Soil-based environmental DNA enables detection of Oncomelania hupensis quadrasi and Schistosoma japonicum microhabitats for schistosomiasis japonica surveillance and control in the Philippines

TL;DR

This study shows that soil samples can detect snails and parasites linked to schistosomiasis, offering a better way to monitor and control the disease in the Philippines.

Contribution

The study demonstrates the first use of soil-based eDNA to detect both snail hosts and parasites in schistosomiasis surveillance.

Findings

Soil-based eDNA detected snails and parasites in more sites than traditional surveys, even where snails were not visible.

eDNA detection outperformed classical malacological surveys in identifying microhabitats for snails and parasites.

Soil pH was the only parameter significantly different between eDNA-positive and eDNA-negative sites.

Abstract

Schistosomiasis japonica, caused by Schistosoma japonicum, remains a significant public health concern in the Philippines, where 12.4 million people are at risk due to persistent transmission in endemic regions. The distribution of schistosomiasis is closely linked to the distribution of its snail intermediate host. This study aims to assess the potential of using soil samples to detect the environmental presence of Oncomelania hupensis quadrasi and Schistosoma japonicum.

This cross-sectional observational study utilized a soil-based environmental DNA (eDNA) detection system for simultaneous detection of O. h. quadrasi, and S. japonicum mitochondrially encoded cytochrome c oxidase subunit 1 gene in multiplex quantitative real-time PCR and digital PCR platforms. A two-phase sample collection and testing were carried out in December 2023 (Phase 1) and March 2024 (Phase 2) across 30 selected sampling sites in Ekiran village, Leyte, Philippines. Wilcoxon two-sample/Mann-Whitney U test was used to determine whether there was a significant difference in eDNA presence and edaphic factors, while percent agreement was used to assess the concordance among methods.

This study reveals that S. japonicum eDNA can be detected in soil samples and confirms the strong applicability of soil-based eDNA for detecting O. h. quadrasi snails and even in sites without visible snail presence. Furthermore, it demonstrates the superiority of soil-eDNA system compared to classical malacological surveys in detecting O. h. quadrasi and S. japonicum microhabitats: in Phase 1, eDNA detected O. h. quadrasi and S. japonicum in 50% (3/6) and 66.67% (4/6) of sites, respectively, while malacological surveys detected them in only 50% and 16.67% (1/6) of sites. In Phase 2, eDNA detected O. h. quadrasi in 20% (6/30) of sites compared to only 10% (3/30) by malacological survey, and S. japonicum was detected only by eDNA in 10% (3/30) of sites. Among the measured soil parameters, only pH showed a statistically significant difference between eDNA-positive and eDNA-negative sites (P = 0.04).

Soil-based eDNA sensitively detected O. h. quadrasi and S. japonicum, enabling scalable, non-invasive transmission site identification and outperforming traditional surveys without visible snails. Its ability to detect S. japonicum highlights its value for comprehensive schistosomiasis monitoring.

The online version contains supplementary material available at 10.1186/s40249-025-01374-w.

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