Pseudomonas aeruginosa populations in the cystic fibrosis lung lose susceptibility to newly applied β-lactams within 3 days

Penicillin binding protein 3 is a common adaptive target among Pseudomonas aeruginosa isolates from adult cystic fibrosis patients treated with β-lactams

(2019) Shawn T. Clark et al.   INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS

Pseudomonas aeruginosatranscriptome during human infection

(2018) Daniel M. Cornforth et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Antibiotic combination efficacy (ACE) networks for a Pseudomonas aeruginosa model

(2018) Camilo Barbosa et al.   PLOS BIOLOGY

Chronic but not intermittent infection withPseudomonas aeruginosais associated with global changes of the lung microbiome in cystic fibrosis

(2017) Sébastien Boutin et al.   EUROPEAN RESPIRATORY JOURNAL

Phenotypic shift in Pseudomonas aeruginosa populations from cystic fibrosis lungs after 2-week antipseudomonal treatment

(2017) Laia Fernández-Barat et al.   Journal of Cystic Fibrosis

Evolved Aztreonam Resistance Is Multifactorial and Can Produce Hypervirulence in Pseudomonas aeruginosa

(2017) Peter Jorth et al.   mBio

Evolution of the Pseudomonas aeruginosa mutational resistome in an international Cystic Fibrosis clone

(2017) Carla López-Causapé et al.   Scientific Reports

The Microbiome in Cystic Fibrosis

(2016) Yvonne J. Huang et al.   CLINICS IN CHEST MEDICINE

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Pseudomonas aeruginosa Evolutionary Adaptation and Diversification in Cystic Fibrosis Chronic Lung Infections

(2016) Craig Winstanley et al.   TRENDS IN MICROBIOLOGY

Antimicrobial resistance, respiratory tract infections and role of biofilms in lung infections in cystic fibrosis patients

(2015) Oana Ciofu et al.   ADVANCED DRUG DELIVERY REVIEWS

Mutations in β-Lactamase AmpC Increase Resistance of Pseudomonas aeruginosa Isolates to Antipseudomonal Cephalosporins

(2015) M. Berrazeg et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Temporal variation in antibiotic environments slows down resistance evolution in pathogenicPseudomonas aeruginosa

(2015) Roderich Roemhild et al.   Evolutionary Applications

In vivoevolution of resistance ofPseudomonas aeruginosastrains isolated from patients admitted to an intensive care unit: mechanisms of resistance and antimicrobial exposure

(2015) Mar Solé et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Selective Sweeps and Parallel Pathoadaptation Drive Pseudomonas aeruginosa Evolution in the Cystic Fibrosis Lung

(2015) Julio Diaz Caballero et al.   mBio

High Individuality of Respiratory Bacterial Communities in a Large Cohort of Adult Cystic Fibrosis Patients under Continuous Antibiotic Treatment

(2015) Rolf Kramer et al.   PLoS One

AliView: a fast and lightweight alignment viewer and editor for large datasets

(2014) Anders Larsson   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Convergent evolution and adaptation of Pseudomonas aeruginosa within patients with cystic fibrosis

(2014) Rasmus Lykke Marvig et al.   NATURE GENETICS

Biological Cost of Different Mechanisms of Colistin Resistance and Their Impact on Virulence in Acinetobacter baumannii

(2013) Alejandro Beceiro et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Is the Improvement of CF Patients, Hospitalized for Pulmonary Exacerbation, Correlated to a Decrease in Bacterial Load?

(2013) Pieter Deschaght et al.   PLoS One

Pseudomonas aeruginosa: new insights into pathogenesis and host defenses

(2013) Shaan L. Gellatly et al.   Pathogens and Disease

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Adaptation of Pseudomonas aeruginosa to the cystic fibrosis airway: an evolutionary perspective

(2012) Anders Folkesson et al.   NATURE REVIEWS MICROBIOLOGY

The Adult Cystic Fibrosis Airway Microbiota Is Stable over Time and Infection Type, and Highly Resilient to Antibiotic Treatment of Exacerbations

(2012) Anthony A. Fodor et al.   PLoS One

Incidence and Risk Factors for Pulmonary Exacerbation Treatment Failures in Patients With Cystic Fibrosis Chronically Infected With Pseudomonas aeruginosa

(2011) Michael D. Parkins et al.   CHEST

Does bacterial density in cystic fibrosis sputum increase prior to pulmonary exacerbation?

(2011) Franziska A. Stressmann et al.   Journal of Cystic Fibrosis

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Evolutionary dynamics of bacteria in a human host environment

(2011) L. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pseudomonas aeruginosa: all roads lead to resistance

(2011) Elena B.M. Breidenstein et al.   TRENDS IN MICROBIOLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Bacterial hypermutation in cystic fibrosis, not only for antibiotic resistance

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

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

In vivo development of antimicrobial resistance in Pseudomonas aeruginosa strains isolated from the lower respiratory tract of Intensive Care Unit patients with nosocomial pneumonia and receiving antipseudomonal therapy

(2010) Mickaël Riou et al.   INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS

Mutators in cystic fibrosis chronic lung infection: Prevalence, mechanisms, and consequences for antimicrobial therapy

(2010) Antonio Oliver   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Comparison of the sensitivity of culture, PCR and quantitative real-time PCR for the detection of Pseudomonas aeruginosa in sputum of cystic fibrosis patients

(2009) Pieter Deschaght et al.   BMC MICROBIOLOGY

Fluctuations in phenotypes and genotypes within populations of Pseudomonas aeruginosa in the cystic fibrosis lung during pulmonary exacerbations

(2009) J. L. Fothergill et al.   JOURNAL OF MEDICAL MICROBIOLOGY

Effect of mutatorP. aeruginosaon antibiotic resistance acquisition and respiratory function in cystic fibrosis

(2009) Agnes Ferroni et al.   PEDIATRIC PULMONOLOGY

β-Lactam Resistance Response Triggered by Inactivation of a Nonessential Penicillin-Binding Protein

(2009) Bartolomé Moya et al.   PLoS Pathogens

Pseudomonas aeruginosa lasR mutants are associated with cystic fibrosis lung disease progression

(2008) Lucas R. Hoffman et al.   Journal of Cystic Fibrosis