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The distribution of plasmid fitness effects explains plasmid persistence in bacterial communities

https://doi.org/10.1101/2020.08.01.230672

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Systematic Review and Meta‐Analysis

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Parallel Compensatory Evolution Stabilizes Plasmids across the Parasitism-Mutualism Continuum

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Intestinal co-colonization with different carbapenemase-producing Enterobacterales isolates is not a rare event in an OXA-48 endemic area

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Plasmid-mediated horizontal gene transfer is a coevolutionary process

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Rates of Lateral Gene Transfer in Prokaryotes: High but Why?

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Evolution of Plasmid-Mediated Antibiotic Resistance in the Clinical Context

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Exploring the costs of horizontal gene transfer

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Contact isolation versus standard precautions to decrease acquisition of extended-spectrum β-lactamase-producing Enterobacterales in non-critical care wards: a cluster-randomised crossover trial

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Noise in a minimal regulatory network: plasmid copy number control

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Evolution of a bacteria/plasmid association

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

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Broad host range plasmids can invade an unexpectedly diverse fraction of a soil bacterial community

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Positive selection and compensatory adaptation interact to stabilize non-transmissible plasmids

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

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The distribution of fitness effects of new mutations

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Spatial structure, cooperation and competition in biofilms

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Mobile genetic elements: the agents of open source evolution

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Integrative analysis of fitness and metabolic effects of plasmids in Pseudomonas aeruginosa PAO1

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Rethinking gut microbiome residency and the Enterobacteriaceae in healthy human adults

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Plasmids persist in a microbial community by providing fitness benefit to multiple phylotypes

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Persistence and reversal of plasmid-mediated antibiotic resistance

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SMARCAD1 ATPase activity is required to silence endogenous retroviruses in embryonic stem cells

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

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Large-scale network analysis captures biological features of bacterial plasmids

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Multicopy plasmids potentiate the evolution of antibiotic resistance in bacteria

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Compensatory mutations improve general permissiveness to antibiotic resistance plasmids

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Coevolution of host–plasmid pairs facilitates the emergence of novel multidrug resistance

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Epidemic of carbapenem-resistant Klebsiella pneumoniae in Europe is driven by nosocomial spread

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Host dependent maintenance of a blaNDM-1-encoding plasmid in clinical Escherichia coli isolates

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Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae , an urgent threat to public health

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SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

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QUAST: quality assessment tool for genome assemblies

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Prokka: rapid prokaryotic genome annotation

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Trimmomatic: a flexible trimmer for Illumina sequence data

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AcCNET (Accessory Genome Constellation Network): comparative genomics software for accessory genome analysis using bipartite networks

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Fecal Colonization With Extended-spectrum Beta-lactamase–Producing Enterobacteriaceae and Risk Factors Among Healthy Individuals: A Systematic Review and Metaanalysis

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Carbapenemase-Producing Organisms: A Global Scourge

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Natural Selection, Infectious Transfer and the Existence Conditions for Bacterial Plasmids

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Amelioration of the Cost of Conjugative Plasmid Carriage in Eschericha coli K12

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THE POPULATION BIOLOGY OF BACTERIAL PLASMIDS: A PRIORI CONDITIONS FOR THE EXISTENCE OF CONJUGATIONALLY TRANSMITTED FACTORS

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Identification of acquired antimicrobial resistance genes

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Low biological cost of carbapenemase-encoding plasmids following transfer from Klebsiella pneumoniae to Escherichia coli

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Characterization of carbapenemase-producing Enterobacteriaceae from colonized patients in a university hospital in Madrid, Spain, during the R-GNOSIS project depicts increased clonal diversity over time with maintenance of high-risk clones

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Evolving Populations in Biofilms Contain More Persistent Plasmids

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IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

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Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy

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RefSeq: an update on prokaryotic genome annotation and curation

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Interspecies Bacterial Comjugation by Plasmids from Marine Environments Visualized by gfp Expression

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The evolution of a conjugative plasmid and its ability to increase bacterial fitness

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A Mathematical Method for Analysing Plasmid Stability in Micro-organisms

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Estimating the rate of plasmid transfer: an end-point method

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Hospital outbreak of carbapenem-resistant Enterobacterales associated with a bla OXA-48 plasmid carried mostly by Escherichia coli ST399

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Stability of a promiscuous plasmid in different hosts: no guarantee for a long-term relationship

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Dissemination routes of the carbapenem resistance plasmid pOXA-48 in a hospital setting

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

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TESTING FOR PHYLOGENETIC SIGNAL IN COMPARATIVE DATA: BEHAVIORAL TRAITS ARE MORE LABILE

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Local Indicators of Spatial Association—LISA

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How to measure and test phylogenetic signal

