Biology of antimicrobial resistance and approaches to combat it

Mycobacterial genomics and structural bioinformatics: opportunities and challenges in drug discovery

(2019) Vaishali P. Waman et al.   Emerging Microbes & Infections

Effect of various drugs on differentially detectable persisters of Mycobacterium tuberculosis generated by long-term lipid diet

(2019) Shaheb Raj Khan et al.   TUBERCULOSIS

Opposing reactions in coenzyme A metabolism sensitize Mycobacterium tuberculosis to enzyme inhibition

(2019) Elaine Ballinger et al.   SCIENCE

Clarifying the Link between Toxin-Antitoxin Modules and Bacterial Persistence

(2019) Séverin Ronneau et al.   JOURNAL OF MOLECULAR BIOLOGY

The Isoniazid Paradigm of Killing, Resistance, and Persistence in Mycobacterium tuberculosis

(2019) Catherine Vilchèze et al.   JOURNAL OF MOLECULAR BIOLOGY

Bedaquiline kills persistent Mycobacterium tuberculosis with no disease relapse: an in vivo model of a potential cure

(2019) Yanmin Hu et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Investigating function roles of hypothetical proteins encoded by the Mycobacterium tuberculosis H37Rv genome

(2019) Zhiyuan Yang et al.   BMC GENOMICS

A White-Box Machine Learning Approach for Revealing Antibiotic Mechanisms of Action

(2019) Jason H. Yang et al.   CELL

Gamblers: An Antibiotic-Induced Evolvable Cell Subpopulation Differentiated by Reactive-Oxygen-Induced General Stress Response

(2019) John P. Pribis et al.   MOLECULAR CELL

Metabolomics-Driven Exploration of the Chemical Drug Space to Predict Combination Antimicrobial Therapies

(2019) Adrian I. Campos et al.   MOLECULAR CELL

Publisher Correction: Definitions and guidelines for research on antibiotic persistence

(2019) Nathalie Q. Balaban et al.   NATURE REVIEWS MICROBIOLOGY

Post-stress bacterial cell death mediated by reactive oxygen species

(2019) Yuzhi Hong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reactive oxygen species as the long arm of bactericidal antibiotics

(2019) Aviram Rasouly et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The challenge of antimicrobial resistance: What economics can contribute

(2019) Laurence S. J. Roope et al.   SCIENCE

Tuberculosis drugs’ distribution and emergence of resistance in patient’s lung lesions: A mechanistic model and tool for regimen and dose optimization

(2019) Natasha Strydom et al.   PLOS MEDICINE

Bacterial Metabolism and Antibiotic Efficacy

(2019) Jonathan M. Stokes et al.   Cell Metabolism

Large-scale chemical–genetics yields new M. tuberculosis inhibitor classes

(2019) Eachan O. Johnson et al.   NATURE

Lysine harvesting is an antioxidant strategy and triggers underground polyamine metabolism

(2019) Viridiana Olin-Sandoval et al.   NATURE

Mechanisms and clinical relevance of bacterial heteroresistance

(2019) Dan I. Andersson et al.   NATURE REVIEWS MICROBIOLOGY

Artificial intelligence enabled parabolic response surface platform identifies ultra-rapid near-universal TB drug treatment regimens comprising approved drugs

(2019) Daniel L. Clemens et al.   PLoS One

Subcellular antibiotic visualization reveals a dynamic drug reservoir in infected macrophages

(2019) Daniel J. Greenwood et al.   SCIENCE

Laboratory mice born to wild mice have natural microbiota and model human immune responses

(2019) Stephan P. Rosshart et al.   SCIENCE

Slow growth determines nonheritable antibiotic resistance in Salmonella enterica

(2019) Mauricio H. Pontes et al.   Science Signaling

Antimicrobial Tolerance and Metabolic Adaptations in Microbial Biofilms

(2019) Aurélie Crabbé et al.   TRENDS IN MICROBIOLOGY

Common Variants in the Glycerol Kinase Gene Reduce Tuberculosis Drug Efficacy

(2019) Michelle M. Bellerose et al.   mBio

Antibiotic combinations that exploit heteroresistance to multiple drugs effectively control infection

