次世代定序技術於公共衛生領域之應用──以總體基因體學定序檢出福氏內格里原蟲為例

Application of Next-generation Sequencing in Public Health - Detection of Naegleria fowleri by Using Metagenomic Sequencing

次世代定序(Next-Generation Sequencing, NGS)兼具不受限檢驗數目及高輸出量之優勢，常應用於病原體全基因定序及總體基因體學(metagenomics)研究。衛生福利部疾病管制署為強化傳染病監測工作，除架構通報法定傳染病之傳染病通報系統，亦部署不明原因感染原監測網絡，以監測社區中不明原因重症肺炎、不明原因腦炎及不明原因死亡個案。本次由北部某醫院於2023年7月底送驗1例不明原因腦炎病例，衛生福利部疾病管制署經收集該病例檢體並經qPCR檢驗後，檢出福氏內格里原蟲(Naegleria fowleri)，接續進行NGS總體基因體學定序，並經多元生物資訊軟體分析後，組裝出完整福氏內格里原蟲粒線體基因序列，成功運用NGS分析之科學實證，強化檢驗結果之正確性。本事件除讓國人瞭解從事水域活動時衛生安全之重要性外，也凸顯部署不明原因感染原監測網絡、推展不明原因病原體之精準檢驗技術、精進檢測不明原因病原體之NGS總體基因體學定序技術，為後新冠疫情時代之重要防疫整備工作。

Next-generation sequencing (NGS) offers high-throughput sequence capacity and the ability to target unlimited sequences, and is often used in whole-genome sequencing and metagenomics research. To enhance infectious disease surveillance, the Taiwan Centers for Disease Control (Taiwan CDC) established the National Infectious Disease Reporting System to report notifiable infectious diseases. In addition, a surveillance network was established to monitor unknown infectious agents causing severe pneumonia, encephalitis, and deaths in the community.
A case of encephalitis due to an unknown cause was reported to the Taiwan CDC from a hospital in northern Taiwan in July 2023. Naegleria fowleri was detected in specimens collected from the case using quantitative polymerase chain reaction (qPCR). Further analysis using NGS and bioinformatic software allowed for the assembly of the complete mitochondrial sequence of Naegleria fowleri. The scientific evidence provided by NGS analysis successfully verified the results of qPCR.
This event underscores the importance of hygiene and safety when engaging in water activities. It also highlights the importance of establishing a surveillance network to identify unknown infectious agents, promoting technologies to detect unknown pathogens, and improving metagenomic sequencing. These are crucial preparedness activities in the post-pandemic era.