Metagenomic assembly and binning analyses the prevalence and spread of antibiotic resistome in water and fish gut microbiomes along an environmental gradient

Characterization of the human skin resistome and identification of two microbiota cutotypes

(2021) Zhiming Li et al.   Microbiome

Occurrence and distribution characteristics of antibiotic resistance genes in sediments between urban and rural of the Liaohe River Basin, China

(2021) Guangshui Na et al.   ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH

Impact of sulfamethoxazole on a riverine microbiome

(2021) Chiara Borsetto et al.   WATER RESEARCH

Abundance and environmental host range of the SXT/R391 ICEs in aquatic environmental communities

(2021) Veronica L. Roman et al.   ENVIRONMENTAL POLLUTION

Chitosan as additive affects the bacterial community, accelerates the removals of antibiotics and related resistance genes during chicken manure composting

(2021) Hongdou Liu et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Homogeneous selection drives antibiotic resistome in two adjacent sub-watersheds, China

(2020) Anyi Hu et al.   JOURNAL OF HAZARDOUS MATERIALS

Vibrio parahaemolyticus

(2020) Jaime Martinez-Urtaza et al.   TRENDS IN MICROBIOLOGY

Co‐occurrence of antibiotic, biocide, and heavy metal resistance genes in bacteria from metal and radionuclide contaminated soils at the Savannah River Site

(2020) Jesse C. Thomas et al.   Microbial Biotechnology

Aeromonas veronii Infection in Commercial Freshwater Fish: A Potential Threat to Public Health

(2020) Tong Li et al.   Animals

Distribution of antibiotic resistance genes in an agriculturally disturbed lake in China: Their links with microbial communities, antibiotics, and water quality

(2020) Zhi Wang et al.   JOURNAL OF HAZARDOUS MATERIALS

Impact of anthropogenic activities on the occurrence and distribution of toxic metals, extending-spectra β-lactamases and carbapenem resistance in sub-Saharan African urban rivers

(2020) Amandine Laffite et al.   SCIENCE OF THE TOTAL ENVIRONMENT

The Role of Integrative and Conjugative Elements in Antibiotic Resistance Evolution

(2020) João Botelho et al.   TRENDS IN MICROBIOLOGY

Metagenomic profiling of antibiotic resistance genes and their associations with bacterial community during multiple disinfection regimes in a full-scale drinking water treatment plant

(2020) Shuyu Jia et al.   WATER RESEARCH

River contamination shapes the microbiome and antibiotic resistance in sharpbelly (Hemiculter leucisculus)

(2020) Xue Xue et al.   ENVIRONMENTAL POLLUTION

Abundance, diversity and mobility potential of antibiotic resistance genes in pristine Tibetan Plateau soil as revealed by soil metagenomics

(2020) Bo Li et al.   FEMS MICROBIOLOGY ECOLOGY

Demonstrating an Integrated Antibiotic Resistance Gene Surveillance Approach in Puerto Rican Watersheds Post-Hurricane Maria

(2020) Benjamin C. Davis et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Does lipid stress affect performance, fate of antibiotic resistance genes and microbial dynamics during anaerobic digestion of food waste?

(2020) Jiaying Ma et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Selection of antibiotic resistance genes on biodegradable and non-biodegradable microplastics

(2020) Yuanze Sun et al.   JOURNAL OF HAZARDOUS MATERIALS

Mobile antibiotic resistome in wastewater treatment plants revealed by Nanopore metagenomic sequencing

(2019) You Che et al.   Microbiome

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

(2019) Pablo Fresia et al.   Microbiome

Oral administration of antibiotics increased the potential mobility of bacterial resistance genes in the gut of the fish Piaractus mesopotamicus

(2019) Johan S. Sáenz et al.   Microbiome

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

(2019) Zongbao Liu et al.   ENVIRONMENT INTERNATIONAL

Freshwater environments as reservoirs of antibiotic resistant bacteria and their role in the dissemination of antibiotic resistance genes

(2019) Chika F. Nnadozie et al.   ENVIRONMENTAL POLLUTION

Metagenomic assembly provides a deep insight into the antibiotic resistome alteration induced by drinking water chlorination and its correlations with bacterial host changes

(2019) Shuyu Jia et al.   JOURNAL OF HAZARDOUS MATERIALS

Identification and quantification of bacterial genomes carrying antibiotic resistance genes and virulence factor genes for aquatic microbiological risk assessment