(2019) Victor I. Band et al.   Nature Microbiology

Salmonella persisters promote the spread of antibiotic resistance plasmids in the gut

(2019) Erik Bakkeren et al.   NATURE

Mode-of-action profiling reveals glutamine synthetase as a collateral metabolic vulnerability of M. tuberculosis to bedaquiline

(2019) Zhe Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phase variation in Mycobacterium tuberculosis glpK produces transiently heritable drug tolerance

(2019) Hassan Safi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacterial metabolic state more accurately predicts antibiotic lethality than growth rate

(2019) Allison J. Lopatkin et al.   Nature Microbiology

Mycobacterium smegmatis moxifloxacin persister cells produce high levels of hydroxyl radical, generating genetic resisters selectable not only with moxifloxacin, but also with ethambutol and isoniazid

(2019) Sharmada Swaminath et al.   MICROBIOLOGY-SGM

Bacterial Heterogeneity and Antibiotic Survival: Understanding and Combatting Persistence and Heteroresistance

(2019) Liselot Dewachter et al.   MOLECULAR CELL

Targeting redox heterogeneity to counteract drug tolerance in replicating Mycobacterium tuberculosis

(2019) Richa Mishra et al.   Science Translational Medicine

Transcriptomic Signatures Predict Regulators of Drug Synergy and Clinical Regimen Efficacy against Tuberculosis

(2019) Shuyi Ma et al.   mBio

Implementation of permeation rules leads to a FabI inhibitor with activity against Gram-negative pathogens

(2019) Erica N. Parker et al.   Nature Microbiology

Differentially Culturable Tubercule Bacilli Are Generated during Nonpulmonary Tuberculosis Infection

(2018) Andrew Rosser et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

DNA-encoded libraries – an efficient small molecule discovery technology for the biomedical sciences

(2018) Verena Kunig et al.   BIOLOGICAL CHEMISTRY

Timing of DNA damage responses impacts persistence to fluoroquinolones

(2018) Wendy W. K. Mok et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reassessing the Role of Type II Toxin-Antitoxin Systems in Formation of Escherichia coli Type II Persister Cells

(2018) Frédéric Goormaghtigh et al.   mBio

Posttranslational modification of a histone-like protein regulates phenotypic resistance to isoniazid in mycobacteria

(2018) Alexandra Sakatos et al.   Science Advances

Bacterial Factors That Predict Relapse after Tuberculosis Therapy

(2018) Roberto Colangeli et al.   NEW ENGLAND JOURNAL OF MEDICINE

The kinases HipA and HipA7 phosphorylate different substrate pools in Escherichia coli to promote multidrug tolerance

(2018) Maja Semanjski et al.   Science Signaling

Modeling Diversity: Do Homogeneous Laboratory Strains Limit Discovery?

(2018) Clare M. Smith et al.   TRENDS IN MICROBIOLOGY

Clinically prevalent mutations in Mycobacterium tuberculosis alter propionate metabolism and mediate multidrug tolerance

(2018) Nathan D. Hicks et al.   Nature Microbiology

Analysis of the clinical antibacterial and antituberculosis pipeline

(2018) Ursula Theuretzbacher et al.   LANCET INFECTIOUS DISEASES

Inhibiting the Evolution of Antibiotic Resistance

(2018) Mark N. Ragheb et al.   MOLECULAR CELL

ATP-Dependent Dynamic Protein Aggregation Regulates Bacterial Dormancy Depth Critical for Antibiotic Tolerance

(2018) Yingying Pu et al.   MOLECULAR CELL

Heterogeneity in efflux pump expression predisposes antibiotic-resistant cells to mutation

