Genome-driven elucidation of phage-host interplay and impact of phage resistance evolution on bacterial fitness

Genomics of an endemic cystic fibrosis Burkholderia multivorans strain reveals low within-patient evolution but high between-patient diversity

(2021) Cédric Lood et al.   PLoS Pathogens

Integrative omics analysis of Pseudomonas aeruginosa virus PA5oct highlights the molecular complexity of jumbo phages

(2020) Cédric Lood et al.   ENVIRONMENTAL MICROBIOLOGY

Phages and their potential to modulate the microbiome and immunity

(2020) Sara Federici et al.   Cellular & Molecular Immunology

The effect of bacterial mutation rate on the evolution of CRISPR-Cas adaptive immunity

(2019) Anne Chevallereau et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Investigation of Pseudomonas aeruginosa strain PcyII-10 variants resisting infection by N4-like phage Ab09 in search for genes involved in phage adsorption

(2019) Libera Latino et al.   PLoS One

The Population Structure of Pseudomonas aeruginosa Is Characterized by Genetic Isolation of exoU+ and exoS+ Lineages

(2019) Egon A Ozer et al.   Genome Biology and Evolution

Resistance Evolution against Phage Combinations Depends on the Timing and Order of Exposure

(2019) Rosanna C. T. Wright et al.   mBio

The pan-immune system of bacteria: antiviral defence as a community resource

(2019) Aude Bernheim et al.   NATURE REVIEWS MICROBIOLOGY

Pseudomonas aeruginosa PA5oct Jumbo Phage Impacts Planktonic and Biofilm Population and Reduces Its Host Virulence

(2019) Tomasz Olszak et al.   Viruses-Basel

Pseudomonas aeruginosa MutL promotes large chromosomal deletions through non-homologous end joining to prevent bacteriophage predation

(2018) Mengyu Shen et al.   NUCLEIC ACIDS RESEARCH

CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins

(2018) David Couvin et al.   NUCLEIC ACIDS RESEARCH

Diversity-Generating Machines: Genetics of Bacterial Sugar-Coating

(2018) Rafał J. Mostowy et al.   TRENDS IN MICROBIOLOGY

Mutation-Driven Evolution of Pseudomonas aeruginosa in the Presence of either Ceftazidime or Ceftazidime-Avibactam

(2018) Fernando Sanz-García et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

The Pseudomonas aeruginosa Pan-Genome Provides New Insights on Its Population Structure, Horizontal Gene Transfer, and Pathogenicity

(2018) Luca Freschi et al.   Genome Biology and Evolution

Cross-resistance is modular in bacteria–phage interactions

(2018) Rosanna C. T. Wright et al.   PLOS BIOLOGY

A Genotypic Analysis of Five P. aeruginosa Strains after Biofilm Infection by Phages Targeting Different Cell Surface Receptors

(2017) Diana P. Pires et al.   Frontiers in Microbiology

Pyomelanin-producing Pseudomonas aeruginosa selected during chronic infections have a large chromosomal deletion which confers resistance to pyocins

(2016) Didier Hocquet et al.   ENVIRONMENTAL MICROBIOLOGY

Prophages mediate defense against phage infection through diverse mechanisms

(2016) Joseph Bondy-Denomy et al.   ISME Journal

Pseudolysogeny and sequential mutations build multiresistance to virulent bacteriophages in Pseudomonas aeruginosa

(2016) Libera Latino et al.   MICROBIOLOGY-SGM

PHASTER: a better, faster version of the PHAST phage search tool

(2016) David Arndt et al.   NUCLEIC ACIDS RESEARCH

A proposed integrated approach for the preclinical evaluation of phage therapy in Pseudomonas infections

(2016) Katarzyna Danis-Wlodarczyk et al.   Scientific Reports

Diversity of Pseudomonas Genomes, Including Populus-Associated Isolates, as Revealed by Comparative Genome Analysis

(2015) Se-Ran Jun et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

Phenotypic characterization of an international Pseudomonas aeruginosa reference panel: strains of cystic fibrosis (CF) origin show less in vivo virulence than non-CF strains

(2015) Louise Cullen et al.   MICROBIOLOGY-SGM

Genetically and Phenotypically Distinct Pseudomonas aeruginosa Cystic Fibrosis Isolates Share a Core Proteomic Signature

(2015) Anahit Penesyan et al.   PLoS One

Characterization of the Newly Isolated Lytic Bacteriophages KTN6 and KT28 and Their Efficacy against Pseudomonas aeruginosa Biofilm

(2015) Katarzyna Danis-Wlodarczyk et al.   PLoS One

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

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

Comparative genomics of defense systems in archaea and bacteria

(2013) Kira S. Makarova et al.   NUCLEIC ACIDS RESEARCH

Pseudomonas aeruginosa: new insights into pathogenesis and host defenses

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

Developing an internationalPseudomonas aeruginosareference panel

(2013) Anthony De Soyza et al.   MicrobiologyOpen

Snakemake--a scalable bioinformatics workflow engine

(2012) J. Koster et al.   BIOINFORMATICS

Innate and adaptive immunity in bacteria: mechanisms of programmed genetic variation to fight bacteriophages

(2011) David Bikard et al.   CURRENT OPINION IN IMMUNOLOGY

Defense Islands in Bacterial and Archaeal Genomes and Prediction of Novel Defense Systems

(2011) K. S. Makarova et al.   JOURNAL OF BACTERIOLOGY

Persister Cells

(2010) Kim Lewis   Annual Review of Microbiology

Bacteriophage resistance mechanisms

(2010) Simon J. Labrie et al.   NATURE REVIEWS MICROBIOLOGY

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Molecular and physiological analysis of three Pseudomonas aeruginosa phages belonging to the “N4-like viruses”

(2010) Pieter-Jan Ceyssens et al.   VIROLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Representational Difference Analysis (RDA) of bacteriophage genomes

(2009) Elke Lammens et al.   JOURNAL OF MICROBIOLOGICAL METHODS