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. 2018 Mar 20;8:4910. doi: 10.1038/s41598-018-23337-y

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© The Author(s) 2018

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Phylogenetic analysis of M. tuberculosis isolates from TBM and PulTB patients. The phylogenetic tree was inferred using the maximum likelihood method with general time reversible and gamma distribution model using 4,490 high-confidence SNPs and compared to the H37Rv reference genome. The bootstrap consensus tree was inferred from 1,000 replicates. Blue circles refer to bootstrap values and the size of each circle is proportional to its value (most of the bootstrap values are 100). Black, red and orange branches and letters refer to Mtb isolates from sputum (SPT) of PulTB cases, cerebrospinal fluid (CSF) of TBM cases, and extrapulmonary (ExP) samples other than CSF, respectively. The upper portion of the tree has been magnified as an inset. Two small clusters of Mtb isolated from TBM patients are indicated in green boxes. Numbers in the outer ring (e.g. 2009) refer to year of collection and NA indicates unavailable data.