Quantifying the effects of antibiotic resistance and within-host competition on strain fitness inStreptococcus pneumoniae

• DOI: 10.1101/2025.03.09.642042
• Publication Date: 2025-03-14T02:40:11Z
• Authors: Aswin Krishna; Gerry Tonkin-Hill; Thibaut Morel-Jou...; Stephen Bentley; Paul Turner; François Blanquart; Sonja Lehtinen

Competition plays a key role in shaping the structure and diversity of bacterial populations. In many clinically important bacterial species, strains compete at multiple scales: at the between-host scale for new hosts to colonise, and at the within-host scale during co-colonisation. Characterising these multiple facets of competition plays an important role in understanding bacterial ecology. This is particularly relevant for antibiotic resistance, where competition between antibioticsusceptible and resistant strains determines resistance dynamics. In this work, we perform survival analyses on a large longitudinal dataset ofStreptococcus pneumoniaecarriage to quantify how within-host competition affects the rates of clearance and establishment of pneumococcal strains. We find that the presence of a within-host competitor is associated with a 33% increase in clearance and a 54% reduction in establishment. Priority effects and serotype differences partially predict the outcomes of this within-host competition. Further, we quantify the effects of antibiotic resistance on between- and within-host components of fitness. Antibiotic consumption is associated with increased clearance rate for both susceptible and resistant strains, albeit to a higher extent in susceptible strains. In the absence of antibiotics, we find some evidence that resistance is associated with increased susceptibility to within-host competition, suggesting a fitness cost of resistance. Overall, our work provides quantitative insights into pneumococcal competition across scales and the role of this competition in shaping pneumococcal epidemiology.