Genomic heterogeneity underlies multidrug resistance in Pseudomonas aeruginosa: A population-level analysis beyond susceptibility testing

Genomic evolution of antibiotic resistance is contingent on genetic background following a long-term experiment with Escherichia coli

(2021) Kyle J. Card et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

It’s Not Easy Being Green: A Narrative Review on the Microbiology, Virulence and Therapeutic Prospects of Multidrug-Resistant Pseudomonas aeruginosa

(2021) Payam Behzadi et al.   Antibiotics-Basel

Phenotypic and Genomic Variability of Serial Peri-Lung Transplantation Pseudomonas aeruginosa Isolates From Cystic Fibrosis Patients

(2021) Rucha Datar et al.   Frontiers in Microbiology

Compensatory evolution of Pseudomonas aeruginosa’s slow growth phenotype suggests mechanisms of adaptation in cystic fibrosis

(2021) Ruggero La Rosa et al.   Nature Communications

Antibiotic collateral sensitivity is contingent on the repeatability of evolution

(2019) Daniel Nichol et al.   Nature Communications

Phenazine production promotes antibiotic tolerance and metabolic heterogeneity in Pseudomonas aeruginosa biofilms

(2019) Konstanze T. Schiessl et al.   Nature Communications

Rapid ultrasensitive detection platform for antimicrobial susceptibility testing

(2019) Mehmet F. Cansizoglu et al.   PLOS BIOLOGY

Antibiotic combinations that exploit heteroresistance to multiple drugs effectively control infection

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

Human pleural fluid triggers global changes in the transcriptional landscape of Acinetobacter baumannii as an adaptive response to stress

(2019) Jasmine Martinez et al.   Scientific Reports

Historical contingency in the evolution of antibiotic resistance after decades of relaxed selection

(2019) Kyle J. Card et al.   PLOS BIOLOGY

EnrichedHeatmap: an R/Bioconductor package for comprehensive visualization of genomic signal associations

(2018) Zuguang Gu et al.   BMC GENOMICS

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools

(2018) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

Contingency and determinism in evolution: Replaying life’s tape

(2018) Zachary D. Blount et al.   SCIENCE

Relevance of multidrug-resistant Pseudomonas aeruginosa infections in cystic fibrosis

(2017) S. Stefani et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

Increasing Incidence of Multidrug Resistance Among Cystic Fibrosis Respiratory Bacterial Isolates

(2017) W. Cliff Rutter et al.   Microbial Drug Resistance

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database

(2016) Baofeng Jia 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

Antibiotic failure mediated by a resistant subpopulation in Enterobacter cloacae

(2016) Victor I. Band et al.   Nature Microbiology

Divergent, CoexistingPseudomonas aeruginosaLineages in Chronic Cystic Fibrosis Lung Infections

(2015) David Williams et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

Regional Isolation Drives Bacterial Diversification within Cystic Fibrosis Lungs

(2015) Peter Jorth et al.   Cell Host & Microbe

Impact of alginate-producing Pseudomonas aeruginosa on alveolar macrophage apoptotic cell clearance

(2015) Charles A. McCaslin et al.   Journal of Cystic Fibrosis

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

(2014) Rasmus Lykke Marvig et al.   NATURE GENETICS

Persistence ofPseudomonas aeruginosain a pulmonary nodule with late relapse

(2014) S. Ronkainen et al.   Transplant Infectious Disease

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Rapid Whole-Genome Sequencing for Detection and Characterization of Microorganisms Directly from Clinical Samples

(2013) H. Hasman et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Use of Collateral Sensitivity Networks to Design Drug Cycling Protocols That Avoid Resistance Development

(2013) L. Imamovic et al.   Science Translational Medicine

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

(2012) Pablo Cingolani et al.   FLY

Reduced airway surface pH impairs bacterial killing in the porcine cystic fibrosis lung

(2012) Alejandro A. Pezzulo et al.   NATURE

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance

(2011) A.-P. Magiorakos et al.   CLINICAL MICROBIOLOGY AND INFECTION

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

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Genetic adaptation of Pseudomonas aeruginosa during chronic lung infection of patients with cystic fibrosis: strong and weak mutators with heterogeneous genetic backgrounds emerge in mucA and/or lasR mutants

(2009) O. Ciofu et al.   MICROBIOLOGY-SGM

Assessing Genetic Heterogeneity within Bacterial Species Isolated from Gastrointestinal and Environmental Samples: How Many Isolates Does It Take?

(2008) D. Dopfer et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH