Unleashing Modern Genomics for Precision Public Health Surveillance of Cryptosporidium
This project aims to improve the way we deal with Cryptosporidium in a public health context.
To achieve this, I will:
- Improve the DNA yield from Cryptosporidium clinical samples, leading to higher quality sequencing data.
- Develop a set of bioinformatic tools which can be used to carry out modern high-resolution epidemiological investigation and phylogenomic analysis of Cryptosporidium samples which pass through the Public Health Wales-hosted UK Cryptosporidium Reference Unit.
- Develop a bleeding edge whole genome typing scheme using a set of highly discriminatory single nucleotide variations (SNVs), which can be used to define and distinguish clinically important populations of Cryptosporidium.
- Use these SNVs to investigate the population structure of Cryptosporidium, and the difference in recombination between outbreak and non-outbreak clinical samples, and consequently improve our understanding of biological factors which lead to Cryptosporidium outbreaks.
Each of these aims are essential to improve understanding of the population structure, epidemiology, and transmission dynamics of Cryptosporidium. With collaborators at the Public Health Wales Cryptosporidium Reference and Pathogen Genomics Units (CRU and PenGU respectively), I will implement the wet-lab protocols developed to deal with low DNA yield samples of Cryptosporidium, the bioinformatic software required to manage sample data storage and carry out epidemiological and investigation, and the novel typing scheme. PenGU and the CRU both currently possess standard processes for sample extraction and sequencing that are ISO accredited. My work will build on these to further optimise and validate these for sequencing Cryptosporidium. This means that while the work is novel and significant, it builds upon existing expertise and processes, reducing the risk of elements not working. I will utilise the developed sample preparation protocol to enrich and sequence the genomic DNA from historical and contemporary Cryptosporidium samples which pass through the CRU to produce 80 new clinical Cryptosporidium NGS datasets. This will represent one of the largest single contributions ever made to the global database of Cryptosporidium clinical genomic data.
Key Hypotheses: Alongside the project aims, I will examine two key hypotheses over the course of this project:
- Typing through interrogation of all single nucleotide polymorphisms throughout the genome of Cryptosporidium is more informative than conventional single and multi-locus genotyping paradigms.
- Recombination events during outbreaks of Cryptosporidium occur at a more rapid rate than during non-outbreak cases.
The work proposed in this project has been developed in collaboration with two units of Public Health Wales (the CRU and PenGU) to tackle the domain specific challenges presented in mounting a public health response to Cryptosporidium in Wales specifically, but also in the broader UK and globally.
The CRU has a UK-wide role in characterising Cryptosporidium, and so the benefits of this project will be felt across the UK, as well as potentially forming the basis for attracting investment into Wales. This project will be the first step into utilising genomics for real-time Cryptosporidium prevention by a public health agency. It will also function as a blueprint for handling many other eukaryotic pathogens which face similar domain specific problems, such as Cyclospora and Toxoplasma.