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Research Project: Source attribution and early warning of water-borne pathogens using hybrid-capture sequencing.

Lead Supervisor: Ed Feil

External Partner: UKHSA & Cefas

The application of genomic technologies is central to the objectives of wastewater-based epidemiology, but there are important trade-offs between methods that provide detailed characterisation of specific pathogens down to the sub-species level (eg single colony sequencing), and those that capture broader community profiles (eg metagenomics). The PCR is widely used to detect and quantify the presence of specific resistance genes, but designing primers with optimal specificity, and high-level multiplexing, can be technically challenging.  This project will develop methods based on probe capture enrichment, which can circumvent these limitations by providing detailed data on a broad range of targeted pathogenic species simultaneously, even when the targeted sequences are rare relative to non-target noise. The approach has been applied to wastewater samples, primarily to detect viruses but, although commercial kits are available, no standard workflow exists for public health monitoring [1].  This project will be to develop and validate probe enrichment pipelines for use on wastewater and river samples collected as part of the ongoing research at the WBE@BATH Centre of Excellence.