Tracking and tackling goat farm-associated pneumonia using a metagenomics approach

Project: PhD

Project Details


In the Netherlands, an increased incidence of community-acquired pneumonia near goat farms has been reported, leading to the question if this is due to exposure to bioaerosols from goat farms. At present, there is no clear link to one or more specific causative agent(s) due to a lack of knowledge on the temporal and spatial patterns of goat farm microbiota and the health effects they have on their environment. The proposed research attempts to obtain more knowledge about this, using both a metagenomics and a One Health approach. A primary objective will be to identify molecular signatures or ultimately the agent(s) that cause goat-related community-acquired pneumonia in humans. It features multiple sampling sites per goat farm. These will be sampled multiple times over the course of at least one year, in order to accurately determine the contribution of each potential source to goat farm microbial emissions through metagenomics. These samples serve as a source of inference of the potential transmission routes within the goat farm and the potential emission routes from the farm to nearby human-inhabited areas. Consecutively, the relation between farm management practices and the occurrence of genomic material of zoonotic pathogens will be studied using machine learning methods. Subsequently, if one or more causative agents would be established in conjunction with parallel research projects directed at pneumonia in nearby residents, intervention strategies can be developed and their effectiveness can be evaluated through metagenomics surveillance practices. Successful development of the methods used to reach these objectives allows for usability of these methods in other monitoring or experimental setups on various scales, e.g. similar approaches could be applied to livestock farms of other species. This potentially turns metagenomics analyses into effective surveillance tools.
Effective start/end date1/06/19 → …


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