(2019) Jinsong Liang et al.   WATER RESEARCH

OUP accepted manuscript

(2018)   BIOINFORMATICS

Review of antibiotic resistance in China and its environment

(2018) Min Qiao et al.   ENVIRONMENT INTERNATIONAL

Ecological effects of antibiotics on natural ecosystems: A review

(2018) Paola Grenni et al.   MICROCHEMICAL JOURNAL

PlasFlow: predicting plasmid sequences in metagenomic data using genome signatures

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

Occurrence and distribution of antibiotics and antibiotic resistance genes in Ba River, China

(2018) Jia Jia et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Transmission of IMI-2 carbapenemase-producing Enterobacteriaceae from river water to human

(2018) Chrislène Laurens et al.   Journal of Global Antimicrobial Resistance

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

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

Mobile Genetic Elements Associated with Antimicrobial Resistance

(2018) Sally R. Partridge et al.   CLINICAL MICROBIOLOGY REVIEWS

The Prevalence of Colistin Resistant Strains and Antibiotic Resistance Gene Profiles in Funan River, China

(2018) Hongmei Tuo et al.   Frontiers in Microbiology

Analysis of Bacterial Community Characteristics, Abundance of Antibiotics and Antibiotic Resistance Genes Along a Pollution Gradient of Ba River in Xi’an, China

(2018) Yongjing Guan et al.   Frontiers in Microbiology

High-throughput profiling of antibiotic resistance gene dynamic in a drinking water river-reservoir system

(2018) Yihan Chen et al.   WATER RESEARCH

River Ganges water as reservoir of microbes with antibiotic and metal ion resistance genes: High throughput metagenomic approach

(2018) Bhaskar Reddy et al.   ENVIRONMENTAL POLLUTION

Aquatic animals promote antibiotic resistance gene dissemination in water via conjugation: Role of different regions within the zebra fish intestinal tract, and impact on fish intestinal microbiota

(2017) Jialun Fu et al.   MOLECULAR ECOLOGY

Metagenomic analysis reveals wastewater treatment plants as hotspots of antibiotic resistance genes and mobile genetic elements

(2017) Jianhua Guo et al.   WATER RESEARCH

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

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Bacterial Community Shift Drives Antibiotic Resistance Promotion during Drinking Water Chlorination

(2015) Shuyu Jia et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Comparative Genomics of Environmental and ClinicalStenotrophomonas maltophiliaStrains with Different Antibiotic Resistance Profiles

(2015) Benjamin Youenou et al.   Genome Biology and Evolution

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

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

Occurrence of antibiotics and antibiotic resistance genes in hospital and urban wastewaters and their impact on the receiving river

(2015) Sara Rodriguez-Mozaz et al.   WATER RESEARCH

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

(2015) Dongwan D. Kang et al.   PeerJ

Bacterial multidrug efflux pumps: Mechanisms, physiology and pharmacological exploitations

(2014) Jingjing Sun et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

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

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

Occurrence and removal of antibiotic resistance genes in municipal wastewater and rural domestic sewage treatment systems in eastern China

(2013) Hong Chen et al.   ENVIRONMENT INTERNATIONAL

BacMet: antibacterial biocide and metal resistance genes database

(2013) Chandan Pal et al.   NUCLEIC ACIDS RESEARCH

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

Ecology drives a global network of gene exchange connecting the human microbiome

(2011) Chris S. Smillie et al.   NATURE

Antibiotic resistance is ancient

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

ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria

(2011) Dexi Bi et al.   NUCLEIC ACIDS RESEARCH

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Antibiotic resistance in the environment: a link to the clinic?

(2010) Gerard D Wright   CURRENT OPINION IN MICROBIOLOGY

Antibiotic resistance and its cost: is it possible to reverse resistance?

(2010) Dan I. Andersson et al.   NATURE REVIEWS MICROBIOLOGY

Class 1 integrons in benthic bacterial communities: abundance, association with Tn402-like transposition modules and evidence for coselection with heavy-metal resistance

(2009) Carly P. Rosewarne et al.   FEMS MICROBIOLOGY ECOLOGY

SOAP: short oligonucleotide alignment program

(2008) R. Li et al.   BIOINFORMATICS