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

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.

Strain-Level Resolution and Pneumococcal Carriage Dynamics by Single Molecule Real Time (SMRT) Sequencing of The Plyncr Marker: A Longitudinal Study In Swiss Infants.

“…Based on our ndings, the median age to rst acquisition (147 days) was much higher in our study compared to reports from higher carriage countries such as, South Africa, Malawi, Indonesia and the Gambia [24,26,32,33]. Given higher rates of PCV uptake in Switzerland [34], the longer time to acquisition in our birth cohort may therefore re ect reduced chances for pneumococcal transmission.…”

Geographic migration and vaccine-induced fitness changes ofStreptococcus pneumoniae

“…To understand whether human mobility can explain the slow spread of the pneumococcus, we built a mechanistic model of geographic spread, fit to the observed province in which our genome sequences were isolated. We used the generation time distribution, time from one person being infected to infecting the next person (estimated mean of 35 days, standard deviation of 35 days [gamma distribution]) to translate branch lengths to the number of generations between pairs of sequences (Figure S6)( 20, 21 ). Each transmission generation is a possible transmission event and an opportunity for pneumococcal mobility.…”

Changes in serotype prevalence of Streptococcus pneumoniae in Southampton, UK between 2006 and 2018

“…Community-level serotype prevalence from a proxy-population will naturally be a poorer substitute for national surveillance and will be hampered by potential geographic and demographic biases. In addition, the analysis of only one isolate from each culture positive individual ignores the impact of colonisation density and multi-serotype carriage as shown elsewhere 38 , 39 . Clearly, there are further data such as immunisation dates, co-carriage of other pathobionts and/or viruses that could be collected.…”