Transmission Estimator

This shiny app is designed to identify transmission clusters among neonatal sepsis bacterial isolates using genomic (genetic distance) and epidemiological (spatiotemporal) data.

Usage instructions

Running locally

Follow these steps to clone the repository, set up the required environment, and run the Shiny app.

1. Clone the Repository

• Install and open RStudio on your machine
• Go to File > New Project > Version Control > Git
• Paste the repository URL (https://github.com/klebgenomics/transmission_estimator.git)
• Choose a location to save the project, and click Create Project

2. Install Required Packages Using renv

This project uses the renv package to manage package dependenciesand ensure that correct versions of packages are installed.

To install renv if it's not already installed, run:

install.packages("renv")

Then, use renv to install the packages specified in the renv.lock file:

renv::restore()

3. Run the Shiny App

Once the dependencies are installed, you can run the app using the following command in the RStudio console:

shiny::runApp()

Alternatively, you can open the app.R file in the root of the repository, and simply click Run App at the top right of the script window.

Note: Adjust the view to fit your screen by pressing Cmd + -/+ on Mac or Ctrl + -/+ on Windows.

Web app

Transmission Estimator is also available as a web app at klebsiella.shinyapps.io/transmission_estimator

Input data

Two input files in TSV or CSV format are required.

• Metadata file
  Metadata file containing epidemiological and other information on the isolates. Required columns include: id, Year, Month, Day, Country, Site, and ST

• Distance matrix file
  Pairwise genetic distance matrix. This can be generated using Pathogenwatch.
  This file must be in square matrix format with the first column labelled 'Name'.

Clustering options

Clusters are identified based on the clustering options / thresholds specified in the Clusters tab.

Clusters comprise isolates with sufficient genetic similarity (as specified with the genetic distance threshold) that were isolated within a given time frame (as specified with the temporal distance threshold) and in the same location (as specified with the spatial clustering variable).

The proportion of cases attributable to transmission is calculated by excluding a hypothetical index case per cluster.

Use the Sensitivity tab to explore the sensitivity of the transmission estimates to the choice of temporal and genetic distance thresholds.

Citation

This tool is still under development. If you use this tool, please cite this repository using this DOI: