Large language model for horizontal transfer of resistance gene: From resistance gene prevalence detection to plasmid conjugation rate evaluation.

Zhang, Jiabin; Zhao, Lei; Wang, Wei; Zhang, Quan; Wang, Xue-Ting; Xing, De-Feng; Ren, Nan-Qi; Lee, Duu-Jong; Chen, Chuan

Zhang, Jiabin; Zhao, Lei; Wang, Wei; Zhang, Quan; Wang, Xue-Ting; Xing, De-Feng; Ren, Nan-Qi; Lee, Duu-Jong; Chen, Chuan.

Afiliación

Zhang J; State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province 150090, China.
Zhao L; State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province 150090, China.
Wang W; State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province 150090, China. Electronic address: wvv9288@163.com.
Zhang Q; State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province 150090, China.
Wang XT; State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province 150090, China.
Xing DF; State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province 150090, China.
Ren NQ; State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province 150090, China; Shenzhen Graduate School, Harbin Institute of Technology, Shenzhen 518055, China.
Lee DJ; Department of Mechanical Engineering, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong.
Chen C; State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province 150090, China. Electronic address: cchen@hit.edu.cn.

Sci Total Environ ; 931: 172466, 2024 Jun 25.

Article en En | MEDLINE | ID: mdl-38626826

ABSTRACT

ABSTRACT

The burgeoning issue of plasmid-mediated resistance genes (ARGs) dissemination poses a significant threat to environmental integrity. However, the prediction of ARGs prevalence is overlooked, especially for emerging ARGs that are potentially evolving gene exchange hotspot. Here, we explored to classify plasmid or chromosome sequences and detect resistance gene prevalence by using DNABERT. Initially, the DNABERT fine-tuned in plasmid and chromosome sequences followed by multilayer perceptron (MLP) classifier could achieve 0.764 AUC (Area under curve) on external datasets across 23 genera, outperforming 0.02 AUC than traditional statistic-based model. Furthermore, Escherichia, Pseudomonas single genera based model were also be trained to explore its predict performance to ARGs prevalence detection. By integrating K-mer frequency attributes, our model could boost the performance to predict the prevalence of ARGs in an external dataset in Escherichia with 0.0281-0.0615 AUC and Pseudomonas with 0.0196-0.0928 AUC. Finally, we established a random forest model aimed at forecasting the relative conjugation transfer rate of plasmids with 0.7956 AUC, drawing on data from existing literature. It identifies the plasmid's repression status, cellular density, and temperature as the most important factors influencing transfer frequency. With these two models combined, they provide useful reference for quick and low-cost integrated evaluation of resistance gene transfer, accelerating the process of computer-assisted quantitative risk assessment of ARGs transfer in environmental field.

Asunto(s)

Transferencia de Gen Horizontal; Plásmidos; Plásmidos/genética; Conjugación Genética; Farmacorresistencia Bacteriana/genética; Pseudomonas/genética

Palabras clave

ARGs prevalence prediction; BERT; Deep learning; Large language model; Plasmid conjugation rate

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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Plásmidos / Transferencia de Gen Horizontal Idioma: En Revista: Sci Total Environ Año: 2024 Tipo del documento: Article País de afiliación: China Pais de publicación: Países Bajos

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