Bayesian inference for multi-strain epidemics with application to Escherichia coli O157: H7 in feedlot cattle

Research output: Contribution to journalArticlepeer-review


External organisations

  • University of Warwick
  • Washington State University
  • Massey University


For most pathogens testing procedures can be used to distinguish between different strains with which individuals are infected. Due to the growing availability of such data, multi-strain models have increased in popularity over the past few years. Quantifying the interactions between different strains of a pathogen is crucial in order to obtain a more complete understanding of the transmission process, but statistical methods for this type of problem are still in the early stages of development. Motivated by this demand, we construct a stochastic epidemic model, that incorporates additional strain information, and propose a statistical algorithm for efficient inference. The model improves upon existing methods in the sense that it allows for both imperfect diagnostic test sensitivities and strain misclassification. Extensive simulation studies were conducted in order to assess the performance of our method, while the utility of the developed methodology is demonstrated on data obtained from a longitudinal study of Escherichia coli O157:H7 strains in feedlot cattle.


Original languageEnglish
Pages (from-to)1925-1944
JournalAnnals of Applied Statistics
Issue number4
Publication statusPublished - 19 Dec 2020
Externally publishedYes


  • multistate Markov model, misclassification, epidemiology, Markov chain Monte Carlo, genotypes