Biofilm antimicrobial susceptibility through an experimental evolutionary lens

Persistence and genetic adaptation of Pseudomonas aeruginosa in patients with chronic obstructive pulmonary disease

(2022) Josefin Eklöf et al.   CLINICAL MICROBIOLOGY AND INFECTION

Tolerance and resistance of microbial biofilms

(2022) Oana Ciofu et al.   NATURE REVIEWS MICROBIOLOGY

Bacterial biofilms predominate in both acute and chronic human lung infections

(2022) Mette Kolpen et al.   THORAX

Modular 3D-Printed Peg Biofilm Device for Flexible Setup of Surface-Related Biofilm Studies

(2022) Greta Zaborskytė et al.   Frontiers in Cellular and Infection Microbiology

Search for a Shared Genetic or Biochemical Basis for Biofilm Tolerance to Antibiotics across Bacterial Species

(2022) Philip S. Stewart et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Visualization of mRNA Expression in Pseudomonas aeruginosa Aggregates Reveals Spatial Patterns of Fermentative and Denitrifying Metabolism

(2022) Jadzia Livingston et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Genomics of diversification of Pseudomonas aeruginosa in cystic fibrosis lung-like conditions

(2022) Alana Schick et al.   Genome Biology and Evolution

The anti-virulence activity of the non-mevalonate pathway inhibitor FR900098 towards Burkholderia cenocepacia is maintained during experimental evolution

(2022) Mona Bové et al.   MICROBIOLOGY-SGM

Population genetics, biofilm recalcitrance, and antibiotic resistance evolution

(2022) Barbora Trubenová et al.   TRENDS IN MICROBIOLOGY

Modulating the evolutionary trajectory of tolerance using antibiotics with different metabolic dependencies

(2022) Erica J. Zheng et al.   Nature Communications

A Microfluidic Chip for Studies of the Dynamics of Antibiotic Resistance Selection in Bacterial Biofilms

(2022) Po-Cheng Tang et al.   Frontiers in Cellular and Infection Microbiology

Pseudomonas aeruginosa Is More Tolerant Under Biofilm Than Under Planktonic Growth Conditions: A Multi-Isolate Survey

(2022) Janne G. Thöming et al.   Frontiers in Cellular and Infection Microbiology

Evolved resistance to a novel cationic peptide antibiotic requires high mutation supply

(2022) Alfonso Santos-Lopez et al.   Evolution Medicine and Public Health

Cefotaxime Exposure Selects Mutations within the CA-Domain of envZ Which Promote Antibiotic Resistance but Repress Biofilm Formation in Salmonella

(2022) Eleftheria Trampari et al.   Microbiology Spectrum

The biofilm life cycle: expanding the conceptual model of biofilm formation

(2022) Karin Sauer et al.   NATURE REVIEWS MICROBIOLOGY

Antibiotic Minimal Selective Concentrations and Fitness Costs during Biofilm and Planktonic Growth

(2022) Karin Hjort et al.   mBio

Evolution of Habitat-Dependent Antibiotic Resistance in Pseudomonas aeruginosa

(2022) Pablo Laborda et al.   Microbiology Spectrum

Microfluidic Evolution‐On‐A‐Chip Reveals New Mutations that Cause Antibiotic Resistance

(2021) Ahmed E. Zoheir et al.   Small

Phenotypic and Genotypic Adaptations in Pseudomonas aeruginosa Biofilms following Long-Term Exposure to an Alginate Oligomer Therapy

(2021) Juliette L. Oakley et al.   mSphere

Exposure of Salmonella biofilms to antibiotic concentrations rapidly selects resistance with collateral tradeoffs

(2021) Eleftheria Trampari et al.   npj Biofilms and Microbiomes

Clinically relevant mutations in core metabolic genes confer antibiotic resistance

(2021) Allison J. Lopatkin et al.   SCIENCE

Evolution of Antibiotic Tolerance Shapes Resistance Development in Chronic Pseudomonas aeruginosa Infections

(2021) Isabella Santi et al.   mBio

Biofilm formation in the lung contributes to virulence and drug tolerance of Mycobacterium tuberculosis

(2021) Poushali Chakraborty et al.   Nature Communications

Pseudomonas aeruginosa aggregates in cystic fibrosis sputum produce exopolysaccharides that likely impede current therapies

(2021) Laura K. Jennings et al.   Cell Reports

The quorum sensing inhibitor furanone C-30 rapidly loses its tobramycin potentiating activity against Pseudomonas aeruginosa biofilms during experimental evolution

(2021) Mona Bové et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Evolutionary Pathways and Trajectories in Antibiotic Resistance

