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Modelling, Bayesian inference, and model assessment for nosocomial pathogens using whole-genome-sequence data.

ABSTRACT: Whole-genome sequencing of pathogens in outbreaks of infectious disease provides the potential to reconstruct transmission pathways and enhance the information contained in conventional epidemiological data. In recent years, there have been numerous new methods and models developed to exploit such high-resolution genetic data. However, corresponding methods for model assessment have been largely overlooked. In this article, we develop both new modelling methods and new model assessment methods, specifically by building on the work of Worby et al. Although the methods are generic in nature, we focus specifically on nosocomial pathogens and analyze a dataset collected during an outbreak of MRSA in a hospital setting.

SUBMITTER: Cassidy R

PROVIDER: S-EPMC7217057 | biostudies-literature | 2020 May

REPOSITORIES: biostudies-literature

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Modelling, Bayesian inference, and model assessment for nosocomial pathogens using whole-genome-sequence data.

Cassidy Rosanna R Kypraios Theodore T O'Neill Philip D PD

Statistics in medicine 20200306 12

Whole-genome sequencing of pathogens in outbreaks of infectious disease provides the potential to reconstruct transmission pathways and enhance the information contained in conventional epidemiological data. In recent years, there have been numerous new methods and models developed to exploit such high-resolution genetic data. However, corresponding methods for model assessment have been largely overlooked. In this article, we develop both new modelling methods and new model assessment methods, ...[more]

PMID: 32142587

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Project description:[This corrects the article DOI: 10.1371/journal.pgen.1008698.].

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