Table 2 Onset, source, and non-SARS-CoV-2 pathogensa by SARS-CoV-2 and testing status
Specimen onset, source, and pathogens n (% positive specimens) | Untested for SARS-CoV-2 | Tested for SARS-CoV-2 | P value | |
|---|---|---|---|---|
SARS-CoV-2 negative | SARS-CoV-2 positive | |||
Any positive non-SARS-CoV-2 specimenb | 73,315 (100%) | 38,753 (100%) | 5012 (100%) | Â |
Timing of non-SARS-CoV-2 pathogen detection |  |  |  | < 0.05 |
 Admission period | 59,016 (80.5%) | 30,141 (77.8%) | 2889 (57.6%) |  |
 Hospital-onset period (> 3 days) | 14,299 (19.5%) | 8612 (22.2%) | 2123 (42.4%) |  |
Non-SARS-CoV-2 specimen source |  |  |  | < 0.05 |
 Urine | 20,807 (28.4%) | 10,077 (26.0%) | 1697 (33.9%) |  |
 Respiratory | 9626 (13.1%) | 5435 (14.0%) | 1228 (24.5%) |  |
 Blood | 11,185 (15.3%) | 9530 (24.6%) | 1020 (20.4%) |  |
 Other | 16,393 (22.4%) | 7474 (19.3%) | 776 (15.5%) |  |
 Skin/Wound | 14,033 (19.1%) | 5698 (14.7%) | 271 (5.3%) |  |
 Intra-abdominal | 1271 (1.7%) | 539 (1.4%) | 20 (0.4%) |  |
Non-SARS-CoV-2 pathogensa | ||||
 Any bacteria | 56,215 (76.7%) | 30,952 (79.9%) | 3972 (79.2%) |  |
  Gram-negative | 31, 887 (43.5%) | 17,087 (44.1%) | 2280 (45.5%) | < 0.05 |
   Enterobacterales | 22,289 (30.4%) | 11,939 (30.8%) | 1594 (31.8%) | 0.06 |
   Pseudomonas aeruginosa | 2729 (3.8%) | 1837 (4.7%) | 324 (6.5%) | < 0.05 |
   Stenotrophomonas maltophilia | 302 (0.4%) | 238 (0.6%) | 39 (0.8%) | < 0.05 |
   Acinetobacter baumannii | 145 (0.2%) | 84 (0.2%) | 13 (0.3%) | 0.56 |
  Gram-positive | 24,035 (32.8%) | 13,532 (34.9%) | 1670 (33.3%) | <  0.05 |
   Staphylococcus aureus | 10,147 (13.8%) | 6120 (15.8%) | 689 (13.7%) | < 0.05 |
   Enterococcus spp. | 4124 (5.6%) | 2357 (6.1%) | 357 (7.1%) | < 0.05 |
   Streptococcus pneumoniae | 682 (0.9%) | 513 (1.3%) | 94 (1.9%) | < 0.05 |
 Non-SARS-CoV-2 virus | 13,150 (17.9) | 5403 (13.9%) | 543 (10.8%) | < 0.05 |
  Respiratory viruses | 4398 (6.0%) | 1170 (3.0%) | 111 (2.2%) | < 0.05 |
 Fungi | 2124 (2.9%) | 1328 (3.4%) | 280 (5.6%) | < 0.05 |
  Candida spp. | 2990 (4.1%) | 1764 (4.6%) | 410 (8.2%) | < 0.05 |
  Aspergillus spp. | 104 (0.1%) | 108 (0.3%) | 6 (0.1%) | < 0.05 |