(2021) F. Baquero et al.   CLINICAL MICROBIOLOGY REVIEWS

The importance of understanding the infectious microenvironment

(2021) Thomas Bjarnsholt et al.   LANCET INFECTIOUS DISEASES

Polygenic Adaptation and Clonal Interference Enable Sustained Diversity in Experimental Pseudomonas aeruginosa Populations

(2021) Katrina B Harris et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ecology and evolution of antibiotic persistence

(2021) L. Verstraete et al.   TRENDS IN MICROBIOLOGY

Adaptation and genomic erosion in fragmented Pseudomonas aeruginosa populations in the sinuses of people with cystic fibrosis

(2021) Catherine R. Armbruster et al.   Cell Reports

Predicting Antimicrobial Activity at the Target Site: Pharmacokinetic/Pharmacodynamic Indices versus Time–Kill Approaches

(2021) Wisse van Os et al.   Antibiotics-Basel

In vivo demonstration of Pseudomonas aeruginosa biofilms as independent pharmacological microcompartments

(2020) Lars Christophersen et al.   Journal of Cystic Fibrosis

Parallel evolutionary paths to produce more than one Pseudomonas aeruginosa biofilm phenotype

(2020) Janne G. Thöming et al.   npj Biofilms and Microbiomes

Evolutionary landscapes of Pseudomonas aeruginosa towards ribosome-targeting antibiotic resistance depend on selection strength

(2020) Fernando Sanz-García et al.   INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS

Allelic polymorphism shapes community function in evolving Pseudomonas aeruginosa populations

(2020) Sheyda Azimi et al.   ISME Journal

Parallel Evolution of Tobramycin Resistance across Species and Environments

(2020) Michelle R. Scribner et al.   mBio

Bacteria under antibiotic attack: Different strategies for evolutionary adaptation

(2020) Etthel M. Windels et al.   PLoS Pathogens

Experimental Evolution In Vivo To Identify Selective Pressures during Pneumococcal Colonization

(2020) Vaughn S. Cooper et al.   mSystems

The evolutionary trajectories of P. aeruginosa in biofilm and planktonic growth modes exposed to ciprofloxacin: beyond selection of antibiotic resistance

(2020) Marwa N. Ahmed et al.   npj Biofilms and Microbiomes

Repeatable ecological dynamics govern the response of experimental communities to antibiotic pulse perturbation

(2020) Johannes Cairns et al.   Nature Ecology & Evolution

Phenotypic Parallelism during Experimental Adaptation of a Free-Living Bacterium to the Zebrafish Gut

(2020) Jarrett F. Lebov et al.   mBio

Pseudomonas aeruginosa adaptation and evolution in patients with cystic fibrosis

(2020) Elio Rossi et al.   NATURE REVIEWS MICROBIOLOGY

Mapping the Role of AcrAB-TolC Efflux Pumps in the Evolution of Antibiotic Resistance Reveals Near-MIC Treatments Facilitate Resistance Acquisition

(2020) Ariel M. Langevin et al.   mSphere

Bacterial persistence promotes the evolution of antibiotic resistance by increasing survival and mutation rates

(2019) Etthel Martha Windels et al.   ISME Journal

In-host evolution of Staphylococcus epidermidis in a pacemaker-associated endocarditis resulting in increased antibiotic tolerance

(2019) Vanina Dengler Haunreiter et al.   Nature Communications

Various Evolutionary Trajectories Lead to Loss of the Tobramycin-Potentiating Activity of the Quorum-Sensing Inhibitor Baicalin Hydrate in Burkholderia cenocepacia Biofilms

(2019) Andrea Sass et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Definitions and guidelines for research on antibiotic persistence

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

Lack of the major multifunctional catalase KatA in P.aeruginosa accelerates evolution of antibiotic resistance in ciprofloxacin-treated biofilms

(2019) Marwa N. Ahmed et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Bacterial Metabolism and Antibiotic Efficacy

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

Antimicrobial Tolerance and Metabolic Adaptations in Microbial Biofilms

(2019) Aurélie Crabbé et al.   TRENDS IN MICROBIOLOGY

Conceptual Model of Biofilm Antibiotic Tolerance that Integrates Phenomena of Diffusion, Metabolism, Gene Expression, and Physiology

(2019) Philip S. Stewart et al.   JOURNAL OF BACTERIOLOGY

Evolutionary pathways to antibiotic resistance are dependent upon environmental structure and bacterial lifestyle

(2019) Alfonso Santos-Lopez et al.   eLife

In vitro evolution of Pseudomonas aeruginosa AA2 biofilms in the presence of cystic fibrosis lung microbiome members

(2019) Eva Vandeplassche et al.   Scientific Reports

Rapid microevolution of biofilm cells in response to antibiotics

(2019) Anahit Penesyan et al.   npj Biofilms and Microbiomes

Evolution of antibiotic resistance in biofilm and planktonic P. aeruginosa populations exposed to sub-inhibitory levels of ciprofloxacin

