Pandemic Social Distancing and Declines in Nasopharyngeal Carriage of Pneumococcus and Related Antimicrobial-Resistant Genes: Evidence From Household-Based Cohort Studies in Lima, Peru

Background Peru implemented restrictive social distancing policies during the COVID-19 pandemic. Few studies have examined patterns of nasopharyngeal pneumococcal carriage and related antimicrobial-resistant genes (ARGs), particularly in community-based settings with intense social distancing policies.Methods Nasopharyngeal swabs were systematically obtained weekly from children and adults enrolled in 2 household-based prospective cohorts in Lima, Peru: prepandemic (2019-2020) and pandemic (2020-2021). Selected samples underwent sequencing-based detection of Streptococcus pneumoniae and related ARGs. We compared detections of pneumococcus and erm genes between cohorts during the same 7 epidemiologic weeks in 2020 and 2021 while accounting for relevant covariates and household clustering by mixed effects logistic regression models.Results An overall 663 specimens from 114 individuals were included: 407 and 256 samples from the prepandemic and pandemic cohorts, respectively. Carriage of pneumococcus was lower in the pandemic cohort (3.5%) as compared with the prepandemic cohort (23.6%; adjusted odds ratio, 0.09; 95% CI, .02-.32). Similarly, erm gene carriage was lower in the pandemic cohort (28.1%) as compared with the prepandemic cohort (58.7%; adjusted odds ratio, 0.21; 95% CI, .10-.46).Conclusions We observed a substantial reduction in the carriage of S pneumoniae and related ARGs in community-dwelling individuals during a pandemic period with intense social distancing in Lima, Peru. In prospective household-based cohort studies in Lima, Peru, we assessed the prevalence of pneumococcal carriage and related antibiotic resistance genes just before and during the COVID-19 pandemic when strict social mitigation measures were in place.