Publication: One Health Approach to Zoonotic Disease Surveillance Utilizing Watering Hole Samples in Laikipia County, Kenya
Date
2023-07-26
Authors
Lilak, Abigail
Journal Title
Journal ISSN
Volume Title
Publisher
Abstract
Emerging and re-emerging pathogens and more specifically, water-borne pathogens continue to be a burden globally. In East Africa, water-borne infectious diseases include cholera, cryptosporidiosis, giardia, hepatitis A and E, leptospirosis, schistosomiasis, and typhoid. Watering holes are an understudied environment for surveillance, in Laikipia County, Kenya. These locations provide a unique perspective as it is a shared environment between animals, livestock, and humans and allow the ability to conduct pathogen surveillance under a One Health framework. Throughout Laikipia County, 10 watering holes were sampled. Within Kenya, there have been outbreaks of cholera, schistosomiasis is considered endemic, and leptospirosis has a high global burden (Chadeka et al., 2019). To our knowledge, there has not been a study in Laikipia County studying water samples from watering holes for zoonotic infectious diseases. Of increasing concern, due to climate change, there has been a scarcity of resources, and certain watering holes are now almost or completely empty during portions of the year. In addition, there has been an ongoing drought which has led to an increase in the shared usage of watering holes and made water a valuable resource amongst humans and animals. From May 2020 until March 2022, 122 pooled water samples were collected from 10 watering holes within Laikipia County. The samples were processed and sequenced using a Mk1C MinION, with output sequences analyzed through a data pipeline. Partial reads from the following microorganisms were detected: Acanthamoeba castellanii, Aeromonas veronii, Brevibacillus brevis, Gardnerella vaginalis, Legionella pneumophila, Orientia tsutsugamushi, Plesiomonas shigelloides, Staphylococcus aureus, Staphylococcus capitis, Staphylococcus epidermidis, Staphylococcus haemolyticus and Vibrio cholerae. Samples were further examined for potential contigs, many of the samples had limited mapping to the reference genome, often with no coverage overlapping. These findings highlight the potential uses of metagenomics for environmental surveillance and the need for more studies conducting work with environmental DNA and metagenomics. Additionally, this thesis starts to contribute towards a larger conversation within science about the reliability and confidence or working with and analyzing genetic data.
Description
Keywords
water, metagenomics, surveillance, NATURAL SCIENCES::Biology::Terrestrial, freshwater and marine ecology, zoonotic, Kenya