Freshwater viral metagenome reveals novel and functional phage-borne antibiotic resistance genes

Bacteriophages as Environmental Reservoirs of Antibiotic Resistance

(2019) William Calero-Cáceres et al.   TRENDS IN MICROBIOLOGY

Viruses as key reservoirs of antibiotic resistance genes in the environment

(2019) Didier Debroas et al.   ISME Journal

Detecting contamination in viromes using ViromeQC

(2019) Moreno Zolfo et al.   NATURE BIOTECHNOLOGY

IMP-68, a Novel IMP-Type Metallo-β-Lactamase in Imipenem-Susceptible Klebsiella pneumoniae

(2019) Hiroaki Kubota et al.   mSphere

How do bacteriophages promote antibiotic resistance in the environment?

(2018) J.L. Balcázar   CLINICAL MICROBIOLOGY AND INFECTION

Phage particles harboring antibiotic resistance genes in fresh-cut vegetables and agricultural soil

(2018) Olatz Larrañaga et al.   ENVIRONMENT INTERNATIONAL

Functional metagenomics reveals a novel carbapenem-hydrolyzing mobile beta-lactamase from Indian river sediments contaminated with antibiotic production waste

(2018) Nachiket P. Marathe et al.   ENVIRONMENT INTERNATIONAL

Estimating the contribution of bacteriophage to the dissemination of antibiotic resistance genes in pig feces

(2018) Mianzhi Wang et al.   ENVIRONMENTAL POLLUTION

Antibiotic resistance genes in phage particles isolated from human faeces and induced from clinical bacterial isolates

(2018) Maryury Brown-Jaque et al.   INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS

Rates of Mutation and Recombination in Siphoviridae Phage Genome Evolution over Three Decades

(2018) Anne Kupczok et al.   MOLECULAR BIOLOGY AND EVOLUTION

Metagenomics Sheds Light on the Ecology of Marine Microbes and Their Viruses

(2018) Felipe Hernandes Coutinho et al.   TRENDS IN MICROBIOLOGY

The Growing Genetic and Functional Diversity of Extended Spectrum Beta-Lactamases

(2018) Sadeeq ur Rahman et al.   Biomed Research International

Detection of Bacteriophage Particles Containing Antibiotic Resistance Genes in the Sputum of Cystic Fibrosis Patients

(2018) Maryury Brown-Jaque et al.   Frontiers in Microbiology

Antibiotic resistance genes in bacteriophages from diverse marine habitats

(2018) William Calero-Cáceres et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Exploring the contribution of bacteriophages to antibiotic resistance

(2017) Itziar Lekunberri et al.   ENVIRONMENTAL POLLUTION

Contribution of bacteriophage and plasmid DNA to the mobilization of antibiotic resistance genes in a river receiving treated wastewater discharges

(2017) Itziar Lekunberri et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Viromes As Genetic Reservoir for the Microbial Communities in Aquatic Environments: A Focus on Antimicrobial-Resistance Genes

(2017) Stefano Colombo et al.   Frontiers in Microbiology

Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut

(2017) Natalya Yutin et al.   Nature Microbiology

Bacterial GCN5-Related N-Acetyltransferases: From Resistance to Regulation

(2016) Lorenza Favrot et al.   BIOCHEMISTRY

Viral metabolic reprogramming in marine ecosystems

(2016) Bonnie L Hurwitz et al.   CURRENT OPINION IN MICROBIOLOGY

Metagenomic analysis reveals that bacteriophages are reservoirs of antibiotic resistance genes

(2016) Jéssica Subirats et al.   INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS

Phages rarely encode antibiotic resistance genes: a cautionary tale for virome analyses

(2016) François Enault et al.   ISME Journal

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

MEGARes: an antimicrobial resistance database for high throughput sequencing

(2016) Steven M. Lakin et al.   NUCLEIC ACIDS RESEARCH

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

(2016) Baofeng Jia et al.   NUCLEIC ACIDS RESEARCH

Persistence of naturally occurring antibiotic resistance genes in the bacteria and bacteriophage fractions of wastewater

(2016) William Calero-Cáceres et al.   WATER RESEARCH

Dissemination of Antimicrobial Resistance in Microbial Ecosystems through Horizontal Gene Transfer

(2016) Christian J. H. von Wintersdorff et al.   Frontiers in Microbiology

Novel thermostable antibiotic resistance enzymes from the Atlantis II Deep Red Sea brine pool

(2016) Ali H. A. Elbehery et al.   Microbial Biotechnology

Metagenomic Characterisation of the Viral Community of Lough Neagh, the Largest Freshwater Lake in Ireland

