Dissemination of Cephalosporin Resistance Genes between Escherichia coli Strains from Farm Animals and Humans by Specific Plasmid Lineages

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

Recent Recombination Events in the Core Genome Are Associated with Adaptive Evolution in Enterococcus faecium

(2013) Mark de Been et al.   Genome Biology and Evolution

The Evolutionary Path to Extraintestinal Pathogenic, Drug-Resistant Escherichia coli Is Marked by Drastic Reduction in Detectable Recombination within the Core Genome

(2013) Alan McNally et al.   Genome Biology and Evolution

Identical plasmid AmpC beta-lactamase genes and plasmid types in E. coli isolates from patients and poultry meat in the Netherlands

(2013) Guido M. Voets et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Whole Genome Sequencing versus Traditional Genotyping for Investigation of a Mycobacterium tuberculosis Outbreak: A Longitudinal Molecular Epidemiological Study

(2013) Andreas Roetzer et al.   PLOS MEDICINE

Extended-Spectrum β-Lactamase–Producing Escherichia coli From Retail Chicken Meat and Humans: Comparison of Strains, Plasmids, Resistance Genes, and Virulence Factors

(2012) Jan A. J. W. Kluytmans et al.   CLINICAL INFECTIOUS DISEASES

Sales of veterinary antibacterial agents in nine European countries during 2005-09: trends and patterns

(2012) K. Grave et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Extended-spectrum- -lactamase- and AmpC- -lactamase-producing Escherichia coli in Dutch broilers and broiler farmers

(2012) C. Dierikx et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Rapid Whole-Genome Sequencing for Investigation of a Neonatal MRSA Outbreak

(2012) Claudio U. Köser et al.   NEW ENGLAND JOURNAL OF MEDICINE

Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011

(2012) Y. H. Grad et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Horizontal Transfer of Antibiotic Resistance Genes on Abiotic Touch Surfaces: Implications for Public Health

(2012) S. L. Warnes et al.   mBio

BIGSdb: Scalable analysis of bacterial genome variation at the population level

(2011) Keith A Jolley et al.   BMC BIOINFORMATICS

Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies

(2011) M. C. Schatz et al.   BRIEFINGS IN BIOINFORMATICS

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Rates of Mutation and Host Transmission for an Escherichia coli Clone over 3 Years

(2011) Peter R. Reeves et al.   PLoS One

Mortality and Hospital Stay Associated with Resistant Staphylococcus aureus and Escherichia coli Bacteremia: Estimating the Burden of Antibiotic Resistance in Europe

(2011) Marlieke E. A. de Kraker et al.   PLOS MEDICINE

Rapid detection of TEM, SHV and CTX-M extended-spectrum β-lactamases in Enterobacteriaceae using ligation-mediated amplification with microarray analysis

(2010) J. Cohen Stuart et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

CTX-M-producing Escherichia coli in a maternity ward: a likely community importation and evidence of mother-to-neonate transmission

(2010) V. Dubois et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Mobility of Plasmids

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

Increased detection of extended spectrum beta-lactamase producing Salmonella enterica and Escherichia coli isolates from poultry

(2010) Cindy Dierikx et al.   VETERINARY MICROBIOLOGY

Attributable Hospital Cost and Length of Stay Associated with Health Care-Associated Infections Caused by Antibiotic-Resistant Gram-Negative Bacteria

(2009) P. D. Mauldin et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Complete Nucleotide Sequences of Plasmids pEK204, pEK499, and pEK516, Encoding CTX-M Enzymes in Three Major Escherichia coli Lineages from the United Kingdom, All Belonging to the International O25:H4-ST131 Clone

(2009) N. Woodford et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Extended-spectrum and CMY-type b-lactamase-producing Escherichia coli in clinical samples and retail meat from Pittsburgh, USA and Seville, Spain

(2009) Y. Doi et al.   CLINICAL MICROBIOLOGY AND INFECTION

Characterization of plasmids encoding CMY-2 AmpC β-lactamases from Escherichia coli in Canadian intensive care units

(2009) Patricia J. Baudry et al.   DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE

The changing epidemiology of resistance

(2009) P. M. Hawkey et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Selection and Persistence of CTX-M-Producing Escherichia coli in the Intestinal Flora of Pigs Treated with Amoxicillin, Ceftiofur, or Cefquinome

(2008) L. M. Cavaco et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Diversity of Extended-Spectrum  -Lactamases and Class C  -Lactamases among Cloacal Escherichia coli Isolates in Belgian Broiler Farms

(2008) A. Smet et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

Multilocus sequence typing of IncI1 plasmids carrying extended-spectrum β-lactamases in Escherichia coli and Salmonella of human and animal origin

(2008) Aurora García-Fernández et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Antibiotic resistance integrons and extended-spectrum  -lactamases among Enterobacteriaceae isolates recovered from chickens and swine in Portugal

(2008) E. Machado et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY