Love this! I'm so upset this is not available in Switzerland. I'm following it vicariously by listening to Marina Hyde and Richard Osman talk about it on this is entertainment - and now also statistics blogging.

Very proud of @krishnaaswin77.bsky.social first PhD paper and grateful to all the excellent collaborators!

A key motivation for this study was to estimate resistance fitness costs in natura. It’s interesting they remain so elusive. In these data, we can only quantify effects associated with clearance and establishment, not transmission - so one possibility is that we’d see clearer effects there.

We did find some evidence that resistant strains are worse within-host competitors than sensitive strains, particularly for macrolide resistance. The direction of the overall effect across all analysed antibiotics is consistent with a fitness cost, but with CIs overlapping zero.

We were also interested in quantifying the fitness cost of resistance. We checked whether there's a cost on clearance rate, but resistant strains are associated with lower clearance. We think this is because resistance is more beneficial on longer carried strains. www.pnas.org/doi/abs/10.1...

We also quantified the fitness effects of antibiotics and antibiotic resistance. Antibiotic exposure is associated with a 71% increase in clearance rate of sensitive strains and, interestingly, a 40% increase in the clearance rate of resistant strains.

We find that the presence of another pneumococcal strain (i.e. competitor) in the host is associated with a 33% increase in clearance rate and a 54% reduction in the probability of establishment.

We used survival analysis to quantify how the presence of a within-host competitor affects the establishment and clearance of serotypes in the Maela pneumococcal carriage study (~1000 infants, sampled monthly over a 2 year period).