Transcontinental spread and evolution of Mycobacterium tuberculosis W148 European/Russian clade toward extensively drug resistant tuberculosis

[1]  V. Chongsuvivatwong,et al.  Revised nomenclature and SNP barcode for Mycobacterium tuberculosis lineage 2 , 2021, Microbial genomics.

[2]  T. Wirth.  When specialized clones go global , 2021, Nature Microbiology.

[3]  R. Antoine,et al.  Intragenic Distribution of IS6110 in Clinical Mycobacterium tuberculosis Strains: Bioinformatic Evidence for Gene Disruption Leading to Underdiagnosed Antibiotic Resistance , 2021, Microbiology spectrum.

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

[5]  T. Dallman,et al.  Emergence and global spread of Listeria monocytogenes main clinical clonal complex , 2020, bioRxiv.

[6]  Charles L. Dulberger,et al.  Mutations in dnaA and a cryptic interaction site increase drug resistance in Mycobacterium tuberculosis , 2020, PLoS pathogens.

[7]  L. Rigouts,et al.  Characterization of genomic variants associated with resistance to bedaquiline and delamanid in naïve Mycobacterium tuberculosis clinical strains , 2020, bioRxiv.

[8]  F. Vandenesch,et al.  Applied phyloepidemiology: Detecting drivers of pathogen transmission from genomic signatures using density measures , 2020, Evolutionary applications.

[9]  C. Köser,et al.  Systematic review of mutations associated with resistance to the new and repurposed Mycobacterium tuberculosis drugs bedaquiline, clofazimine, linezolid, delamanid and pretomanid. , 2020, The Journal of antimicrobial chemotherapy.

[10]  Laurent Jacob,et al.  Niche specialization and spread of Staphylococcus capitis involved in neonatal sepsis , 2020, Nature Microbiology.

[11]  J. Parkhill,et al.  Phylogenetically informative mutations in genes implicated in antibiotic resistance in Mycobacterium tuberculosis complex , 2020, Genome Medicine.

[12]  Richard Bonneau,et al.  Pre-detection history of extensively drug-resistant tuberculosis in KwaZulu-Natal, South Africa , 2019, Proceedings of the National Academy of Sciences.

[13]  Matthew W. Snyder,et al.  GWAS for quantitative resistance phenotypes in Mycobacterium tuberculosis reveals resistance genes and regulatory regions , 2019, Nature Communications.

[14]  Joseph Crispell,et al.  HomoplasyFinder: a simple tool to identify homoplasies on a phylogeny , 2019, Microbial genomics.

[15]  Stefan Niemann,et al.  MTBseq: a comprehensive pipeline for whole genome sequence analysis of Mycobacterium tuberculosis complex isolates , 2018, PeerJ.

[16]  T. Clark,et al.  Global expansion of Mycobacterium tuberculosis lineage 4 shaped by colonial migration and local adaptation , 2018, Science Advances.

[17]  B. Zhao,et al.  Clinically prevalent mutations in Mycobacterium tuberculosis alter propionate metabolism and mediate multidrug tolerance , 2018, Nature Microbiology.

[18]  A. Diacon,et al.  Perspectives for personalized therapy for patients with multidrug‐resistant tuberculosis , 2018, Journal of internal medicine.

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

[20]  S. Boisset,et al.  Changing patterns of human migrations shaped the global population structure of Mycobacterium tuberculosis in France , 2018, Scientific Reports.

[21]  A. Pain,et al.  Mutations in ppe38 block PE_PGRS secretion and increase virulence of Mycobacterium tuberculosis , 2018, Nature Microbiology.

[22]  T. Clark,et al.  Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis , 2018, Nature Genetics.

[23]  C. Khatchikian,et al.  tipdatingbeast: an r package to assist the implementation of phylogenetic tip‐dating tests using beast , 2017, Molecular ecology resources.

[24]  K. Dooley,et al.  The epidemiology, pathogenesis, transmission, diagnosis, and management of multidrug-resistant, extensively drug-resistant, and incurable tuberculosis. , 2017, The Lancet. Respiratory medicine.

[25]  S. Boisset,et al.  Strain-specific estimation of epidemic success provides insights into the transmission dynamics of tuberculosis , 2017, Scientific Reports.

[26]  Andrew Kitchen,et al.  Armed conflict and population displacement as drivers of the evolution and dispersal of Mycobacterium tuberculosis , 2016, Proceedings of the National Academy of Sciences.

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

[28]  Peer Bork,et al.  Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees , 2016, Nucleic Acids Res..

