Prospecting a pathogen : pathogen, host and environmental dynamics driving the emerging Batrachochytrium salamandrivorans epidemic

Emerging infectious diseases are a major force contributing to global biodiversity declines. Amphibians are emblematic of this pattern- the last 50 years have seen global declines and extinctions in hundreds of species, making this group the most threatened Class within the animal Kingdom. One of the most recently described emerging infectious diseases contributing to these declines is Batrachochytrium salamandrivorans (Bsal), a chytrid fungus that has been associated with mass mortality events in a growing number of European amphibian populations over the last 10 years. Since its description in 2013, various studies have described key Bsal characteristics such as its lifecycle, suitable conditions for growth and potential species susceptibility. However, these studies focused on the type strain, isolated from the index outbreak site. The aim of this thesis was to characterize variation within the European Bsal epidemic – with a specific focus on pathogen variation, but also considering key elements of host variation that may influence epidemiological outcomes