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. 2022 Aug 30;13:5105. doi: 10.1038/s41467-022-32455-1

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© The Author(s) 2022

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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Fig. 3 — a Bayesian time tree based on 5264 variable positions (SNPs) among the 720 W148 strains and 11 lineage 2 outgroup strains. The different crowns are showing the presence (filled box) or absence (empty box) of mutations conferring resistance to different drugs: INH Isoniazid, SM Streptomycin, RIF Rifampicin, EMB Ethambutol, PZA Pyrazinamide, FQ Fluoroquinolones, KM Kanamycin, ETH Ethionamide and PAS Para-aminoslicylic acid; strains drug resistance profiles: XDR, Pre-XDR and carrying putative rpoB compensation. b Box plot representing the emergence time of different antibiotic resistances. Highlighted dates indicate emergence of rifampicin resistance on top of pre-existing isoniazid resistance and thus MDR-TB (1991), pyrazinamide resistance (2002), fluoroquinolone resistance and XDR-TB (both 2009). Solid bars indicate median node ages, boxes represent the inter quartile range (IQR), whiskers extend to 1.5× IQR, outliers are shown as individual points.