(2018) Imane El Meouche et al.   SCIENCE

Salmonella persisters undermine host immune defenses during antibiotic treatment

(2018) Daphne A. C. Stapels et al.   SCIENCE

Differentially Detectable Mycobacterium tuberculosis Cells in Sputum from Treatment-Naive Subjects in Haiti and Their Proportionate Increase after Initiation of Treatment

(2018) Kathrine McAulay et al.   mBio

Kunkel Lecture: Fundamental immunodeficiency and its correction

(2017) Carl Nathan   JOURNAL OF EXPERIMENTAL MEDICINE

Deletion of a mycobacterial divisome factor collapses single-cell phenotypic heterogeneity

(2017) E. Hesper Rego et al.   NATURE

Persistent bacterial infections and persister cells

(2017) Robert A. Fisher et al.   NATURE REVIEWS MICROBIOLOGY

Rifamycin action on RNA polymerase in antibiotic-tolerantMycobacterium tuberculosisresults in differentially detectable populations

(2017) Kohta Saito et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Antibiotic tolerance facilitates the evolution of resistance

(2017) Irit Levin-Reisman et al.   SCIENCE

Emerging Approaches to Tuberculosis Drug Development: At Home in the Metabolome

(2017) Robert S. Jansen et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Mechanisms of resistance against NITD-916, a direct inhibitor of Mycobacterium tuberculosis InhA

(2017) Matthew B. McNeil et al.   TUBERCULOSIS

Comprehensive Essentiality Analysis of the Mycobacterium tuberculosis Genome via Saturating Transposon Mutagenesis

(2017) Michael A. DeJesus et al.   mBio

An In Vitro Caseum Binding Assay that Predicts Drug Penetration in Tuberculosis Lesions

(2017) Jansy P. Sarathy et al.   Jove-Journal of Visualized Experiments

Metabolic anticipation in Mycobacterium tuberculosis

(2017) Hyungjin Eoh et al.   Nature Microbiology

Programmable transcriptional repression in mycobacteria using an orthogonal CRISPR interference platform

(2017) Jeremy M. Rock et al.   Nature Microbiology

Efficient measurement and factorization of high-order drug interactions in Mycobacterium tuberculosis

(2017) Murat Cokol et al.   Science Advances

Detection and Quantification of Differentially Culturable Tubercle Bacteria in Sputum from Patients with Tuberculosis

(2016) Melissa D. Chengalroyen et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

De Novo Emergence of Genetically Resistant Mutants of Mycobacterium tuberculosis from the Persistence Phase Cells formed against Antituberculosis Drugs In Vitro

(2016) Jees Sebastian et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Immune activation of the host cell induces drug tolerance inMycobacterium tuberculosisboth in vitro and in vivo

(2016) Yancheng Liu et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Enhanced Efflux Activity Facilitates Drug Tolerance in Dormant Bacterial Cells

(2016) Yingying Pu et al.   MOLECULAR CELL

Bacterial persistence is an active σSstress response to metabolic flux limitation

(2016) Jakub Leszek Radzikowski et al.   Molecular Systems Biology

Chemogenomics and orthology‐based design of antibiotic combination therapies

(2016) Sriram Chandrasekaran et al.   Molecular Systems Biology

Distinguishing between resistance, tolerance and persistence to antibiotic treatment

(2016) Asher Brauner et al.   NATURE REVIEWS MICROBIOLOGY

Mechanisms of bacterial persistence during stress and antibiotic exposure

(2016) Alexander Harms et al.   SCIENCE

Tuberculosis Susceptibility and Vaccine Protection Are Independently Controlled by Host Genotype

(2016) Clare M. Smith et al.   mBio

The essential mycobacterial amidotransferase GatCAB is a modulator of specific translational fidelity

(2016) Hong-Wei Su et al.   Nature Microbiology

Network analysis identifies Rv0324 and Rv0880 as regulators of bedaquiline tolerance in Mycobacterium tuberculosis

