Recent advances in sequencing technology have revolutionised our ability to track infectious disease dynamics using pathogen genomes, such as during outbreak investigations. However, these tools remain underutilised for addressing endemic disease threats, especially those affecting human and animal health in low-resource settings.

Anthrax is a classic example of a neglected bacterial zoonosis, affecting marginalised communities in many parts of the global south, including much of Sub-Saharan Africa. It causes significant mortality in people as well as livestock losses, but tends to be undiagnosed and underreported. Although vaccination of livestock plays a key role in preventing infection in both people and animals, it is often not affordable. Moreover, because the spores of the anthrax bacterium Bacillus anthracis can remain infectious within the environment for decades, it is not clear how long livestock vaccination would have to be maintained before a measurable reduction in infection risk is achieved. Obtaining genome data from detected cases, and incorporating genomic and epidemiological data into phylodynamic models provide a novel and powerful means to track residual anthrax transmission and quantify progress towards its elimination.

This project aims to create the necessary framework for guiding anthrax control programmes in endemic settings through the use of pathogen genomics and phylodynamic modelling. Building on robust partnerships and research platforms established in northern Tanzania by the Glasgow supervisors, including existing genomic data, our project will:

1. Extend current analytical tools and molecular clock models to accommodate the alternation between extended environmental persistence and periodic rapid replication typical for B. anthracis

2. Develop a simulation model combining genomic, spatial, temporal and epidemiological information to examine the effect of vaccination on B. anthracis genetic diversity and transmission in silico

Validate this model by generating genomic data obtained during a livestock vaccination program expected to start in the study area in 2019.

The project would create a new interdisciplinary collaboration between the two universities that brings together complementary skills and expertise in bacterial zoonoses, field epidemiology, one health interventions and molecular epidemiology (Lembo, Forde, Biek), as well as pathogen phylodynamics and population modeling (Lycett). It builds on existing research led by Glasgow in the Ngorongoro Conservation Area (NCA), Tanzania, a hyperendemic area for anthrax. This provides extensive collections of data and samples, of which >70 have already yielded whole genomes. The project is timely given the expected initiation of livestock vaccination in the NCA, which offers a platform for real-time monitoring of the campaign.

Supervisors:

Dr Roman Biek (University of Glasgow)
Dr Samantha Lycett (Roslin Institute, University of Edinburgh)
Dr Tiziana Lembo (University of Glasgow)
Dr Taya Forde (University of Glasgow)