Detection of zoonotic bacteria in rodent samples from Africa using 16s metagenomic sequencing. 01/04/2022 - 31/03/2023

Abstract

Although most emerging infectious diseases originate from animals, the ecological mechanisms that explain how parasites persist in wildlife and spill-over to humans are not well understood. Collecting data during outbreaks is difficult because epidemics usually remain undetected until they spillover to humans and wild animals are not part of surveillance programs (e.g. in contrast to livestock). As part of my postdoc project, I will investigate how zoonotic bacteria persist in rodent communities in sub- Saharan Africa. I will disentangle the rodent community to check which rodent species are reservoirs of these bacteria and which are secondary host. This will allow to test two import questions in disease ecology: (i) Which factors drive the persistence of multi-host pathogens?; (ii) Does the rodent community structure affect co-infection patterns. To test these questions, I trapped rodents in the Democratic Republic of Congo and Tanzania in different habitats where the rodent communities differ. While I initially proposed to screen these samples using two model bacteria (anaplasma and bartonella) that we frequently find in rodent communities using PCR and Sanger sequencing, the additional BOF funding will be used to screen samples on the presence of all bacteria using MinION sequencing. The MinION is a third-generation sequencer with the capacity to sequence large DNA fragments reads. This will significantly improve the quality of the work as it will allow to screen all samples on all possible pathogenic bacteria in multiplex. Indeed, metagenomics sequencing will detect many more pathogens that infect multiple rodent host and co-occur in the same individual. Therefore, it is clear that this approach will allow to answer the two research questions more convincingly.

Researcher(s)

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Project type(s)

  • Research Project

Who infects whom? Disentangling multi-host transmission of pathogens in rodent populations. 01/11/2020 - 31/10/2023

Abstract

Although most emerging infectious diseases are caused by animalborne pathogens that originate from wildlife, the ecological mechanisms that explain how these pathogens spread and persist in the natural environment remain unclear. This research gap arises from the practical challenges of gathering convincing field data due to the stochastic nature of epidemics and the fact that these are longterm, population-level processes. In this project, I propose to investigate how differences in rodent communities influence the prevalence, persistence and control of pathogens that infect multiplehost species. These mechanisms lie at the root of an ongoing debate in conservation biology: whether biodiversity loss will lead to an increase or decrease of infectious disease that might spillover from animals to humans. The work will be based on the analysis of a unique collection of rodent samples that were captured during earlier fieldwork performed in the DRC and Tanzania and will be tested on the presence of different pathogens. By combining this data collection with additional field experiments and mathematical models, my project will test three main hypotheses: (i) pathogens tend to infect multiple host species, (ii) pathogen persistence is often driven by a key host species, and (iii) targeting this key host species suffices for pathogen control.

Researcher(s)

Research team(s)

Project type(s)

  • Research Project