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

PLoS One. 2024 Dec 5;19(12):e0315081. doi: 10.1371/journal.pone.0315081. eCollection 2024.

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.

MeSH terms

  • Adult
  • COVID-19* / epidemiology
  • COVID-19* / microbiology
  • Carrier State* / epidemiology
  • Carrier State* / microbiology
  • Child
  • Child, Preschool
  • Female
  • Humans
  • Infant
  • Male
  • Nasopharynx* / microbiology
  • Nasopharynx* / virology
  • Pneumococcal Infections* / epidemiology
  • Pneumococcal Infections* / microbiology
  • SARS-CoV-2 / isolation & purification
  • Spain / epidemiology
  • Streptococcus pneumoniae* / genetics
  • Streptococcus pneumoniae* / isolation & purification

Grants and funding

This study has been funded by the Kids Corona Project, Hospital Sant Joan de Déu, Barcelona, and by the Pla strategic de recerca I innovació en salut - PERIS, Health Department, Generalitat of Catalonia. ISGlobal acknowledges support from the grant CEX2018-000806-S funded by MCIN/AEI/ 10.13039/501100011033, and support from the Generalitat de Catalunya through the CERCA Program. CISM is supported by the Government of Mozambique and the Spanish Agency for International Development (AECID). The funding sources had not role in the writing up of the manuscript and in the decision to submit for publication.