Statistical analysis. The geometric mean was used to summarize the distribution of Ct values from lytA and piaB of nasopharyngeal and oropharyngeal samples. To look for associations between Ct values from nursing home vs family home and nasopharynx vs oropharynx an adjusted generalized linear model (GLM) using a Gaussian distribution and a log link function was used. The McNemar's test was used to compare culture and real-time PCR methods based on paired individuals. The Chi-square test was used to compare prevalence of S. pneumoniae between nasopharyngeal and oropharyngeal samples and between nursing home and family home by real-time PCR or culture-based methods. A p-value of <0.05 was considered statistically significant for all the tests used. The Gini-Simpson index of diversity (GSID) was used to calculate serotype diversity. All analyses were performed using R version 3.2.3 41. ethics statement. This study was conducted in accordance with the European Statements for Good Clinical Practice and the declaration of Helsinki of the World Health Medical Association. In addition, it was registered and approved at health care centers of Oeiras and Montemor-o-Novo that report to Administração Regional de Saúde (ARS, "Regional Health Administration") of Lisboa e Vale do Tejo, and Alentejo, respectively, from the Ministry of Health. Informed written consent was obtained from all participants. All samples and questionnaires were attributed a numeric code and were processed anonymously.

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