Skip to main content

Table 2 Onset, source, and non-SARS-CoV-2 pathogensa by SARS-CoV-2 and testing status

From: A multicenter analysis of the clinical microbiology and antimicrobial usage in hospitalized patients in the US with or without COVID-19

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%)  
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
  1. aAny bacteria, fungus, or virus other than SARS-CoV-2
  2. bPatients could have more than one positive specimen and pathogen