Understanding how infectious diseases spread (epidemiology) is important to public health policy, responsive infection control and individual patient management. Traditionally, epidemiologists rely upon high-quality surveillance data. However, obtaining such data depends upon comprehensive monitoring of patients and their contacts throughout an outbreak, which is often infeasible in the real world.
But what if, rather than just considering the patient, it was possible to get this information directly from the pathogen? When microbes reproduce in order to transmit and infect another person, they have to copy their genome – and frequently they make mistakes, known as mutations. These mutations accumulate over generations, chronicling the organism’s ancestry. Thanks to modern genomic sequencing techniques, it is now possible to read this inbuilt historical record. This data can be used to infer much about the dynamics of infection in the population at large, such as: the prevalence of the infection in the population; its speed of transmission; when it crossed into humans; what groups are at risk; and potential targets for treatment. Bethany’s research has specifically dealt with norovirus in hospitals, the spread of Campylobacter (the major cause of gastroenteritis) from farmyard animals to humans, and HIV.