Juliana M. Ruzante, Katherine Olin, Breda Munoz, Jeff Nawrocki, Rangaraj Selvarangan, Lindsay Meyers
Abstract
Acute gastrointestinal infection (AGI) represents a significant public health concern. To control and treat AGI, it is critical to quickly and accurately identify its causes. The use of novel multiplex molecular assays for pathogen detection and identification provides a unique opportunity to improve pathogen detection, and better understand risk factors and burden associated with AGI in the community. In this study, de-identified results from BioFire® FilmArray® Gastrointestinal (GI) Panel were obtained from January 01, 2016 to October 31, 2018 through BioFire® Syndromic Trends (Trend), a cloud database. Data was analyzed to describe the occurrence of pathogens causing AGI across United States sites and the relative rankings of pathogens monitored by FoodNet, a CDC surveillance system were compared
Introduction
Every year around the world, 1.5 to 2.5 million children under the age of five die from diarrhea, one of the main symptoms of acute gastrointestinal infections (AGI) [1]. In the United States, AGI accounts for 178.8 million cases a year [2], representing a significant burden to public health. AGI can be caused by a wide range of noninfectious and infectious agents. To effectively control and reduce the disease burden associated with AGI, it is critical to understand which agent is causing the disease, how frequently and when infection occurs in the population, and the potential sources of exposure. Surveillance systems often rely on cases that are reported to public health authorities to compile and analyze this information and monitor the occurrence of illnesses in a population.
Among the critical events that must occur for a disease to be reported to authorities is the identification of the AGI agent(s) by clinical laboratories [3]. The quick and accurate identification of the cause of illness is also essential for the effective treatment of AGI patients, which can result in shorter hospital stays, appropriate use of antimicrobials, avoidance of unnecessary isolation of patients, and cost savings [4, 5]..
Materials and methods
BioFire Trend GI data was extracted in July 2019 for the period of January 01, 2016 to October 31, 2018 (34 months). The dataset contained de-identified clinical test variables, anonymized at the participating site level, and included: laboratory location, organism(s) detected, approximate date of the test (obfuscated for privacy) for all participating BioFire Trend sites using the BioFire GI Panel. The test time obfuscation process imports tests from each site in sets of three tests, leading to an average of hours to a couple days between actual time and time recorded in BioFire Trend. To ensure the panel was being routinely used for patient testing and not for test validation, only sites utilizing an average of 10 or more GI tests per month with a median monthly test count within 20% of the mean were included in this study.
Discussion
This is the first study to summarize and evaluate a large dataset of test results for 22 GI pathogens obtained from 29 clinical laboratories across the United States that use a multiplex real-time PCR assay, the BioFire GI Panel. The results were obtained from BioFire’s cloud database, BioFire Trend, Syndromic Trends (Trend), which collects, aggregates, and displays calculated de-identified test results in near real-time for participating sites. BioFire Trend data represents patients who seek medical care in institutions that not only used the BioFire GI Panel, but also participated in BioFire Trend.
For those reasons, results are not representative of the United States. Nevertheless, the overall percentage of positives, negatives, co-detection rate, as well as the most frequently detected pathogens (i.e.: C. difficile, EPEC, norovirus, EAEC, and Campylobacter) reported in this study were similar to what has been reported in previous studies that used the BioFire GI Panel in clinical settings [12, 17–21].
Citation: Ruzante JM, Olin K, Munoz B, Nawrocki J, Selvarangan R, Meyers L (2021) Real-time gastrointestinal infection surveillance through a cloud-based network of clinical laboratories. PLoS ONE 16(4): e0250767. https://doi.org/10.1371/journal.pone.0250767.
Editor: Baochuan Lin, Defense Threat Reduction Agency, UNITED STATES
Received: July 21, 2020; Accepted: April 14, 2021; Published: April 30, 2021.
Copyright: © 2021 Ruzante et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Data Availability: There are both legal and ethical restrictions on sharing the data publicly. The data obtained by BioFire is subject to the terms and conditions of a Data Use Agreement (DUA) by and between BioFire and each facility participating in the Trend program. Primarily, the DUA is intended to protect the patient’s privacy and comply with applicable privacy laws and regulations. If a data set is requested, BioFire will review such request internally to ensure that any disclosure does not conflict with BioFire’s obligations and restrictions set forth in the DUA. For more information, contact Joel Hartsell (joel.hartsell@biofiredx.com).
Funding: This study was funded by BioFire Diagnostics. BioFire Diagnostics funded the study at RTI International and provided support in the form of salaries for the following authors: KO, JN, and LM (LM is no longer an employee of BioFire). The specific roles of these authors are articulated in the ‘author contributions’ section. The funders had no additional role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: The authors have read the journal’s policy, and the authors of the manuscript have the following competing interests to declare: At the time that the study was conducted, KO, JN, and LM were all paid employees of BioFire. KO, JN, and LM hold stocks and shares of BioMérieux (owner of BioFire). RS is also on BioFire’s Scientific Advisory Board, and has received funding for research, unrelated to the present study, from: BioFire Diagnostics; Cepheid; Abbott; Becton and Dickinson; Hologic; Diasorin; Luminex; Merck; and Bacterioscan. This does not alter our adherence to PLOS ONE policies on sharing data and materials. There are no patents, products in development or marketed products associated with this research to declare.
