Development of high throughput SNP marker panels for genotyping of pathogenic bacteria

Abstract

Bacteria colonise almost every known habitat on earth and pose some of the greatest threats to public health. They do this through the great genetic variation between and within species. These traits allow colonies to develop new strategies to survive e.g. evading host immune responses or becoming resistant to antibiotics. In this project we have taken advantage of the swathes of sequence data available for a range of bacteria and used this to identify key single nucleotide polymorphisms (SNPs) in each species. These SNPs were ranked by our minimal marker pipeline in order of resolving power to create SNP marker panels which could be used to discriminate between hundreds of isolates of the same species. Our results showed that, for most species tested, over 99% of isolates of a single species could be resolved from one another using between just seven and 15 SNP markers. A panel of the most informative SNP markers for Campylobacter jejuni was created and used to genotype DNA samples from eight unseen isolates in the lab. The alleles displayed by each isolate at the 13 SNP markers used displayed sufficient diversity to allow us to discriminate between all eight isolates.

Date of Award	6 Dec 2022
Original language	English
Awarding Institution	University of Bristol
Supervisor	Gary L A Barker (Supervisor) & Andy M Bailey (Supervisor)