NCRD: A non-redundant comprehensive database for detecting antibiotic resistance genes

Yujie Mao; Xiaohui Liu; Na Zhang; Zhi Wang; Maozhen Han

iScience (Nov 2023)

NCRD: A non-redundant comprehensive database for detecting antibiotic resistance genes

Yujie Mao,
Xiaohui Liu,
Na Zhang,
Zhi Wang,
Maozhen Han

Affiliations

Yujie Mao: Key Laboratory for Environment and Disaster Monitoring and Evaluation of Hubei, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430077, China; School of Life Sciences, Anhui Medical University, Hefei, Anhui 230032, China; University of Chinese Academy of Sciences, Beijing 100049, China
Xiaohui Liu: College of Environmental Science and Engineering, Ocean University of China, Qingdao 266003, China; Key Laboratory of Marine Environmental Science and Ecology, Ministry of Education, Ocean University of China, Qingdao 266003, China
Na Zhang: School of Life Sciences, Anhui Medical University, Hefei, Anhui 230032, China
Zhi Wang: Key Laboratory for Environment and Disaster Monitoring and Evaluation of Hubei, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430077, China; Corresponding author
Maozhen Han: School of Life Sciences, Anhui Medical University, Hefei, Anhui 230032, China; Corresponding author

Journal volume & issue: Vol. 26, no. 11
p. 108141

Abstract

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Summary: Antibiotic resistance genes (ARGs) are emerging pollutants present in various environments. Identifying ARGs has become a growing concern in recent years. Several databases, including the Antibiotic Resistance Genes Database (ARDB), Comprehensive Antibiotic Resistance Database (CARD), and Structured Antibiotic Resistance Genes (SARG), have been applied to detect ARGs. However, these databases have limitations, which hinder the comprehensive profiling of ARGs in environmental samples. To address these issues, we constructed a non-redundant antibiotic resistance genes database (NRD) by consolidating sequences from ARDB, CARD, and SARG. We identified the homologous proteins of NRD from Non-redundant Protein Database (NR) and the Protein DataBank Database (PDB) and clustered them to establish a non-redundant comprehensive antibiotic resistance genes database (NCRD) with similarities of 100% (NCRD100) and 95% (NCRD95). To demonstrate the advantages of NCRD, we compared it with other databases by using metagenome datasets. Results revealed its strong ability in detecting potential ARGs.

Published in iScience

ISSN: 2589-0042 (Online)
Publisher: Elsevier
Country of publisher: United States
LCC subjects: Science
Website: http://www.cell.com/iscience/home

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