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

DOI: 10.6524/TEB.202410_40(19).0002

Yu-Chi Lin¹, Meng-Shan Li¹, Jen-Che Chang¹, Song-En Huang², Chih-Peng Tseng³, Fang-Tzy Wu¹, Ming-Tsan Liu¹, Shu-Ying Li¹, Jung-Jung Mu^1*

2024 Vol.40 NO.19

Correspondence Author： Jung-Jung Mu^1*

Abstract：

        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.