ARGA, a pipeline for primer evaluation on antibiotic resistance genes.

Anti-Bacterial Agents / pharmacology Databases, Genetic Drug Resistance, Microbial / genetics Metagenome
ARGs Annotation Nucleotide Primer assessment Protein Sequence database

Journal

Environment international
ISSN: 1873-6750
Titre abrégé: Environ Int
Pays: Netherlands
ID NLM: 7807270

Informations de publication

Date de publication:
07 2019
Historique:
received: 03 02 2019
revised: 11 04 2019
accepted: 12 04 2019
pubmed: 6 5 2019
medline: 12 11 2019
entrez: 5 5 2019
Statut: ppublish

Résumé

Molecular biology techniques have assisted in the investigation of antibiotic resistance genes (ARGs) from various environments. However, their accuracy relies on primer quality and data interpretation, both of which require a full-coverage sequence database for ARGs. Here, based upon the abandoned Antibiotic Resistance Genes Database (ARDB), we created an updated sequence database of antibiotic resistance genes (SDARG). A total of 1,260,069 protein sequences and 1,164,479 nucleotide sequences, 56 times more sequences than ARDB, from 448 types of ARGs (enabling resistance to 18 categories of antibiotics) were collected and integrated with different hierarchical credibility and full-scale taxonomic information. Based on this comprehensive sequence database, an online pipeline - ARG analyzer (ARGA, http://mem.rcees.ac.cn:8083/) was developed to assess current ARGs primers, as well as annotate ARGs from environmental metagenomes. Thereafter, a list of 658 published primer pairs, targeting 173 ARGs, was evaluated using ARGA and integrated in ARGA as ARGs primer database. The results showed that 65.05% primers are of high specificity (≥90%), while only 29.79% primers cover >50% of targeted sequences, indicating a divergence in the quality of current ARG primers. Hence, primer assessment or redesign is highly recommended to improve the accuracy of ARGs studies. ARGs primer database was attached in ARGA to provide researchers alternatives to better survey ARGs in the environment.

Identifiants

DOI: 10.1016/j.envint.2019.04.030 PMID: 31054477
pubmed: 31054477
pii: S0160-4120(19)30374-5
doi: 10.1016/j.envint.2019.04.030
pii:
doi:

Substances chimiques

Anti-Bacterial Agents 0

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

137-145

Informations de copyright

Copyright © 2019 The Authors. Published by Elsevier Ltd.. All rights reserved.

Auteurs

Ziyan Wei (Z)

Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China; Key Laboratory of Environmental Biotechnology of CAS, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.

Yueni Wu (Y)

Key Laboratory of Environmental Biotechnology of CAS, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.

Kai Feng (K)

Key Laboratory of Environmental Biotechnology of CAS, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.

Min Yang (M)

State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.

Yu Zhang (Y)

State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.

Qichao Tu (Q)

Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China.

Jun Wang (J)

College of Resources and Environment, Shandong Agricultural University, Taian 271018, China.

Ye Deng (Y)

Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China; Key Laboratory of Environmental Biotechnology of CAS, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China. Electronic address: yedeng@rcees.ac.cn.

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Classifications MeSH

questionsmedicales.fr › Actions chimiques et utilisations › Actions pharmacologiques › Utilisations thérapeutiques › Anti-infectieux › Antibactériens › ARGA, a pipeline for primer evaluation on...
questionsmedicales.fr › Sciences de l'information › Mémorisation et recherche des informations › Bases de données comme sujet › Bases de données factuelles › Bases de données génétiques › ARGA, a pipeline for primer evaluation on...
questionsmedicales.fr › Phénomènes physiologiques › Phénomènes pharmacologiques et toxicologiques › Phénomènes pharmacologiques › Résistance aux substances › Résistance microbienne aux médicaments › ARGA, a pipeline for primer evaluation on...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Métagénome › ARGA, a pipeline for primer evaluation on...