Que Tengcheng, Li Wen, Zhang Zhining, He Yunlin, He Kangming, Qiu Hong, Huang Juan, Lu Zhiwei, Jiang Chunlan, Huang Yongjian, Huang Hui, Wu Qiuyu, Chen Panyu, Hu Yanling, Liu Wenjian
Faculty of Data Science, City University of Macau, Macau, Macau SAR, China.
School of Basic Medical Sciences, Youjiang Medical University for Nationalities, Baise, Guangxi, China.
Front Cell Infect Microbiol. 2025 May 2;15:1580165. doi: 10.3389/fcimb.2025.1580165. eCollection 2025.
Unbiased metagenomic sequencing (mNGS) is crucial for infectious disease diagnosis and epidemiological surveillance. However, its analysis requires specialized bioinformatics skills, creating barriers for clinicians. We developed HPD-Kit (Henbio Pathogen Detection Toolkit) with an integrated pathogen database to simplify pathogen detection and analysis for both human and animal pathogens.
HPD-Kit includes a specifically curated pathogen database and optimized bioinformatics pipeline. We evaluated its performance using simulated datasets at varying pathogen abundances and clinical samples. The toolkit provides both open-source software and a web interface for streamlined one-click analysis.
Validation with simulated data showed HPD-Kit maintains high detection accuracy even at low pathogen abundance. Clinical dataset analysis demonstrated superior pathogen identification compared to conventional methods. The web interface retained this performance while significantly improving usability.
HPD-Kit effectively addresses the bioinformatics barrier in mNGS analysis while maintaining high accuracy. Its dual open-source and web-based implementation facilitates clinical and public health applications, promoting wider adoption of mNGS technology in diagnostic settings.
无偏宏基因组测序（mNGS）对于传染病诊断和流行病学监测至关重要。然而，其分析需要专业的生物信息学技能，这给临床医生带来了障碍。我们开发了HPD-Kit（亨氏生物病原体检测工具包），它集成了病原体数据库，以简化对人类和动物病原体的检测与分析。
HPD-Kit包括一个经过专门策划的病原体数据库和优化的生物信息学流程。我们使用不同病原体丰度的模拟数据集和临床样本评估了其性能。该工具包提供开源软件和网络界面，以实现简化的一键式分析。
对模拟数据的验证表明，即使在病原体丰度较低的情况下，HPD-Kit仍能保持较高的检测准确性。临床数据集分析表明，与传统方法相比，其病原体识别能力更优。网络界面在显著提高可用性的同时保持了这种性能。
HPD-Kit有效解决了mNGS分析中的生物信息学障碍，同时保持了高准确性。其开源和基于网络的双重实现方式便于临床和公共卫生应用，促进了mNGS技术在诊断环境中的更广泛应用。
