Transmission is a key driver of extensively drug-resistant tuberculosis.

Multidrug-resistant tuberculosis (MDR-TB) and extensively drug-resistant (XDR) TB are threatening global TB control. The World Health Organization has recently endorsed new regimens for the treatment of MDR-TB that rely on the new and repurposed drugs bedaquiline, pretomanid and linezolid with or without moxifloxacin (BPaL(M)). As BPaL(M) is being rolled-out, resistance to these new drugs is already emerging, leading to acquired XDR-TB. Importantly, instances of transmitted XDR-TB have been reported. The spread of highly drug-resistant M. tuberculosis (MTB) strains pose at risk novel TB treatments that took decades to develop. In this study, we analyzed 6,926 MTB genomes from a 13-year nationwide study in Georgia, a known geographical hotspot of MDR-TB, together with more than 80,000 MTB genomes from public sources to estimate the relative contribution of transmission to the burden of XDR-TB. We show that XDR-TB is already geographically widespread, occurring in at least 27 countries across four continents. Moreover, we estimated that a quarter of the XDR-TB cases identified are likely the consequence of transmission. Our findings call for urgent improvements in the global diagnostic capacity, infection control, and surveillance of XDR-TB.

[1]  A. Gabrielian,et al.  Genetic diversity within diagnostic sputum samples is mirrored in the culture of Mycobacterium tuberculosis , 2024, bioRxiv.

[2]  I. Barilar,et al.  Emergence of bedaquiline-resistant tuberculosis and of multidrug-resistant and extensively drug-resistant Mycobacterium tuberculosis strains with rpoB Ile491Phe mutation not detected by Xpert MTB/RIF in Mozambique: a retrospective observational study. , 2023, The Lancet. Infectious diseases.

[3]  A. Witney,et al.  Baseline and acquired resistance to bedaquiline, linezolid and pretomanid, and impact on treatment outcomes in four tuberculosis clinical trials containing pretomanid , 2023, PLOS global public health.

[4]  J. Alffenaar,et al.  Pretomanid resistance: an update on emergence, mechanisms and relevance for clinical practice. , 2023, International journal of antimicrobial agents.

[5]  Sebastian M. Gygli,et al.  The relative transmission fitness of multidrug-resistant Mycobacterium tuberculosis in a drug resistance hotspot , 2023, Nature Communications.

[6]  S. Niemann,et al.  Transcontinental spread and evolution of Mycobacterium tuberculosis W148 European/Russian clade toward extensively drug resistant tuberculosis , 2022, Nature Communications.

[7]  Daniel J. Wilson,et al.  High fluoroquinolone resistance proportions among multidrug-resistant tuberculosis driven by dominant L2 Mycobacterium tuberculosis clones in the Mumbai Metropolitan Region , 2022, Genome Medicine.

[8]  Z. Iqbal,et al.  A data compendium associating the genomes of 12,289 Mycobacterium tuberculosis isolates with quantitative resistance phenotypes to 13 antibiotics , 2022, PLoS biology.

[9]  Sufyan bin Uzayr GitHub , 2022, Mastering Git.

[10]  T. Cohen,et al.  Phylogeography and transmission of M. tuberculosis in Moldova: A prospective genomic analysis , 2022, PLoS medicine.

[11]  Sebastian M. Gygli,et al.  Prisons as ecological drivers of fitness-compensated multidrug-resistant Mycobacterium tuberculosis , 2021, Nature Medicine.

[12]  I. Comas,et al.  Contaminant DNA in bacterial sequencing experiments is a major source of false genetic variability , 2020, BMC Biology.

[13]  Olga Chernomor,et al.  IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era , 2019, bioRxiv.

[14]  S. Niemann,et al.  Compensatory evolution drives multidrug-resistant tuberculosis in Central Asia , 2018, bioRxiv.

[15]  S. Gagneux Ecology and evolution of Mycobacterium tuberculosis , 2018, Nature Reviews Microbiology.

[16]  Qian Gao,et al.  Transmission of multidrug-resistant Mycobacterium tuberculosis in Shanghai, China: a retrospective observational study using whole-genome sequencing and epidemiological investigation. , 2017, The Lancet. Infectious diseases.

[17]  Liliana K. Rutaihwa,et al.  Mycobacterium tuberculosis Lineage 4 comprises globally distributed and geographically restricted sublineages , 2016, Nature Genetics.

[18]  G. Bloemberg,et al.  Acquired Resistance to Bedaquiline and Delamanid in Therapy for Tuberculosis. , 2015, The New England journal of medicine.

[19]  F. Balloux,et al.  Four decades of transmission of a multidrug-resistant Mycobacterium tuberculosis outbreak strain , 2015, Nature Communications.

[20]  Francesc Coll,et al.  A robust SNP barcode for typing Mycobacterium tuberculosis complex strains , 2014, Nature Communications.

[21]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[22]  Derrick E. Wood,et al.  Kraken: ultrafast metagenomic sequence classification using exact alignments , 2014, Genome Biology.

[23]  Jukka Corander,et al.  Evolution and transmission of drug resistant tuberculosis in a Russian population , 2014, Nature Genetics.

[24]  T. Walker,et al.  Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study , 2013, The Lancet. Infectious diseases.

[25]  J. Kalinowski,et al.  rplC T460C Identified as a Dominant Mutation in Linezolid-Resistant Mycobacterium tuberculosis Strains , 2012, Antimicrobial Agents and Chemotherapy.

[26]  M. DePristo,et al.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.

[27]  J. Galagan,et al.  Human T cell epitopes of Mycobacterium tuberculosis are evolutionarily hyperconserved , 2010, Nature Genetics.

[28]  Andrew R. Francis,et al.  The epidemiological fitness cost of drug resistance in Mycobacterium tuberculosis , 2009, Proceedings of the National Academy of Sciences.

[29]  C. D. Long,et al.  The Competitive Cost of Antibiotic Resistance in Mycobacterium tuberculosis , 2006, Science.