Hotspot mutations and ColE1 plasmids contribute to the fitness of Salmonella Heidelberg in poultry litter

Cheating fosters species co-existence in well-mixed bacterial communities

(2017) Anne Leinweber et al.   ISME Journal

Conflicting selection alters the trajectory of molecular evolution in a tripartite bacteria-plasmid-phage interaction

(2017) Ellie Harrison et al.   MOLECULAR ECOLOGY

Carriage of type II toxin-antitoxin systems by the growing group of IncX plasmids

(2017) Paula Bustamante et al.   PLASMID

Ordering the mob: Insights into replicon and MOB typing schemes from analysis of a curated dataset of publicly available plasmids

(2017) Alex Orlek et al.   PLASMID

The evolution of plasmid stability: Are infectious transmission and compensatory evolution competing evolutionary trajectories?

(2017) James P.J. Hall et al.   PLASMID

Antibiotic stress selects against cooperation in the pathogenic bacteriumPseudomonas aeruginosa

(2017) Marie Vasse et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Impact of treatments for recycled broiler litter on the viability and infectivity of microorganisms

(2017) Daiane Voss-Rech et al.   VETERINARY MICROBIOLOGY

Persistence and reversal of plasmid-mediated antibiotic resistance

(2017) Allison J. Lopatkin et al.   Nature Communications

Compensatory mutations improve general permissiveness to antibiotic resistance plasmids

(2017) Wesley Loftie-Eaton et al.   Nature Ecology & Evolution

Bacterial Quorum Sensing Stabilizes Cooperation by Optimizing Growth Strategies

(2016) Eric L. Bruger et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Water activity of poultry litter: Relationship to moisture content during a grow-out

(2016) Mark W. Dunlop et al.   JOURNAL OF ENVIRONMENTAL MANAGEMENT

Virulence characteristics of extraintestinal pathogenic Escherichia coli deletion of gene encoding the outer membrane protein X

(2016) Xianrong MENG et al.   JOURNAL OF VETERINARY MEDICAL SCIENCE

A Novel 6′-N-Aminoglycoside Acetyltransferase, AAC(6′)-Ial, from a Clinical Isolate ofSerratia marcescens

(2016) Tatsuya Tada et al.   Microbial Drug Resistance

Toxin-antitoxin systems in bacterial growth arrest and persistence

(2016) Rebecca Page et al.   Nature Chemical Biology

CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database

(2016) Baofeng Jia et al.   NUCLEIC ACIDS RESEARCH

National Outbreak of Multidrug Resistant Salmonella Heidelberg Infections Linked to a Single Poultry Company

(2016) Laura Gieraltowski et al.   PLoS One

Multicopy plasmids potentiate the evolution of antibiotic resistance in bacteria

(2016) Alvaro San Millan et al.   Nature Ecology & Evolution

Plasmid carriage can limit bacteria–phage coevolution

(2015) Ellie Harrison et al.   Biology Letters

Microbial Evolution: Towards Resolving the Plasmid Paradox

(2015) R. Craig MacLean et al.   CURRENT BIOLOGY

Parallel Compensatory Evolution Stabilizes Plasmids across the Parasitism-Mutualism Continuum

(2015) Ellie Harrison et al.   CURRENT BIOLOGY

Diversity of Cyclic Di-GMP-Binding Proteins and Mechanisms

(2015) Shan-Ho Chou et al.   JOURNAL OF BACTERIOLOGY

Usefulness of High-Quality Core Genome Single-Nucleotide Variant Analysis for Subtyping the Highly Clonal and the Most Prevalent Salmonella enterica Serovar Heidelberg Clone in the Context of Outbreak Investigations

(2015) S. Bekal et al.   JOURNAL OF CLINICAL MICROBIOLOGY

A new perspective on lysogeny: prophages as active regulatory switches of bacteria

(2015) Ron Feiner et al.   NATURE REVIEWS MICROBIOLOGY

Identification of a Novel 6′-N-Aminoglycoside Acetyltransferase, AAC(6′)-Iak, from a Multidrug-Resistant Clinical Isolate of Stenotrophomonas maltophilia

(2014) Tatsuya Tada et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Comparative Genomic Analysis and Virulence Differences in Closely Related Salmonella enterica Serotype Heidelberg Isolates from Humans, Retail Meats, and Animals

(2014) Maria Hoffmann et al.   Genome Biology and Evolution

A widespread bacteriophage abortive infection system functions through a Type IV toxin–antitoxin mechanism

