Data for: Identifying human encounters that shape the transmission of Streptococcus pneumoniae and other acute respiratory infections

Published: 26 July 2018| Version 1 | DOI: 10.17632/rdskdgxrh3.1
Olivier le Polain de Waroux, Donny Ndazima, Celine Langendorf, john edmunds, Juliet Mwanga-Amumpaire, Adam Kucharski, Sandra Cohuet, Stefan Flasche, Rebecca Grais


This dataset contained the data that was used in the analysis of the manuscript entitled "Identifying human encounters that shape the transmission of Streptococcus pneumoniae and other acute respiratory infections". The study was conducted in Sheema North Sub-District (South-West Uganda) between January and March 2014. Sixty clusters were randomly selected from the 215 villages and two small district towns (Kabwohe and Itendero) in the study area, proportionally to the population size of each village and town. In each cluster, from 29 or 30 individuals randomly sampled from different households for inclusion in a nasopharyngeal carriage study, a subset of 11 or 12 individuals were selected to answer questions about their social contacts and their history of respiratory illness in the last two weeks, in addition to having a nasopharyngeal swab taken. For the social contact questionnaire, participants were first asked to list all the individuals with whom they had a two-way conversational contact lasting for ≥5 minutes during a period of approximately 24 hours prior to the survey day (from wake up the previous day until wake up on the survey day). Such encounters were defined as ‘ordinary contacts’. For each reported ordinary contact, participants (or their parent/guardian) were asked to estimate the contact’s age (or estimated age), how long the encounter lasted for and whether it involved skin-to-skin touch or utensils passed from mouth to mouth (either of those defining ‘physical contacts’). For very short social encounters (<5 minutes), which were defined as ‘casual contacts’ (e.g. seeing someone on the way, encounter in a shop etc.), participants were asked to estimate the number of encounters based on pre-defined categories (<10 contacts, 10-19 contacts, 20-29 contacts, ≥30 contacts), but not to provide further details about each contact. Next, participants were asked about respiratory symptoms experienced in the two weeks prior to the survey, including any of the following: cough, runny nose, sneezing, sore throat, difficulty breathing. Finally, after the interview was completed, a nasopharyngeal swab was taken from each participant. The data dictionary for this dataset can be found in the corresponding manuscript files



Epidemiology, Infectious Disease, Modelling