Abundance and diversity of the faecal resistome in slaughter pigs and broilers in nine European countries

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

(2016) Patrick Munk et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Quantitative assessment of antimicrobial resistance in livestock during the course of a nationwide antimicrobial use reduction in the Netherlands

(2016) Alejandro Dorado-García et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Interconnected microbiomes and resistomes in low-income human habitats

(2016) Erica C. Pehrsson et al.   NATURE

Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system

(2016) Karthik Anantharaman et al.   Nature Communications

A reference gene catalogue of the pig gut microbiome

(2016) Liang Xiao et al.   Nature Microbiology

Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition

(2016) Berith E. Knudsen et al.   mSystems

Impact of library preparation protocols and template quantity on the metagenomic reconstruction of a mock microbial community

(2015) Robert M. Bowers et al.   BMC GENOMICS

Metagenomic Assembly Reveals Hosts of Antibiotic Resistance Genes and the Shared Resistome in Pig, Chicken, and Human Feces

(2015) Liping Ma et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Detection ofmcr-1encoding plasmid-mediated colistin-resistantEscherichia coliisolates from human bloodstream infection and imported chicken meat, Denmark 2015

(2015) Henrik Hasman et al.   Eurosurveillance

A novel gene,optrA, that confers transferable resistance to oxazolidinones and phenicols and its presence inEnterococcus faecalisandEnterococcus faeciumof human and animal origin

(2015) Yang Wang et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Fitting Linear Mixed-Effects Models Usinglme4

(2015) Douglas Bates et al.   Journal of Statistical Software

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

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

Characterization of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli obtained from Danish pigs, pig farmers and their families from farms with high or no consumption of third- or fourth-generation cephalosporins

(2014) Anette M. Hammerum et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

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

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

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

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

Novel resistance functions uncovered using functional metagenomic investigations of resistance reservoirs

(2013) Erica C. Pehrsson et al.   Frontiers in Microbiology

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu 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

Identification of acquired antimicrobial resistance genes

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

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

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