Plasmid fitness costs are caused by specific genetic conflicts enabling resolution by compensatory mutation

Epidemic territorial spread of IncP-2-type VIM-2 carbapenemase-encoding megaplasmids in nosocomial Pseudomonas aeruginosa populations

(2021) Paweł Urbanowicz et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Positive Selection Inhibits Plasmid Coexistence in Bacterial Genomes

(2021) Laura Carrilero et al.   mBio

A megaplasmid family driving dissemination of multidrug resistance in Pseudomonas

(2020) Adrian Cazares et al.   Nature Communications

Abortive Infection: Bacterial Suicide as an Antiviral Immune Strategy

(2020) Anna Lopatina et al.   Annual Review of Virology

Mobile Compensatory Mutations Promote Plasmid Survival

(2019) Martin Zwanzig et al.   mSystems

The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads

(2019) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

Linking the resistome and plasmidome to the microbiome

(2019) Thibault Stalder et al.   ISME Journal

Selective advantages favour high genomic AT-contents in intracellular elements

(2019) Anne-Kathrin Dietel et al.   PLoS Genetics

Emergence of plasmid stability under non-selective conditions maintains antibiotic resistance

(2019) Tanita Wein et al.   Nature Communications

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

Unravelling plasmidome distribution and interaction with its hosting microbiome

(2019) Aya Brown Kav et al.   ENVIRONMENTAL MICROBIOLOGY

A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core

(2018) Lukas Zimmermann et al.   JOURNAL OF MOLECULAR BIOLOGY

Going around in circles: virulence plasmids in enteric pathogens

(2018) Giulia Pilla et al.   NATURE REVIEWS MICROBIOLOGY

Systematic discovery of antiphage defense systems in the microbial pangenome

(2018) Shany Doron et al.   SCIENCE

Conflicting selection alters the trajectory of molecular evolution in a tripartite bacteria-plasmid-phage interaction

(2017) Ellie Harrison et al.   MOLECULAR ECOLOGY

Increased ParB level affects expression of stress response, adaptation and virulence operons and potentiates repression of promoters adjacent to the high affinity binding sites parS3 and parS4 in Pseudomonas aeruginosa

(2017) Adam Kawalek et al.   PLoS One

Persistence and reversal of plasmid-mediated antibiotic resistance

(2017) Allison J. Lopatkin et al.   Nature Communications

Plasmid-Mediated Bioaugmentation for the Bioremediation of Contaminated Soils

(2017) Carlos Garbisu et al.   Frontiers in Microbiology

Adaptive modulation of antibiotic resistance through intragenomic coevolution

(2017) Michael J. Bottery et al.   Nature Ecology & Evolution

Compensatory mutations improve general permissiveness to antibiotic resistance plasmids

(2017) Wesley Loftie-Eaton et al.   Nature Ecology & Evolution

Positive selection inhibits gene mobilization and transfer in soil bacterial communities

(2017) James P. J. Hall et al.   Nature Ecology & Evolution

Emerging patterns of plasmid-host coevolution that stabilize antibiotic resistance

(2017) Thibault Stalder et al.   Scientific Reports

Nested Russian Doll-Like Genetic Mobility Drives Rapid Dissemination of the Carbapenem Resistance GeneblaKPC

(2016) Anna E. Sheppard et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

What drives parallel evolution?

(2016) Susan F. Bailey et al.   BIOESSAYS

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

Vibrio crassostreae, a benign oyster colonizer turned into a pathogen after plasmid acquisition

(2016) Maxime Bruto et al.   ISME Journal

Survival and Evolution of a Large Multidrug Resistance Plasmid in New Clinical Bacterial Hosts

(2016) Andreas Porse et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolved plasmid-host interactions reduce plasmid interference cost

(2016) Hirokazu Yano et al.   MOLECULAR MICROBIOLOGY

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

(2016) David Arndt et al.   NUCLEIC ACIDS RESEARCH

Source–sink plasmid transfer dynamics maintain gene mobility in soil bacterial communities

(2016) James P. J. Hall et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Regulation of genetic flux between bacteria by restriction–modification systems

(2016) Pedro H. Oliveira et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Impact of 18 Ancestral and Horizontally-Acquired Regulatory Proteins upon the Transcriptome and sRNA Landscape of Salmonella enterica serovar Typhimurium

(2016) Aoife M. Colgan et al.   PLoS Genetics

Phylogenomics and sequence-structure-function relationships in the GmrSD family of Type IV restriction enzymes

(2015) Magdalena A. Machnicka et al.   BMC BIOINFORMATICS

Co-occurrence of resistance genes to antibiotics, biocides and metals reveals novel insights into their co-selection potential

(2015) Chandan Pal et al.   BMC GENOMICS

Parallel Compensatory Evolution Stabilizes Plasmids across the Parasitism-Mutualism Continuum

