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. 2021 Jan 8:8:587730.
doi: 10.3389/fped.2020.587730. eCollection 2020.

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

Chrispin Chaguza  1   2 , Madikay Senghore  3 , Ebrima Bojang  3 , Stephanie W Lo  1 , Chinelo Ebruke  3 , Rebecca A Gladstone  1 , Peggy-Estelle Tientcheu  3 , Rowan E Bancroft  3 , Archibald Worwui  3 , Ebenezer Foster-Nyarko  3 , Fatima Ceesay  3 , Catherine Okoi  3 , Lesley McGee  4 , Keith P Klugman  5 , Robert F Breiman  6 , Michael R Barer  7 , Richard A Adegbola  3   8 , Martin Antonio  3   9 , Stephen D Bentley  1   10 , Brenda A Kwambana-Adams  3   11
Affiliations

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

Chrispin Chaguza et al. Front Pediatr. .

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.

Keywords: Africa; acquisition; carriage duration; infants; pneumococcus; serotype.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Flow diagram showing the number of infants and pneumococcal samples included in the analysis. The infants in community 1 were from PCV-unexposed (unvaccinated) villages and received PCV7 after 6 months (control group). The infants in community 2 were also from PCV-unexposed (unvaccinated) and they received PCV7 at 2, 3, and 4 months (direct impact of vaccination). The infants from community 3 came from PCV-exposed (vaccinated) villages and they received PCV7 at 2, 3, and 4 months (direct impact of vaccination and herd immunity).
Figure 2
Figure 2
Temporal prevalence of pneumococcal serotypes during the first year of life. (A) Proportion of infants colonized with any serotype at each sampling point. (B) Proportion of infants co-colonized with multiple serotypes at each sampling point. (C) Proportion of infants colonized by a different number of serotypes at each sampling point. The estimates are shown at bi-weekly sampling points from weeks 1 to 27, and then bi-monthly sampling intervals from weeks 35 to 52.
Figure 3
Figure 3
Network graph showing co-colonization of pneumococcal strains among Gambian infants. The width of the edges connecting a pair of nodes (or serotypes) in the network is proportional to the number of co-occurrences of the pair of serotypes at the same sampling point in the same infant. The shades of color from light green to indigo for each connecting line in the network correspond to the number of detected serotype co-occurrences ranging from 0 to 20.
Figure 4
Figure 4
The Kaplan-Meier survival curves and exponential fit to the longitudinal pneumococcal carriage data. The plots show (A) duration from acquisition to clearance of all serotypes, (B) time until first acquisition of any serotype and (C) time until second acquisition or reacquisition of any serotype. The black curve represents the Kaplan-Meier estimates while the yellow line is the fitted survival curve. The rate parameter in the exponential model is shown at the top of the plots (A–C) represents the mean clearance, acquisition and reacquisition rate, respectively. The inverse of the rate in plots A, B and C equates to mean the carriage duration, time until first acquisition and reacquisition of any serotype, respectively.
Figure 5
Figure 5
Carriage dynamics of pneumococcal serotypes in Gambian infants. Graph showing (A) carriage duration, (B) time to first acquisition, (C) time to acquisition from birth for the first and second colonization episode with the serotype, (D) carriage duration for the first and second colonization episode with the serotype.
Figure 6
Figure 6
Relationship of carriage estimates of pneumococcal serotypes in Gambian infants. (A) Scatter plot showing carriage duration and time to first acquisition. (B) Scatter plot showing carriage duration, second acquisition (reacquisition). (C) Scatter plot showing carriage duration and frequency of serotype/episode, (D) time to first acquisition and frequency of serotypes. (E) Scatter plot showing carriage duration of serotypes in the Gambia and Kenya. (F) Scatter plot showing time to acquisition of serotypes in the Gambia and South Africa.
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