BacAnt: A Combination Annotation Server for Bacterial DNA Sequences to Identify Antibiotic Resistance Genes, Integrons, and Transposable Elements

Xiaoting Hua; Xiaoting Hua; Xiaoting Hua; Qian Liang; Qian Liang; Min Deng; Jintao He; Jintao He; Jintao He; Meixia Wang; Meixia Wang; Wenjie Hong; Wenjie Hong; Jun Wu; Bian Lu; Sebastian Leptihn; Sebastian Leptihn; Yunsong Yu; Yunsong Yu; Yunsong Yu; Huan Chen; Huan Chen; Huan Chen

doi:10.3389/fmicb.2021.649969

Frontiers in Microbiology (Jul 2021)

BacAnt: A Combination Annotation Server for Bacterial DNA Sequences to Identify Antibiotic Resistance Genes, Integrons, and Transposable Elements

Xiaoting Hua,
Xiaoting Hua,
Xiaoting Hua,
Qian Liang,
Qian Liang,
Min Deng,
Jintao He,
Jintao He,
Jintao He,
Meixia Wang,
Meixia Wang,
Wenjie Hong,
Wenjie Hong,
Jun Wu,
Bian Lu,
Sebastian Leptihn,
Sebastian Leptihn,
Yunsong Yu,
Yunsong Yu,
Yunsong Yu,
Huan Chen,
Huan Chen,
Huan Chen

Affiliations

Xiaoting Hua: Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
Xiaoting Hua: Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou, China
Xiaoting Hua: Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
Qian Liang: Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou, China
Qian Liang: National Medical Products Administration Key Laboratory for Testing and Risk Warning of Pharmaceutical Microbiology, Zhejiang Institute of Microbiology, Hangzhou, China
Min Deng: Department of Infectious Diseases, The First Hospital of Jiaxing, The First Affiliated Hospital of Jiaxing University, Jiaxing, China
Jintao He: Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
Jintao He: Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou, China
Jintao He: Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
Meixia Wang: Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou, China
Meixia Wang: National Medical Products Administration Key Laboratory for Testing and Risk Warning of Pharmaceutical Microbiology, Zhejiang Institute of Microbiology, Hangzhou, China
Wenjie Hong: Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou, China
Wenjie Hong: National Medical Products Administration Key Laboratory for Testing and Risk Warning of Pharmaceutical Microbiology, Zhejiang Institute of Microbiology, Hangzhou, China
Jun Wu: Lin’an Center for Disease Control and Prevention, Lin’an, China
Bian Lu: Xiaoshan Center for Disease Control and Prevention, Hangzhou, China
Sebastian Leptihn: Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
Sebastian Leptihn: Zhejiang University-University of Edinburgh Institute, School of Medicine, Zhejiang University, Hangzhou, China
Yunsong Yu: Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
Yunsong Yu: Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou, China
Yunsong Yu: Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
Huan Chen: Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
Huan Chen: Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou, China
Huan Chen: National Medical Products Administration Key Laboratory for Testing and Risk Warning of Pharmaceutical Microbiology, Zhejiang Institute of Microbiology, Hangzhou, China

DOI: https://doi.org/10.3389/fmicb.2021.649969
Journal volume & issue: Vol. 12

Abstract

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Whole genome sequencing (WGS) of bacteria has become a routine method in diagnostic laboratories. One of the clinically most useful advantages of WGS is the ability to predict antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) in bacterial sequences. This allows comprehensive investigations of such genetic features but can also be used for epidemiological studies. A plethora of software programs have been developed for the detailed annotation of bacterial DNA sequences, such as rapid annotation using subsystem technology (RAST), Resfinder, ISfinder, INTEGRALL and The Transposon Registry. Unfortunately, to this day, a reliable annotation tool of the combination of ARGs and MGEs is not available, and the generation of genbank files requires much manual input. Here, we present a new webserver which allows the annotation of ARGs, integrons and transposable elements at the same time. The pipeline generates genbank files automatically, which are compatible with Easyfig for comparative genomic analysis. Our BacAnt code and standalone software package are available at https://github.com/xthua/bacant with an accompanying web application at http://bacant.net.

Published in Frontiers in Microbiology

ISSN: 1664-302X (Online)
Publisher: Frontiers Media S.A.
Country of publisher: Switzerland
LCC subjects: Science: Microbiology
Website: http://www.frontiersin.org/journals/microbiology

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