Globally distributed mining-impacted environments are underexplored hotspots of multidrug resistance genes

Nanopore-based metagenomics analysis reveals prevalence of mobile antibiotic and heavy metal resistome in wastewater

(2021) Cristina Martin et al.   ECOTOXICOLOGY

Heavy metal pollution promotes antibiotics resistance potential in the aquatic environment

(2021) Majid Komijani et al.   ENVIRONMENTAL POLLUTION

PathoFact: a pipeline for the prediction of virulence factors and antimicrobial resistance genes in metagenomic data

(2021) Laura de Nies et al.   Microbiome

Shotgun metagenome guided exploration of anthropogenically driven resistomic hotspots within Lonar soda lake of India

(2020) Jaya Chakraborty et al.   ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY

Novel phosphate-solubilizing bacteria enhance soil phosphorus cycling following ecological restoration of land degraded by mining

(2020) Jie-Liang Liang et al.   ISME Journal

Coastal urbanization influences human pathogens and microdebris contamination in seafood

(2020) Raechel A. Littman et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Determining Hosts of Antibiotic Resistance Genes: A Review of Methodological Advances

(2020) Eric W. Rice et al.   Environmental Science & Technology Letters

Co-selection of antibiotic-resistant bacteria in a paddy soil exposed to As(III) contamination with an emphasis on potential pathogens

(2020) Jiayao Cao et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Metagenomic exploration of multi-resistance genes linked to microbial attributes in active nonferrous metal(loid) tailings

(2020) Jian-li Liu et al.   ENVIRONMENTAL POLLUTION

Fecal pollution can explain antibiotic resistance gene abundances in anthropogenically impacted environments

(2019) Antti Karkman et al.   Nature Communications

Comparative genomics of 16 Microbacterium spp. that tolerate multiple heavy metals and antibiotics

(2019) Deric R. Learman et al.   PeerJ

Urban metagenomics uncover antibiotic resistance reservoirs in coastal beach and sewage waters

(2019) Pablo Fresia et al.   Microbiome

Antibiotics in the Soil Environment—Degradation and Their Impact on Microbial Activity and Diversity

(2019) Mariusz Cycoń et al.   Frontiers in Microbiology

Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage

(2019) Rene S. Hendriksen et al.   Nature Communications

Pollution from azithromycin-manufacturing promotes macrolide-resistance gene propagation and induces spatial and seasonal bacterial community shifts in receiving river sediments

(2019) Milena Milaković et al.   ENVIRONMENT INTERNATIONAL

Shifting interactions among bacteria, fungi and archaea enhance removal of antibiotics and antibiotic resistance genes in the soil bioelectrochemical remediation

(2019) Xiaodong Zhao et al.   Biotechnology for Biofuels

Metagenomic and metatranscriptomic analyses reveal activity and hosts of antibiotic resistance genes in activated sludge

(2019) Zongbao Liu et al.   ENVIRONMENT INTERNATIONAL

MEGARes 2.0: a database for classification of antimicrobial drug, biocide and metal resistance determinants in metagenomic sequence data

(2019) Enrique Doster et al.   NUCLEIC ACIDS RESEARCH

The Transposon Registry

(2019) Supathep Tansirichaiya et al.   Mobile DNA

Clinical class 1 integron-integrase gene – A promising indicator to monitor the abundance and elimination of antibiotic resistance genes in an urban wastewater treatment plant

(2019) Wanlin Zheng et al.   ENVIRONMENT INTERNATIONAL

Inhibition of histone deacetylase 1 (HDAC1) and HDAC2 enhances CRISPR/Cas9 genome editing

(2019) Bin Liu et al.   NUCLEIC ACIDS RESEARCH

Diversity of herbaceous plants and bacterial communities regulates soil resistome across forest biomes

(2018) Hang-Wei Hu et al.   ENVIRONMENTAL MICROBIOLOGY

Bacterial community structure and abundances of antibiotic resistance genes in heavy metals contaminated agricultural soil

(2018) Fengli Zhang et al.   ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH

Detection of blaNDM-1 in Stenotrophomonas maltophilia isolated from Brazilian soil

(2018) João Pedro Rueda Furlan et al.   MEMORIAS DO INSTITUTO OSWALDO CRUZ

PlasFlow: predicting plasmid sequences in metagenomic data using genome signatures

(2018) Pawel S Krawczyk et al.   NUCLEIC ACIDS RESEARCH

Antibiotic resistome in landfill leachate from different cities of China deciphered by metagenomic analysis

(2018) Renxin Zhao et al.   WATER RESEARCH

DeepARG: a deep learning approach for predicting antibiotic resistance genes from metagenomic data

(2018) Gustavo Arango-Argoty et al.   Microbiome

Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy

(2018) Christian M. K. Sieber et al.   Nature Microbiology

PRISMA Extension for Scoping Reviews (PRISMA-ScR): Checklist and Explanation

(2018) Andrea C. Tricco et al.   ANNALS OF INTERNAL MEDICINE

Wastewater treatment plant resistomes are shaped by bacterial composition, genetic exchange, and upregulated expression in the effluent microbiomes

