title: Real-Time Sequencing of Mycobacterium tuberculosis: Are We There Yet?
abstract: Whole-genome sequencing has taken a leading role in epidemiologic studies of tuberculosis, but thus far, its real-time clinical utility has been low, in part because of the requirement for culture. In their report in this issue, Votintseva et al. (A. A. Votintseva, P. Bradley, L. Pankhurst, C. del Ojo Elias, M. Loose, K. Nilgiriwala, A. Chatterjee, E. G. Smith, N. Sanderson, T. M. Walker, M. R. Morgan, D. H. Wyllie, A. S. Walker, T. E. A. Peto, D. W. Crook, and Z. Iqbal, J Clin Microbiol 55:1285-1298, 2017, https://doi.org/10.1128/JCM.02483-16) present a new method for extractingMycobacterium tuberculosisDNA directly from smear-positive respiratory samples, making it feasible to generate drug resistance predictions and phylogenetic trees in 44 h with the Illumina MiSeq. They also illustrate the potential for a <24-h turnaround time from DNA extraction to clinically relevant results with Illumina MiniSeq and Oxford Nanopore Technologies MinION. We comment on the promise and limitations of these approaches.
authors.affiliation: Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia.|Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne, Melbourne, Victoria, Australia.
authors.forename: Robyn S
authors.initials: RS
authors.lastname: Lee
authors.affiliation: McGill International TB Centre, Montréal, Québec, Canada madhukar.pai@mcgill.ca.|McGill Global Health Programs, McGill University, Montréal, Québec, Canada.|Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec, Canada.
authors.forename: Madhukar
authors.initials: M
authors.lastname: Pai
mesh_terms: D004269:DNA, Bacterial / Q000032:analysis*; D016680:Genome, Bacterial / Q000235:genetics*; D006801:Humans; D008826:Microbial Sensitivity Tests; D009169:Mycobacterium tuberculosis / Q000187:drug effects* / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods; D014397:Tuberculosis, Pulmonary / Q000175:diagnosis* / Q000188:drug therapy / Q000382:microbiology
chemical_list: D004269:DNA, Bacterial