Removing the bottleneck in whole genome sequencing of Mycobacterium tuberculosis for rapid drug resistance analysis: a call to action

International Journal of Infectious Diseases

Volumn 56, Issue , 2017, Pages 130-135

  McNerney, Ruth ^a   Clark, Taane G ^b   Campino, Susana ^b   Rodrigues, Camilla ^c   Dolinger, David ^d   Smith, Liezel ^a   Cabibbe, Andrea M ^e   Dheda, Keertan ^a   Schito, Marco ^f  

^a UNIVERSITY OF CAPE TOWN   (South Africa)

^b LONDON SCHOOL OF HYGIENE AND TROPICAL MEDICINE   (United Kingdom)

^c P D HINDUJA NATIONAL HOSPITAL   (India)

^d FIND   (Switzerland)

^e SAN RAFFAELE HOSPITAL   (Italy)

^f CRITICAL PATH INSTITUTE   (United States)

Author keywords

Clinical isolate; Drug resistance; Next generation sequencing; Sputum; Tuberculosis

Indexed keywords

BACTERIAL DNA; DNA; OLIGONUCLEOTIDE; TUBERCULOSTATIC AGENT;

ANTIBIOTIC RESISTANCE; BACTERIUM CULTURE; DRUG RESISTANT TUBERCULOSIS; ENRICHMENT CULTURE; ENRICHMENT TECHNIQUE; GENE AMPLIFICATION; HUMAN; MYCOBACTERIUM TUBERCULOSIS; NEXT GENERATION SEQUENCING; NONHUMAN; REVIEW; SOLVENT EXTRACTION; SPUTUM ANALYSIS; WHOLE GENOME SEQUENCING; DNA SEQUENCE; DRUG EFFECTS; GENETICS; GENOTYPING TECHNIQUE; MICROBIOLOGY; NUCLEOTIDE SEQUENCE; PROCEDURES; SPECIMEN HANDLING; SPUTUM; TUBERCULOSIS, MULTIDRUG-RESISTANT;

ANTITUBERCULAR AGENTS; BASE SEQUENCE; DNA, BACTERIAL; GENOTYPING TECHNIQUES; HUMANS; MYCOBACTERIUM TUBERCULOSIS; SEQUENCE ANALYSIS, DNA; SPECIMEN HANDLING; SPUTUM; TUBERCULOSIS, MULTIDRUG-RESISTANT;

EID: 85009452509     PISSN: 12019712     EISSN: 18783511     Source Type: Journal    
DOI: 10.1016/j.ijid.2016.11.422     Document Type: Review

References (59)

