Within-host whole genome analysis of an antibiotic resistant Pseudomonas aeruginosa strain sub-type in cystic fibrosis

Aminoglycoside resistance ofPseudomonas aeruginosain cystic fibrosis results from convergent evolution in themexZgene

(2016) Michelle H Prickett et al.   THORAX

Assess drug-resistance phenotypes, not just genotypes

(2016) Laura J. V. Piddock   Nature Microbiology

Divergent, CoexistingPseudomonas aeruginosaLineages in Chronic Cystic Fibrosis Lung Infections

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

New Inhaled Antimicrobial Formulations for Use in the Cystic Fibrosis Patient Population

(2015) Christopher T. Campbell et al.   ANNALS OF PHARMACOTHERAPY

Bandage: interactive visualization ofde novogenome assemblies: Fig. 1.

(2015) Ryan R. Wick et al.   BIOINFORMATICS

PROVEAN web server: a tool to predict the functional effect of amino acid substitutions and indels

(2015) Yongwook Choi et al.   BIOINFORMATICS

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

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

(2015) Julio Diaz Caballero et al.   mBio

The social network of cystic fibrosis centre care and shared Pseudomonas aeruginosa strain infection: a cross-sectional analysis

(2015) Timothy J Kidd et al.   Lancet Respiratory Medicine

Genotypic Diversity within a Single Pseudomonas aeruginosa Strain Commonly Shared by Australian Patients with Cystic Fibrosis

(2015) Anna Sze Tai et al.   PLoS One

The Resistome of Pseudomonas aeruginosa in Relationship to Phenotypic Susceptibility

(2014) Veronica N. Kos et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

A comparison of two informative SNP-based strategies for typing Pseudomonas aeruginosa isolates from patients with cystic fibrosis

(2014) Melanie W Syrmis et al.   BMC INFECTIOUS DISEASES

Structural and Functional Characterization of Pseudomonas aeruginosa Global Regulator AmpR

(2014) O. Caille et al.   JOURNAL OF BACTERIOLOGY

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

(2014) Rasmus Lykke Marvig et al.   NATURE GENETICS

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

(2014) Nicholas J. Croucher et al.   NUCLEIC ACIDS RESEARCH

Coexistence and Within-Host Evolution of Diversified Lineages of Hypermutable Pseudomonas aeruginosa in Long-term Cystic Fibrosis Infections

(2014) Sofía Feliziani et al.   PLoS Genetics

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

The Comprehensive Antibiotic Resistance Database

(2013) Andrew G. McArthur et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Evolutionary genomics of epidemic and nonepidemic strains of Pseudomonas aeruginosa

(2013) J. R. Dettman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome Analysis of a Transmissible Lineage of Pseudomonas aeruginosa Reveals Pathoadaptive Mutations and Distinct Evolutionary Paths of Hypermutators

(2013) Rasmus Lykke Marvig et al.   PLoS Genetics

Quantitative Contributions of Target Alteration and Decreased Drug Accumulation to Pseudomonas aeruginosa Fluoroquinolone Resistance

(2012) Sebastian Bruchmann et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

SharedPseudomonas aeruginosagenotypes are common in Australian cystic fibrosis centres

(2012) Timothy J. Kidd et al.   EUROPEAN RESPIRATORY JOURNAL

Transmissible strains ofPseudomonas aeruginosain cystic fibrosis lung infections

(2012) Joanne L. Fothergill et al.   EUROPEAN RESPIRATORY JOURNAL

Synergistic antibacterial efficacy of early combination treatment with tobramycin and quorum-sensing inhibitors against Pseudomonas aeruginosa in an intraperitoneal foreign-body infection mouse model

(2012) L. D. Christensen et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Identification of acquired antimicrobial resistance genes

(2012) E. Zankari et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Genomic Variation among Contemporary Pseudomonas aeruginosa Isolates from Chronically Infected Cystic Fibrosis Patients

(2012) Jade C. S. Chung et al.   JOURNAL OF BACTERIOLOGY

Results of antibiotic susceptibility testing do not influence clinical outcome in children with cystic fibrosis

(2012) M.N. Hurley et al.   Journal of Cystic Fibrosis

EvolView, an online tool for visualizing, annotating and managing phylogenetic trees

(2012) Huangkai Zhang et al.   NUCLEIC ACIDS RESEARCH

Pseudomonas aeruginosaPopulation Diversity and Turnover in Cystic Fibrosis Chronic Infections

(2011) Eilidh Mowat et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

SHRiMP2: Sensitive yet Practical Short Read Mapping

(2011) Matei David et al.   BIOINFORMATICS

BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons

(2011) Nabil-Fareed Alikhan et al.   BMC GENOMICS

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

PHAST: A Fast Phage Search Tool

(2011) Y. Zhou et al.   NUCLEIC ACIDS RESEARCH

Infection With Transmissible Strains of Pseudomonas aeruginosa and Clinical Outcomes in Adults With Cystic Fibrosis

(2010) Shawn D. Aaron et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

(2010) Aaron E. Darling et al.   PLoS One

Extended-Spectrum Cephalosporinases in Pseudomonas aeruginosa

(2009) J.-M. Rodriguez-Martinez et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Classification of OprD sequence and correlation with antimicrobial activity of carbapenem agents inPseudomonas aeruginosaclinical isolates collected in Japan

(2009) Yumiko Sanbongi et al.   MICROBIOLOGY AND IMMUNOLOGY

Emergence of Carbapenem Resistance inPseudomonas aeruginosaIsolates from a Patient with Cystic Fibrosis in the Absence of Carbapenem Therapy

(2008) Daniel J. Wolter et al.   CLINICAL INFECTIOUS DISEASES

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

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