Genomic network analysis of environmental and livestock F-type plasmid populations

Large-scale network analysis captures biological features of bacterial plasmids

(2020) Mislav Acman et al.   Nature Communications

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

Characterizing Antimicrobial Resistant Escherichia coli and Associated Risk Factors in a Cross-Sectional Study of Pig Farms in Great Britain

(2020) Manal AbuOun 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

Detection of extended‐spectrum β‐lactam, AmpC and carbapenem resistance in Enterobacteriaceae in beef cattle in Great Britain in 2015

(2019) M. Velasova et al.   JOURNAL OF APPLIED MICROBIOLOGY

Selective advantages favour high genomic AT-contents in intracellular elements

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

Genomic analysis unveils important aspects of population structure, virulence, and antimicrobial resistance in Klebsiella aerogenes

(2019) Hemanoel Passarelli‐Araujo et al.   FEBS Journal

Genomic analysis of a multidrug‐resistant clinical Providencia rettgeri (PR002) strain with the novel integron ln 1483 and an A/C plasmid replicon

(2019) Nontombi Marylucy Mbelle et al.   Annals of the New York Academy of Sciences

Validating the NCBI AMRFinder Tool and Resistance Gene Database Using Antimicrobial Resistance Genotype-Phenotype Correlations in a Collection of NARMS Isolates

(2019) Michael Feldgarden et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Genomic comparison of diverse Salmonella serovars isolated from swine

(2019) Sushim K. Gupta et al.   PLoS One

An Escherichia coli ST131 pangenome atlas reveals population structure and evolution across 4,071 isolates

(2019) Arun Gonzales Decano et al.   Scientific Reports

Klebsiella pneumoniae as a key trafficker of drug resistance genes from environmental to clinically important bacteria

(2018) Kelly L .Wyres et al.   CURRENT OPINION IN MICROBIOLOGY

Plasmids carrying antimicrobial resistance genes in Enterobacteriaceae

(2018) M Rozwandowicz et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Extended-Spectrum Beta-Lactamase-Producing Enterobacteriaceae in Dairy Farm Environments: A New Zealand Perspective

(2018) Rose M. Collis et al.   Foodborne Pathogens and Disease

Plasmid ATLAS: plasmid visual analytics and identification in high-throughput sequencing data

(2018) Tiago F Jesus et al.   NUCLEIC ACIDS RESEARCH

Clustal Omega for making accurate alignments of many protein sequences

(2017) Fabian Sievers et al.   PROTEIN SCIENCE

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

(2017) Ryan R. Wick et al.   PLoS Computational Biology

Plasmid Classification in an Era of Whole-Genome Sequencing: Application in Studies of Antibiotic Resistance Epidemiology

(2017) Alex Orlek et al.   Frontiers in Microbiology

CTX-M-15-Producing E. coli Isolates from Food Products in Germany Are Mainly Associated with an IncF-Type Plasmid and Belong to Two Predominant Clonal E. coli Lineages

(2017) Alexandra Irrgang et al.   Frontiers in Microbiology

blaCTX-M-15 carried by IncF-type plasmids is the dominant ESBL gene in Escherichia coli and Klebsiella pneumoniae at a hospital in Ghana

(2016) Alex Agyekum et al.   DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE

Antimicrobial Resistance in Agriculture

(2016) Sophie Thanner et al.   mBio

ggtree: anrpackage for visualization and annotation of phylogenetic trees with their covariates and other associated data

(2016) Guangchuang Yu et al.   Methods in Ecology and Evolution

Antimicrobial resistance in humans, livestock and the wider environment

(2015) M. Woolhouse et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Faster unfolding of communities: Speeding up the Louvain algorithm

(2015) V. A. Traag   PHYSICAL REVIEW E

ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes

(2015) Xavier Didelot et al.   PLoS Computational Biology

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

Replicon sequence typing of IncF plasmids carrying virulence and resistance determinants

(2010) Laura Villa et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Fast unfolding of communities in large networks

(2008) Vincent D Blondel et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT