1093/database/bau069. View

14.

Brynildsrud O, Pepperell C, Suffys P, Grandjean L, Monteserin J, Debech N . Global expansion of lineage 4 shaped by colonial migration and local adaptation. Sci Adv. 2018; 4(10):eaat5869. PMC: 6192687. DOI: 10.1126/sciadv.aat5869. View

15.

Millet J, Streit E, Berchel M, Bomer A, Schuster F, Paasch D . A systematic follow-up of Mycobacterium tuberculosis drug-resistance and associated genotypic lineages in the French Departments of the Americas over a seventeen-year period. Biomed Res Int. 2014; 2014:689852. PMC: 3971487. DOI: 10.1155/2014/689852. View

16.

Sanchez-Padilla E, Merker M, Beckert P, Jochims F, Dlamini T, Kahn P . Detection of drug-resistant tuberculosis by Xpert MTB/RIF in Swaziland. N Engl J Med. 2015; 372(12):1181-2. DOI: 10.1056/NEJMc1413930. View

17.

Boritsch E, Brosch R . Evolution of Mycobacterium tuberculosis: New Insights into Pathogenicity and Drug Resistance. Microbiol Spectr. 2016; 4(5). DOI: 10.1128/microbiolspec.TBTB2-0020-2016. View

18.

Bellerose M, Baek S, Huang C, Moss C, Koh E, Proulx M . Common Variants in the Glycerol Kinase Gene Reduce Tuberculosis Drug Efficacy. mBio. 2019; 10(4). PMC: 6667613. DOI: 10.1128/mBio.00663-19. View

19.

Wilson B, Eisenstein M, Soh H . High-Fidelity Nanopore Sequencing of Ultra-Short DNA Targets. Anal Chem. 2019; 91(10):6783-6789. PMC: 6533607. DOI: 10.1021/acs.analchem.9b00856. View

20.

Eldholm V, Monteserin J, Rieux A, Lopez B, Sobkowiak B, Ritacco V . Four decades of transmission of a multidrug-resistant Mycobacterium tuberculosis outbreak strain. Nat Commun. 2015; 6:7119. PMC: 4432642. DOI: 10.1038/ncomms8119. View