title: Rates of acquisition and clearance of pneumococcal serotypes in the nasopharynges of children in Kilifi District, Kenya.
abstract: BACKGROUND
  To understand and model the impact of pneumococcal conjugate vaccines at the population level, we need to know the transmission dynamics of individual pneumococcal serotypes. We estimated serotype-specific clearance and acquisition rates of nasopharyngeal colonization among Kenyan children.
  
  
  METHODS
  Children aged 3-59 months who were identified as carriers in a cross-sectional survey were followed-up approximately 1, 2, 4, 8, 16, and 32 days later and monthly thereafter until culture of 2 consecutive swabs yielded an alternative serotype or no pneumococcus. Serotype-specific clearance rates were estimated by exponential regression of interval-censored carriage durations. Duration was estimated as the reciprocal of the clearance rate, and acquisition rates were estimated on the basis of prevalence and duration, assuming an equilibrium state.
  
  
  RESULTS
  Of 2840 children sampled between October 2006 and December 2008, 1868 were carriers. The clearance rate was 0.032 episodes/day (95% confidence interval [CI], .030-.034), for a carriage duration of 31.3 days, and the rate varied by serotype (P< .0005). Carriage durations for the 28 serotypes with ≥ 10 carriers ranged from 6.7 to 50 days. Clearance rates increased with year of age, adjusted for serotype (hazard ratio, 1.21; 95% CI, 1.15-1.27). The acquisition rate was 0.061 episodes/day (95% CI, .055-.067), which did not vary with age. Serotype-specific acquisition rates varied from 0.0002 to 0.0022 episodes/day. Serotype-specific acquisition rates correlated with prevalence (r=0.91; P< .00005) and with acquisition rates measured in a separate study involving 1404 newborns in Kilifi (r=0.87; P< .00005).
  
  
  CONCLUSIONS
  The large sample size and short swabbing intervals provide a precise description of the prevalence, duration, and acquisition of carriage of 28 pneumococcal serotypes. In Kilifi, young children experience approximately 8 episodes of carriage per year. The declining prevalence with age is attributable to increasing clearance rates.
authors: Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya. oabdulla@hsph.harvard.edu
authors: Osman
authors: O
authors: Abdullahi
authors: Angela
authors: A
authors: Karani
authors: Caroline C
authors: CC
authors: Tigoi
authors: Daisy
authors: D
authors: Mugo
authors: Stella
authors: S
authors: Kungu
authors: Eva
authors: E
authors: Wanjiru
authors: Jane
authors: J
authors: Jomo
authors: Robert
authors: R
authors: Musyimi
authors: Marc
authors: M
authors: Lipsitch
authors: J Anthony G
authors: JA
authors: Scott
mesh_terms: D002353:Carrier State / Q000453:epidemiology* / Q000382:microbiology; D002675:Child, Preschool; D006801:Humans; D015994:Incidence; D007223:Infant; D007630:Kenya / Q000453:epidemiology; D008137:Longitudinal Studies; D009302:Nasopharyngeal Diseases / Q000453:epidemiology* / Q000382:microbiology; D011008:Pneumococcal Infections / Q000453:epidemiology* / Q000382:microbiology; D015995:Prevalence; D013296:Streptococcus pneumoniae