Related references
Note: Only part of the references are listed.The population genetics of pathogenicEscherichia coli
Erick Denamur et al.
NATURE REVIEWS MICROBIOLOGY (2021)
Beyond horizontal gene transfer: the role of plasmids in bacterial evolution
Jeronimo Rodriguez-Beltran et al.
NATURE REVIEWS MICROBIOLOGY (2021)
Conjugative plasmids interact with insertion sequences to shape the horizontal transfer of antimicrobial resistance genes
You Che et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)
Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae
Liam P. Shaw et al.
SCIENCE ADVANCES (2021)
SCAPP: an algorithm for improved plasmid assembly in metagenomes
David Pellow et al.
MICROBIOME (2021)
First genomic insights into carbapenem-resistant Klebsiella pneumoniae from Malaysia
Han Ming Gan et al.
JOURNAL OF GLOBAL ANTIMICROBIAL RESISTANCE (2020)
Plasmids Shaped the Recent Emergence of the Major Nosocomial Pathogen Enterococcus faecium
S. Arredondo-Alonso et al.
MBIO (2020)
gplas: a comprehensive tool for plasmid analysis using short-read graphs
Sergio Arredondo-Alonso et al.
BIOINFORMATICS (2020)
PlasClass improves plasmid sequence classification
David Pellow et al.
PLoS Computational Biology (2020)
Origin, maintenance and spread of antibiotic resistance genes within plasmids and chromosomes of bloodstream isolates of Escherichia coli
Cosmika Goswami et al.
MICROBIAL GENOMICS (2020)
F Plasmids Are the Major Carriers of Antibiotic Resistance Genes in Human-Associated Commensal Escherichia coli
Craig Stephens et al.
MSPHERE (2020)
Platon: identification and characterization of bacterial plasmid contigs in short-read draft assemblies exploiting protein sequence-based replicon distribution scores
Oliver Schwengers et al.
MICROBIAL GENOMICS (2020)
A Nosocomial Respiratory Infection Outbreak of Carbapenem-ResistantEscherichia coliST131 With Multiple TransmissibleblaKPC-2Carrying Plasmids
Lin Gong et al.
FRONTIERS IN MICROBIOLOGY (2020)
Tracking of Antibiotic Resistance Transfer and Rapid Plasmid Evolution in a Hospital Setting by Nanopore Sequencing
Silke Peter et al.
MSPHERE (2020)
Genome-based characterization of Escherichia coli causing bloodstream infection through next-generation sequencing
Rafika Indah Paramita et al.
PLOS ONE (2020)
Isolation of Drug-Resistant Gallibacterium anatis from Calves with Unresponsive Bronchopneumonia, Belgium
Laura Van Driessche et al.
EMERGING INFECTIOUS DISEASES (2020)
Opportunities and challenges in long-read sequencing data analysis
Shanika L. Amarasinghe et al.
GENOME BIOLOGY (2020)
Fast and flexible bacterial genomic epidemiology with PopPUNK
John A. Lees et al.
GENOME RESEARCH (2019)
Mosaic plasmids are abundant and unevenly distributed across prokaryotic taxa
Mitchell W. Pesesky et al.
PLASMID (2019)
PPR-Meta: a tool for identifying phages and plasmids from metagenomic fragments using deep learning
Zhencheng Fang et al.
GIGASCIENCE (2019)
In vivo acquisition of fosfomycin resistance in Escherichia coli by fosA transmission from commensal flora
Thijs ten Doesschate et al.
JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY (2019)
Using Genomics to Track Global Antimicrobial Resistance
Rene S. Hendriksen et al.
FRONTIERS IN PUBLIC HEALTH (2019)
Attributable deaths and disability-adjusted life-years caused by infections with antibiotic-resistant bacteria in the EU and the European Economic Area in 2015: a population-level modelling analysis
Alessandro Cassini et al.
