Research
I am currently an SNSF PRIMA group leader at ETH Zurich - and will be moving to the University of Lausanne this summer. There will be PhD and postdoc positions advertised soon - come join us! More info here.
My group is interested in how ecological and evolutionary mechanisms shape the structure and diversity of bacterial populations and, in particular, the dynamics of public health relevant traits, such as antibiotic resistance.
We use mathematical and statistical modelling, and genomic and surveillance data - both publicly available and collected as part of our own studies - to develop evolutionary and epidemiological insights.
We focus on species that share a similar lifestyle: mostly commensal but occasionally pathogenic (e.g. Streptococcus pneumoniae, Escherichia coli) and of high clinical relevance.
For more information about the group, see here.
Antibiotic resistance dynamics
Much of my work has focused on explaining puzzling trends in the frequencies of antibiotic resistance in bacteria, particularly S. pneumoniae. These projects include explaining why resistant bacteria are not out-competing sensitive bacteria; exploring why frequencies of multidrug resistance are higher than expected; and analysing the relative importance of selection and horizontal gene transfer in the dynamics of antibiotic resistance.
Competition across scales
Our current work focuses on understanding how the interaction of within- and between-host scales shapes the competition between different strains (e.g. antibiotic sensitive and resistant strains). As part of this work, 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 have also began developing some related theory on the effects of bacterial fratricide on strain dynamics at the epidemiological (i.e. host population) scale.
Gut microbiome study
We are running a longitudinal study of E. coli colonisation in children. 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.
Plasmid ecology and evolution
Plasmids play an important role in bacterial evolution, in particular through their role as vehicles of horizontal gene transfer. Some genes, such as antibiotic resistance, are more likely to be found on plasmids than the chromosome. In recent work, we suggest a priority effect arising from positive frequency-dependent selection may explain this observation. In related work, we explore the effects of plasmid co-infection on the evolutionary and ecological dynamics of plasmids.
Other projects
Other project include work on how the timing of SARS-CoV-2 transmission impacts quarantine and contact tracing and work on protein interaction networks during my PhD.