(2018) Marwa N. Ahmed et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Targeting Antibiotic Tolerance, Pathogen by Pathogen

(2018) Sylvain Meylan et al.   CELL

Experimental Design, Population Dynamics, and Diversity in Microbial Experimental Evolution

(2018) Bram Van den Bergh et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Spatial structure facilitates the accumulation and persistence of antibiotic-resistant mutants in biofilms

(2018) Michael T. France et al.   Evolutionary Applications

Rapid diversification of Pseudomonas aeruginosa in cystic fibrosis lung-like conditions

(2018) Alana Schick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Consequences of Being in an Infectious Biofilm: Microenvironmental Conditions Governing Antibiotic Tolerance

(2017) Majken Sønderholm et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Co-evolution with Staphylococcus aureus leads to lipopolysaccharide alterations in Pseudomonas aeruginosa

(2017) Mikael Tognon et al.   ISME Journal

Experimental evolution and the dynamics of adaptation and genome evolution in microbial populations

(2017) Richard E Lenski   ISME Journal

Using experimental evolution to identify druggable targets that could inhibit the evolution of antimicrobial resistance

(2017) Heer H Mehta et al.   JOURNAL OF ANTIBIOTICS

The fate of inhaled antibiotics after deposition in cystic fibrosis: How to get drug to the bug?

(2017) Aukje C. Bos et al.   Journal of Cystic Fibrosis

Metabolic constraints on the evolution of antibiotic resistance

(2017) Mattia Zampieri et al.   Molecular Systems Biology

Antibiotic tolerance facilitates the evolution of resistance

(2017) Irit Levin-Reisman et al.   SCIENCE

The Role of Reactive Oxygen Species in Antibiotic-Mediated Killing of Bacteria

(2017) Heleen Van Acker et al.   TRENDS IN MICROBIOLOGY

A shifting mutational landscape in 6 nutritional states: Stress-induced mutagenesis as a series of distinct stress input–mutation output relationships

(2017) Ram P. Maharjan et al.   PLOS BIOLOGY

Anaerobically Grown Escherichia coli Has an Enhanced Mutation Rate and Distinct Mutational Spectra

(2017) Sonal Shewaramani et al.   PLoS Genetics

Visualizing Antimicrobials in Bacterial Biofilms: Three-Dimensional Biochemical Imaging Using TOF-SIMS

(2017) Sarah K. Davies et al.   mSphere

Evolution of Pseudomonas aeruginosa Antimicrobial Resistance and Fitness under Low and High Mutation Rates

(2016) Gabriel Cabot et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

In VitroEmergence of High Persistence upon Periodic Aminoglycoside Challenge in the ESKAPE Pathogens

(2016) Joran Elie Michiels et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

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

Critical review on biofilm methods

(2016) Joana Azeredo et al.   CRITICAL REVIEWS IN MICROBIOLOGY

Combinations of mutations inenvZ,ftsI,mrdA,acrBandacrRcan cause high-level carbapenem resistance inEscherichia coli

(2016) Marlen Adler et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Laboratory Evolution of Microbial Interactions in Bacterial Biofilms

(2016) Marivic Martin et al.   JOURNAL OF BACTERIOLOGY

Persistence and resistance as complementary bacterial adaptations to antibiotics

(2016) T. Vogwill et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Distinguishing between resistance, tolerance and persistence to antibiotic treatment

(2016) Asher Brauner et al.   NATURE REVIEWS MICROBIOLOGY

Frequency of antibiotic application drives rapid evolutionary adaptation of Escherichia coli persistence

(2016) Bram Van den Bergh et al.   Nature Microbiology

Insights into the evolutionary trajectories of fluoroquinolone resistance inStreptococcus pneumoniae

(2015) Gang Zhang et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Antibiotic penetration and bacterial killing in a Pseudomonas aeruginosa biofilm model

(2015) B. Cao et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Acinetobacter baumannii Repeatedly Evolves a Hypermutator Phenotype in Response to Tigecycline That Effectively Surveys Evolutionary Trajectories to Resistance

(2015) Troy G. Hammerstrom et al.   PLoS One

Extracellular Polymeric Substance Architecture Influences Natural Genetic Transformation of Acinetobacter baylyi in Biofilms

(2014) Robin T. Merod et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Experimental evolution as an efficient tool to dissect adaptive paths to antibiotic resistance

(2014) Gunther Jansen et al.   DRUG RESISTANCE UPDATES

Parallel evolution of small colony variants in Burkholderia cenocepacia biofilms

(2014) Vaughn S. Cooper et al.   GENOMICS

Optimization of lag time underlies antibiotic tolerance in evolved bacterial populations

