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Diversity of Mycobacterium tuberculosis across evolutionary scales

https://doi.org/10.1101/014217
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Revised structure of a trehalose-containing immunoreactive glycolipid of Mycobacterium tuberculosis
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Mycobacterium tuberculosis transporter MmpL7 is a potential substrate for kinase PknD
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Deep resequencing of serial sputum isolates of Mycobacterium tuberculosis during therapeutic failure due to poor compliance reveals stepwise mutation of key resistance genes on an otherwise stable genetic background
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TubercuList – 10 years after
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Recent advances in deciphering the contribution of Mycobacterium tuberculosis lipids to pathogenesis
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Molecular cloning and sequencing of the gene for mycocerosic acid synthase, a novel fatty acid elongating multifunctional enzyme, from Mycobacterium tuberculosis var. bovis Bacillus Calmette-Guerin.
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Identification of a Mycobacterium tuberculosis gene cluster encoding the biosynthetic enzymes for assembly of the virulence-conferring siderophore mycobactin
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Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence
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CD1c-mediated T-cell recognition of isoprenoid glycolipids in Mycobacterium tuberculosis infection
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Complex lipid determines tissue-specific replication of Mycobacterium tuberculosis in mice
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A glycolipid of hypervirulent tuberculosis strains that inhibits the innate immune response
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R-loops and nicks initiate DNA breakage and genome instability in non-growing Escherichia coli
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A mutation burst during the acute phase of Helicobacter pylori infection in humans and rhesus macaques
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Pseudomonas aeruginosa adaptation in the nasopharyngeal reservoir leads to migration and persistence in the lungs
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Mycobacterium tuberculosis mutation rate estimates from different lineages predict substantial differences in the emergence of drug-resistant tuberculosis
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Genome sequencing of 161 Mycobacterium tuberculosis isolates from China identifies genes and intergenic regions associated with drug resistance
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Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans
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Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis
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Genetic variation of a bacterial pathogen within individuals with cystic fibrosis provides a record of selective pressures
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Natural selection has driven population differentiation in modern humans
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A framework for variation discovery and genotyping using next-generation DNA sequencing data
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Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection
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Parallel bacterial evolution within multiple patients identifies candidate pathogenicity genes
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Identification of a virulence gene cluster of Mycobacterium tuberculosis by signature‐tagged transposon mutagenesis
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Evaluation of a nutrient starvation model of Mycobacterium tuberculosis persistence by gene and protein expression profiling
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Disruption of msl3 abolishes the synthesis of mycolipanoic and mycolipenic acids required for polyacyltrehalose synthesis in Mycobacterium tuberculosis H37Rv and causes cell aggregation
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Linkage disequilibrium between minisatellite loci supports clonal evolution of Mycobacterium tuberculosis in a high tuberculosis incidence area
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Genes required for mycobacterial growth defined by high density mutagenesis
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Deficiency in mycolipenate- and mycosanoate-derived acyltrehaloses enhances early interactions of Mycobacterium tuberculosis with host cells
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Stable association between strains of Mycobacterium tuberculosis and their human host populations
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The temporal expression profile of Mycobacterium tuberculosis infection in mice
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The nonredundant roles of two 4′-phosphopantetheinyl transferases in vital processes of Mycobacteria
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Lipidomics reveals control of Mycobacterium tuberculosis virulence lipids via metabolic coupling
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Dispersal of Mycobacterium tuberculosis via the Canadian fur trade
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Helicobacter pylori genome evolution during human infection
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Diarylcoumarins inhibit mycolic acid biosynthesis and kill Mycobacterium tuberculosis by targeting FadD32
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Evolutionary history of tuberculosis shaped by conserved mutations in the PhoPR virulence regulator
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The role of Rel Mtb -mediated adaptation to stationary phase in long-term persistence of Mycobacterium tuberculosis in mice
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Genetic requirements for mycobacterial survival during infection
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Hypervirulent mutant of Mycobacterium tuberculosis resulting from disruption of the mce1 operon
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Prevention of phagosome-lysosome fusion in cultured macrophages by sulfatides of Mycobacterium tuberculosis.