1. 1 Cole, S.T., Brosch, R., Parkhill, J., Garnier, T., Churcher, C., Harris, D., et al. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393 (1998), 537–544.
2. 2 Delcher, A.L., Kasif, S., Fleischmann, R.D., Peterson, J., White, O., Salzberg, S.L., Alignment of whole genomes. Nucleic Acids Res 27 (1999), 2369–2376.
3. 3 Fleischmann, R.D., Alland, D., Eisen, J.A., Carpenter, L., White, O., Peterson, J., et al. Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains. J Bacteriol 184 (2002), 5479–5490.
4. 4 Brites, D., Gagneux, S., Co-evolution of Mycobacterium tuberculosis and Homo sapiens. Immunol Rev 264 (2015), 6–24.
5. 5 Phelan, J., Coll, F., McNerney, R., Ascher, D.B., Pires, D.E., Furnham, N., et al. Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance. BMC Med, 14, 2016, 31.
6. 6 Guerra-Assuncao, J.A., Crampin, A.C., Houben, R.M., Mzembe, T., Mallard, K., Coll, F., et al. Large-scale whole genome sequencing of M. tuberculosis provides insights into transmission in a high prevalence area. eLife, 4, 2015, e05166.
7. 7 Glynn, J.R., Guerra-Assuncao, J.A., Houben, R.M., Sichali, L., Mzembe, T., Mwaungulu, L.K., et al. Whole genome sequencing shows a low proportion of tuberculosis disease is attributable to known close contacts in rural Malawi. PLoS One, 10, 2015, e0132840.
8. 8 Casali, N., Nikolayevskyy, V., Balabanova, Y., Harris, S.R., Ignatyeva, O., Kontsevaya, I., et al. Evolution and transmission of drug-resistant tuberculosis in a Russian population. Nat Genet 46 (2014), 279–286.
9. 9 Farhat, M.R., Sultana, R., Iartchouk, O., Bozeman, S., Galagan, J., Sisk, P., et al. Genetic determinants of drug resistance in Mycobacterium tuberculosis and their diagnostic value. Am J Respir Crit Care Med 194 (2016), 621–630.
10. 10 Hatherell, H.A., Colijn, C., Stagg, H.R., Jackson, C., Winter, J.R., Abubakar, I., Interpreting whole genome sequencing for investigating tuberculosis transmission: a systematic review. BMC Med, 14, 2016, 21.
11. 11 Faksri, K., Tan, J.H., Chaiprasert, A., Teo, Y.Y., Ong, R.T., Bioinformatics tools and databases for whole genome sequence analysis of Mycobacterium tuberculosis. Infect Genet Evol 45 (2016), 359–368.
12. 12 Coll, F., McNerney, R., Preston, M.D., Guerra-Assuncao, J.A., Warry, A., Hill-Cawthorne, G., et al. Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences. Genome Med, 7, 2015, 51.
13. 13 Bradley, P., Gordon, N.C., Walker, T.M., Dunn, L., Heys, S., Huang, B., et al. Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis. Nat Commun, 6, 2015, 10063.
14. 14 Feuerriegel, S., Schleusener, V., Beckert, P., Kohl, T.A., Miotto, P., Cirillo, D.M., et al. PhyResSE: a Web tool delineating Mycobacterium tuberculosis antibiotic resistance and lineage from whole-genome sequencing data. J Clin Microbiol 53 (2015), 1908–1914.
15. 15 Iwai, H., Kato-Miyazawa, M., Kirikae, T., Miyoshi-Akiyama, T., CASTB (the comprehensive analysis server for the Mycobacterium tuberculosis complex): a publicly accessible Web server for epidemiological analyses, drug-resistance prediction and phylogenetic comparison of clinical isolates. Tuberculosis (Edinb) 95 (2015), 843–844.
16. 16 Witney, A.A., Gould, K.A., Arnold, A., Coleman, D., Delgado, R., Dhillon, J., Clinical application of whole-genome sequencing to inform treatment for multidrug-resistant tuberculosis cases. J Clin Microbiol 53 (2015), 1473–1483.
17. 17 Colman, R.E., Anderson, J., Lemmer, D., Lehmkuhl, E., Georghiou, S.B., Heaton, H., et al. Rapid drug susceptibility testing of drug-resistant Mycobacterium tuberculosis isolates directly from clinical samples by use of amplicon sequencing: a proof-of-concept study. J Clin Microbiol 54 (2016), 2058–2067.
18. 18 Brown, A.C., Bryant, J.M., Einer-Jensen, K., Holdstock, J., Houniet, D.T., Chan, J.Z., et al. Rapid whole-genome sequencing of Mycobacterium tuberculosis isolates directly from clinical samples. J Clin Microbiol 53 (2015), 2230–2237.