(2016) Eliza J. R. Peterson et al.   Nature Microbiology

Persister formation in Staphylococcus aureus is associated with ATP depletion

(2016) Brian P. Conlon et al.   Nature Microbiology

Stressed Mycobacteria Use the Chaperone ClpB to Sequester Irreversibly Oxidized Proteins Asymmetrically Within and Between Cells

(2015) Julien Vaubourgeix et al.   Cell Host & Microbe

Stress and Host Immunity Amplify Mycobacterium tuberculosis Phenotypic Heterogeneity and Induce Nongrowing Metabolically Active Forms

(2015) Giulia Manina et al.   Cell Host & Microbe

Forecasting Accuracy of the Hollow Fiber Model of Tuberculosis for Clinical Therapeutic Outcomes

(2015) Tawanda Gumbo et al.   CLINICAL INFECTIOUS DISEASES

Antibiotic Body Burden of Chinese School Children: A Multisite Biomonitoring-based Study

(2015) Hexing Wang et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Global trends in antimicrobial use in food animals

(2015) Thomas P. Van Boeckel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ranking of persister genes in the same Escherichia coli genetic background demonstrates varying importance of individual persister genes in tolerance to different antibiotics

(2015) Nan Wu et al.   Frontiers in Microbiology

Bacterial Resistance to Leucyl-tRNA Synthetase Inhibitor GSK2251052 Develops during Treatment of Complicated Urinary Tract Infections

(2014) Karen O'Dwyer et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

The Cyclic Peptide Ecumicin Targeting ClpC1 Is Active against Mycobacterium tuberculosis In Vivo

(2014) Wei Gao et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Phenotypic bistability in Escherichia coli's central carbon metabolism

(2014) O. Kotte et al.   Molecular Systems Biology

Optimization of lag time underlies antibiotic tolerance in evolved bacterial populations

(2014) Ofer Fridman et al.   NATURE

Antibiotic Resistance — Problems, Progress, and Prospects

(2014) Carl Nathan et al.   NEW ENGLAND JOURNAL OF MEDICINE

Nutrient Transitions Are a Source of Persisters in Escherichia coli Biofilms

(2014) Stephanie M. Amato et al.   PLoS One

Antibiotics induce redox-related physiological alterations as part of their lethality

(2014) D. J. Dwyer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mycobacterial mistranslation is necessary and sufficient for rifampicin phenotypic resistance

(2014) B. Javid et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Isocitrate lyase mediates broad antibiotic tolerance in Mycobacterium tuberculosis

(2014) Madhumitha Nandakumar et al.   Nature Communications

The importance of the viable but non-culturable state in human bacterial pathogens

(2014) Laam Li et al.   Frontiers in Microbiology

Dormancy Is Not Necessary or Sufficient for Bacterial Persistence

(2013) Mehmet A. Orman et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Lipoamide Channel-Binding Sulfonamides Selectively Inhibit Mycobacterial Lipoamide Dehydrogenase

(2013) Ruslana Bryk et al.   BIOCHEMISTRY

The Normalcy of Dormancy: Common Themes in Microbial Quiescence

(2013) Emily S.C. Rittershaus et al.   Cell Host & Microbe

Microbial Persistence and the Road to Drug Resistance

(2013) Nadia R. Cohen et al.   Cell Host & Microbe

Potentiating antibacterial activity by predictably enhancing endogenous microbial ROS production

(2013) Mark P Brynildsen et al.   NATURE BIOTECHNOLOGY

A genetic strategy to identify targets for the development of drugs that prevent bacterial persistence

(2013) J.-H. Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Direct observation of single stationary-phase bacteria reveals a surprisingly long period of constant protein production activity

(2013) O. Gefen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Activation of heme biosynthesis by a small molecule that is toxic to fermenting Staphylococcus aureus

(2013) L. A. Mike et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multifunctional essentiality of succinate metabolism in adaptation to hypoxia in Mycobacterium tuberculosis

(2013) H. Eoh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cell Death from Antibiotics Without the Involvement of Reactive Oxygen Species

