Carriage Dynamics of Pneumococcal Serotypes in Naturally Colonized Infants in a Rural African Setting During the First Year of Life.

Chrispin Chaguza,Chinelo Ebruke,Stephen D Bentley,Ebrima Bojang,Archibald Worwui,Robert F Breiman,Richard A Adegbola,Catherine Okoi,Michael R Barer,Rebecca A Gladstone,Lesley Mcgee,Peggy-Estelle Tientcheu,Fatima Ceesay,Ebenezer Foster-Nyarko,Keith P Klugman,Madikay Senghore,Martín Antonio ,Rowan E Bancroft ,Stephanie Lo ,Brenda Kwambana-Adams

doi:10.3389/fped.2020.587730

Abstract

Streptococcus pneumoniae (the pneumococcus) carriage precedes invasive disease and influences population-wide strain dynamics, but limited data exist on temporal carriage patterns of serotypes due to the prohibitive costs of longitudinal studies. Here, we report carriage prevalence, clearance and acquisition rates of pneumococcal serotypes sampled from newborn infants bi-weekly from weeks 1 to 27, and then bi-monthly from weeks 35 to 52 in the Gambia. We used sweep latex agglutination and whole genome sequencing to serotype the isolates. We show rapid pneumococcal acquisition with nearly 31% of the infants colonized by the end of first week after birth and quickly exceeding 95% after 2 months. Co-colonization with multiple serotypes was consistently observed in over 40% of the infants at each sampling point during the first year of life. Overall, the mean acquisition time and carriage duration regardless of serotype was 38 and 24 days, respectively, but varied considerably between serotypes comparable to observations from other regions. Our data will inform disease prevention and control measures including providing baseline data for parameterising infectious disease mathematical models including those assessing the impact of clinical interventions such as pneumococcal conjugate vaccines.

Highlights

The pneumococcus continues to kill >320,000 children under 5 years old every year globally despite the use of highly effective serotype-specific pneumococcal conjugate vaccines (PCV) [1]
We have described the carriage duration and acquisition patterns of pneumococcal serotypes during the first year of life in the Gambia
We found that time from birth to first acquisition and to first reacquisition from birth were similar, which suggests continuous exposure leading to reacquisition of serotypes, possibly among household contacts

Summary

Introduction

The pneumococcus continues to kill >320,000 children under 5 years old every year globally despite the use of highly effective serotype-specific pneumococcal conjugate vaccines (PCV) [1]. Mathematical models are increasingly becoming useful for investigating disease dynamics This includes understanding transmission patterns [7], antibiotic resistance [5, 8], and impact of infant vaccination programs [9]. The accuracy of these models depends on the availability of reliable data to initialize the parameters; it is crucial to conduct studies to generate such required information. Such data include carriage dynamics time to and rates of acquisition/reacquisition, and carriage duration and clearance rates of different strains. Studies to describe carriage dynamics should be conducted in different countries to account for the geographical heterogeneity, which may result in accurate inferences from the models

Methods

Results

Conclusion