19. 19 Tyler, A.D., Christianson, S., Knox, N.C., Mabon, P., Wolfe, J., Van Domselaar, G., et al. Comparison of sample preparation methods used for the next-generation sequencing of Mycobacterium tuberculosis. PLoS One, 11, 2016, e0148676.
20. 20 Daum, L.T., Rodriguez, J.D., Worthy, S.A., Ismail, N.A., Omar, S.V., Dreyer, A.W., et al. Next-generation ion torrent sequencing of drug resistance mutations in Mycobacterium tuberculosis strains. J Clin Microbiol 50 (2012), 3831–3837.
21. 21 Phelan J, O'Sullivan DM, Machado D, Ramos J, Whale AS, O'Grady J, et al. The reliability of whole genome sequencing technology for detecting resistance to anti-tuberculous drugs. Genome Med 2016:.
22. 22 Illumina. Solexa technology. Illumina; 2016. Available at: http://www.illumina.com/technology/next-generation-sequencing/solexa-technology.html (accessed September 20, 2016).
23. 23 Thermo Fisher Scientific. Ion Torrent™ next-generation sequencing technology. Available at: https://www.thermofisher.com/za/en/home/life-science/sequencing/next-generation-sequencing/ion-torrent-next-generation-sequencing-technology.html (accessed September 20, 2016).
24. 24 Pacific Biosciences. SMRT sequencing. Available at: http://www.pacb.com/smrt-science/smrt-sequencing/ (accessed September 20, 2016).
25. 25 Feng, Y., Zhang, Y., Ying, C., Wang, D., Du, C., Nanopore-based fourth-generation DNA sequencing technology. Genomics Proteomics Bioinformatics 13 (2015), 4–16.
26. 26 Schmidt, K., Mwaigwisya, S., Crossman, L.C., Doumith, M., Munroe, D., Pires, C., et al. Identification of bacterial pathogens and antimicrobial resistance directly from clinical urines by nanopore-based metagenomic sequencing. J Antimicrob Chemother 72 (2016), 104–114.
27. 27 McNerney, R., Advice on samples for tuberculosis testing. 2010, You Tube.
28. 28 Weiszhar, Z., Horvath, I., Induced sputum analysis: step by step. Breathe 9 (2013), 300–306.
29. 29 Hernandez, P., Punchak, M., Camacho, M., Hepple, P., McNerney, R., Investigating the quality of expectorated sputum for tuberculosis diagnosis in Bolivia. Int J Tuberc Lung Dis 19 (2015), 1065–1067.
30. nded, 1991, Bureau of Hygiene and tropical Diseases, London.
31. 31 Hadad, D.J., Morais, C.G., Vinhas, S.A., Fennelly, K.P., Dietze, R., Nascimento, C.P., et al. Evaluation of processing methods to equitably aliquot sputa for mycobacterial testing. J Clin Microbiol 50 (2012), 1440–1442.
32. 32 Kaser, M., Ruf, M.T., Hauser, J., Marsollier, L., Pluschke, G., Optimized method for preparation of DNA from pathogenic and environmental mycobacteria. Appl Environ Microbiol 75 (2009), 414–418.
33. sted, 2014, Stop TB Partnership.
34. 34 Kubica, G.P., Dye, W.E., Cohn, M.L., Middlebrook, G., Sputum digestion and decontamination with N-acetyl-L-cysteine–sodium hydroxide for culture of mycobacteria. Am Rev Respir Dis 87 (1963), 775–779.
35. 35 Chatterjee, M., Bhattacharya, S., Karak, K., Dastidar, S.G., Effects of different methods of decontamination for successful cultivation of Mycobacterium tuberculosis. Indian J Med Res 138 (2013), 541–548.
36. 36 Wang, T.Y., Wang, L., Zhang, J.H., Dong, W.H., A simplified universal genomic DNA extraction protocol suitable for PCR. Genet Mol Res 10 (2011), 519–525.
37. 37 Sambrook, J., Fritsch, E.F., Maniatis, T., Molecular cloning: a laboratory manual. 1989, Cold Spring Harbor Laboratory Press, New York.
38. 38 Hayatsu, H., Pan, S., Ukita, T., Reaction of sodium hypochlorite with nucleic acids and their constituents. Chem Pharm Bull (Tokyo) 19 (1971), 2189–2192.
39. 39 Donoghue, H.D., Spigelman, M., O'Grady, J., Szikossy, I., Pap, I., Lee, O.Y., et al. Ancient DNA analysis—an established technique in charting the evolution of tuberculosis and leprosy. Tuberculosis (Edinb) 95:Suppl 1 (2015), S140–S144.
40. 40 Lim, Y.W., Schmieder, R., Haynes, M., Willner, D., Furlan, M., Youle, M., et al. Metagenomics and metatranscriptomics: windows on CF-associated viral and microbial communities. J Cyst Fibros 12 (2013), 154–164.
