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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

From: Evaluating the potential for respiratory metagenomics to improve treatment of secondary infection and detection of nosocomial transmission on expanded COVID-19 intensive care units

  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
  1. aOne patient was SARS-CoV-2 RNA PCR-negative but had clinical diagnosis of COVID-19
  2. 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