Changes in global climate and land use are leading to shifts in the geographical distribution, prevalence, and host ranges of pathogens. At the same time, antibiotics are becoming increasingly ineffective in treating bacterial infections due to the emergence and spread of multidrug resistant pathogens. To develop better strategies to mitigate this combined threat to global health, we urgently need to better understand how antibiotic resistance is gained and lost across different host species.
The increasing availability of large collections of genome sequence data from natural populations of bacterial pathogens, and a better understanding of the diverse microbial communities of particular within-host niches, has created an opportunity to better characterise the evolutionary dynamics of antibiotic resistance genes, across bacterial communities and host environments. This project will develop and apply population genetic and phylogenetic models of bacterial evolution to genome sequence data to investigate how resistance is gained and lost across different host populations, and infer the sources of resistance genes. Depending on the interests of the PhD student there is potential for a data collection or laboratory component of the project.
While the findings of the project will have broad relevance for the emergence and spread of resistant pathogens, the suggested initial focus is Staphylococcus aureus (MRSA). S. aureus is a WHO global priority antibiotic-resistant pathogen that has been estimated to cause the deaths of more than 100,000 people globally each year. It is also found across a wide range of other species, including birds, bats, reptiles, aquatic mammals and fish.