Sample collection and microbiological methods.

<div><p>Background</p><p>Despite growing evidence of reduced invasive and non-invasive pneumococcal disease attributed to public health measures against the COVID-19 pandemic, the effect of these measures on pneumococcal carriage remains unclear. This study aimed to assess pneumococcal nasopharyngeal carriage among children and adults self-confined at home during the COVID-19 national lockdown in Spain while identifying predictors of pneumococcal carriage in children.</p><p>Methods</p><p>Household study conducted across the metropolitan area of Barcelona (Spain) between April-June 2020. Nasopharyngeal samples were collected from young children and adults for real-time PCR pneumococcal <i>lytA</i> and <i>wgz</i> gene detection, quantification, and serotyping, as well as for detection of respiratory viruses.</p><p>Results</p><p>Among 332 children (median age: 3.1 years [IQR: 1.9–4.0 years]; 59% male) and 278 adults (median age: 38.9 years [IQR: 36.1–41.3 years]; 64% female), pneumococcal carriage rates were 28.3% and 2.5%, respectively. Highly invasive serotypes 3, 7F/7A, and 19A were detected in 14.0% of samples from children carriers. Pneumococcal co-infections with <i>respiratory syncytial virus</i> (RSV), <i>human metapneumovirus</i> (hMPV), and <i>influenza virus</i> (IV) were not identified in children. Attendance to kindergarten before the lockdown (aOR: 2.65; IQR: 1.57–4.47; <i>p</i><0.001) and household crowding (aOR: 1.85; IQR: 1.09–3.15; <i>p</i> = 0.02) were independent risk factors for children’s pneumococcal carriage.</p><p>Conclusions</p><p>Pneumococcal carriage rate among quarantined children during a full COVID-19 lockdown was moderate and correlated with limited presence of highly invasive serotypes and absence of pneumococcal co-infections with RSV, hMPV, and IV. Pre-lockdown daycare and household crowding predisposed children to carriage.</p></div>