Mycobacterium tuberculosis and whole genome sequencing: a practical guide and online tools available for the clinical microbiologist

Clinical Microbiology and Infection

Volumn 23, Issue 2, 2017, Pages 69-72

  Satta, G ^a,b   Atzeni, A ^a   McHugh, T D ^a  

^a UNIVERSITY COLLEGE LONDON   (United Kingdom)

^b IMPERIAL COLLEGE HEALTHCARE NHS TRUST   (United Kingdom)

Author keywords

Mycobacterium tuberculosis; Online tools; Phylogenetic analysis; Rapid susceptibility testing; Whole genome sequencing

Indexed keywords

GENOMIC DNA; TUBERCULOSTATIC AGENT;

CLINICAL PRACTICE; MYCOBACTERIUM TUBERCULOSIS; NEXT GENERATION SEQUENCING; NONHUMAN; ONLINE SYSTEM; PHYLOGENY; PRIORITY JOURNAL; REVIEW; SEQUENCE ANALYSIS; SOFTWARE; WHOLE GENOME SEQUENCING; BACTERIAL GENOME; BACTERIUM IDENTIFICATION; BIOLOGY; CLASSIFICATION; DNA SEQUENCE; DRUG EFFECTS; GENETICS; HUMAN; MICROBIAL SENSITIVITY TEST; MICROBIOLOGY; PROCEDURES; STANDARDS; TUBERCULOSIS; WEB BROWSER;

ANTITUBERCULAR AGENTS; BACTERIAL TYPING TECHNIQUES; COMPUTATIONAL BIOLOGY; GENOME, BACTERIAL; HUMANS; MICROBIAL SENSITIVITY TESTS; MYCOBACTERIUM TUBERCULOSIS; PHYLOGENY; SEQUENCE ANALYSIS, DNA; SOFTWARE; TUBERCULOSIS; WEB BROWSER;

EID: 85005954418     PISSN: 1198743X     EISSN: 14690691     Source Type: Journal    
DOI: 10.1016/j.cmi.2016.09.005     Document Type: Review

References (38)

