Comparison of next-generation droplet digital PCR with quantitative PCR for enumeration of Naegleria fowleri in environmental water and clinical samples

Abstract

Naegleria fowleri in recreational waters is a serious health threat. A rapid and accurate method to determine this pathogen in water is vital to develop effective control strategies. In this study, we compared two molecular methods: droplet digital polymerase chain reaction (ddPCR) and quantitative PCR (qPCR) assays in identifying N. fowleri from clinical and environmental samples. Strong agreement between ddPCR and qPCR methods over clinical DNA samples was observed. The limit of detection (LOD) for ddPCR and qPCR assays were 2·5 and 25 N. fowleri per reaction respectively. In the comparative analysis using N. fowleri genomic DNA, quantitative results obtained from ddPCR and qPCR assays showed no significant difference. The assay specificity for ddPCR and qPCR assays were 100 and 86% respectively. Results from both PCR assays indicated N. fowleri was present in surface water samples from Lake Pontchartrain during our study period. In general, the ddPCR performance demonstrated in this study on clinical and environmental samples lead to greater confidence of ddPCR technology on field application. For precise quantification using qPCR, we recommend using ddPCR to quantify the standard materials before qPCR application.

Significance and impact of the study: This study explored the application of ddPCR and qPCR methods in identifying Naegleria fowleri from both clinical and environmental water samples. Strong agreement between ddPCR and qPCR methods over clinical DNA samples was observed. Naegleria fowleri was present in surface water samples from Lake Pontchartrain during our study period. The ability of N. fowleri to survive in brackish water is therefore a potential risk factor for people who engage in water-related recreational activities. The ddPCR performance demonstrated in this study on clinical and environmental samples lead to greater confidence of ddPCR technology on field application.

Keywords: LOD; Naegleria fowleri; qPCR; ddPCR; primary amoebic meningoencephalitis; specificity.