(2018) Feng Ju et al.   ISME Journal

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis

(2018) Gherman V. Uritskiy et al.   Microbiome

ICEberg 2.0: an updated database of bacterial integrative and conjugative elements

(2018) Meng Liu et al.   NUCLEIC ACIDS RESEARCH

Anthropogenic influence shapes the distribution of antibiotic resistant bacteria (ARB) in the sediment of Sundarban estuary in India

(2018) Anish Bhattacharyya et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Evidence for co-selection of antibiotic resistance genes and mobile genetic elements in metal polluted urban soils

(2018) Yi Zhao et al.   SCIENCE OF THE TOTAL ENVIRONMENT

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

Integrative and conjugative elements and their hosts: composition, distribution and organization

(2017) Jean Cury et al.   NUCLEIC ACIDS RESEARCH

Changes in microbial community composition following phytostabilization of an extremely acidic Cu mine tailings

(2017) Tao-tao Yang et al.   SOIL BIOLOGY & BIOCHEMISTRY

Effect of the environment on horizontal gene transfer between bacteria and archaea

(2017) Clara A. Fuchsman et al.   PeerJ

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

(2017) Jian-Qiang Su et al.   Microbiome

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

(2017) Donovan H. Parks et al.   Nature Microbiology

Continental-scale pollution of estuaries with antibiotic resistance genes

(2017) Yong-Guan Zhu et al.   Nature Microbiology

Field-based evidence for copper contamination induced changes of antibiotic resistance in agricultural soils

(2016) Hang-Wei Hu et al.   ENVIRONMENTAL MICROBIOLOGY

Co-occurrence of antibiotic and metal resistance genes revealed in complete genome collection

(2016) Li-Guan Li et al.   ISME Journal

MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets

(2015) Yu-Wei Wu et al.   BIOINFORMATICS

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

Co-occurrence of resistance genes to antibiotics, biocides and metals reveals novel insights into their co-selection potential

(2015) Chandan Pal 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

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

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

(2015) Bing Li et al.   ISME Journal

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

(2015) Dongwan D. Kang et al.   PeerJ

Pseudomonas hunanensis sp. nov., Isolated from Soil Subjected to Long-Term Manganese Pollution

(2014) Jian Gao et al.   CURRENT MICROBIOLOGY

Bacterial phylogeny structures soil resistomes across habitats

(2014) Kevin J. Forsberg et al.   NATURE

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Nonpareil: a redundancy-based approach to assess the level of coverage in metagenomic datasets

(2013) Luis M. Rodriguez-R et al.   BIOINFORMATICS

BacMet: antibacterial biocide and metal resistance genes database

(2013) Chandan Pal et al.   NUCLEIC ACIDS RESEARCH

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

PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes

(2013) Nicola Segata et al.   Nature Communications

Gene and translation initiation site prediction in metagenomic sequences

(2012) Doug Hyatt et al.   BIOINFORMATICS

Biosynthesis of the Respiratory Toxin Bongkrekic Acid in the Pathogenic Bacterium Burkholderia gladioli

(2012) Nadine Moebius et al.   CHEMISTRY & BIOLOGY

Susceptibility of archaea to antimicrobial agents: applications to clinical microbiology

(2012) S. Khelaifia et al.   CLINICAL MICROBIOLOGY AND INFECTION

Antibiotic resistance gene abundances associated with antibiotics and heavy metals in animal manures and agricultural soils adjacent to feedlots in Shanghai; China

(2012) Xiuling Ji et al.   JOURNAL OF HAZARDOUS MATERIALS

Heavy metal driven co-selection of antibiotic resistance in soil and water bodies impacted by agriculture and aquaculture

(2012) Claudia Seiler et al.   Frontiers in Microbiology

Spatial and Temporal Analysis of the Microbial Community in the Tailings of a Pb-Zn Mine Generating Acidic Drainage

(2011) Li-Nan Huang et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Complete genome and comparative analysis of Streptococcus gallolyticus subsp. gallolyticus, an emerging pathogen of infective endocarditis

(2011) Dennis Hinse et al.   BMC GENOMICS

Antibiotic resistance is ancient

(2011) Vanessa M. D’Costa et al.   NATURE

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy

(2011) I. Letunic et al.   NUCLEIC ACIDS RESEARCH

Origins and Evolution of Antibiotic Resistance

(2010) J. Davies et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

INTEGRALL: a database and search engine for integrons, integrases and gene cassettes

(2009) A. Moura et al.   BIOINFORMATICS

Stenotrophomonas maltophilia: an emerging opportunist human pathogen

(2009) W John Looney et al.   LANCET INFECTIOUS DISEASES

The Genome of Burkholderia cenocepacia J2315, an Epidemic Pathogen of Cystic Fibrosis Patients

(2008) M. T. G. Holden et al.   JOURNAL OF BACTERIOLOGY