Abstract

Waterborne pathogens pose a significant global health threat, however, their detection is challenged by ultra-low concentrations in environmental samples, necessitating complex enrichment steps that hinder field testing. Although molecular methods such as PCR offer speed and sensitivity, they are constrained by small reaction volumes and the requirement for sample DNA preparation, which increases complexity and contamination risk. To address these limitations, spiky silica nanoparticles (SSNPs) with tunable inter-spike distances were engineered to capture and concentrate bacterial DNA from large water volumes. We demonstrated that SSNPs not only capture DNA efficiently but also enable direct PCR amplification without elution, thereby eliminating extra processing steps. This one-pot method is capable of detecting Escherichia coli ( E. coli ) at 1 CFU per 100 mL, meeting WHO sensitivity guidelines, and outperforms a commercial kit. The method successfully identifies specific pathogens ( Escherichia coli and Streptococcus suis ) as well as total bacterial communities (via universal bacterial 16S rRNA) in diverse environmental water samples. Further studies suggested that the total available surface area is the key indicator of whether direct PCR would be successful. In this study, by integrating sample concentration and amplification into a single reaction, this novel SSNP-based platform provides a rapid, sensitive, and field-deployable strategy for water quality monitoring, particularly suited for resource-limited settings.