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.

Methods
These data have been synthesized from studies that report Streptococcus pneumoniae colonization and co-colonization in children populations worldwide. We provide primary data files (metadata and extracted epidemiological variables as well as serotype compositions), processed data files, and some auxiliary R codes for analysis. The main purpose of our initial analyses was to investigate the stress-gradient-hypothesis in pneumococcus, and to link the mathematical modeling framework in previous papers (Gjini and Madec, 2021; Madec and Gjini 2021) to a concrete epidemiological context. 

Gjini, Erida, and Sten Madec. "The ratio of single to co‐colonization is key to complexity in interacting systems with multiple strains." Ecology and Evolution 11.13 (2021): 8456-8474. https://doi.org/10.1002/ece3.7259 
Madec, Sten, and Erida Gjini. "Predicting N-strain coexistence from co-colonization interactions: epidemiology meets ecology and the replicator equation." Bulletin of Mathematical Biology 82.11 (2020): 142. https://doi.org/10.1007/s11538-020-00816-w