Longitudinal characterization of nasopharyngeal colonization with Streptococcus pneumoniae in a South African birth cohort post 13-valent pneumococcal conjugate vaccine implementation

Abstract

Monitoring changes in pneumococcal carriage is key to understanding vaccination-induced shifts in the ecology of carriage and impact on health. We longitudinally investigated pneumococcal carriage dynamics in infants. Pneumococcal isolates were obtained from nasopharyngeal (NP) swabs collected 2-weekly from 137 infants enrolled from birth through their first year of life. Pneumococci were serotyped by sequetyping, confirmed by Quellung. Pneumococci were isolated from 54% (1809/3331) of infants. Median time to first acquisition was 63 days. Serotype-specific acquisition rates ranged from 0.01 to 0.88 events/child-year and did not differ between PCV13 and non-PCV13 serotypes (0.11 events/child-year [95% CI 0.07–0.18] vs. 0.11 events/child-year [95% CI 0.06–0.18]). There was no difference in carriage duration between individual PCV13 and non-PCV13 serotypes (40.6 days [95% CI 31.9–49.4] vs. 38.6 days [95% CI 35.1–42.1]), however cumulatively the duration of carriage of non-PCV13 serotypes was greater than PCV13 serotypes (141.2 days (95% CI 126.6–155.8) vs. 30.7 days (95% CI 22.3–39.0). Frequently carried PCV13 serotypes included 19F, 9V, 19A and 6A, while non-PCV13 serotypes included 15B/15C, 21, 10A, 16F, 35B, 9N and 15A. Despite high immunization coverage in our setting, PCV13 serotypes remain in circulation in this cohort, comprising 22% of isolates. Individual PCV13 serotypes were acquired, on average, at equivalent rate to non-PCV13 serotypes, and carried for a similar duration, although the most common non-PCV13 serotypes were more frequently acquired than PCV13 serotypes.

Carriage of penicillin-non-susceptible pneumococci among children in northern Tanzania in the 13-valent pneumococcal vaccine era

“…In this study, the pneumococcal carriage detected by culture was 31%, which is in accordance with the results of a previous study performed in Dar es Salaam, Tanzania, which showed a 35% pre-vaccination pneumococcal carriage rate (Moyo et al, 2012), and a study performed in Ghana, where the pneumococcal carriage rate among children was 34% (Dayie et al, 2013). However, similar studies in other regions of Africa have reported higher pneumococcal carriage both pre-and post-vaccination (Hammitt et al, 2014;Kobayashi et al, 2017;Mills et al, 2015;Dube et al, 2018;Adetifa et al, 2012). This variation can be attributed to differences in the study populations and consequently more or less exposure to risk factors, as well variances in the detection methods used (Bogaert et al, 2004;Satzke et al, 2013).…”

“…In this study, serotypes/groups 6, 19F, 23F, and 14 were the most prevalent serotypes/serogroups of those included in PCV13. These serotypes are considered colonizers and tend to be carried within the nasopharynx for prolonged periods of time compared with more invasive and immunogenic serotypes such as serotypes 1 and 3 (Dube et al, 2018;Sleeman et al, 2006). Among the non-PCV13 serotypes/groups, 15B/C, 19B, and 10A were the most prevalent.…”

“…Serotype/group 15B/C has been reported as one of the predominant serotypes/groups recovered after PCV13 introduction in both low-and high-income countries (Devine et al, 2017;Ho et al, 2015;Dube et al, 2018). Other studies in Africa have reported a high prevalence of serotypes/groups 15B/C, 10A, 11, and 19A (Birindwa et al, 2018;Kwambana-Adams et al, 2017;Dube et al, 2018). However, the relatively high prevalence of serotype 19B in this study was unexpected and appears not to have been reported in other recently published African studies.…”

Pneumococcal lineages associated with serotype replacement and antibiotic resistance in childhood invasive pneumococcal disease in the post-PCV13 era: an international whole-genome sequencing study

“…Furthermore, given that nasopharyngeal carriage of pneumococcus could be a risk for proceeding into invasive disease, frequent colonisers, such as serotypes 15B/C and 35B, might be sufficiently prevalent in carriage for expansion to result in significant disease replacement. 51,52 Despite the overall reductions in prevalence of antibiotic resistance in pneumococci after the use of PCVs, signi ficant increases in penicillin and erythromycin resistance among non-vaccine-type isolates were observed in the PCV13 period. Penicillin is the first-line antibiotic in the treatment of pneumococcal disease.…”

Pneumococcal carriage, density, and co-colonization dynamics: A longitudinal study in Indonesian infants

“…Definitions of pneumococcal carriage episodes were based on the identification of an individual serotype, and estimates of dates of acquisition (midpoint between last negative swab and first positive swab) and clearance (midpoint between last positive swab and subsequent negative swab) were consistent with published longitudinal carriage studies (Turner et al, 2012;Heinsbroek et al, 2016;Dube et al, 2018;Tigoi et al, 2012). For infants carrying pneumococci at enrolment, the date of acquisition was estimated as the midpoint between birth and visit 1.…”