mBio · 2019 · 120 citations · 38 references
Life SciencesGeneticsMolecular GeneticsBiochemical GeneticsMetabolismMicrobial GeneticsAntibiotic ResistanceAntibiotic Resistance EvolutionAntibiotic Resistance GeneticsAntibiotic Resistance MechanismsDrug Metabolism GenomicsDrug Resistance GenomicsCommon Genetic VariantsDuration Of Antibiotic TreatmentMetabolic Degradation PathwaysMolecular Drug ResistanceMutational Pathways Of ResistanceResistance ClonesResistance In Clinical IsolatesTuberculosis Drug Resistance
TB control is limited in part by the length of antibiotic treatment needed to prevent recurrent disease. To probe mechanisms underlying survival under antibiotic pressure, we performed a genetic screen for M. tuberculosis mutants with altered susceptibility to treatment using the mouse model of TB. We identified multiple genes involved in a range of functions which alter sensitivity to antibiotics. In particular, we found glycerol catabolism mutants were less susceptible to treatment and that common variation in a homopolymeric region in the glpK gene was associated with drug resistance in clinical isolates. These studies indicate that reversible high-frequency variation in carbon metabolic pathways can produce phenotypically drug-tolerant clones and have a role in the development of resistance.
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The Sequence Alignment/Map format and SAMtools
Heng Li, Alec Wysoker, Tim Fennell et al. · Bioinformatics · 2009 · 67.5K citations · Full text
PHYLIP-Phylogeny inference package (Version 3.2)
Joe Felsenstein · Cladistics · 1989 · 17.9K citations
PAML 4: Phylogenetic Analysis by Maximum Likelihood
Molecular Biology and Evolution · 2007 · 14.8K citations · Full text
A framework for variation discovery and genotyping using next-generation DNA sequencing data
Mark A. DePristo, Eric Banks, Ryan Poplin et al. · Nature Genetics · 2011 · 12.4K citations · Full text