Table 1 Clinical characteristics and results of routine microbiological tests performed on intubated COVID-19 patients during the CMg study across 7 linked dedicated COVID-19 intensive care units on Guy’s and St Thomas’ Hospital sites
| Â | Non-metagenomics group (n = 141) | Metagenomics groupa (n = 34) |
|---|---|---|
Median age (IQR) | 56 (46–61) | 52 (41–58) |
Sex–male | 101 (72%) | 23 (70%) |
Ethnicity | ||
  White | 49 (35%) | 16 (47%) |
  Black and minority ethnicities | 74 (52%) | 15 (44%) |
  Not known | 19 (13%) | 3 (9%) |
Mortality | 34 (25%) | 8 (24%) |
Length of stay (IQR) | 25 days (15–45) | 32 days (24–47) |
Respiratory cultures in ICUb | ||
Median samples per patient (IQR) | 2 (1–3) | 4 (4–6) |
Total number of samples/patients tested | 372/117 | 180/34 |
Organisms from respiratory culture whilst in ICU (number of individuals who ever had the following organisms in any sample) | ||
Klebsiella spp. | 48 (34%) | 18 (53%) |
Staphylococcus aureus | 14 (10%) | 3 (9%) |
Citrobacter spp. | 14 (10%) | 5 (15%) |
Escherichia coli | 7 (5%) | 3 (9%) |
Pseudomonas spp. | 10 (7%) | 1 (3%) |
Corynebacterium striatum | 8 (6%) | 8 (24%) |
Enterococcus spp. | 12 (9%) | 4 (12%) |
Serratia spp. | 9 (6%) | 2 (6%) |
Enterobacter spp. | 6 (4%) | 1 (3%) |
Haemophilus spp. | 2 (1%) | 0 (0%) |
Stenotrophomonas maltophilia | 4 (3%) | 1 (3%) |
Proteus spp. | 0 (0%) | 4 (12%) |
Morganella spp. | 0 (0%) | 1 (3%) |
Acinetobacter spp. | 0 (0%) | 1 (3%) |
Streptococcus pyogenes | 3 (2%) | 0 (0%) |
Candida albicans | 40 (28%) | 13 (38%) |
Candida spp. (non-albicans) | 10 (7%) | 5 (15%) |
Aspergillus spp. | 1 (1%) | 3 (9%) |
 No organisms isolated | 40 (30%) | 2 (6%) |
Galactomannans (GMs) | ||
Bronchoalveolar lavage (BAL) GMs | ||
Number of tests/patients tested | 38/28 | 25/16 |
 Positive tests/patients positive | 0/0 | 6/5 |
Serum GMs | ||
Number of tests/patients tested | 74/50 | 34/22 |
 Positive tests/patients positive | 4/4 | 3/3 |