[29]  Lin Sun,et al.  Compensatory Mutations of Rifampin Resistance Are Associated with Transmission of Multidrug-Resistant Mycobacterium tuberculosis Beijing Genotype Strains in China , 2016, Antimicrobial Agents and Chemotherapy.

[30]  Andrew Rambaut,et al.  Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen) , 2016, Virus evolution.

[31]  Thomas Abeel,et al.  Evolution of Extensively Drug-Resistant Tuberculosis over Four Decades: Whole Genome Sequencing and Dating Analysis of Mycobacterium tuberculosis Isolates from KwaZulu-Natal , 2015, PLoS medicine.

[32]  T. Wirth.  Massive lineage replacements and cryptic outbreaks of Salmonella Typhi in eastern and southern Africa , 2015, Nature Genetics.

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

[34]  M. Shulgina,et al.  Tuberculosis in Russia. Its history and its status today. , 2015, American journal of respiratory and critical care medicine.

[35]  Nalin Rastogi,et al.  Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage , 2015, Nature Genetics.

[36]  Dong Xie,et al.  BEAST 2: A Software Platform for Bayesian Evolutionary Analysis , 2014, PLoS Comput. Biol..

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

[38]  V. Govorun,et al.  Unusual Large-Scale Chromosomal Rearrangements in Mycobacterium tuberculosis Beijing B0/W148 Cluster Isolates , 2014, PloS one.

[39]  Dongfang Li,et al.  Genome sequencing of 161 Mycobacterium tuberculosis isolates from China identifies genes and intergenic regions associated with drug resistance , 2013, Nature Genetics.

[40]  Marc Lipsitch,et al.  Mycobacterium tuberculosis mutation rate estimates from different lineages predict substantial differences in the emergence of drug resistant tuberculosis , 2013, Nature Genetics.

[41]  I. Mokrousov.  Insights into the Origin, Emergence, and Current Spread of a Successful Russian Clone of Mycobacterium tuberculosis , 2013, Clinical Microbiology Reviews.

[42]  A. Skrahina,et al.  Multidrug-resistant Tuberculosis in Belarus: the Size of the Problem and Associated Risk Factors , 2022 .

[43]  L. Liljas,et al.  Fitness‐compensatory mutations in rifampicin‐resistant RNA polymerase , 2012, Molecular microbiology.

[44]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[45]  G. Cooke,et al.  International Spread of MDR TB from Tugela Ferry, South Africa , 2011, Emerging infectious diseases.

[46]  O. Gascuel,et al.  New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. , 2010, Systematic biology.

[47]  Emmanuel Paradis,et al.  pegas: an R package for population genetics with an integrated-modular approach , 2010, Bioinform..

[48]  P. V. van Helden,et al.  Evidence for a rapid rate of molecular evolution at the hypervariable and immunogenic Mycobacterium tuberculosis PPE38 gene region , 2009, BMC Evolutionary Biology.

[49]  Andreas Handel,et al.  The Role of Compensatory Mutations in the Emergence of Drug Resistance , 2006, PLoS Comput. Biol..

[50]  D. Reich,et al.  Principal components analysis corrects for stratification in genome-wide association studies , 2006, Nature Genetics.

[51]  Korbinian Strimmer,et al.  APE: Analyses of Phylogenetics and Evolution in R language , 2004, Bioinform..

[52]  Tanya Parish,et al.  Deletion of Two-Component Regulatory Systems Increases the Virulence of Mycobacterium tuberculosis , 2003, Infection and Immunity.

[53]  Barun Mathema,et al.  Global dissemination of the Mycobacterium tuberculosis W-Beijing family strains. , 2002, Trends in microbiology.

[54]  Marti J. Anderson,et al.  Permutation Tests for Linear Models , 2001 .

[55]  J. Gowrishankar,et al.  trans-Acting Mutations in Loci Other than kdpDE That Affect kdp Operon Regulation inEscherichia coli: Effects of Cytoplasmic Thiol Oxidation Status and Nucleoid Protein H-NS on kdpExpression , 2001, Journal of bacteriology.

[56]  A. Renton,et al.  Epidemics of syphilis in the newly independent states of the former Soviet Union. , 1998, Sexually Transmitted Infections.

[57]  D. Wares,et al.  Tuberculosis in Russia , 1997, The Lancet.

[58]  S. Dittmann,et al.  Current situation and control strategies for resurgence of diphtheria in newly independent states of the former Soviet Union , 1996, The Lancet.