An automated Dashboard to improve laboratory COVID-19 diagnostics management

Abstract

Background: In response to the CoVID-19 pandemic, our microbial diagnostic laboratory located in a university hospital has implemented several distinct SARS-CoV-2 RT-PCR systems in a very short time. Thanks to our automated molecular diagnostic platform, more than 140 000 SARS-CoV-2 RT-PCR tests were achieved over 12 months, with peaks higher than 1 500 daily tests. A dashboard was developed to give access to Key Performance Indicators (KPIs) to improve laboratory operational management. Methods: RT-PCR data extraction of four respiratory viruses - SARS-CoV-2, influenza A and B and RSV - from our laboratory information system (LIS), was automated. Important KPIs were identified and the visualization was achieved using an in-house dashboard based on the open-source language R (Shiny). Information is updated every 4 hours. Results: The dashboard is organized into three main parts. The Filter page presents all the KPIs, divided into five sections: i) general and gender-related indicators, ii) number of tests and positivity rate, iii) cycle threshold and viral load, iv) test durations, and v) not valid results. Filtering allows to select a given period, a dedicated instrument, a given specimen, or a requester for instance. The Comparison page allows a custom charting of all the available variables, which represents more than 182 combinations. The Data page gives the user access to the raw data in table format, with the possibility of filtering, allowing for a deeper analysis and data download in Excel format. Conclusions: The dashboard, that gives a rapid access to a huge number of up-to-date information, represents a reliable and user-friendly tool improving the decision-making process, resource planning and quality management. The dashboard represent an added value for diagnosric laboratories during a pandemic, where rapid and efficient adaptation is mandatory.

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An iteratively optimised process for improving the efficiency and effectiveness of an industrial SARS-CoV-2 diagnostic facility

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