Analysis of longitudinal bacterial carriage studies accounting for sensitivity of swabbing: an application to Neisseria meningitidis

Longitudinal carriage studies of colonizing bacteria such as Neisseria meningitidis can provide important insights into the transmission dynamics of these organisms. Carriage is detected by culturing from a nasopharyngeal swab, but the sensitivity of this technique is low and varies between studies. This paper applies a statistical method for estimating the sensitivity of swabbing, infection rate, recovery rate and initial prevalence of carriage to three longitudinal carriage studies of N. meningitidis. These parameters and 95% confidence intervals were estimated using maximum likelihood techniques. The sensitivity of swabbing was estimated to be 60-83% and this should be taken into account when interpreting carriage studies. The estimates of force of infection and recovery rates seem to be consistent with estimates from more traditional methods. Differences in the parameter estimates between datasets may be due to differences in study design. This method could be used to assist in the design of future carriage studies.