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The Virulence-associated Two-component PhoP-PhoR System Controls the Biosynthesis of Polyketide-derived Lipids in Mycobacterium tuberculosis
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The Pks13/FadD32 Crosstalk for the Biosynthesis of Mycolic Acids in Mycobacterium tuberculosis
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The Role of MmpL8 in Sulfatide Biogenesis and Virulence of Mycobacterium tuberculosis
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A Novel Interaction Linking the FAS-II and Phthiocerol Dimycocerosate (PDIM) Biosynthetic Pathways
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Transcriptional Adaptation of Mycobacterium tuberculosis within Macrophages
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Mycobacterium tuberculosis pks12 Produces a Novel Polyketide Presented by CD1c to T Cells
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CD1c tetramers detect ex vivo T cell responses to processed phosphomycoketide antigens
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Genetic Requirements for the Survival of Tubercle Bacilli in Primates
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Fast and accurate short read alignment with Burrows–Wheeler transform
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trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
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The Sequence Alignment/Map format and SAMtools
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PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq)
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RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
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Prokka: rapid prokaryotic genome annotation
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Mapping of Genotype–Phenotype Diversity among Clinical Isolates of Mycobacterium tuberculosis by Sequence-Based Transcriptional Profiling
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Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.
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Dynamic Population Changes in Mycobacterium tuberculosis During Acquisition and Fixation of Drug Resistance in Patients
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Molecular basis and mechanisms of drug resistance in Mycobacterium tuberculosis: classical and new drugs
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Bacterial Genetic Signatures of Human Social Phenomena among M. tuberculosis from an Aboriginal Canadian Population
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Evidence for Diversifying Selection in a Set of Mycobacterium tuberculosis Genes in Response to Antibiotic- and Nonantibiotic-Related Pressure
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The COG database: a tool for genome-scale analysis of protein functions and evolution
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Mycolipenates and Mycolipanolates of Trehalose from Mycobacterium tuberculosis
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Disruption of the serine/threonine protein kinase H affects phthiocerol dimycocerosates synthesis in Mycobacterium tuberculosis
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Selection of transposon mutants of Mycobacterium tuberculosis with increased macrophage infectivity identifies fadD23 to be involved in sulfolipid production and association with macrophages
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Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system
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OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
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Mycobacterial Di-O-Acyl-Trehalose Inhibits Mitogen- and Antigen-Induced Proliferation of Murine T Cells In Vitro
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Mixed-Strain Mycobacterium tuberculosis Infections and the Implications for Tuberculosis Treatment and Control
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Signature-Tagged Transposon Mutagenesis Identifies Novel Mycobacterium tuberculosis Genes Involved in the Parasitism of Human Macrophages
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Mycobacterium tuberculosis Strains Lacking Surface Lipid Phthiocerol Dimycocerosate Are Susceptible to Killing by an Early Innate Host Response
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A Genetic Screen forMycobacterium tuberculosisMutants Defective for Phagosome Maturation Arrest Identifies Components of the ESX-1 Secretion System
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The Largest Open Reading Frame ( pks12 ) in the Mycobacterium tuberculosis Genome Is Involved in Pathogenesis and Dimycocerosyl Phthiocerol Synthesis
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Contribution of theMycobacterium tuberculosisMmpL Protein Family to Virulence and Drug Resistance
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The Stringent Response of Mycobacterium tuberculosis Is Required for Long-Term Survival
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Requirement of themymAOperon for Appropriate Cell Wall Ultrastructure and Persistence ofMycobacterium tuberculosisin the Spleens of Guinea Pigs
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Extensive Within-Host Diversity in Fecally Carried Extended-Spectrum-Beta-Lactamase-Producing Escherichia coli Isolates: Implications for Transmission Analyses
