About the Project
This project is one of a number that are in competition for funding from the Red-ALERT CDT for entry in September 2025.
Overview of the Research:
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. Methods development will consider all steps from panel design, sample preparation, sequencing and bioinformatics, and will be steered towards two distinct aims:
1. Source attribution of common bacterial pathogens. We will develop targets identified from current bioinformatics projects leveraging large volumes of genomic data for E. coli and Klebsiella from diverse animal hosts and ecological settings.
2. Early warning of rare pathogens, including those arising from zoonotic spillovers. Here we will consider a broad range of pathogenic taxa, including bacteria (eg Leptospirosis), viruses (eg Mpox, polio), parasites (eg cryptosporidium) and fungi (eg Candida).
Project Keywords: Pathogen, Probe Enrichment, Microbial Source-Tracking (MST), Water, Early-Warning
Industrial Partner:
The UK Health Security Agency are the industrial partner on this project.
Candidate Requirements:
Applicants should hold, or expect to receive, a First Class or good Upper Second-Class UK Honours degree (or the equivalent) in in Biology, preferably Microbiology or a related subject.
Some bioinformatics experience would be an advantage, as would a master’s level qualification.
*Non-UK applicants must meet the programme’s English language requirement prior to a formal offer being made.
Equality, Diversity, and Inclusion:
We value a diverse research environment and aim to be an inclusive university, where difference is celebrated and respected. We welcome and encourage applications from under-represented groups.
If you have circumstances that you feel we should be aware of that have affected your educational attainment, then please feel free to tell us about it in your application form. The best way to do this is a short paragraph at the end of your personal statement.
Enquiries and Applications:
Formal applications should be submitted via the Red-ALERT CDT online application form prior to the closing date of this advert.
Funding Notes
Candidates may be considered for a NERC Red-ALERT studentship tenable for 3.5 years. Funding covers tuition fees, a stipend (ÂŁ19,237 p/a in 2024/5) and access to a training support budget.
References
1. Kantor RS, Jiang M. Considerations and Opportunities for Probe Capture Enrichment Sequencing of Emerging Viruses from Wastewater. Environ Sci Technol. 2024 May 14;58(19):8161-8168. doi: 10.1021/acs.est.4c02638. Epub 2024 May 1. PMID: 38691513; PMCID: PMC11097388.
