Extensive metagenomic analysis of the porcine gut resistome to identify indicators reflecting antimicrobial resistance

Expanded catalog of microbial genes and metagenome-assembled genomes from the pig gut microbiome

(2021) Congying Chen et al.   Nature Communications

Man-made microbial resistances in built environments

(2019) Alexander Mahnert et al.   Nature Communications

1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses

(2019) Yuanqiang Zou et al.   NATURE BIOTECHNOLOGY

Antimicrobial Effects on Swine Gastrointestinal Microbiota and Their Accompanying Antibiotic Resistome

(2019) Mohamed Zeineldin et al.   Frontiers in Microbiology

Antibiotic resistomes of healthy pig faecal metagenomes

(2019) Aoife Joyce et al.   Microbial Genomics

Global trends in antimicrobial resistance in animals in low- and middle-income countries

(2019) Thomas P. Van Boeckel et al.   SCIENCE

Characterization of the Pig Gut Microbiome and Antibiotic Resistome in Industrialized Feedlots in China

(2019) Chunlai Wang et al.   mSystems

CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database

(2019) Brian P Alcock et al.   NUCLEIC ACIDS RESEARCH

Gut resistomes, microbiota and antibiotic residues in Chinese patients undergoing antibiotic administration and healthy individuals

(2019) Yujing Duan et al.   SCIENCE OF THE TOTAL ENVIRONMENT

The fecal resistome of dairy cattle is associated with diet during nursing

(2019) Jinxin Liu et al.   Nature Communications

Occurrence and distribution of clinical and veterinary antibiotics in the faeces of a Chinese population

(2019) Qing Wang et al.   JOURNAL OF HAZARDOUS MATERIALS

OUP accepted manuscript

(2018)   BIOINFORMATICS

The diversity of uncharacterized antibiotic resistance genes can be predicted from known gene variants—but not always

(2018) Johan Bengtsson-Palme   Microbiome

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

(2018) Patrick Munk et al.   Nature Microbiology

BASTA - Taxonomic classification of sequences and sequence bins using Last Common Ancestor estimations

(2018) Tim Kahlke et al.   Methods in Ecology and Evolution

Recovery of gut microbiota of healthy adults following antibiotic exposure

(2018) Albert Palleja et al.   Nature Microbiology

Environmental Escherichia coli : ecology and public health implications-a review

(2017) J. Jang et al.   JOURNAL OF APPLIED MICROBIOLOGY

Reducing antimicrobial use in food animals

(2017) Thomas P. Van Boeckel et al.   SCIENCE

Differences in Microbiota Membership along the Gastrointestinal Tract of Piglets and Their Differential Alterations Following an Early-Life Antibiotic Intervention

(2017) Chunlong Mu et al.   Frontiers in Microbiology

Next-Generation Beneficial Microbes: The Case of Akkermansia muciniphila

(2017) Patrice D. Cani et al.   Frontiers in Microbiology

Metagenomics of urban sewage identifies an extensively shared antibiotic resistome in China

(2017) Jian-Qiang Su et al.   Microbiome

Diversity of the Tetracycline Mobilome within a Chinese Pig Manure Sample

(2016) Sébastien Olivier Leclercq et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices

(2016) Dinghua Li et al.   METHODS

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

(2016) Baofeng Jia et al.   NUCLEIC ACIDS RESEARCH

The structure and diversity of human, animal and environmental resistomes

(2016) Chandan Pal et al.   Microbiome

A reference gene catalogue of the pig gut microbiome

(2016) Liang Xiao et al.   Nature Microbiology

Novel opportunities for next-generation probiotics targeting metabolic syndrome

(2015) Patrice D Cani et al.   CURRENT OPINION IN BIOTECHNOLOGY

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

Comprehensive Evaluation of Antibiotics Emission and Fate in the River Basins of China: Source Analysis, Multimedia Modeling, and Linkage to Bacterial Resistance

(2015) Qian-Qian Zhang et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

The Rise of Fluoroquinolone-ResistantEscherichia coliin the Community: Scarier Than We Thought

(2015) Brad Spellberg et al.   JOURNAL OF INFECTIOUS DISEASES

Update on the antibiotic resistance crisis

(2014) Gian Maria Rossolini et al.   CURRENT OPINION IN PHARMACOLOGY

Variations in the sales and sales patterns of veterinary antimicrobial agents in 25 European countries

(2014) K. Grave et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

An integrated catalog of reference genes in the human gut microbiome

(2014) Junhua Li et al.   NATURE BIOTECHNOLOGY

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

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

(2014) Mark de Been et al.   PLoS Genetics

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Toward Effective Probiotics for Autism and Other Neurodevelopmental Disorders

(2013) Jack A. Gilbert et al.   CELL

Faecalibacterium prausnitzii and human intestinal health

(2013) S Miquel et al.   CURRENT OPINION IN MICROBIOLOGY

Diverse and abundant antibiotic resistance genes in Chinese swine farms

(2013) Yong-Guan Zhu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metagenome-wide analysis of antibiotic resistance genes in a large cohort of human gut microbiota

(2013) Yongfei Hu et al.   Nature Communications

A metagenome-wide association study of gut microbiota in type 2 diabetes

(2012) Junjie Qin et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

Insights into a Multidrug Resistant Escherichia coli Pathogen of the Globally Disseminated ST131 Lineage: Genome Analysis and Virulence Mechanisms

(2011) Makrina Totsika et al.   PLoS One

Expression of Multidrug Efflux Pump GenesacrAB-tolC,mdfA, andnorEinEscherichia coliClinical Isolates as a Function of Fluoroquinolone and Multidrug Resistance

(2010) Michelle C. Swick et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Overexpression of Resistance-Nodulation-Cell Division Pump AdeFGH Confers Multidrug Resistance in Acinetobacter baumannii

(2010) S. Coyne et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Ab initio gene identification in metagenomic sequences

(2010) Wenhan Zhu et al.   NUCLEIC ACIDS RESEARCH

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

MRSA in livestock animals—an epidemic waiting to happen?

(2008) M. Wulf et al.   CLINICAL MICROBIOLOGY AND INFECTION

The safety ofBacillus subtilisandBacillus indicusas food probiotics

(2008) H.A. Hong et al.   JOURNAL OF APPLIED MICROBIOLOGY

Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients

(2008) H. Sokol et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Antimicrobial resistance in swine production

(2008) Frank M. Aarestrup et al.   ANIMAL HEALTH RESEARCH REVIEWS