(2016) Timofey Skvortsov et al.   PLoS One

Isolation of Polyvalent Bacteriophages by Sequential Multiple-Host Approaches

(2015) Pingfeng Yu et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Structural Basis for Carbapenem-Hydrolyzing Mechanisms of Carbapenemases Conferring Antibiotic Resistance

(2015) Jeong Jeon et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Metagenomic and network analysis reveal wide distribution and co-occurrence of environmental antibiotic resistance genes

(2015) Bing Li et al.   ISME Journal

metaxa2: improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data

(2015) Johan Bengtsson-Palme et al.   Molecular Ecology Resources

Transfer of antibiotic-resistance genes via phage-related mobile elements

(2015) Maryury Brown-Jaque et al.   PLASMID

Patterns and ecological drivers of ocean viral communities

(2015) J. R. Brum et al.   SCIENCE

VirSorter: mining viral signal from microbial genomic data

(2015) Simon Roux et al.   PeerJ

Potential for Reduction of Streptogramin A Resistance Revealed by Structural Analysis of Acetyltransferase VatA

(2014) Peter J. Stogios et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Rapid evaluation and quality control of next generation sequencing data with FaQCs

(2014) Chien-Chi Lo et al.   BMC BIOINFORMATICS

Diversity of viral photosystem-I psaA genes

(2014) Gur Hevroni et al.   ISME Journal

Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology

(2014) Molly K Gibson et al.   ISME Journal

Quinolone resistance genes (qnrA and qnrS) in bacteriophage particles from wastewater samples and the effect of inducing agents on packaged antibiotic resistance genes

(2014) M. Colomer-Lluch et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Structural basis for the evolution of vancomycin resistance D,D-peptidases

(2014) D. Meziane-Cherif et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacteriophages as Vehicles for Antibiotic Resistance Genes in the Environment

(2014) Jose Luis Balcazar   PLoS Pathogens

Mechanisms of polymyxin resistance: acquired and intrinsic resistance in bacteria

(2014) Abiola O. Olaitan et al.   Frontiers in Microbiology

Molecular Aspects and Comparative Genomics of Bacteriophage Endolysins

(2013) H. Oliveira et al.   JOURNAL OF VIROLOGY

Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome

(2013) Sheetal R. Modi et al.   NATURE

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

(2013) Ross Overbeek et al.   NUCLEIC ACIDS RESEARCH

Metagenomic analysis reveals significant changes of microbial compositions and protective functions during drinking water treatment

(2013) Yuanqing Chao et al.   Scientific Reports

Novel resistance functions uncovered using functional metagenomic investigations of resistance reservoirs

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

Kinetic and Crystallographic Studies of Extended-Spectrum GES-11, GES-12, and GES-14 β-Lactamases

(2012) Heinrich Delbrück et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

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

(2012) Y. Peng et al.   BIOINFORMATICS

The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools

(2012) Andreas Wilke et al.   BMC BIOINFORMATICS

Evaluation of methods to concentrate and purify ocean virus communities through comparative, replicated metagenomics

(2012) Bonnie L. Hurwitz et al.   ENVIRONMENTAL MICROBIOLOGY

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

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

Bacteriophages Carrying Antibiotic Resistance Genes in Fecal Waste from Cattle, Pigs, and Poultry

(2011) Marta Colomer-Lluch et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

Antibiotic Resistance Genes in the Bacteriophage DNA Fraction of Environmental Samples

(2011) Marta Colomer-Lluch et al.   PLoS One

Acquired Antibiotic Resistance Genes: An Overview

(2011) Angela H. A. M. van Hoek et al.   Frontiers in Microbiology

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Viral Mutation Rates

(2010) R. Sanjuan et al.   JOURNAL OF VIROLOGY

A simple and efficient method for concentration of ocean viruses by chemical flocculation

(2010) Seth G. John et al.   Environmental Microbiology Reports

Plasmid-Mediated Quinolone Resistance: a Multifaceted Threat

(2009) J. Strahilevitz et al.   CLINICAL MICROBIOLOGY REVIEWS

Laboratory procedures to generate viral metagenomes

(2009) Rebecca V Thurber et al.   Nature Protocols

Functional Diversity among Metallo- -Lactamases: Characterization of the CAR-1 Enzyme of Erwinia carotovora

(2008) M. Stoczko et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

(2008) F Meyer et al.   BMC BIOINFORMATICS

The Sorcerer II Global Ocean Sampling Expedition: Metagenomic Characterization of Viruses within Aquatic Microbial Samples

(2008) Shannon J. Williamson et al.   PLoS One

Unifying classical and molecular taxonomic classification: analysis of the Podoviridae using BLASTP-based tools

(2008) Rob Lavigne et al.   RESEARCH IN MICROBIOLOGY