A sampling and metagenomic sequencing-based methodology for monitoring antimicrobial resistance in swine herds

Determining the optimal number of individual samples to pool for quantification of average herd levels of antimicrobial resistance genes in Danish pig herds using high-throughput qPCR

(2016) Julie Clasen et al.   VETERINARY MICROBIOLOGY

Metagenomic insights into tetracycline effects on microbial community and antibiotic resistance of mouse gut

(2015) Jinbao Yin et al.   ECOTOXICOLOGY

EBI metagenomics in 2016 - an expanding and evolving resource for the analysis and archiving of metagenomic data

(2015) Alex Mitchell et al.   NUCLEIC ACIDS RESEARCH

The livestock reservoir for antimicrobial resistance: a personal view on changing patterns of risks, effects of interventions and the way forward

(2015) F. M. Aarestrup   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Sampling and Pooling Methods for Capturing Herd Level Antibiotic Resistance in Swine Feces using qPCR and CFU Approaches

(2015) Gunilla Veslemøy Schmidt et al.   PLoS One

Meta-genomic analysis of toilet waste from long distance flights; a step towards global surveillance of infectious diseases and antimicrobial resistance

(2015) Thomas Nordahl Petersen et al.   Scientific Reports

Prevalence of Antibiotic Resistance Genes and Bacterial Pathogens in Long-Term Manured Greenhouse Soils As Revealed by Metagenomic Survey

(2014) Hua Fang et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

A Comprehensive Insight into Tetracycline Resistant Bacteria and Antibiotic Resistance Genes in Activated Sludge Using Next-Generation Sequencing

(2014) Kailong Huang et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Faecal Escherichia coli from patients with E. coli urinary tract infection and healthy controls who have never had a urinary tract infection

(2014) Karen L. Nielsen et al.   JOURNAL OF MEDICAL MICROBIOLOGY

Bacterial phylogeny structures soil resistomes across habitats

(2014) Kevin J. Forsberg et al.   NATURE

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes

(2014) H Bjørn Nielsen et al.   NATURE BIOTECHNOLOGY

What is a resistance gene? Ranking risk in resistomes

(2014) José L. Martínez et al.   NATURE REVIEWS MICROBIOLOGY

In Silico Analysis of Antibiotic Resistance Genes in the Gut Microflora of Individuals from Diverse Geographies and Age-Groups

(2014) Tarini Shankar Ghosh et al.   PLoS One

Impact of treatment strategies on cephalosporin and tetracycline resistance gene quantities in the bovine fecal metagenome

(2014) Neena Kanwar et al.   Scientific Reports

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

(2014) Paul J. McMurdie et al.   PLoS Computational Biology

Country-specific antibiotic use practices impact the human gut resistome

(2013) K. Forslund et al.   GENOME RESEARCH

Correlation between veterinary antimicrobial use and antimicrobial resistance in food-producing animals: a report on seven countries

(2013) I. Chantziaras et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Genome assembly and haplotyping with Hi-C

(2013) Jan O Korbel et al.   NATURE BIOTECHNOLOGY

EBI metagenomics—a new resource for the analysis and archiving of metagenomic data

(2013) Sarah Hunter et al.   NUCLEIC ACIDS RESEARCH

Sea Surface Temperature of the mid-Piacenzian Ocean: A Data-Model Comparison

(2013) Harry J. Dowsett et al.   Scientific Reports

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

Voluntary ban on cephalosporin use in Danish pig production has effectively reduced extended-spectrum cephalosporinase-producing Escherichia coli in slaughter pigs

(2012) Yvonne Agersø et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing

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

In-feed antibiotic effects on the swine intestinal microbiome

(2012) T. Looft et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pseudomonas Aeruginosa: Resistance to the Max

(2011) Keith Poole   Frontiers in Microbiology

Two Novel Antibiotic Resistance Genes, tet(44) and ant(6)-Ib, Are Located within a Transferable Pathogenicity Island in Campylobacter fetus subsp. fetus

(2010) C. Abril et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Functional Characterization of the Antibiotic Resistance Reservoir in the Human Microflora

(2009) M. O. A. Sommer et al.   SCIENCE

Harmonised monitoring of antimicrobial resistance in Salmonella and Campylobacter isolates from food animals in the European Union

(2008) S. Bronzwaer   CLINICAL MICROBIOLOGY AND INFECTION