Temporal Changes in Nasopharyngeal Pneumococcal Colonization Density Associated With Respiratory Syncytial Virus and Influenza in a South African Household Cohort Study, 2016-2018.

Background: Respiratory syncytial virus (RSV) and influenza infections are associated with increased pneumococcal colonization and disease risk. We assessed the impact of RSV and influenza on pneumococcal colonization density and factors influencing density changes during viral infection.

Methods: Over 3 years, 1658 individuals from 325 households were enrolled, with nasopharyngeal swabs collected twice weekly for pneumococcus, RSV, and influenza A/B detection by real-time polymerase chain reaction. We analyzed samples from 2 weeks before, during, and 2 and 8 weeks after infection. Pneumococcal density was compared across infection periods by t tests, and multivariable regression identified factors influencing density changes.

Results: Pneumococcal density increased during RSV infection (log mean before vs during infection, 9.3 vs 10.2 genomic copies/mL; P < .01) but showed no significant overall increase with influenza (log mean before vs during infection, 9.6 vs 9.9 genomic copies/mL; P = .2). However, the following were correlated with increased pneumococcal density: higher influenza viral loads (cycle threshold [Ct] value <25: coefficient, 2.8; 95% CI 1.4-4.2) and RSV viral loads (viral Ct value <25: coefficient, 2.5 [95% CI, 1.1-3.9; P < .01]; viral Ct value of 25-29: coefficient, 1.1 [95% CI, .1-2.2; P = .04]; vs viral Ct value of 30-34). Participants who were underweight had lower pneumococcal density differences (coefficient, -1.8; 95% CI, -3.5 to -.1; P = .04) than those with a normal body mass index.

Conclusions: RSV infection, especially with higher viral loads, increases pneumococcal colonization, while individuals who are underweight exhibit lower density changes.