Scabies in residential care homes: Modelling, inference and interventions for well-connected population sub-units

• Published in: PLoS computational biology 2018-03, Vol.14 (3), p.e1006046-e1006046
• Main Authors: Kinyanjui, Timothy, Middleton, Jo, Güttel, Stefan, Cassell, Jackie, Ross, Joshua, House, Thomas
• Format: Article
• Language: English
• Subjects: Approximation; Bayes Theorem; Bayesian analysis; Biology and Life Sciences; Calibration; Communicable Disease Control - methods; Communicable Disease Control - statistics & numerical data; Communicable Diseases - transmission; Computational mathematics; Computer simulation; Councils; Cross infection; Differential equations; Disease; Goodness of fit; Health aspects; Households; Houses; Humans; Infectious diseases; Inference; Ivermectin; Ivermectin - therapeutic use; Markov analysis; Markov Chains; Mathematical models; Medicine and Health Sciences; Methods; Monte Carlo Method; Monte Carlo simulation; Numerical analysis; Numerical methods; Nursing homes; Parameter uncertainty; Physical Sciences; Population; Population (statistical); Primary care; Public health; Research and Analysis Methods; Residential Facilities; Risk factors; Scabies; Scabies - epidemiology; Scabies - parasitology; Scabies - prevention & control; Social Sciences; Software; Statistical analysis; Stochastic models; Supervision
• ISSN: 1553-7358; 1553-734X; 1553-7358
• DOI: 10.1371/journal.pcbi.1006046

In the context of an ageing population, understanding the transmission of infectious diseases such as scabies through well-connected sub-units of the population, such as residential care homes, is particularly important for the design of efficient interventions to mitigate against the effects of those diseases. Here, we present a modelling methodology based on the efficient solution of a large-scale system of linear differential equations that allows statistical calibration of individual-based random models to real data on scabies in residential care homes. In particular, we review and benchmark different numerical methods for the integration of the differential equation system, and then select the most appropriate of these methods to perform inference using Markov chain Monte Carlo. We test the goodness-of-fit of this model using posterior predictive intervals and propagate forward the resulting parameter uncertainty in a Bayesian framework to consider the economic cost of delayed interventions against scabies, quantifying the benefits of prompt action in the event of detection. We also revisit the previous methodology used to assess the safety of treatments in small population sub-units-in this context ivermectin-and demonstrate that even a very slight relaxation of the implicit assumption of homogeneous death rates significantly increases the plausibility of the hypothesis that ivermectin does not cause excess mortality based upon the data of Barkwell and Shields.