1. [1] World Health Organization website, accessed on 1 July 2016. Available at: http://www.who.int/tb/publications/global_report/en/.
2. [2] Pfyffer, G.E., Wittwer, F., Incubation time of mycobacterial cultures: how long is long enough to issue a final negative report to the clinician?. J Clin Microbiol 50 (2012), 4188–4189.
3. [3] Boehme, C.C., Nabeta, P., Hillemann, D., Nicol, M.P., Shenai, S., Krapp, F., et al. Rapid molecular detection of tuberculosis and rifampin resistance. N Engl J Med. 363:11 (2010), 1005–1015.
4. [4] Witney, A.A., Cosgrove, C.A., Arnold, A., Hinds, J., Stoker, N.G., Butcher, P.D., Clinical use of whole genome sequencing for Mycobacterium tuberculosis. BMC Med, 14, 2016, 46.
5. [5] Walker, T.M., Ip, C.L., Harrell, R.H., Evans, J.T., Kapatai, G., et al. Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study. Lancet Infect Dis 13:2 (2013), 137–146.
6. [6] Wellcome Trust Sanger Institute website, accessed on 28 June 2016. Available at: http://www.sanger.ac.uk/science/tools/categories/analysis/all.
7. [7] The Galaxy project website, accessed on 28 June 2016. Available at: https://galaxyproject.org/.
8. [8] Broad Institute website, accessed on 28 June 2015. Available at: http://www.broadinstitute.org/scientific-community/software.
9. [9] Käser, M., Ruf, M.T., Hauser, J., Pluschke, G., Optimized DNA preparation from mycobacteria. Cold Spring Harb Protoc, 2010, 2010 pdb.prot5408.
10. [10] Broad Institute website, Sample Quality and Quantiy Specifications, accessed on 23 August 2016. Available at: https://www.broadinstitute.org/scientific-community/science/platforms/genomics/sample-quality-and-quantity-specifications.
11. [11] Belisle, J.T., Mahaffey, S.B., Hill, P.J., Isolation of Mycobacterium species genomic DNA. Methods Mol Biol 465 (2009), 1–12.
12. [12] Kent, L., McHugh, T.D., Billington, O., Dale, J.W., Gillespie, S.H., Demonstration of homology between IS6110 of Mycobacterium tuberculosis and DNAs of other Mycobacterium spp.?. J Clin Microbiol 33 (1995), 2290–2293.
13. [13] van Soolingen, D., Hermans, P.W., de Haas, P.E., Soll, D.R., van Embden, J.D., Occurrence and stability of insertion sequences in Mycobacterium tuberculosis complex strains: evaluation of an insertion sequence-dependent DNA polymorphism as a tool in the epidemiology of tuberculosis. J Clin Microbiol 29 (1991), 2578–2586.
14. [14] 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.
15. [15] 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.
16. [16] Robin, J.D., Ludlow, A.T., LaRanger, R., Wright, W.E., Shay, J.W., Comparison of DNA quantification methods for next generation sequencing. Sci Rep, 6, 2016, 24067.
17. [17] University of Wisconsin – Madison, Biotechnology Center website, accessed 13 July 2016. Available at: https://www.biotech.wisc.edu/services/dnaseq/sequencing/Ion_Torrent_PGM/file_formats.
18. [18] Linux website, accessed 1 July 2016. Available at: https://www.linux.com/what-is-linux.
19. [19] Mykrobe predictor website, accessed on 3 July 2016 at: http://www.mykrobe.com/products/predictor/#tb.
20. [20] 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.
21. [21] TB Profiler website, accessed on 3rd July 2016 at: http://tbdr.lshtm.ac.uk.
22. [22] Coll, F., McNerney, R., Preston, M.D., Guerra-Assunção, 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.
23. [23] Total genotyping solution for Mycobacterium tuberculosis (TGS-TB) website, accessed on 3rd July 2016. Available at: https://gph.niid.go.jp/tgs-tb/index_tb.html.
24. [24] Sekizuka, T., Yamashita, A., Murase, Y., Iwamoto, T., Mitarai, S., Kato, S., et al. TGS-TB: total genotyping solution for Mycobacterium tuberculosis using short-read whole-genome sequencing. PLoS ONE, 10(11), 2015, e0142951.
25. [25] Phylo-Resistance Search Engine (PhyResSE) website, accessed on 3 July 2016. Available at: http://phyresse.org.
26. [26] Feuerriegel, S., Schleusener, V., Beckert, P., Kohl, T.A., Miotto, P., Cirillo, D.M., et al. PhyResSE: web tool delineating Mycobacterium tuberculosis antibiotic resistance and lineage from whole-genome sequencing data. J Clin Microbiol 53 (2015), 1908–1914.
27. [27] Köser, C.U., Ellington, M.J., Cartwright, E.J., Gillespie, S.H., Brown, N.M., Farrington, M., et al. Routine use of microbial whole genome sequencing in diagnostic and public health microbiology. PLoS Pathog., 8(8), 2012, e1002824.
28. [28] 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.
29. [29] EUCAST website, last accessed on 3rd July 2016. Available at: http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Consultation/2016/EUCAST_WGS_report_consultation_20160511.pdf.
30. [30] Javid, B., Török, M.E., Whole-genome sequencing for the diagnosis of drug-resistant tuberculosis. Lancet Infect Dis, 16, 2016, 17.
31. [31] Malik, S., Willby, M., Sikes, D., Tsodikov, O.V., Posey, J.E., New insights into fluoroquinolone resistance in Mycobacterium tuberculosis: functional genetic analysis of gyrA and gyrB mutations. PLoS One, 7, 2012, e39754.
32. [32] Eilertson, B., Maruri, F., Blackman, A., Herrera, M., Samuels, D.C., Sterling, T.R., High proportion of heteroresistance in gyrA and gyrB in fluoroquinolone-resistant Mycobacterium tuberculosis clinical isolates. Antimicrob Agents Chemother 58 (2014), 3270–3275.
33. [33] Robinson, E., Bawa, Z., Smith, E.G., Diagnosis of tuberculosis in England in the molecular genomic era. Bull R Coll Patholog 175 (2016), 163–166.
34. [34] Gardy, J.L., Johnston, J.C., Sui, S.J.H., Cook, V.J., Shah, L., Brodkin, E., et al. Whole-genome sequencing and social-network analysis of a tuberculosis outbreak. N Engl J Med 364 (2011), 730–739.
35. [35] Török, M.E., Reuter, S., Bryant, J., Köser, C.U., Stinchcombe, S.V., Nazareth, B., et al. Rapid whole-genome sequencing for investigation of a suspected tuberculosis outbreak. J Clin Microbiol 51 (2013), 611–614.
36. [36] Satta, G., Witney, A.A., Shorten, R.J., Karlikowska, M., Lipman, M., McHugh, T.D., Genetic variation in Mycobacterium tuberculosis isolates from a London outbreak associated with isoniazid resistance. BMC Med, 14, 2016, 117.
37. [37] Bryant, J.M., Harris, S.R., Parkhill, J., Dawson, R., Diacon, A.H., van Helden, P., et al. Whole-genome sequencing to establish relapse or re-infection with Mycobacterium tuberculosis: a retrospective observational study. Lancet Respir Med 1 (2013), 786–792.
38. [38] Robinson, E.R., Walker, T.M., Pallen, M.J., Genomics and outbreak investigation: from sequence to consequence. Genome Med, 5, 2013, 36.