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. 2017 Dec 15;7:17672. doi: 10.1038/s41598-017-17705-3

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© The Author(s) 2017

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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Maximum-likelihood tree of 139 Mycobacterium tuberculosis complex isolates from Djibouti. The tree was calculated by using the general time reversible substitution model with gamma distribution and bootstrap resampling based on single-nucleotide polymorphisms identified by whole-genome sequencing. Substitution models were tested and the tree generated by using MetaPiga software version 3.1 and the maximum-likelihood ratio test. Midpoint rooting was performed. Distinct colors were chosen for the lineages identified; the Coll-nomenclature inferred from the whole-genome sequencing data. MDR-TB strains resistant to second line injectable drugs are highlighted in bold. Asterisks indicate clustered MDR-TB isolates from patients aged ≥55 years. Clusters with rifampicin resistant isolates are indicated as RR, while clusters with rifampicin susceptible isolates are indicated as RS. Scale bar indicates nucleotide substitutions per site.