Since the outbreak of coronavirus disease 2019, hospital laboratories have become an important place for testing all kinds of specimens of patients with suspected or confirmed coronavirus disease 2019. There may be a high load of severe acute respiratory syndrome coronavirus 2 in clinical specimens of confirmed patients, and the biosafety risk is high, so it poses a challenge to the hospital laboratory testing process. This paper compares the microbial pre-processing, culture, identification and drug sensitivity analysis of the traditional clinical microbial detection process and the fully automated microbial pipeline, expounds the biosafety risks of the traditional manual detection process of pathogenic microorganisms in the epidemic situation, and discusses the role and dilemma of the fully automated microbial pipeline in the biosafety assurance of the epidemic situation. The purpose is to provide a basis for the promotion of fully automated microbial pipeline in the future.