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GO analysis revealed significant difference (P less then 0.05) in gene expressions of biological process (BP), cellular component (CC), and molecular function (MF) among original, AgR, and ANR E. faecalis. These findings provided a significant basis for further understanding and managing the silver-resistance of E. faecalis in infection-control environments. The mechanism behind Ag+/AgNPs resistance of E. faecalis needs to be further investigated.This paper presents a dynamic tree-based item response (IRTree) model as a novel exten