Competition across scales
Much of our current work focuses on understanding how the interaction of within- and between-host scales shapes competition between strains. This is important for understanding (e.g.) the dynamics of antibiotic resistance.
On the empirical side, we used a large longitudinal dataset of pneumococcal carriage to quantify how competition affects strain fitness. We also looked at how antibiotic resistance affects fitness in presence and absence of antibiotics. You can read more about it here.
On the theory side, we are developing modelling approaches to understand how the inter-play of within- and between-host processes shapes the ecology and evolution of bacterial populations and communities.
We are also interested in what mediates competition between strains. At the moment, we are focusing on the role of bacteriocins using both theory and genomics.
Longitudinal gut microbiome study
We are conducting a longitudinal stool sampling study in a nursery cohort to investigate strain dynamics within-host and transmission from host to host. We use both culture and metagenomic techniques to characterise the species and strain composition of the gut microbiota. We are interested in understanding how different E. coli strains interact with each other and other species in the gut, and how these interactions affect the onward transmission of strains.
Antibiotic resistance dynamics
We are interested in understanding and predicting the dynamics of antibiotic resistance.
In recent work, we characterised long-term temporal trends in resistance frequencies using a statistical modelling approach. We found evidence that, contrary to an intuitive model of resistance evolution, trajectories show signs of stabilising at intermediate frequencies.
This stabilising trend is intriguing and not fully explained (yet). Some of our theoretical work focuses on this puzzling observation. We are also interested in the role of horizontal gene transfer, and particularly plasmids, in resistance dynamics.
Horizontal gene transfer and strain structure
Many bacterial species exist as distinct strains that are stable through time. This is interesting, because in principle, horizontal gene transfer between strains should act to degrade such structure over time. We are using both genomic and modelling approaches to study the mechanisms that maintain strain structure in the presence of horizontal gene transfer. This will help us better understand the circumstances under which selection acts to change the frequency of genes vs the frequency of genotypes.