(2013) Y. Liu et al.   SCIENCE

Killing by Bactericidal Antibiotics Does Not Depend on Reactive Oxygen Species

(2013) I. Keren et al.   SCIENCE

Dynamic Persistence of Antibiotic-Stressed Mycobacteria

(2013) Y. Wakamoto et al.   SCIENCE

HipA-mediated antibiotic persistence via phosphorylation of the glutamyl-tRNA-synthetase

(2013) Ilana Kaspy et al.   Nature Communications

A Genome-Wide Screen in Yeast Identifies Specific Oxidative Stress Genes Required for the Maintenance of Sub-Cellular Redox Homeostasis

(2012) Anita Ayer et al.   PLoS One

Large mutational target size for rapid emergence of bacterial persistence

(2012) H. S. Girgis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Oxidation of the Guanine Nucleotide Pool Underlies Cell Death by Bactericidal Antibiotics

(2012) J. J. Foti et al.   SCIENCE

Para-Aminosalicylic Acid Acts as an Alternative Substrate of Folate Metabolism in Mycobacterium tuberculosis

(2012) S. Chakraborty et al.   SCIENCE

Fresh Approaches to Anti-Infective Therapies

(2012) C. Nathan   Science Translational Medicine

Drug Tolerance in Replicating Mycobacteria Mediated by a Macrophage-Induced Efflux Mechanism

(2011) Kristin N. Adams et al.   CELL

Making Space for Anti-Infective Drug Discovery

(2011) Carl Nathan   Cell Host & Microbe

Virulence of Mycobacterium tuberculosis Depends on Lipoamide Dehydrogenase, a Member of Three Multienzyme Complexes

(2011) Aditya Venugopal et al.   Cell Host & Microbe

GENETIC VARIATION FOR ANTIBIOTIC PERSISTENCE IN ESCHERICHIA COLI

(2011) Balint Stewart et al.   EVOLUTION

Role of persister cells in chronic infections: clinical relevance and perspectives on anti-persister therapies

(2011) M. Fauvart et al.   JOURNAL OF MEDICAL MICROBIOLOGY

Active Starvation Responses Mediate Antibiotic Tolerance in Biofilms and Nutrient-Limited Bacteria

(2011) D. Nguyen et al.   SCIENCE

H2S: A Universal Defense Against Antibiotics in Bacteria

(2011) K. Shatalin et al.   SCIENCE

Characterization and Transcriptome Analysis of Mycobacterium tuberculosis Persisters

(2011) I. Keren et al.   mBio

Nitazoxanide Disrupts Membrane Potential and Intrabacterial pH Homeostasis of Mycobacterium tuberculosis

(2011) Luiz Pedro S. de Carvalho et al.   ACS Medicinal Chemistry Letters

Fitness Landscape of Antibiotic Tolerance in Pseudomonas aeruginosa Biofilms

(2011) Sasan Amini et al.   PLoS Pathogens

Simple Model for Testing Drugs against Nonreplicating Mycobacterium tuberculosis

(2010) C. Sala et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Mycobacterium tuberculosis persistence mutants identified by screening in isoniazid-treated mice

(2010) N. Dhar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A chemical genetic screen in Mycobacterium tuberculosis identifies carbon-source-dependent growth inhibitors devoid of in vivo efficacy

(2010) Kevin Pethe et al.   Nature Communications

Resuscitation-promoting Factors Reveal an Occult Population of Tubercle Bacilli in Sputum

(2009) Galina V. Mukamolova et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Inhibitors selective for mycobacterial versus human proteasomes

(2009) Gang Lin et al.   NATURE

Endogenous Nitric Oxide Protects Bacteria Against a Wide Spectrum of Antibiotics

(2009) I. Gusarov et al.   SCIENCE

Molecular Mechanisms of HipA-Mediated Multidrug Tolerance and Its Neutralization by HipB

(2009) M. A. Schumacher et al.   SCIENCE

Selective Killing of Nonreplicating Mycobacteria

(2008) Ruslana Bryk et al.   Cell Host & Microbe