PLM-ARG: antibiotic resistance gene identification using a pretrained protein language model.

Journal: Bioinformatics (Oxford, England)
Published Date: Nov 1, 2023

Abstract

MOTIVATION: Antibiotic resistance presents a formidable global challenge to public health and the environment. While considerable endeavors have been dedicated to identify antibiotic resistance genes (ARGs) for assessing the threat of antibiotic resistance, recent extensive investigations using metagenomic and metatranscriptomic approaches have unveiled a noteworthy concern. A significant fraction of proteins defies annotation through conventional sequence similarity-based methods, an issue that extends to ARGs, potentially leading to their under-recognition due to dissimilarities at the sequence level.

Authors

  • Jun Wu
    Department of Emergency, Zhuhai Integrated Traditional Chinese and Western Medicine Hospital, Zhuhai, 519020, Guangdong Province, China. quanshabai43@163.com.
  • Jian Ouyang
    Center for Bioinformatics and Computational Biology, and The Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China.
  • Haipeng Qin
    Center for Bioinformatics and Computational Biology, and The Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China.
  • Jiajia Zhou
    Shanghai Mental Health Center, Shanghai Jiao Tong University, School of Medicine, Shanghai, China.
  • Ruth Roberts
    c ApconiX Ltd , Alderley Edge , UK.
  • Rania Siam
    Biology Department, School of Sciences and Engineering, The American University in Cairo, New Cairo 11835, Egypt.
  • Lan Wang
    The Center of Psychosomatic Medicine, Sichuan Provincial Center for Mental Health, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 611731, China.
  • Weida Tong
    National Center for Toxicological Research, Division of Bioinformatics and Biostatistics, U.S. Food and Drug Administration, Jefferson, AR, United States.
  • Zhichao Liu
    a Division of Bioinformatics and Biostatistics , National Center for Toxicological Research, U.S. Food and Drug Administration , Jefferson , AR , USA.
  • Tieliu Shi
    Center for Bioinformatics and Computational Biology, and The Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China.

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