Nanopore-based long-read metagenomics uncover the resistome intrusion by antibiotic resistant bacteria from treated wastewater in receiving water body

Efficient assembly of nanopore reads via highly accurate and intact error correction

(2021) Ying Chen et al.   Nature Communications

Long-read sequencing revealed cooccurrence, host range, and potential mobility of antibiotic resistome in cow feces

(2021) Xun Qian et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An omics-based framework for assessing the health risk of antimicrobial resistance genes

(2021) An-Ni Zhang et al.   Nature Communications

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

(2019) You Che et al.   Microbiome

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

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

Drug combinations: a strategy to extend the life of antibiotics in the 21st century

(2019) Mike Tyers et al.   NATURE REVIEWS MICROBIOLOGY

Metagenomic insights into the abundance and composition of resistance genes in aquatic environments: Influence of stratification and geography

(2019) Yuyi Yang et al.   ENVIRONMENT INTERNATIONAL

NanoARG: a web service for detecting and contextualizing antimicrobial resistance genes from nanopore-derived metagenomes

(2019) G. A. Arango-Argoty et al.   Microbiome

Characterization and source-tracking of antibiotic resistomes in the sediments of a peri-urban river

(2019) Haiyang Chen et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Screening and evaluation of heavy metals facilitating antibiotic resistance gene transfer in a sludge bacterial community

(2019) Hai Lin et al.   SCIENCE OF THE TOTAL ENVIRONMENT

ARGs-OAP v2.0 with an expanded SARG database and Hidden Markov Models for enhancement characterization and quantification of antibiotic resistance genes in environmental metagenomes

(2018) Xiaole Yin et al.   BIOINFORMATICS

NanoPack: visualizing and processing long-read sequencing data

(2018) Wouter De Coster et al.   BIOINFORMATICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

Conserved phylogenetic distribution and limited antibiotic resistance of class 1 integrons revealed by assessing the bacterial genome and plasmid collection

(2018) An Ni Zhang et al.   Microbiome

A Novel aadA Aminoglycoside Resistance Gene in Bovine and Porcine Pathogens

(2018) Andrew Cameron et al.   mSphere

Antibiotic resistome in a large-scale healthy human gut microbiota deciphered by metagenomic and network analyses

(2017) Jie Feng et al.   ENVIRONMENTAL MICROBIOLOGY

PAHs accelerate the propagation of antibiotic resistance genes in coastal water microbial community

(2017) Jing Wang et al.   ENVIRONMENTAL POLLUTION

The Prevalence of Integrons as the Carrier of Antibiotic Resistance Genes in Natural and Man-Made Environments

(2017) Liping Ma et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Microbial strain-level population structure and genetic diversity from metagenomes

(2017) Duy Tin Truong et al.   GENOME RESEARCH

Discharge of KPC-2 genes from the WWTPs contributed to their enriched abundance in the receiving river

(2017) Fengxia Yang et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Identification of new bacteria harboring qnrS and aac(6′)-Ib/cr and mutations possibly involved in fluoroquinolone resistance in raw sewage and activated sludge samples from a full-scale WWTP

(2017) Magna C. Paiva et al.   WATER RESEARCH

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

(2017) Ryan R. Wick et al.   PLoS Computational Biology

Catalogue of antibiotic resistome and host-tracking in drinking water deciphered by a large scale survey

(2017) Liping Ma et al.   Microbiome

Co-occurrence of integrase 1, antibiotic and heavy metal resistance genes in municipal wastewater treatment plants

(2016) Andrea Di Cesare et al.   WATER RESEARCH

Propagation of New Delhi Metallo-β-lactamase Genes (blaNDM-1) from a Wastewater Treatment Plant to Its Receiving River

(2016) Fengxia Yang et al.   Environmental Science & Technology Letters

Genomics of high molecular weight plasmids isolated from an on-farm biopurification system

(2016) María C. Martini et al.   Scientific Reports

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

Unravelling core microbial metabolisms in the hypersaline microbial mats of Shark Bay using high-throughput metagenomics

(2015) Rendy Ruvindy et al.   ISME Journal

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Using the class 1 integron-integrase gene as a proxy for anthropogenic pollution

(2014) Michael R Gillings et al.   ISME Journal

MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island

(2014) Philip M Ashton et al.   NATURE BIOTECHNOLOGY

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Fate of antibiotic resistance genes in sewage treatment plant revealed by metagenomic approach

(2014) Ying Yang et al.   WATER RESEARCH

Exploring Variation of Antibiotic Resistance Genes in Activated Sludge over a Four-Year Period through a Metagenomic Approach

(2013) Ying Yang et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

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

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

(2012) Limin Fu et al.   BIOINFORMATICS

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

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

The Shared Antibiotic Resistome of Soil Bacteria and Human Pathogens

(2012) K. J. Forsberg et al.   SCIENCE

BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons

(2011) Nabil-Fareed Alikhan et al.   BMC GENOMICS

Bayesian community-wide culture-independent microbial source tracking

(2011) Dan Knights et al.   NATURE METHODS

Trends in Antibiotic Resistance Genes Occurrence in the Haihe River, China

(2010) Yi Luo et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Incorporating sequence quality data into alignment improves DNA read mapping

(2010) Martin C. Frith et al.   NUCLEIC ACIDS RESEARCH

Phenotyping and Genotyping of Antibiotic-Resistant Escherichia coli Isolated from a Natural River Basin

(2008) Jianying Hu et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY