Diagnostic System for Monitoring Patients on Ventilators for Secondary Infection

Project Goal: Create an interface for doctors to view and analyze metagenomic next-generation sequencing, or mNGS, data, allowing for rapid diagnosis and treatment of secondary infections for patients on ventilators.

During the COVID-19 pandemic, many patients are being hospitalized and intubated. Intubation increases the risk of developing secondary infections, which can be fatal in patients who are already very ill. Currently, it takes several days to diagnose secondary infections in intubated patients.

Metagenomic next-generation sequencing, or mNGS, can identify infections more quickly than current methods. However, it is not widely used in clinical settings, largely because clinicians are not yet comfortable with the technology. This project strives to push mNGS technology from "bench to bedside" by making the technology accessible and convenient within current infrastructure.

To make mNGS more accessible, the team created an interface for doctors to view and evaluate data. Lab personnel can upload data to the RShiny-based web interface, and doctors can choose how they’d like to view the data from among several formats. One option is to view the data in a format similar to existing reports, which the doctors are already familiar with. In addition, the app contains several unique analytical tools, including some to monitor the relative size of multiple infections over time, which is not currently possible.