HMD-ARG: hierarchical multi-task deep learning for annotating antibiotic resistance genes.

Journal: Microbiome
Published Date: Feb 8, 2021

Abstract

BACKGROUND: The spread of antibiotic resistance has become one of the most urgent threats to global health, which is estimated to cause 700,000 deaths each year globally. Its surrogates, antibiotic resistance genes (ARGs), are highly transmittable between food, water, animal, and human to mitigate the efficacy of antibiotics. Accurately identifying ARGs is thus an indispensable step to understanding the ecology, and transmission of ARGs between environmental and human-associated reservoirs. Unfortunately, the previous computational methods for identifying ARGs are mostly based on sequence alignment, which cannot identify novel ARGs, and their applications are limited by currently incomplete knowledge about ARGs.

Authors

  • Yu Li
    Department of Public Health, Shihezi University School of Medicine, 832000, China.
  • Zeling Xu
    School of Biological Sciences, The University of Hong Kong, Hong Kong, People's Republic of China.
  • Wenkai Han
    Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955, Saudi Arabia.
  • Huiluo Cao
    Carol Yu Center for Infection and Department of Microbiology, The University of Hong Kong, Hong Kong, People's Republic of China.
  • Ramzan Umarov
    Electrical and Mathematical Sciences and Engineering Division (CEMSE), Computational Bioscience Research Center (CBRC), Computer, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
  • Aixin Yan
    School of Biological Sciences, The University of Hong Kong, Hong Kong, People's Republic of China.
  • Ming Fan
    Institute of Biomedical Engineering and Instrumentation, Hangzhou Dianzi University, Hangzhou 310018, China.
  • Huan Chen
    Beijing Guangqumen Middle School, Beijing, 100062, China.
  • Carlos M Duarte
    Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955, Saudi Arabia.
  • Lihua Li
    College of Life Information Science and Instrument Engineering, Hangzhou Dianzi University, Hangzhou 310018, China. Electronic address: lilh@hdu.edu.cn.
  • Pak-Leung Ho
    Carol Yu Center for Infection and Department of Microbiology, The University of Hong Kong, Hong Kong, People's Republic of China.
  • Xin Gao
    Department of Computer Science, New Jersey Institute of Technology, Newark, New Jersey, USA.

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