Streptococcus pneumoniae Serotype Distribution Among Adults Admitted with Community-Acquired Pneumonia Across South Africa in the COVID-19 Era

Abstract

Introduction Recommendations for pneumococcal vaccination require periodic updating considering the ever- changing pneumococcal epidemiology and licensure of new vaccines. Pneumococcal epidemiology especially oronasopharyngeal (ONP) carriage in the coronavirus disease 2019 (COVID-19) era remains unclear in South Africa (SA). This study investigated pneumococcal serotype distribution among adults hospitalized with Community Acquired Pneumonia (CAP) in the COVID-19 era in SA. Methods Secondary analysis of ONP and blood serotypes from autolysin gene polymerase chain reaction (lytA PCR) positive samples of 317 adults admitted between March 2020 and October 2021 and followed up for two years. Prevalence and incidence rates (IR) of pneumococcal serotypes were calculated, and incidence drivers were explored by Poisson regression. Serotype-associated mortality rates were calculated and mortality predictors were assessed using logistic regression, Kaplan Meier survival analysis, and Cox regression. Results Of the 317 participants enrolled in this study, 171 (54%) were males, 299 (94%) were blacks, 126 (40%) were aged 35-49 years, 143 (45%) had no source of income, 125 (39%) were alcohol users, 99 (31%) were current smokers and 203 (64%) were people living with HIV (PLWH) of which 122 (60%) were on antiretroviral therapy (ART). Pneumococcal CAP prevalence was 22,638 cases per 100,000 persons (95% CI: 20,098 -25,338). Serotypes 1, 3, 4, 5, 8, 9A/V, 12A/B/F/44/46, 19F, 22A/F, 33A/F/37 had leading prevalence and IR in the oronasopharynx while serotypes 1, 3, 4, 8, 6A/B, 11A/D, 19A had leading prevalence in blood. The oronasopharyngeal prevalence for all serotypes was 20,888 serotypes per 100,000 persons (95% CI: 18,919-22,964) and that of the 13-valent pneumococcal conjugate vaccine (PCV13) serotypes alone was 13,571 serotypes per 100,000 persons (95% CI: 11,929 - 15,348). The ONP carriage prevalence for all serotypes was significantly higher in males (70%), participants aged 35-49 years (75%), current smokers (73%) and alcohol users (72%) while prevalence for the 23- valent pneumococcal polysaccharide vaccine (PPSV23) serotypes was significantly higher in PLWH on ART (66%). IR varied with the period of testing with the lowest all-serotype IR in March 2020-October 2020 when compared to March 2021-June 2021 (IRR= 0.30, 95% CI: 0.07- v 1.20). ONP serotypes 1, 3, 4, 5, 15A/F, 18A/B/C/F, 23A, 33A/F/37 were associated with leading mortality. Mortality was significantly higher in participants with CURB-65 score 1 (adjusted OR= 3.30, 95% CI:1.38-7.90, p=0.007) and in underweight participants (adjusted OR=4.82, 95% CI: 1.76-13.15, p=0.002). There was increased mortality risk among participants carrying ONP serotype 1 (adjusted HR=2.56, 95% CI=1.24- 5.30, p= 0.011) and those who required oxygen supplementation (adjusted HR= 1.98, 95% CI=1.11-3.54, p= 0.021). Conclusion S. pneumoniae remains important in CAP epidemiology in SA although there was a big decline in incidence in 2020 following the COVID-19 outbreak. Most of the serotypes circulating among adults in the COVID-19 era are included in PCV20, which is not used in SA.