An Integrated Platform For Rapid Intelligent Pathogen Detection And Analysis

In recent years,the frequent occurrence of infectious disease outbreaks has posed severe challenges worldwide.High-throughput sequencing(HTS)technology has demonstrated broad application prospects in the field of pathogen detection and has played a crucial role in pathogen identification and tracing.However,the practical application of high-throughput sequencing still faces challenges,such as high data analysis learning costs,incomplete pathogen databases,and difficulties in storing and managing the massive HTS data.To address these issues,this study has designed and constructed a platform for rapid and intelligent pathogen detection and analysis.This platform integrates the experimental and data analysis procedures used in pathogen detection.The platform provides a graphical user interface based on a web browser,allows users to easily manage HTS data,initiate analysis tasks,and view analysis results through the frontend interface,and achieve visualization of the platform operations.The platform integrates commonly used bioinformatics softwares and designs specific analysis workflows for metagenomic samples and pure culture samples.Upon initiating an analysis task through the graphical interface,the platform automatically executes the pre-set analysis steps and generates a visualized result report.Furthermore,to support pathogen identification and tracing analysis tasks,this study has successfully constructed a pathogen tracing analysis database containing pathogen gene sequences,species classification information,and sample origin information.Users can select appropriate sub-databases based on specific clinical indications when using the platform for analysis tasks,ensuring fast and accurate analysis.The platform and database constructed in this study have been applied to operations,the platform can finish species identification for a pure culture sample with 1 GB sequencing data within 10 min of initiating the analysis,and detailed analysis results,including data assembly,species annotation,traceability analysis,and resistance/virulence gene prediction,can be obtained within 3 hr.For a metagenomic sample with 3 GB sequencing data,species identification results can be obtained within 15 min of initiating the analysis,and detailed analysis results,including data assembly,species annotation,and resistance/virulence gene prediction,can be obtained within 1 hr.This platform can simultaneously address various challenges in using high-throughput sequencing for pathogen detection work,such as high costs in data analysis learning and difficulties in balancing database sizes,provide rapid and accurate pathogen identification,and offer basic support for the timely control of infectious disease outbreaks.