Overview of bioinformatic methods for analysis of antibiotic resistome from genome and metagenome data

Kihyun Lee; Dae-Wi Kim; Chang-Jun Cha

doi:10.1007/s12275-021-0652-4

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Overview of bioinformatic methods for analysis of antibiotic resistome from genome and metagenome data: Kihyun Lee ^1,2, Dae-Wi Kim ³, Chang-Jun Cha ¹; Journal of Microbiology 2021;59(3):270-280.
DOI: https://doi.org/10.1007/s12275-021-0652-4
Published online: February 23, 2021

¹Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong 17546, Republic of Korea, ²ChunLab, Inc., Seoul 06194, Republic of Korea, ³Division of Life Sciences, Jeonbuk National University, Jeonju 54896, Republic of Korea¹Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong 17546, Republic of Korea, ²ChunLab, Inc., Seoul 06194, Republic of Korea, ³Division of Life Sciences, Jeonbuk National University, Jeonju 54896, Republic of Korea

Corresponding author: Chang-Jun Cha ,

Received: 11 December 2020 • Revised: 28 January 2021 • Accepted: 29 January 2021

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Abstract

Whole genome and metagenome sequencing are powerful approaches that enable comprehensive cataloging and profiling of antibiotic resistance genes at scales ranging from a single clinical isolate to ecosystems. Recent studies deal with genomic and metagenomic data sets at larger scales; therefore, designing computational workflows that provide high efficiency and accuracy is becoming more important. In this review, we summarize the computational workflows used in the research field of antibiotic resistome based on genome or metagenome sequencing. We introduce workflows, software tools, and data resources that have been successfully employed in this rapidly developing field. The workflow described in this review can be used to list the known antibiotic resistance genes from genomes and metagenomes, quantitatively profile them, and investigate the epidemiological and evolutionary contexts behind their emergence and transmission. We also discuss how novel antibiotic resistance genes can be discovered and how the association between the resistome and mobilome can be explored.

Keywords: Bradyrhizobium japonicum;dilution;gene expression;symbiotic nitrogen fixation;water stress

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Overview of bioinformatic methods for analysis of antibiotic resistome from genome and metagenome data

J. Microbiol. 2021;59(3):270-280. Published online February 23, 2021

DOI: https://doi.org/10.1007/s12275-021-0652-4

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