Characterization of Fungal Infections in COVID-19 Infected and Mechanically Ventilated Patients in ICU

Currently, ICU patients with ARDS, whatever the etiology, are not systematically screened for the detection of respiratory fungal infections.

Here, the protocol will be in two steps:

First step

COVID-19 patients hospitalized in ICU for ARDS will benefit for a systematic screening with a fungal respiratory syndromic panel once or twice a week from entry to discharge from ICU, with minimum 3 samples when discharge occurs after 15 days::

• Sample: tracheal aspiration, bronchial aspiration, BAL
• Fungal respiratory panel: samples will be processed in each lab for culture without direct examination nor stained smears, and real-time PCR will be performed for Aspergillus, Pneumocystis jirovecii and mucormycetes
• Results will be given to ICU in order to optimize the management of the patient Second step

Complementary analysis will be performed in order to finalize the diagnostic and to differentiate between colonization and infection, with:

• Serum detection of galactomannan and serum Aspergillus PCR in case of positive respiratory sample for Aspergillus
• Serum/plasma beta-D-glucan detection in case of positive respiratory sample for Pneumocystis jirovecii
• Serum mucorales PCR in case of positive respiratory sample for mucorales This second step is possible in most of the labs, but when necessary a confirmation test can be externalized. A process of DNA transmission to a reference lab within each region will be implemented.

This second step will allow to classify infections as probable or proven according to international recommendations.

Case report form (CRF) A short but standardized CRF will be proposed to all centers in order to collect demographic data and the essential clinical and laboratory data during the survey.

Inclusion criteria

• ICU patients COVID-19 diagnosed by RT-PCR
• Intubated and mechanically ventilated patients
• Adult patients
• Patients (or legal representative) informed on the research without opposition

Non-inclusion criteria :

• Patients <18 years old
• People of full age who are the subject of a judicial safeguard,

Exclusion criteria

• Patient, or legal representative opposing the pursuit of the research
• Patients under judicial protection will be excluded as soon as the investigator becomes aware of their status.