Machine Learning Suggests That Small Size Helps Broaden Plasmid Host Range

HOTSPOT: hierarchical host prediction for assembled plasmid contigs with transformer

(2023) Yongxin Ji et al.   BIOINFORMATICS

Restriction-modification systems have shaped the evolution and distribution of plasmids across bacteria

(2023) Liam P Shaw et al.   NUCLEIC ACIDS RESEARCH

Global transmission of broad-host-range plasmids derived from the human gut microbiome

(2023) Lili Yang et al.   NUCLEIC ACIDS RESEARCH

Plasmid classifications

(2023) M. Pilar Garcillán-Barcia et al.   PLASMID

Emergence of new IncHI2 multidrug-resistance plasmids carrying VIM-1 metallo-β-lactamase in Escherichia coli in Norway

(2023) Nachiket P Marathe et al.   Lancet Microbe

Structural and functional diversity of type IV secretion systems

(2023) Tiago R. D. Costa et al.   NATURE REVIEWS MICROBIOLOGY

Resistome expansion in disease-associated human gut microbiomes

(2023) Simen Fredriksen et al.   Microbiome

Biology and evolution of bacterial toxin–antitoxin systems

(2022) Dukas Jurėnas et al.   NATURE REVIEWS MICROBIOLOGY

PlasmidHostFinder: Prediction of Plasmid Hosts Using Random Forest

(2022) Derya Aytan-Aktug et al.   mSystems

Metabolic genes on conjugative plasmids are highly prevalent in Escherichia coli and can protect against antibiotic treatment

(2022) Alana Palomino et al.   ISME Journal

CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database

(2022) Brian P Alcock et al.   NUCLEIC ACIDS RESEARCH

Epidemiology of Plasmid Lineages Mediating the Spread of Extended-Spectrum Beta-Lactamases among Clinical Escherichia coli

(2022) Bejan Mahmud et al.   mSystems

Targeted bacterial conjugation mediated by synthetic cell-to-cell adhesions

(2022) Marta Robledo et al.   NUCLEIC ACIDS RESEARCH

A Brief History of Plasmids

(2022) Donald R. Helinski   EcoSal Plus

Indirect Selection against Antibiotic Resistance via Specialized Plasmid-Dependent Bacteriophages

(2021) Reetta Penttinen et al.   Microorganisms

COPLA, a taxonomic classifier of plasmids

(2021) Santiago Redondo-Salvo et al.   BMC BIOINFORMATICS

Protein Transfer through an F Plasmid-Encoded Type IV Secretion System Suppresses the Mating-Induced SOS Response

(2021) Abu Amar M. Al Mamun et al.   mBio

Re-evaluating the evidence for a universal genetic boundary among microbial species

(2021) Connor S. Murray et al.   Nature Communications

AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence

(2021) Michael Feldgarden et al.   Scientific Reports

Deeplasmid: deep learning accurately separates plasmids from bacterial chromosomes

(2021) William B Andreopoulos et al.   NUCLEIC ACIDS RESEARCH

PLSDB: advancing a comprehensive database of bacterial plasmids

(2021) Georges P Schmartz et al.   NUCLEIC ACIDS RESEARCH

Ecological and evolutionary solutions to the plasmid paradox

(2021) Michael A. Brockhurst et al.   TRENDS IN MICROBIOLOGY

Analysis of COMPASS, a New Comprehensive Plasmid Database Revealed Prevalence of Multireplicon and Extensive Diversity of IncF Plasmids

(2020) Pierre-Emmanuel Douarre et al.   Frontiers in Microbiology

Pathways for horizontal gene transfer in bacteria revealed by a global map of their plasmids

(2020) Santiago Redondo-Salvo et al.   Nature Communications

A comparative analysis of gradient boosting algorithms

(2020) Candice Bentéjac et al.   ARTIFICIAL INTELLIGENCE REVIEW

Universal whole-sequence-based plasmid typing and its utility to prediction of host range and epidemiological surveillance

(2020) James Robertson et al.   Microbial Genomics

On the emergence of P-Loop NTPase and Rossmann enzymes from a Beta-Alpha-Beta ancestral fragment

(2020) Liam M Longo et al.   eLife

Defining and combating antibiotic resistance from One Health and Global Health perspectives

(2019) Sara Hernando-Amado et al.   Nature Microbiology

Environmental and clinical antibiotic resistomes, same only different

(2019) Gerard D Wright   CURRENT OPINION IN MICROBIOLOGY

Plasmid persistence: costs, benefits, and the plasmid paradox

(2018) Amanda C. Carroll et al.   CANADIAN JOURNAL OF MICROBIOLOGY

PlasFlow: predicting plasmid sequences in metagenomic data using genome signatures

(2018) Pawel S Krawczyk et al.   NUCLEIC ACIDS RESEARCH

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

(2018) Chirag Jain et al.   Nature Communications

β-Lactams and β-Lactamase Inhibitors: An Overview

(2016) Karen Bush et al.   Cold Spring Harbor Perspectives in Medicine

Tackling antibiotic resistance: the environmental framework

(2015) Thomas U. Berendonk et al.   NATURE REVIEWS MICROBIOLOGY

In SilicoDetection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing

(2014) Alessandra Carattoli et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

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

(2014) Tom Vogwill et al.   Evolutionary Applications

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

(2014) Uli Klümper et al.   ISME Journal

Plasmid Flux in Escherichia coli ST131 Sublineages, Analyzed by Plasmid Constellation Network (PLACNET), a New Method for Plasmid Reconstruction from Whole Genome Sequences

(2014) Val F. Lanza et al.   PLoS Genetics

Subcellular location of the coupling protein TrwB and the role of its transmembrane domain

(2013) Rosa L. Segura et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Mobility of Plasmids

(2010) C. Smillie et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

BcsQ is an essential component of theEscherichia colicellulose biosynthesis apparatus that localizes at the bacterial cell pole

(2009) Benjamin Le Quéré et al.   MOLECULAR MICROBIOLOGY

The structural biology of type IV secretion systems

(2009) Rémi Fronzes et al.   NATURE REVIEWS MICROBIOLOGY

Differential Regulation of Horizontally Acquired and Core Genome Genes by the Bacterial Modulator H-NS

(2009) Rosa C. Baños et al.   PLoS Genetics