Data and code for: Pneumococcus co-colonization and the stress-gradient-hypothesis

Pneumococcus serotype co-colonization, caused by the polymorphic bacteria Streptococcus pneumoniae, has been increasingly investigated and reported in recent years. Yet, there is limited information on how co-colonization patterns vary globally, critical for understanding the evolution and transmission dynamics of these bacteria. Here we report on a rich dataset of cross-sectional pneumococcal colonization studies collected from the literature, where we quantified patterns of transmission intensity and co-colonization variation in children populations across different epidemiological settings. Fitting these data to an SIS model with co-colonization under the assumption of quasi-neutrality among multiple interacting strains,  our analysis reveals strong patterns of negative co-variation between transmission intensity R₀ and susceptibility to co-colonization k, in support of the stress-gradient-hypothesis (SGH) in ecology. According to this hypothesis, ecological interactions between organisms shift positively as environmental stress increases. In our model higher environmental stress is represented via lower values of the basic reproduction number R₀, and a shift towards positive interactions is represented via higher vulnerability to co-colonization (higher k) between pneumococcus serotypes.