(2014) Ron L. Dy et al.   NUCLEIC ACIDS RESEARCH

Pervasive domestication of defective prophages by bacteria

(2014) L.-M. Bobay et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2014) A. San Millan et al.   Nature Communications

The Kil Peptide of Bacteriophage λ Blocks Escherichia coli Cytokinesis via ZipA-Dependent Inhibition of FtsZ Assembly

(2014) Daniel P. Haeusser et al.   PLoS Genetics

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

(2013) Alvaro San Millan et al.   ISME Journal

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Novel 6′-N-Aminoglycoside Acetyltransferase AAC(6′)-Iaj from a Clinical Isolate of Pseudomonas aeruginosa

(2012) Tatsuya Tada et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Characterization of Multidrug-Resistant Salmonella enterica Serovar Heidelberg from a Ground Turkey-Associated Outbreak in the United States in 2011

(2012) Jason P. Folster et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Interaction between relaxase MbeA and accessory protein MbeC of the conjugally mobilizable plasmid ColE1

(2012) Athanasia Varsaki et al.   FEBS LETTERS

Convergent Molecular Evolution of Genomic Cores in Salmonella enterica and Escherichia coli

(2012) Sujay Chattopadhyay et al.   JOURNAL OF BACTERIOLOGY

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

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

Influence of Primer Sequences and DNA Extraction Method on Detection of Non-O157 Shiga Toxin–Producing Escherichia coli in Ground Beef by Real-Time PCR Targeting theeae, stx, and Serogroup-Specific Genes

(2012) JAMIE L. WASILENKO et al.   JOURNAL OF FOOD PROTECTION

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

Sequencing of IncX-Plasmids Suggests Ubiquity of Mobile Forms of a Biofilm-Promoting Gene Cassette Recruited from Klebsiella pneumoniae

(2012) Mette Burmølle et al.   PLoS One

The Molecular Diversity of Adaptive Convergence

(2012) O. Tenaillon et al.   SCIENCE

PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs

(2011) H. E. L. Lischer et al.   BIOINFORMATICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Agar Disk Diffusion and Automated Microbroth Dilution Produce Similar Antimicrobial Susceptibility Testing Results for Salmonella Serotypes Newport, Typhimurium, and 4,5,12:i-, But Differ in Economic Cost

(2011) Karin Hoelzer et al.   Foodborne Pathogens and Disease

PHAST: A Fast Phage Search Tool

(2011) Y. Zhou et al.   NUCLEIC ACIDS RESEARCH

Design and Synthesis of a Quintessential Self-Transmissible IncX1 Plasmid, pX1.0

(2011) Lars H. Hansen et al.   PLoS One

Research on Salmonella in broiler litter reused for up to 14 consecutive flocks

(2011) V. F. B. Roll et al.   POULTRY SCIENCE

TonB-Dependent Transporters: Regulation, Structure, and Function

(2010) Nicholas Noinaj et al.   Annual Review of Microbiology

Interrelations between the Microbiotas in the Litter and in the Intestines of Commercial Broiler Chickens

(2010) M. D. Cressman et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Mobility of Plasmids

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

Sociobiological Control of Plasmid Copy Number in Bacteria

(2010) Mukta M. Watve et al.   PLoS One

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

(2010) Aaron E. Darling et al.   PLoS One

Cryptic prophages help bacteria cope with adverse environments

(2010) Xiaoxue Wang et al.   Nature Communications

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Contribution of Gene Amplification to Evolution of Increased Antibiotic Resistance in Salmonella typhimurium

(2009) Song Sun et al.   GENETICS

The Glycerol-3-Phosphate Permease GlpT Is the Only Fosfomycin Transporter in Pseudomonas aeruginosa

(2009) A. Castaneda-Garcia et al.   JOURNAL OF BACTERIOLOGY

High frequency of hotspot mutations in core genes of Escherichia coli due to short-term positive selection

(2009) S. Chattopadhyay et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Periplasmic Cu,Zn superoxide dismutase and cytoplasmic Dps concur in protecting Salmonella enterica serovar Typhimurium from extracellular reactive oxygen species

(2008) Francesca Pacello et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Analysis of ColE1 MbeC Unveils an Extended Ribbon-Helix-Helix Family of Nicking Accessory Proteins

(2008) A. Varsaki et al.   JOURNAL OF BACTERIOLOGY

Cross-talk suppression between the CpxA-CpxR and EnvZ-OmpR two-component systems inE. coli

(2008) Albert Siryaporn et al.   MOLECULAR MICROBIOLOGY