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

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

本数据集收录了用于分析题为《识别塑造肺炎链球菌及其他急性呼吸道感染传播的人类接触》的手稿中所用数据。该研究于2014年1月至3月间在乌干达西南部的希马北区（Sheema North Sub-District）进行。根据每个村庄和城镇的人口规模，从研究区域内的215个村庄和两个小型地区城镇（卡布韦和伊滕德罗）中随机选取了60个集群。在每个集群中，从不同家庭中随机抽取29至30名个体参与鼻咽部携带研究，并从中选取11至12名个体回答关于其社会接触及其过去两周内呼吸道疾病史的问卷，同时采集鼻咽拭子。在社会接触问卷中，参与者首先被要求列出在调查日之前约24小时内（从前一天醒来至调查日醒来）与其进行持续时间≥5分钟双向对话的所有个体。此类遭遇被定义为‘普通接触’。对于每项报告的普通接触，参与者（或其父母/监护人）被要求估计接触者的年龄（或估计年龄）、遭遇持续时间以及是否涉及皮肤接触或口对口传递餐具（这些均定义为‘物理接触’）。对于持续时间很短的社会遭遇（<5分钟），这些被定义为‘偶遇’（例如，在路上遇到某人、商店中的遭遇等），参与者被要求根据预先定义的类别（<10次接触、10-19次接触、20-29次接触、≥30次接触）估计遭遇次数，但无需提供关于每次接触的详细信息。接下来，参与者被询问在调查前两周内经历的呼吸道症状，包括以下任何一项：咳嗽、流鼻涕、打喷嚏、喉咙痛、呼吸困难。最后，在访谈结束后，从每位参与者处采集鼻咽拭子。本数据集的数据字典可在对应的手稿文件中找到。