Molecular detection of respiratory pathogens
The ePlex results demonstrated that 30.1% (241/799) of patients tested positive for any respiratory pathogen, with 2% of the total specimens having co-infections (16/799) (Fig 1A). The composition of different pathogens detected is summarized in Figure 1B. RhV/EV was the most common pathogen detected (32.7% of the total detections: mono- or co-infections), followed by IAV (26.1%), CoV and hMPV (both 10.9%), and RSV (9.3%). Overall, 28.4% (69/241) of positives were infected with influenza (IAV or IBV). Less common pathogens were AdV (3.5%), PIV (3.1%), IBV (2.3%), and M. pneumo (1.2%).
Sixteen patients had co-infections (32 detections total), the composition of which is shown in Fig 1B and C. IAV (7/16, 43.8%), RhV/EV (7/16, 43.8%), and AdV (6/16, 37.5%) were the most frequently detected pathogens in individuals with co-infections. For individuals infected with AdV, co-infections (N=6, 66.6%) were more common than mono-infections (N=3, 33.3%), ratio of 2.0 (Fig 1B).
Geographical analysis
The prevalence of pathogens at the four sites were compared (Figure 2). The lowest rate of any pathogen detection was seen at JHH; 22.9% (60/262) of specimens positive (Fig 2A). This was significantly different than those seen at MMC, 39.3% (59/150, p = 0.007, Fig 2B), TMC 31.5% (53/168, p = 0.003, Fig 2C), and OVM 31.5% (69/219, p = 0.04, Fig 2D). Co-infections were most commonly found at MMC: 5.3% of specimens compared to approximately 1% at other sites.
All respiratory pathogens detected were observed at each site, with the exception of M. pneumoniae (N=2), which was only detected at MMC (Fig 2G). While not statistically significant, other differences were observed in the composition of pathogens between sites (Fig 2E-H). MMC had the greatest number of unique pathogens detected. RSV was the greatest at TMC (14.9%). hMPV was identified in greater numbers and proportion at the Western EDs (14.9% at MMC and 12.7% at OVM) compared to the Eastern ED (6.3% at JHH).