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
| 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 |
aOne patient was SARS-CoV-2 RNA PCR-negative but had clinical diagnosis of COVID-19
bOne patient in the metagenomics group and 48 patients from the non-metagenomics group had no respiratory specimens collected whilst on ICU during the study period