Research Joachim Mariën

Abstract

The past century has seen unprecedented changes of natural biotopes due to human activities, in Africa perhaps even more than elsewhere. This has affected the distribution and dynamics of infectious diseases, particularly zoonotic infections, transmitted from wildlife to humans. In addition, changes in human demography, agriculture and other human activities in the environment, including health care interventions, have also changed the disease dynamics. Understanding the relative contribution of these factors may help in predicting what the effects can be of future environmental changes to the spread of diseases. This FED-tWIN profile will use museum collections and historical archives to retrospectively study the impact of environmental and anthropogenic changes on vector and disease dynamics. Despite their enormous potential, this 'unexplored heritage' is vastly underused in epidemiological research. Here we will combine longitudinal series of vector collections and zoonotic disease carriers from the RMCA and, in a later stage, also other institutes, with historical archives such as medical records, aerial pictures and scientific publications. By taking a multidisciplinary approach, combining ecology, geography, modeling and semi-quantitative methods, we will document the changes in the presence, diversity and distribution of pathogens, vectors and animal reservoirs and relate these to changes in 1) human demography, 2) climate, and 3) land cover and land use on the spread of vector-borne and zoonotic diseases. By including socio-ecological studies and historical records of disease control efforts, we can draw lessons in order to improve current health policy ('historical epidemiology'). RECORDED has a perspective of 10 years, but as a starting point we will focus on three vector-borne diseases that are strongly affected by environmental and anthropogenic change and that fall within the expertise of and/or historical documentation at both institutes: schistosomiasis, sleeping sickness and bubonic plague. The initial geographical focus lies on Kisangani (DRCongo), in the heart of the Congolese rainforest, because of the wealth of historical archives and collections that exist in our museums due to our colonial history, but also because it is a fast-growing economical center, linked with Kinshasa through the Congo River. Due to increased globalization, changing disease dynamics in Kisangani will therefore also be linked to other areas in the world.

Researcher(s)

• Promoter: Leirs Herwig
• Fellow: Mariën Joachim

Research team(s)

• Evolutionary ecology group (EVECO)

Project type(s)

• Research Project

Abstract

To mitigate and prevent zoonotic disease to humans, it is necessary to understand how pathogens are transmitted in populations of their wildlife reservoir. In fact, most wildlife pathogens circulate endemically within communities of multiple host species that differ in density, susceptibility, infectiousness and behaviour. One of the main questions within this one-health perspective is whether increasing biodiversity will lead to a decrease or increase in infection prevalence, termed the dilution and amplification effects, respectively. In this project, we will investigate these mechanisms focusing on viruses in rodent communities using a unique combination of empirical data, existing sample sets, and state-of the art metagenomic sequencing and modelling. More specifically we will integrate a CRISPR-Cas-based host depletion technique into existing metagenomic sequencing pipeline that will allow us to deplete any target (e.g. host gene, adapters) of any type (DNA or RNA), in any sample (acellular vs cellular), and in any species. This will greatly expand the diagnostic range for human and wildlife samples at ITM and UAntwerp and more importantly provide a more in-depth understanding of the ecology and evolution of zoonotic viruses.

Researcher(s)

• Promoter: Leirs Herwig
• Co-promoter: Mariën Joachim

Research team(s)

• Evolutionary ecology group (EVECO)

Project type(s)

• Research Project

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)

• Promoter: Mariën Joachim

Research team(s)

• Evolutionary ecology group (EVECO)

Project website

Project type(s)

• Research Project

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)

• Promoter: Leirs Herwig
• Fellow: Mariën Joachim

Research team(s)

• Evolutionary ecology group (EVECO)

Project type(s)

• Research Project