Understanding, predicting and manipulating the genotypic evolution of antibiotic resistance

[1]  Arti Kapi The evolving threat of antimicrobial resistance: Options for action , 2014 .

[2]  J. Davies,et al.  Enhancing antibiotic activity: a strategy to control Acinetobacter infections. , 2009, The Journal of antimicrobial chemotherapy.

[3]  Hila Sheftel,et al.  Automated imaging with ScanLag reveals previously undetectable bacterial growth phenotypes , 2010, Nature Methods.

[4]  R. Lenski,et al.  Microbial genetics: Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation , 2003, Nature Reviews Genetics.

[5]  Remy Chait,et al.  Drug interactions modulate the potential for evolution of resistance , 2008, Proceedings of the National Academy of Sciences.

[6]  Alison K. Hottes,et al.  Global Discovery of Adaptive Mutations , 2009, Nature Methods.

[7]  Remy Chait,et al.  Optimal Drug Synergy in Antimicrobial Treatments , 2010, PLoS Comput. Biol..

[8]  M. Morar,et al.  The genomic enzymology of antibiotic resistance. , 2010, Annual review of genetics.

[9]  G. B. Golding,et al.  Antibiotic resistance is ancient , 2011, Nature.

[10]  Stefan Niemann,et al.  Whole-genome sequencing of rifampicin-resistant Mycobacterium tuberculosis strains identifies compensatory mutations in RNA polymerase genes , 2011 .

[11]  David L Paterson Resistance in gram-negative bacteria: enterobacteriaceae. , 2006, The American journal of medicine.

[12]  A. Moya,et al.  Evolutionary Trajectories of Beta-Lactamase CTX-M-1 Cluster Enzymes: Predicting Antibiotic Resistance , 2010, PLoS pathogens.

[13]  D. Hartl,et al.  An Equivalence Principle for the Incorporation of Favorable Mutations in Asexual Populations , 2006, Science.

[14]  Daniel J. Wilson,et al.  Transforming clinical microbiology with bacterial genome sequencing , 2012, Nature Reviews Genetics.

[15]  R. Kishony,et al.  Chemical decay of an antibiotic inverts selection for resistance. , 2010, Nature chemical biology.

[16]  D. Falush,et al.  Inference of Bacterial Microevolution Using Multilocus Sequence Data , 2007, Genetics.

[17]  D. Hughes,et al.  Sampling the Antibiotic Resistome , 2006, Science.

[18]  A. Sousa,et al.  Positive Epistasis Drives the Acquisition of Multidrug Resistance , 2009, PLoS genetics.

[19]  S Bonhoeffer,et al.  Evaluating treatment protocols to prevent antibiotic resistance. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[20]  K. Lewis,et al.  Antibiotics: Recover the lost art of drug discovery , 2012, Nature.

[21]  J. Krug,et al.  Quantifying the Adaptive Potential of an Antibiotic Resistance Enzyme , 2012, PLoS genetics.

[22]  S. Baldauf,et al.  Phylogeny for the faint of heart: a tutorial. , 2003, Trends in genetics : TIG.

[23]  Julian Parkhill,et al.  Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study , 2013, The Lancet. Infectious Diseases.

[24]  R. Kishony,et al.  Antibiotic interactions that select against resistance , 2007, Nature.

[25]  Julian Parkhill,et al.  Evolution of MRSA During Hospital Transmission and Intercontinental Spread , 2010, Science.

[26]  R. MacLean,et al.  EPISTASIS BUFFERS THE FITNESS EFFECTS OF RIFAMPICIN‐ RESISTANCE MUTATIONS IN PSEUDOMONAS AERUGINOSA , 2011, Evolution; international journal of organic evolution.

[27]  D. Hartl,et al.  Accelerated evolution of resistance in multidrug environments , 2008, Proceedings of the National Academy of Sciences.

[28]  J. Handelsman,et al.  Uncultured soil bacteria are a reservoir of new antibiotic resistance genes. , 2004, Environmental microbiology.

[29]  Stefan Niemann,et al.  Whole-genome sequencing of rifampicin-resistant M. tuberculosis strains identifies compensatory mutations in RNA polymerase , 2011, Nature Genetics.

[30]  Nigel F. Delaney,et al.  Darwinian Evolution Can Follow Only Very Few Mutational Paths to Fitter Proteins , 2006, Science.

[31]  Remy Chait,et al.  Evolutionary paths to antibiotic resistance under dynamically sustained drug selection , 2011, Nature Genetics.

[32]  Roy Kishony,et al.  Drug interactions and the evolution of antibiotic resistance , 2009, Nature Reviews Microbiology.

[33]  Diarmaid Hughes,et al.  Antibiotic resistance and its cost: is it possible to reverse resistance? , 2010, Nature Reviews Microbiology.

[34]  Julian Parkhill,et al.  Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak. , 2012, The New England journal of medicine.

[35]  Joanna B. Goldberg,et al.  Parallel bacterial evolution within multiple patients identifies candidate pathogenicity genes , 2011, Nature Genetics.

[36]  Nigel F. Delaney,et al.  FREQ-Seq: A Rapid, Cost-Effective, Sequencing-Based Method to Determine Allele Frequencies Directly from Mixed Populations , 2012, PloS one.

[37]  J. Gore,et al.  Hidden randomness between fitness landscapes limits reverse evolution. , 2011, Physical review letters.

[38]  J. Collins,et al.  Bacterial charity work leads to population-wide resistance , 2010, Nature.

[39]  Evan S Snitkin,et al.  Tracking a Hospital Outbreak of Carbapenem-Resistant Klebsiella pneumoniae with Whole-Genome Sequencing , 2012, Science Translational Medicine.

[40]  Alison K. Hottes,et al.  Genetic Architecture of Intrinsic Antibiotic Susceptibility , 2009, PloS one.

[41]  D. J. Kiviet,et al.  Empirical fitness landscapes reveal accessible evolutionary paths , 2007, Nature.

[42]  Alexander Tomasz,et al.  Tracking the in vivo evolution of multidrug resistance in Staphylococcus aureus by whole-genome sequencing , 2007, Proceedings of the National Academy of Sciences.

[43]  Thanat Chookajorn,et al.  Stepwise acquisition of pyrimethamine resistance in the malaria parasite , 2009, Proceedings of the National Academy of Sciences.

[44]  T. Mukhtar,et al.  Inactivation of the Lipopeptide Antibiotic Daptomycin by Hydrolytic Mechanisms , 2011, Antimicrobial Agents and Chemotherapy.

[45]  Dan S. Tawfik,et al.  Initial Mutations Direct Alternative Pathways of Protein Evolution , 2011, PLoS genetics.

[46]  A. Camilli,et al.  Tn-seq; high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms , 2009, Nature Methods.

[47]  J. Burton,et al.  Rapid Pneumococcal Evolution in Response to Clinical Interventions , 2011, Science.

[48]  George M Church,et al.  The human microbiome harbors a diverse reservoir of antibiotic resistance genes , 2010, Virulence.

[49]  Elena R. Lozovsky,et al.  Compensatory mutations restore fitness during the evolution of dihydrofolate reductase. , 2010, Molecular biology and evolution.

[50]  Chih-kuan Tung,et al.  Acceleration of Emergence of Bacterial Antibiotic Resistance in Connected Microenvironments , 2011, Science.

[51]  Ted Cohen,et al.  Modeling epidemics of multidrug-resistant M. tuberculosis of heterogeneous fitness , 2004, Nature Medicine.