Table 3.
Results of infectious disease testing among 316 patients presenting with acute respiratory illness and tested for COVID-19.
| COVID-19 positive (n = 33) | COVID-19 negative (n = 283) | P value | |
|---|---|---|---|
| Other viral testing performed | 82% (27/33) | 69% (194/283) | 0.116 |
| Influenza/Respiratory syncytial virus PCR | 27% (9/33) | 32% (90/283) | 0.596 |
| 12-target respiratory virus PCR panel | 55% (18/33) | 54% (153/283) | 0.958 |
| Metagenomic next generation sequencing | 42% (14/33) | 29% (83/283) | 0.123 |
| Positive identification of virus other than SARS-CoV-2* | 0% (0/27) | 16% (31/194) | 0.025 |
| I nfluenza A† | 0/27 | 5/194 | |
| Influenza B† | 0/27 | 2/194 | |
| Respiratory syncytial virus† | 0/27 | 3/194 | |
| Rhinovirus‡ | 0/26 | 9/188 | |
| Metapneumovirus‡ | 0/26 | 8/188 | |
| Parainfluenza‡ | 0/26 | 1/188 | |
| Coronavirus-229E§ | 0/14 | 2/83 | |
| Coronavirus-NL63§ | 0/14 | 1/83 | |
| Bocavirus§ | 0/14 | 1/83 | |
| Blood culture ordered | 19/33 (58%) | 139/283 (49%) | 0.358 |
| Blood culture positive | 1/19 (5%) | 10/139 (7%) | 1.000 |
| Enterococcus faecalis | 0/19 | 1/139 | |
| Enterococcus faecium | 1/19 | 1/139 | |
| E. coli | 0/19 | 1/139 | |
| Group A Streptococcus | 0/19 | 2/139 | |
| Group C Streptococcus | 0/19 | 1/139 | |
| Group G Streptococcus | 0/19 | 1/139 | |
| Klebsiella pneumoniae | 0/19 | 1/139 | |
| Staphylococcus aureus | 0/19 | 1/139 | |
| Candida glabrata | 0/19 | 1/139 | |
| Sputum or lower respiratory culture ordered | 9/33 (27%) | 33/283 (12%) | 0.012 |
| Sputum or lower respiratory culture positive| | 1/9 (11%) | 6/33 (18%) | 1.000 |
| Enterobacter cloacae complex | 0/9 | 1/33 | |
| H. parainfluenzae | 0/9 | 3/33 | |
| Staphylococcus aureus | 0/9 | 1/33 | |
| Pseudomonas aeruginosa | 0/9 | 2/33 | |
| Stenotrophomonas maltophilia | 1/9 | 0/33 |
Legend: COVID-19 - Coronavirus Disease 2019; PCR - polymerase chain reaction.
One case of viral co-infection identified (i.e., 32 pathogenic viruses in 31 patients).
ascertained by Influenza/RSV PCR or 12-target respiratory viral PCR panel or metagenomic next generation sequencing; 194 patients without COVID-19 and 27 with COVID-19 had any additional viral testing done.
ascertained by 12-target respiratory viral PCR panel or metagenomic next generation sequencing; 188 patients without COVID-19 and 26 with COVID-19 had either test performed.
ascertained by mNGS only; 83 patients without COVID-19 and 14 with COVID-19 had mNGS testing performed.
One case of multiple bacterial pathogens identified by sputum culture (i.e., 7 pathogenic bacteria in 6 patients).