41. 41 Doughty, E.L., Sergeant, M.J., Adetifa, I., Antonio, M., Pallen, M.J., Culture-independent detection and characterisation of Mycobacterium tuberculosis and M. africanum in sputum samples using shotgun metagenomics on a benchtop sequencer. PeerJ, 2, 2014, e585.
42. 42 DiaSorin Ireland Ltd. Bugs'n Beads Kit—instructions for use. DiaSorin Ireland Ltd; 2012. Available at: http://uk.werfen.com/∼/media/il%20uk/docs/diasorin/ifu%20120102%20%20%20bugs%20n%20beads%20english.pdf (accessed December 10, 2016).
43. 43 Wilson, S., Lane, A., Rosedale, R., Stanley, C., Concentration of Mycobacterium tuberculosis from sputum using ligand-coated magnetic beads. Int J Tuberc Lung Dis 14 (2010), 1164–1168.
44. 44 Rodrigue, S., Malmstrom, R.R., Berlin, A.M., Birren, B.W., Henn, M.R., Chisholm, S.W., Whole genome amplification and de novo assembly of single bacterial cells. PLoS One, 4, 2009, e6864.
45. 45 Chitsaz, H., Yee-Greenbaum, J.L., Tesler, G., Lombardo, M.J., Dupont, C.L., Badger, J.H., et al. Efficient de novo assembly of single-cell bacterial genomes from short-read data sets. Nat Biotechnol 29 (2011), 915–921.
46. 46 Spits, C., Le Caignec, C., De Rycke, M., Van Haute, L., Van Steirteghem, A., Liebaers, I., et al. Whole-genome multiple displacement amplification from single cells. Nat Protoc 1 (2006), 1965–1970.
47. 47 Martinez, E., Bustamante, A., Menon, R., Wang, Q., Jelfs, P., Marais, B., et al. Whole-genome sequencing of Mycobacterium tuberculosis for rapid diagnostics: feasibility of a decentralised model. Lancet Respir Med 4 (2016), e13–e14.
48. 48 Pankhurst, L.J., Del Ojo Elias, C., Votintseva, A.A., Walker, T.M., Cole, K., Davies, J., et al. Rapid, comprehensive, and affordable mycobacterial diagnosis with whole-genome sequencing: a prospective study. Lancet Respir Med 4 (2016), 49–58.
49. 49 Koser, C.U., Bryant, J.M., Becq, J., Torok, M.E., Ellington, M.J., Marti-Renom, M.A., et al. Whole-genome sequencing for rapid susceptibility testing of M. tuberculosis. N Engl J Med 369 (2013), 290–292.
50. 50 Belisle, J.T., Sonnenberg, M.G., Isolation of genomic DNA from mycobacteria. Parish, T., Stoker, N.G., (eds.) Mycobacteria Protocols, 1998, Humana Press Inc, New Jersey, USA, 31–44.
51. 51 Zhang, Z.Q., Ishaque, M., Evaluation of methods for isolation of DNA from slowly and rapidly growing mycobacteria. Int J Lepr Other Mycobact Dis 65 (1997), 469–476.
52. 52 van Helden, P.D., Victor, T.C., Warren, R.M., van Helden, E.G., Isolation of DNA from Mycobacterium tuberculosis. Methods Mol Med 54 (2001), 19–30.
53. 53 Yuan, S., Cohen, D.B., Ravel, J., Abdo, Z., Forney, L.J., Evaluation of methods for the extraction and purification of DNA from the human microbiome. PLoS One, 7, 2012, e33865.
54. 54 van Embden, J.D., Cave, M.D., Crawford, J.T., Dale, J.W., Eisenach, K.D., Gicquel, B., et al. Strain identification of Mycobacterium tuberculosis by DNA fingerprinting: recommendations for a standardized methodology. J Clin Microbiol 31 (1993), 406–409.
55. 55 Baess, I., Isolation and purification of deoxyribonucleic acid from mycobacteria. Acta Pathol Microbiol Scand B Microbiol Immunol 82 (1974), 780–784.
56. 56 Dheda, K., Gumbo, T., Gandhi, N.R., Murray, M., Theron, G., Udwadia, Z., et al. Global control of tuberculosis: from extensively drug-resistant to untreatable tuberculosis. Lancet Respir Medicine 2 (2014), 321–338.
57. 57 World Health Organization, WHO treatment guidelines for drug-resistant tuberculosis 2016 update. 2016, WHO, Geneva, Switzerland.
58. 58 Schito, M., Dolinger, D.L., A collaborative approach for “ReSeq-ing” Mycobacterium tuberculosis drug resistance: convergence for drug and diagnostic developers. EBioMedicine 2 (2015), 1262–1265.
59. 59 Votintseva, A.A., Pankhurst, L.J., Anson, L.W., Morgan, M.R., Gascoyne-Binzi, D., Walker, T.M., et al. Mycobacterial DNA extraction for whole-genome sequencing from early positive liquid (MGIT) cultures. J Clin Microbiol 53 (2015), 1137–1143.