TY - JOUR T1 - Whole Genome Sequencing of <em>Mycobacterium tuberculosis</em> JF - European Respiratory Journal JO - Eur Respir J DO - 10.1183/13993003.01163-2018 SP - 1801163 AU - Andrea M. Cabibbe AU - Timothy M. Walker AU - Stefan Niemann AU - Daniela M. Cirillo Y1 - 2018/01/01 UR - http://erj.ersjournals.com/content/early/2018/09/06/13993003.01163-2018.abstract N2 - Next Generation Sequencing (NGS) technologies using massively parallel processing to interrogate pathogen genomes in days are revolutionising the clinical microbiology practice [1]. Whole genome sequencing (WGS) offers unprecedented resolution for genotyping, outbreak investigation and determination of known sequence variants involved in antimicrobial resistance (AMR), which deep sequencing of selected genomic regions (targeted NGS, tNGS) can further illuminate. WGS-based approach has been proposed for surveillance of bacterial pathogens included in the “priority list” by the World Health Organization (WHO) [2]. At present, proof-of-principle and validation studies have been conducted for WGS from culture samples of Escherichia coli, Klebsiella pneumoniae, Staphylococcus aureus, Streptococcus pneumoniae, Pseudomonas aeruginosa, Salmonella spp., Acinetobacter spp., Neisseria gonorrhoeae and Clostridium difficile included in this list, in addition to the globally established priority group Mycobacteria spp. (including Mycobacterium tuberculosis, MTB) [3].FootnotesThis manuscript has recently been accepted for publication in the European Respiratory Journal. It is published here in its accepted form prior to copyediting and typesetting by our production team. After these production processes are complete and the authors have approved the resulting proofs, the article will move to the latest issue of the ERJ online. Please open or download the PDF to view this article.Conflict of interest: Dr. Cabibbe has nothing to disclose.Conflict of interest: Dr. Walker has nothing to disclose.Conflict of interest: Dr. Niemann reports grants from German Center for Infection Research, grants from Leibniz Science Campus Evolung, during the conduct of the study.Conflict of interest: Dr. Cirillo has nothing to disclose. ER -