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Examination of the Enterotoxigenic Escherichia coli Population Structure during Human Infection
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Environmental Heterogeneity Drives Within-Host Diversification and Evolution of Pseudomonas aeruginosa
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Trans-cyclopropanation of mycolic acids on trehalose dimycolate suppresses Mycobacterium tuberculosis-induced inflammation and virulence
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Evidence for positive selection on Mycobacterium tuberculosis within patients
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EggLib: processing, analysis and simulation tools for population genetics and genomics
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Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems
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Evolution of extensively drug-resistant Mycobacterium tuberculosisfrom a susceptible ancestor in a single patient
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The Population Genetics of dN/dS
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Comprehensive Functional Analysis of Mycobacterium tuberculosis Toxin-Antitoxin Systems: Implications for Pathogenesis, Stress Responses, and Evolution
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Coexistence and Within-Host Evolution of Diversified Lineages of Hypermutable Pseudomonas aeruginosa in Long-term Cystic Fibrosis Infections
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Tuberculosis Drug Resistance Mutation Database
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PhoP: A Missing Piece in the Intricate Puzzle of Mycobacterium tuberculosis Virulence
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Characterization of a Clp Protease Gene Regulator and the Reaeration Response in Mycobacterium tuberculosis
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Genome-Wide Screen for Mycobacterium tuberculosis Genes That Regulate Host Immunity
inferredcites →https://doi.org/10.1371/journal.pone.0015925openalex-snapshot
PoPoolation: A Toolbox for Population Genetic Analysis of Next Generation Sequencing Data from Pooled Individuals
inferredcites →https://doi.org/10.1371/journal.pone.0024301openalex-snapshot
Adaptive Evolution of Staphylococcus aureus during Chronic Endobronchial Infection of a Cystic Fibrosis Patient
inferredcites →https://doi.org/10.1371/journal.pone.0026295openalex-snapshot
Modulation of Transcriptional and Inflammatory Responses in Murine Macrophages by the Mycobacterium tuberculosis Mammalian Cell Entry (Mce) 1 Complex
inferredcites →https://doi.org/10.1371/journal.pone.0058378openalex-snapshot
Transcription of Genes Involved in Sulfolipid and Polyacyltrehalose Biosynthesis of Mycobacterium tuberculosis in Experimental Latent Tuberculosis Infection
inferredcites →https://doi.org/10.1371/journal.pone.0061319openalex-snapshot
Within-Host Evolution of Staphylococcus aureus during Asymptomatic Carriage
inferredcites →https://doi.org/10.1371/journal.pone.0064718openalex-snapshot
Evolution of Smooth Tubercle Bacilli PE and PE_PGRS Genes: Evidence for a Prominent Role of Recombination and Imprint of Positive Selection
inferredcites →https://doi.org/10.1371/journal.pone.0082551openalex-snapshot
Whole Genome Sequencing Reveals Complex Evolution Patterns of Multidrug-Resistant Mycobacterium tuberculosis Beijing Strains in Patients
inferredcites →https://doi.org/10.1371/journal.ppat.1000204openalex-snapshot
Foamy Macrophages from Tuberculous Patients' Granulomas Constitute a Nutrient-Rich Reservoir for M. tuberculosis Persistence
inferredcites →https://doi.org/10.1371/journal.ppat.1001100openalex-snapshot
High Content Phenotypic Cell-Based Visual Screen Identifies Mycobacterium tuberculosis Acyltrehalose-Containing Glycolipids Involved in Phagosome Remodeling
inferredcites →https://doi.org/10.1371/journal.ppat.1002251openalex-snapshot
High-Resolution Phenotypic Profiling Defines Genes Essential for Mycobacterial Growth and Cholesterol Catabolism
inferredcites →https://doi.org/10.1371/journal.ppat.1003543openalex-snapshot
The Role of Selection in Shaping Diversity of Natural M. tuberculosis Populations
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Cutadapt removes adapter sequences from high-throughput sequencing reads
inferredcites →https://doi.org/10.1534/genetics.107.082198openalex-snapshot
Testing for Neutrality in Samples With Sequencing Errors
inferredcites →https://doi.org/10.3109/10409238.2014.896859openalex-snapshot
Biosynthesis of mycobacterial lipids by polyketide synthases and beyond
inferredcites →https://doi.org/10.3201//eid1903.120246openalex-snapshot
Emergence and Spread of Extensively and Totally Drug-Resistant Tuberculosis, South Africa
inferredcites →https://doi.org/10.3201/eid1903.120246openalex-snapshot
Emergence and Spread of Extensively and Totally Drug-Resistant Tuberculosis, South Africa
inferredcites →https://doi.org/10.3201/eid1903.120256openalex-snapshot
Mycobacterial Lineages Causing Pulmonary and Extrapulmonary Tuberculosis, Ethiopia
inferredcites →https://doi.org/10.32614/r.manualsopenalex-snapshot
R: A Language and Environment for Statistical Computing
inferredcites →https://doi.org/10.48550/arxiv.1303.3997openalex-snapshot
Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM
inferredcites →https://doi.org/10.6084/m9.figshare.963153.v1openalex-snapshot
Aligning sequence reads, clone sequences and assembly con*gs with BWA-MEM
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