Detection of mobile genetic elements associated with antibiotic resistance in Salmonella enterica using a newly developed web tool: MobileElementFinder

Four European Salmonella Typhimurium datasets collected to develop WGS-based source attribution methods

(2020) Nanna Munck et al.   Scientific Data

Structures bounded by directly-oriented members of the IS26 family are pseudo-compound transposons.

(2020) Christopher J. Harmer et al.   PLASMID

Cyclic-di-GMP regulation promotes survival of a slow-replicating subpopulation of intracellularSalmonellaTyphimurium

(2019) Erik Petersen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic diversity and delineation of Salmonella Agona outbreak strains by next generation sequencing, Bavaria, Germany, 1993 to 2018

(2019) Alexandra Dangel et al.   Eurosurveillance

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Salmonella genomic island 3 is an integrative and conjugative element and contributes to copper and arsenic tolerance of Salmonella enterica

(2019) Nobuo Arai et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Transient Replication in Specialized Cells Favors Transfer of an Integrative and Conjugative Element

(2019) François Delavat et al.   mBio

The Transposon Registry

(2019) Supathep Tansirichaiya et al.   Mobile DNA

A Bioinformatic Analysis of Integrative Mobile Genetic Elements Highlights Their Role in Bacterial Adaptation

(2019) Matthew G. Durrant et al.   Cell Host & Microbe

A genomic overview of the population structure of Salmonella

(2018) Nabil-Fareed Alikhan et al.   PLoS Genetics

Mobile Genetic Elements Associated with Antimicrobial Resistance

(2018) Sally R. Partridge et al.   CLINICAL MICROBIOLOGY REVIEWS

ICEberg 2.0: an updated database of bacterial integrative and conjugative elements

(2018) Meng Liu et al.   NUCLEIC ACIDS RESEARCH

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

(2018) Chirag Jain et al.   Nature Communications

Antibiotic Resistance Mechanisms in Bacteria: Relationships Between Resistance Determinants of Antibiotic Producers, Environmental Bacteria, and Clinical Pathogens

(2018) Elizabeth Peterson et al.   Frontiers in Microbiology

National Antimicrobial Resistance Monitoring System: Two Decades of Advancing Public Health Through Integrated Surveillance of Antimicrobial Resistance

(2017) Beth E. Karp et al.   Foodborne Pathogens and Disease

Autonomous Replication of the Conjugative Transposon Tn 916

(2016) Laurel D. Wright et al.   JOURNAL OF BACTERIOLOGY

Identification and analysis of integrons and cassette arrays in bacterial genomes

(2016) Jean Cury et al.   NUCLEIC ACIDS RESEARCH

Expression and Genetic Activation of Cyclic Di-GMP-Specific Phosphodiesterases in Escherichia coli

(2015) Alberto Reinders et al.   JOURNAL OF BACTERIOLOGY

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

Movement of IS26-Associated Antibiotic Resistance Genes Occurs via a Translocatable Unit That Includes a Single IS26 and Preferentially Inserts Adjacent to Another IS26

(2014) C. J. Harmer et al.   mBio

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Identification of acquired antimicrobial resistance genes

(2012) E. Zankari et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria

(2012) M. V. Larsen et al.   JOURNAL OF CLINICAL MICROBIOLOGY

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

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Repetitive DNA and next-generation sequencing: computational challenges and solutions

(2011) Todd J. Treangen et al.   NATURE REVIEWS GENETICS

Recombination and Population Structure in Salmonella enterica

(2011) Xavier Didelot et al.   PLoS Genetics

Acquired Antibiotic Resistance Genes: An Overview

(2011) Angela H. A. M. van Hoek et al.   Frontiers in Microbiology

ISsaga is an ensemble of web-based methods for high throughput identification and semi-automatic annotation of insertion sequences in prokaryotic genomes

(2011) Alessandro M Varani et al.   GENOME BIOLOGY

Integrative and conjugative elements: mosaic mobile genetic elements enabling dynamic lateral gene flow

(2010) Rachel A. F. Wozniak et al.   NATURE REVIEWS MICROBIOLOGY

SGI2, a Relative of Salmonella Genomic Island SGI1 with an Independent Origin

(2008) R. S. Levings et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Salmonella challenges: Prevalence in swine and poultry and potential pathogenicity of such isolates1,2

(2007) S. L. Foley et al.   JOURNAL OF ANIMAL SCIENCE