Pneumococcal nasopharyngeal carriage in children and adults self-confined at home during a COVID-19 national lockdown

Abstract

Background: 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. Methods: 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 lytA and wgz gene detection, quantification, and serotyping, as well as for detection of respiratory viruses. Results: 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 respiratory syncytial virus (RSV), human metapneumovirus (hMPV), and influenza virus (IV) were not identified in children. Attendance to kindergarten before the lockdown (aOR: 2.65; IQR: 1.57–4.47; p<0.001) and household crowding (aOR: 1.85; IQR: 1.09–3.15; p = 0.02) were independent risk factors for children’s pneumococcal carriage. Conclusions: 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.