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Effects of new mutations on fitness: insights from models and data

inferredcites →https://doi.org/10.1126/science.1147112openalex-snapshot

Genome-Wide Experimental Determination of Barriers to Horizontal Gene Transfer

inferredcites →https://doi.org/10.1126/science.aad2602openalex-snapshot

The ecology of the microbiome: Networks, competition, and stability

inferredcites →https://doi.org/10.1126/science.aan0797openalex-snapshot

Mutation dynamics and fitness effects followed in single cells

inferredcites →https://doi.org/10.1128/aac.02412-14openalex-snapshot

In Silico Detection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing

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Emergence of Oxacillinase-Mediated Resistance to Imipenem inKlebsiella pneumoniae

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Construction of a Vibrio splendidus Mutant Lacking the Metalloprotease Gene vsm by Use of a Novel Counterselectable Suicide Vector

inferredcites →https://doi.org/10.1128/cmr.00088-17openalex-snapshot

Mobile Genetic Elements Associated with Antimicrobial Resistance

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The Global Ascendency of OXA-48-Type Carbapenemases

inferredcites →https://doi.org/10.1128/genomea.00433-18openalex-snapshot

Complete Genome Sequence of Escherichia coli J53, an Azide-Resistant Laboratory Strain Used for Conjugation Experiments

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Evolutionary History of the Global Emergence of the Escherichia coli Epidemic Clone ST131

inferredcites →https://doi.org/10.1128/microbiolspec.mtbp-0016-2017openalex-snapshot

Fitness Costs of Plasmids: a Limit to Plasmid Transmission

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Mobile Compensatory Mutations Promote Plasmid Survival

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Local prevalence of extended-spectrum beta-lactamase (ESBL) producing Enterobacteriaceae intestinal carriers at admission and co-expression of ESBL and OXA-48 carbapenemase in Klebsiella pneumoniae: a prevalence survey in a Spanish University Hospital

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Cell Genetics and Hereditary Symbiosis

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Fitness of Escherichia coli strains carrying expressed and partially silent IncN and IncP1 plasmids

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Mash: fast genome and metagenome distance estimation using MinHash

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Combined Analysis of Variation in Core, Accessory and Regulatory Genome Regions Provides a Super-Resolution View into the Evolution of Bacterial Populations

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A New and Improved Host-Independent Plasmid System for RK2-Based Conjugal Transfer

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The Population Biology of Bacterial Plasmids: A Hidden Markov Model Approach

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The Persistence of Parasitic Plasmids

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Transfer and Persistence of a Multi-Drug Resistance Plasmid in situ of the Infant Gut Microbiota in the Absence of Antibiotic Treatment

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Modelling Plasmid-Mediated Horizontal Gene Transfer in Biofilms

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Introduction of Plasmid to the Murine Gut via Consumption of an Escherichia coli Carrier and Examining the Impact of Bacterial Dosing and Antibiotics on Persistence

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The ecology of plasmid-coded antibiotic resistance: a basic framework for experimental research and modeling

inferred← citeshttps://doi.org/10.1038/s41467-022-33412-8openalex-snapshot

Two modes of evolution shape bacterial strain diversity in the mammalian gut for thousands of generations

inferred← citeshttps://doi.org/10.1038/s41579-020-00497-1openalex-snapshot

Beyond horizontal gene transfer: the role of plasmids in bacterial evolution

inferred← citeshttps://doi.org/10.1101/2020.10.23.351718openalex-snapshot

Limited and strain-specific transcriptional and growth responses to acquisition of a multidrug resistance plasmid in genetically diverse Escherichia coli lineages

inferred← citeshttps://doi.org/10.1101/2021.04.10.439128openalex-snapshot

Plasmid fitness costs are caused by specific genetic conflicts

inferred← citeshttps://doi.org/10.1101/2022.03.02.482687openalex-snapshot

Bioinformatic analyses of plasmid resistome changes in pOXA-48

inferred← citeshttps://doi.org/10.1128/cmr.00050-19openalex-snapshot

Evolutionary Pathways and Trajectories in Antibiotic Resistance

inferred← citeshttps://doi.org/10.1128/msphere.00008-21openalex-snapshot

Genomic Background Governs Opposing Responses to Nalidixic Acid upon Megaplasmid Acquisition in Pseudomonas

inferred← citeshttps://doi.org/10.1128/msystems.00083-21openalex-snapshot

Limited and Strain-Specific Transcriptional and Growth Responses to Acquisition of a Multidrug Resistance Plasmid in Genetically Diverse Escherichia coli Lineages

inferred← citeshttps://doi.org/10.1186/s12866-022-02546-6openalex-snapshot

Genomic analysis of qnr-harbouring IncX plasmids and their transferability within different hosts under induced stress

inferred← citeshttps://doi.org/10.1371/journal.pbio.3001225openalex-snapshot

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

inferred← citeshttps://doi.org/10.22215/etd/2021-14588openalex-snapshot

The Effect of Genetic Background and Environment on Plasmid Fitness and Persistence

inferred← citeshttps://doi.org/10.3389/fmicb.2021.606396openalex-snapshot

Mathematical Models of Plasmid Population Dynamics

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Collateral sensitivity associated with antibiotic resistance plasmids

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