(2014) Ofer Fridman et al.   NATURE

Molecular mechanisms of antimicrobial tolerance and resistance in bacterial and fungal biofilms

(2014) Heleen Van Acker et al.   TRENDS IN MICROBIOLOGY

Adaptation of Enterococcus faecalis to Daptomycin Reveals an Ordered Progression to Resistance

(2013) Corwin Miller et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

The evolution of antibiotic susceptibility and resistance during the formation of Escherichia coli biofilms in the absence of antibiotics

(2013) Jabus G Tyerman et al.   BMC EVOLUTIONARY BIOLOGY

Persisters and beyond: Mechanisms of phenotypic drug resistance and drug tolerance in bacteria

(2013) Jemila C. Kester et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

Genome dynamics during experimental evolution

(2013) Jeffrey E. Barrick et al.   NATURE REVIEWS GENETICS

Invasion of E. coli biofilms by antibiotic resistance plasmids

(2013) Jaroslaw E. Król et al.   PLASMID

Biofilm-Grown Burkholderia cepacia Complex Cells Survive Antibiotic Treatment by Avoiding Production of Reactive Oxygen Species

(2013) Heleen Van Acker et al.   PLoS One

Transport of Nanoparticles and Tobramycin-loaded Liposomes in Burkholderia cepacia Complex Biofilms

(2013) Anne-Sophie Messiaen et al.   PLoS One

The interconnection between biofilm formation and horizontal gene transfer

(2012) Jonas Stenløkke Madsen et al.   FEMS IMMUNOLOGY AND MEDICAL MICROBIOLOGY

Increased Mutability of Staphylococci in Biofilms as a Consequence of Oxidative Stress

(2012) Victoria J. Ryder et al.   PLoS One

Tangled bank of experimentally evolved Burkholderia biofilms reflects selection during chronic infections

(2012) C. C. Traverse et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Experimental evolution

(2012) Tadeusz J. Kawecki et al.   TRENDS IN ECOLOGY & EVOLUTION

Genomics of Adaptation during Experimental Evolution of the Opportunistic Pathogen Pseudomonas aeruginosa

(2012) Alex Wong et al.   PLoS Genetics

Increased Transfer of a Multidrug Resistance Plasmid in Escherichia coli Biofilms at the Air-Liquid Interface

(2011) Jaroslaw E. Król et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Interfering Waves of Adaptation Promote Spatial Mixing

(2011) Erik A. Martens et al.   GENETICS

Parallel evolution and local differentiation in quinolone resistance in Pseudomonas aeruginosa

(2011) A. Wong et al.   MICROBIOLOGY-SGM

Acceleration of Emergence of Bacterial Antibiotic Resistance in Connected Microenvironments

(2011) Q. Zhang et al.   SCIENCE

Bacterial hypermutation in cystic fibrosis, not only for antibiotic resistance

(2010) A. Oliver et al.   CLINICAL MICROBIOLOGY AND INFECTION

Ecological succession in long-term experimentally evolved biofilms produces synergistic communities

(2010) Steffen R Poltak et al.   ISME Journal

Heterogeneous rpoS and rhlR mRNA Levels and 16S rRNA/rDNA (rRNA Gene) Ratios within Pseudomonas aeruginosa Biofilms, Sampled by Laser Capture Microdissection

(2010) A. C. Perez-Osorio et al.   JOURNAL OF BACTERIOLOGY

In vitro and in vivo model systems to study microbial biofilm formation

(2010) Tom Coenye et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Role of reactive oxygen species in antibiotic action and resistance

(2009) Daniel J Dwyer et al.   CURRENT OPINION IN MICROBIOLOGY

Bacterial competition: surviving and thriving in the microbial jungle

(2009) Michael E. Hibbing et al.   NATURE REVIEWS MICROBIOLOGY

Increased mutability of Pseudomonas aeruginosa in biofilms

(2008) K. Driffield et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Genetic Adaptation of Pseudomonas aeruginosa to the Airways of Cystic Fibrosis Patients Is Catalyzed by Hypermutation

(2008) A. Mena et al.   JOURNAL OF BACTERIOLOGY

Formation of Streptococcus pneumoniae Non-Phase-Variable Colony Variants Is Due to Increased Mutation Frequency Present under Biofilm Growth Conditions

(2008) M. Allegrucci et al.   JOURNAL OF BACTERIOLOGY

Physiological heterogeneity in biofilms

(2008) Philip S. Stewart et al.   NATURE REVIEWS MICROBIOLOGY

Heterogeneous Adaptive Trajectories of Small Populations on Complex Fitness Landscapes

(2008) Daniel E. Rozen et al.   PLoS One

Endogenous oxidative stress produces diversity and adaptability in biofilm communities

(2008) B. R. Boles et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA