Abstract

Soil-transmitted helminths (STHs) are a major global health concern, exacerbating poverty and disease. Traditional diagnostic methods rely on microscopic examination of faecal samples, which can be labour-intensive and have limited sensitivity. Molecular techniques, particularly quantitative polymerase chain reaction (qPCR), offer improved sensitivity, especially in low-prevalence areas, but current assays have been developed using a narrow range of parasite isolates. This is problematic because STHs are genetically diverse, and such variation can affect the accuracy of molecular diagnostics. Unravelling the untapped genetic diversity of STHs could transform the way we understand STH biology and epidemiology. Population genetics studies of STHs are limited, partly due to the difficulty of obtaining adult worm samples. This thesis explores the use of low-depth shotgun metagenomic sequencing (“genome skimming”) and targeted hybridisation enrichment on faecal samples with known STH infections to analyse helminth genetic diversity. Although less sensitive than qPCR, genome skimming enabled the recovery of complete mitochondrial genomes (mtDNA) and revealed substantial genetic variation in nuclear diagnostic targets that can influence diagnostic performance. Given the low abundance of STHs in faecal samples and the large amounts of non-target DNA (e.g., host, bacteria), targeted hybridisation enrichment is a highly efficient method to enrich helminth mtDNA in faecal samples and capture genetic variation. These advances provide a foundation for better understanding STH genetics without relying on adult worms and form a foundational basis for the genomic epidemiology and sustainable control of STHs as a public health concern.