Finding evidence for local transmission of contagious disease in molecular epidemiological datasets

Surveillance systems of contagious diseases record information on cases to monitor incidence of disease and to evaluate effectiveness of interventions. These systems focus on a well-defined population; a key question is whether observed cases are infected through local transmission within the population or whether cases are the result of importation of infection into the population. Local spread of infection calls for different intervention measures than importation of infection. Besides standardized information on time of symptom onset and location of cases, pathogen genotyping or sequencing offers essential information to address this question. Here we introduce a method that takes full advantage of both the genetic and epidemiological data to distinguish local transmission from importation of infection, by comparing inter-case distances in temporal, spatial and genetic data. Cases that are part of a local transmission chain will have shorter distances between their geographical locations, shorter durations between their times of symptom onset and shorter genetic distances between their pathogen sequences as compared to cases that are due to importation. In contrast to generic clustering algorithms, the proposed method explicitly accounts for the fact that during local transmission of a contagious disease the cases are caused by other cases. No pathogen-specific assumptions are needed due to the use of ordinal distances, which allow for direct comparison between the disparate data types. Using simulations, we test the performance of the method in identifying local transmission of disease in large datasets, and assess how sensitivity and specificity change with varying size of local transmission chains and varying overall disease incidence.