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 orga..., 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..., , # Data and code for: Pneumococcus co-colonization and the stress-gradient-hypothesis [https://doi.org/10.5061/dryad.hqbzkh1p0](https://doi.org/10.5061/dryad.hqbzkh1p0) This dataset contains gathered information on pneumococcus colonization and co-colonization in children for a meta-analysis of 19 studies (17 geographic locations around the world) collected between 2000-2017. We extracted prevalences of susceptibles, singly-colonized (hosts carrying one serotype), and co-colonized children (hosts carrying more than 1 serotype) as reported in these studies. We also extracted the sets of serotypes present in any given setting and performed similarity comparisons for serotype composition across sites. Summarized general information can be found in the file: *Metadata_SGH_SPN.xlsx*. The serotypes reported in each study, the statistics of their occurrence/co-occurrence, and rankings in the global dataset are provided in the file: *SerotypesSGH_SPN.xlsx*. We provide also post-processing dat...由多态性细菌肺炎链球菌（Streptococcus pneumoniae）引发的肺炎链球菌血清型共定植现象，近年来受到越来越多的研究关注与报道。然而，关于共定植模式在全球范围内的变异规律的相关信息仍较为匮乏，而这对于阐明该类细菌的演化与传播动态至关重要。本研究基于从公开文献中搜集的大量横断面肺炎链球菌定植研究数据集，量化了不同流行病学背景下儿童群体中的传播强度模式与共定植变异特征。本研究将上述数据拟合至多交互菌株间满足准中性假设的共定植SIS模型，分析结果揭示了传播强度基本再生数R0与共定植易感性k之间存在显著的负协变模式，为生态学中的胁迫梯度假说（stress-gradient hypothesis, SGH）提供了支持依据。根据该假说，不同生物间的生态交互作用……本数据集整合了全球范围内针对儿童群体的肺炎链球菌定植与共定植相关研究数据。本研究提供原始数据文件（包含元数据、提取的流行病学变量及血清型组成信息）、处理后的数据文件，以及用于数据分析的辅助R代码。本研究初始分析的核心目标为验证肺炎链球菌相关的胁迫梯度假说，并将既往研究（Gjini与Madec, 2021；Madec与Gjini, 2021）中的数学建模框架与具体的流行病学场景相结合。 Gjini, Erida, 与 Sten Madec. 《单定植与共定植的比值是多菌株交互系统复杂性的关键调控因素》，Ecology and Evolution 11.13 (2021): 8456-8474. https://doi.org/10.1002/ece3.7259 Madec, Sten, 与 Erida Gjini. 《从共定植交互作用预测N菌株共存：流行病学与生态学及复制者方程的结合》，Bulletin of Mathematical Biology 82…… # 数据集与代码：肺炎链球菌共定植与胁迫梯度假说 https://doi.org/10.5061/dryad.hqbzkh1p0 本数据集涵盖了2000-2017年间搜集的19项研究（覆盖全球17个地理区域）的荟萃分析所需的儿童肺炎链球菌定植与共定植相关信息。我们从这些研究中提取了易感儿童、单定植儿童（携带单一血清型的宿主）与共定植儿童（携带多于1种血清型的宿主）的流行率数据；同时提取了各研究区域内存在的血清型集合，并对不同位点的血清型组成进行了相似性比较。 汇总的基础信息可在文件*Metadata_SGH_SPN.xlsx*中查阅；各研究中报道的血清型、其出现/共现统计数据及全球数据集内的排名信息可在文件*SerotypesSGH_SPN.xlsx*中获取。本研究同时提供后处理数据……