# sourceR: Classification and Source Attribution of Infectious Agents among Heterogeneous Populations

## TL;DR

sourceR is an R package that uses Bayesian modeling and strain typing data to attribute human zoonotic infections to sources, aiding food safety interventions and understanding pathogen behavior.

## Contribution

It introduces a novel Bayesian framework with non-parametric clustering for strain types, improving source attribution accuracy in zoonotic disease studies.

## Key findings

- Successfully applied to Campylobacter jejuni data from New Zealand
- Enables straightforward attribution of human cases to sources
- Detects high-virulence strain types through clustering

## Abstract

Zoonotic diseases are a major cause of morbidity, and productivity losses in both humans and animal populations. Identifying the source of food-borne zoonoses (e.g. an animal reservoir or food product) is crucial for the identification and prioritisation of food safety interventions. For many zoonotic diseases it is difficult to attribute human cases to sources of infection because there is little epidemiological information on the cases. However, microbial strain typing allows zoonotic pathogens to be categorised, and the relative frequencies of the strain types among the sources and in human cases allows inference on the likely source of each infection. We introduce sourceR, an R package for quantitative source attribution, aimed at food-borne diseases. It implements a fully joint Bayesian model using strain-typed surveillance data from both human cases and source samples, capable of identifying important sources of infection. The model measures the force of infection from each source, allowing for varying survivability, pathogenicity and virulence of pathogen strains, and varying abilities of the sources to act as vehicles of infection. A Bayesian non-parametric (Dirichlet process) approach is used to cluster pathogen strain types by epidemiological behaviour, avoiding model overfitting and allowing detection of strain types associated with potentially high 'virulence'. sourceR is demonstrated using Campylobacter jejuni isolate data collected in New Zealand between 2005 and 2008. It enables straightforward attribution of cases of zoonotic infection to putative sources of infection by epidemiologists and public health decision makers. As sourceR develops, we intend it to become an important and flexible resource for food-borne disease attribution studies.