LANCET INFECTIOUS DISEASES (2019)
Plasmid ATLAS: plasmid visual analytics and identification in high-throughput sequencing data
Tiago F. Jesus et al.
NUCLEIC ACIDS RESEARCH (2019)
One Health Genomic Surveillance of Escherichia coli Demonstrates Distinct Lineages and Mobile Genetic Elements in Isolates from Humans versus Livestock
Catherine Ludden et al.
MBIO (2019)
Attributable sources of community-acquired carriage of Escherichia coli containing β-lactam antibiotic resistance genes: a population-based modelling study
Lapo Mughini-Gras et al.
LANCET PLANETARY HEALTH (2019)
Metagenomic analysis reveals the prevalence and persistence of antibiotic- and heavy metal-resistance genes in wastewater treatment plant
Sachin Kumar Gupta et al.
JOURNAL OF MICROBIOLOGY (2018)
PlasFlow: predicting plasmid sequences in metagenomic data using genome signatures
Pawel S. Krawczyk et al.
NUCLEIC ACIDS RESEARCH (2018)
ClermonTyping: an easy-to-use and accurate in silico method for Escherichia genus strain phylotyping
Johann Beghain et al.
MICROBIAL GENOMICS (2018)
mlplasmids: a user-friendly tool to predict plasmid- and chromosome-derived sequences for single species
Sergio Arredondo-Alonso et al.
MICROBIAL GENOMICS (2018)
PlaScope: a targeted approach to assess the plasmidome from genome assemblies at the species level
G. Royer et al.
MICROBIAL GENOMICS (2018)
MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies
James Robertson et al.
MICROBIAL GENOMICS (2018)
Recycler: an algorithm for detecting plasmids from de novo assembly graphs
Roye Rozov et al.
BIOINFORMATICS (2017)
Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads
Ryan R. Wick et al.
PLOS COMPUTATIONAL BIOLOGY (2017)
Global phylogenetic analysis of Escherichia coli and plasmids carrying the mcr-1 gene indicates bacterial diversity but plasmid restriction
Sebastien Matamoros et al.
SCIENTIFIC REPORTS (2017)
The impact of insertion sequences on bacterial genome plasticity and adaptability
Joachim Vandecraen et al.
CRITICAL REVIEWS IN MICROBIOLOGY (2017)
Completing bacterial genome assemblies with multiplex MinION sequencing
Ryan R. Wick et al.
MICROBIAL GENOMICS (2017)
On the (im)possibility of reconstructing plasmids from whole-genome short-read sequencing data
Sergio Arredondo-Alonso et al.
MICROBIAL GENOMICS (2017)
plasmidSPAdes: assembling plasmids from whole genome sequencing data
Dmitry Antipov et al.
BIOINFORMATICS (2016)
Mash: fast genome and metagenome distance estimation using MinHash
Brian D. Ondov et al.
GENOME BIOLOGY (2016)
Insertion Sequence IS26 Reorganizes Plasmids in Clinically Isolated Multidrug-Resistant Bacteria by Replicative Transposition
Susu He et al.
MBIO (2015)
In Silico Detection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing
Alessandra Carattoli et al.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY (2014)
Population-Based Epidemiology and Microbiology of Community-Onset Bloodstream Infections
Kevin B. Laupland et al.
CLINICAL MICROBIOLOGY REVIEWS (2014)
Structure, function and diversity of the healthy human microbiome
Curtis Huttenhower et al.
NATURE (2012)
The mosaicism of plasmids revealed by atypical genes detection and analysis
Emanuele Bosi et al.
BMC GENOMICS (2011)
Cryptic Lineages of the Genus Escherichia
Seth T. Walk et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2009)
New insights into the epidemiology of enteropathogenic Escherichia coli infection
Theresa J. Ochoa et al.
TRANSACTIONS OF THE ROYAL SOCIETY OF TROPICAL MEDICINE AND HYGIENE (2008)