(2015) Ellie Harrison et al.   CURRENT BIOLOGY

Environmentally co-occurring mercury resistance plasmids are genetically and phenotypically diverse and confer variable context-dependent fitness effects

(2015) James P.J. Hall et al.   ENVIRONMENTAL MICROBIOLOGY

The bioenergetic costs of a gene

(2015) Michael Lynch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Building bridges within the bacterial chromosome

(2015) Dan Song et al.   TRENDS IN GENETICS

The Tailocin Tale: Peeling off Phage Tails

(2015) Maarten G.K. Ghequire et al.   TRENDS IN MICROBIOLOGY

Interactions between horizontally acquired genes create a fitness cost in Pseudomonas aeruginosa

(2015) Alvaro San Millan et al.   Nature Communications

Modulation of primary cell function of hostPseudomonasbacteria by the conjugative plasmid pCAR1

(2014) Yurika Takahashi et al.   ENVIRONMENTAL MICROBIOLOGY

Antibiotic resistance correlates with transmission in plasmid evolution

(2014) Paul E. Turner et al.   EVOLUTION

The genetic basis of the fitness costs of antimicrobial resistance: a meta-analysis approach

(2014) Tom Vogwill et al.   Evolutionary Applications

The evolution of bacterial DNA base composition

(2014) Deepa Agashe et al.   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

A sequence-based approach for prediction of CsrA/RsmA targets in bacteria with experimental validation in Pseudomonas aeruginosa

(2014) P. R. Kulkarni et al.   NUCLEIC ACIDS RESEARCH

A unique megaplasmid contributes to stress tolerance and pathogenicity of an emergentSalmonella entericaserovar Infantis strain

(2013) Gili Aviv et al.   ENVIRONMENTAL MICROBIOLOGY

Large Deletions in the pAtC58 Megaplasmid of Agrobacterium tumefaciens Can Confer Reduced Carriage Cost and Increased Expression of Virulence Genes

(2013) Elise R. Morton et al.   Genome Biology and Evolution

Positive epistasis between co-infecting plasmids promotes plasmid survival in bacterial populations

(2013) Alvaro San Millan et al.   ISME Journal

Community-wide plasmid gene mobilization and selection

(2013) Vladimir Sentchilo et al.   ISME Journal

Exploring the costs of horizontal gene transfer

(2013) David A. Baltrus   TRENDS IN ECOLOGY & EVOLUTION

The Gac regulon ofPseudomonas fluorescens SBW25

(2013) Xu Cheng et al.   Environmental Microbiology Reports

Dealing with the Evolutionary Downside of CRISPR Immunity: Bacteria and Beneficial Plasmids

(2013) Wenyan Jiang et al.   PLoS Genetics

ParI, an orphan ParA family protein fromPseudomonas putida KT2440-specific genomic island, interferes with the partition system of IncP-7 plasmids

(2012) Masatoshi Miyakoshi et al.   ENVIRONMENTAL MICROBIOLOGY

Antibiotic-Induced Bacterial Cell Death Exhibits Physiological and Biochemical Hallmarks of Apoptosis

(2012) Daniel J. Dwyer et al.   MOLECULAR CELL

Repeated, Selection-Driven Genome Reduction of Accessory Genes in Experimental Populations

(2012) Ming-Chun Lee et al.   PLoS Genetics

Bacteriophage selection against a plasmid-encoded sex apparatus leads to the loss of antibiotic-resistance plasmids

(2011) M. Jalasvuori et al.   Biology Letters

Trends and barriers to lateral gene transfer in prokaryotes

(2011) Ovidiu Popa et al.   CURRENT OPINION IN MICROBIOLOGY

Measuring Selection Coefficients Below 10−3: Method, Questions, and Prospects

(2011) Romain Gallet et al.   GENETICS

Binding and Spreading of ParB on DNA Determine Its Biological Function in Pseudomonas aeruginosa

(2011) M. Kusiak et al.   JOURNAL OF BACTERIOLOGY

Principles of a switch

(2011) Mark Ptashne   Nature Chemical Biology

Shifts in the host range of a promiscuous plasmid through parallel evolution of its replication initiation protein

(2010) Masahiro Sota et al.   ISME Journal

Conjugative DNA Transfer Induces the Bacterial SOS Response and Promotes Antibiotic Resistance Development through Integron Activation

(2010) Zeynep Baharoglu et al.   PLoS Genetics

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Mobile genetic elements in the genome of the beneficial rhizobacterium Pseudomonas fluorescens Pf-5

(2009) Dmitri V Mavrodi et al.   BMC MICROBIOLOGY

An SOS Inhibitor that Binds to Free RecA Protein: The PsiB Protein

(2009) Vessela Petrova et al.   MOLECULAR CELL

Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens

(2009) Mark W Silby et al.   GENOME BIOLOGY