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Table 2 Univariate analysis of day 90 mortality*

From: Oropharyngeal and intestinal concentrations of opportunistic pathogens are independently associated with death of SARS-CoV-2 critically ill adults

 

HR

95% CI

p

Oropharynx (time-dependent variables)

 Enterococcus spp.

1.268

1.172

1.371

 < 0.0001

 Enterobacterales

0.964

0.862

1.078

0.5231

 Pseudomonas aeruginosa

0.950

0.774

1.165

0.6202

 ESBL-producing Enterobacterales

0.992

0.790

1.246

0.9439

 Candida spp.

1.170

1.065

1.285

0.0010

 S. aureus

1.211

1.081

1.358

0.0010

Rectal (time-dependent variables)

 Enterococcus spp.

1.198

1.095

1.310

 < 0.0001

 Enterobacterales

0.942

0.870

1.020

0.1416

 Pseudomonas aeruginosa

0.980

0.867

1.108

0.7448

 ESBL-producing Enterobacterales

0.914

0.791

1.057

0.2263

 Candida spp.

1.198

1.077

1.332

0.0009

 S. aureus

1.309

1.088

1.573

0.0042

16S/rectal (time-dependent variables)

 Richness

1.000

1.000

1.000

0.1407

 Shannon index

1.006

0.733

1.380

0.9696

 Bacteroides***

2.501

0.530

11.801

0.2467

 Enterococcus***

5.300

2.034

13.814

0.0006

 Finegoldia***

0.013

0.001

0.286

0.0058

 Enterobacterales***

1.224

0.145

10.333

0.8524

 Firmicutes/Bacteroidetes ratio

0.998

0.994

1.001

0.1835

Antimicrobial therapy (time-dependent variables)

 Antifungal treatment active against Candida#

4.298

2.662

6.940

 < 0.0001

 Antibiotic treatment active against Enterococcus spp.#

5.998

3.742

9.614

 < 0.0001

 Fluoroquinolones

0.947

0.339

2.645

0.9168

 Daptomycin/Glycopeptides/Linezolid

7.300

4.564

11.677

 < 0.0001

 Antibiotic treatment active against anaerobic bacteria#

5.895

3.811

9.118

 < 0.0001

General characteristics and treatment during the 1st 48 h of ICU admission

 Age

1.033

1.006

1.061

0.0172

 Female

1.184

0.566

2.477

0.6529

 Obesity

0.658

0.345

1.255

0.2040

 Diabetes

1.666

0.876

3.169

0.1199

 Chronic diseases

1.776

0.958

3.291

0.0681

 SAPS 2*

1.012

1.000

1.025

0.0476

 SOFA score*

1.192

1.087

1.306

0.0002

 C-reactive protein*

1.002

1.000

1.005

0.0884

 Steroids*

1.387

0.709

2.712

0.3389

 Renal replacement therapy**

1.674

0.800

3.502

0.1710

 Vasopressors**

1.591

0.868

2.917

0.1328

 Ventilation status**

 Mechanical ventilation with PEEP > 10 cmH2O

1.992

1.035

3.834

0.0391

 ECMO

1.897

0.757

4.755

0.1719

 Antibiotics**

2.225

0.687

7.207

0.1821

  1. SAPS 2, Simplified Acute Physiology Score; SOFA score, Sequential Organ Failure Assessment score; OUT, Operational Taxonomic Unit; B/F ratio, Bacteroidetes/Firmicutes ratio; ECMO, Extracorporeal Membrane Oxygenation; HR, Hazard ratio on the final model; 95% CI, 95% confidence interval of the adjusted HR
  2. *At admission; **During the first 48 h in ICU; ***Abundance
  3. #Antifungal treatment active against Candida includes intravenous (IV) polyenes, azoles and IV candins. Antibiotic treatment active against Enterococcus/MRSA includes vancomycin, daptomycin and oxazolidinones. Antibiotic treatment active against anaerobic bacteria includes nitro-imidazoles, imipenem, meropenem, clindamycin, piperacillin/tazobactam and amoxicillin/clavulanate
  4. NB: only one patient was colonized with carbapenemase-producing Enterobacterales. The variable was not tested statistically