Automated collection of pathogen-specific diagnostic data for real-time syndromic epidemiological studies

Lindsay Meyers; Christine C. Ginocchio; Aimie N. Faucett; Frederick S. Nolte; Per H. Gesteland; Amy Leber; Diane Janowiak; Virginia Donovan; Jennifer Dien Bard; Silvia Spitzer; Kathleen A. Stellrecht; Hossein Salimnia; Rangaraj Selvarangan; Stefan Juretschko; Judy A. Daly; Jeremy C. Wallentine; Kristy Lindsey; Franklin Moore; Sharon L. Reed; Maria Aguero-Rosenfeld; Paul D. Fey; Gregory A. Storch; Steve J. Melnick; Christine C. Robinson; Jennifer F. Meredith; Camille V. Cook; Robert K. Nelson; Jay D. Jones; Samuel V. Scarpino; Benjamin M. Althouse; Kirk M. Ririe; Bradley A. Malin; Mark A. Poritz

The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. . https://doi.org/10.1101/157156 doi: bioRxiv preprint The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. . https://doi.org/10.1101/157156 doi: bioRxiv preprint Trend data have high temporal, spatial, and organism-specific resolution. These three properties allow for a novel evaluation of co-detections. The observed rates of co-detections should be influenced by the number of circulating pathogens detected by the FilmArray RP test at a particular site. Figure 5A shows the average number of unique organisms detected at each site in a given week (see Methods: Calculation of co-detection rates). This number fluctuates from a 295 summer low of four to a winter high of 11 pathogens. Figure 5B (grey bars) shows that the total rate of organism co-detections in the Trend dataset fluctuates annually with peak rates occurring in the winter months. The average rates have been as high as 12% in the winter of 2016 and as low as 2% in the summer of 2014. 300 From the Trend data, a Measure of Interspecific Encounter (MIE) can be calculated as the probability of a co-detection, weighted by the prevalence of each circulating pathogen at a site.