Study design and participants
The present work is a prospective, exploratory substudy of the ongoing LYMPHONIE trial (ClinicalTrials.gov NCT03505281), initiated in November 2018 at the University Hospital of Dijon-Bourgogne (France). Patients were eligible if they had severe community-acquired pneumonia (CAP): 1) pneumonia (≥ 2 acute signs including cough, purulent sputum, dyspnea, chest pain, temperature < 35 °C or ≥ 38.5 °C, and new radiological pulmonary infiltrate); 2) at least two criteria of the quick-Sequential Organ Failure Assessment (SOFA) score (systolic blood pressure ≤ 100 mm Hg, respiratory rate ≥ 22, Glasgow score < 15) and/or the need for mechanical ventilation (MV) and/or vasopressors; and 3) diagnosed within 48 h following admission. Non-inclusion criteria were: < 18 years, pregnant women, persons under legal protection, decision to limit care, known immune deficiency, chronic disorder known to cause deep lymphopenia (i.e. cirrhosis, lympho- or myeloproliferative syndrome, solid cancer or active systemic lupus), hospitalization for sepsis within the previous 3 months. Non-COVID-19 CAP patients were included until February 20, 2020. COVID-19 patients were eligible if they were tested positive for SARS-CoV-2 by reverse transcriptase-polymerase chain reaction (RT-PCR) on one respiratory sample. Oral consent was obtained from the patient or their legal representative. Approval was obtained from the ethics committee (Comité de Protection des Personnes SUD MEDITERRANEE V; 2017-A03404-49).
Variables of interest, clinical outcomes, and data collection
Clinical and biological parameters, severity scores (SOFA , Simplified Acute Physiology Score (SAPS II)  and Pneumonia Severity Index (PSI) ) were calculated at the time of inclusion. ARDS was defined according to the Berlin definition , and septic shock was defined as persistent hypotension requiring vasopressors and a serum lactate level > 2 mmol/L despite adequate volume resuscitation. Clinical outcomes were recorded up to 30 days after admission, namely: 30-day mortality, hospital- and ICU- length of stay, duration of MV and the occurrence of ventilator-acquired pneumonia (VAP). Dedicated clinical research assistants collected all data using a standardized electronic case report form. Automatic checks were generated for missing or incoherent data.
Ethylenediamine tetraacetic acid blood (plasma biomarker) and heparin anticoagulated blood (cell stimulation) were obtained after inclusion of the patient (within 48 h of hospital admission, with a diagnosis of severe community acquired pneumonia and according to the inclusion and non-inclusion criteria). Within 4 h following sampling, plasma was collected after centrifugation at 2000 x g for 10 min at 4 °C and stored at −80 °C until use, without freeze–thaw cycle. All samples were collected and stored in the biological resource center of Dijon University Hospital (CRB Ferdinand Cabanne; http://www.crbferdinandcabanne.fr/; NF S96-900 certification).
Absolute counts for CD3 + , CD3 + CD4 + ,CD3 + CD8 + , CD3-CD19 + , CD3-CD56 + and/or CD16 + lymphocyte subsets were performed using an AQUIOS CL flow cytometer (Beckman Coulter, Hialeah, FL). The AQUIOS CL is a single platform, fully automated volumetric flow cytometry technology and uses a 488 nm solid state diode laser to measure light diffraction, fluorescence and electronic volume which estimates the relative size of the cells. Whole blood was incubated with the monoclonal antibody reagent followed by no-wash erythrocyte lysis. A ready-to-use mix of antibodies was used. AQUIOS Tetra-1 Panel CD45-FITC/CD4-RD1/CD8-ECD/CD3-PC5 reagent provides identification and enumeration of CD45 + , CD45 + Low SS, and CD3 +/CD4 + , CD3 +/CD8 + , and CD3 + lymphocyte percentages and absolute counts in peripheral whole blood. AQUIOS Tetra-2 + Panel CD45-FITC/(CD56 + CD16)-RD1/CD19-ECD/CD3-PC5 provides identification and enumeration of CD45 + , CD45 + Low SS, and CD3 + , CD3-/CD19 + and CD3-/CD56 + CD16 + lymphocyte percentages and absolute counts in peripheral whole blood. Additionally, both panels provide for CD45 + absolute count and CD45 + Low SS absolute count and percentage. The AQUIOS System Software includes the algorithms and test definitions that provide automated analysis and results for AQUIOS reagents. Normal range (5%–95% reference ranges) values of absolute counts for immune cells and lymphocyte subsets are indicated as Ref. [22, 23].
Measurement of cytokines
Thirty analytes were quantified in plasma using the Human XL Cytokine Magnetic Luminex® assay (R&D Systems, USA) according to the manufacturer’s instructions: C–C motif chemokine ligand (CCL)2, CCL3, CCL4, CCL5, CCL11, CCL19, CCL20, soluble CD40 ligand, fractalkine, CXCL1, CXCL2, CXCL10, FMS-like tyrosine kinase 3 ligand (FLT3L), granulocyte colony-stimulating factor (G-CSF), granulocyte–macrophage colony-stimulating factor (GM-CSF), granzyme B, interferon (IFN)-α, IL-1α, IL-1β, IL-1RA, IL-2, IL-6, IL-7, IL-8, IL-10, IL-15, IL-33, programmed death-ligand 1 (PDL1), transforming growth factor (TGF)-α, TNF-α, and TNF-related apoptosis inducing ligand (TRAIL). All samples were measured in the same experiment. Briefly, on the day of the assay, plasma was centrifuged again at 16,000xg for 4 min immediately prior to use. A twofold dilution with calibrator was used for all samples. The acquisition was performed using Bio-Plex 200 system and analyzed using Bio-Plex ManagerTM software (Bio-rad, Hercules, CA). Cytokine concentrations were automatically determined from standard curves and expressed as pg/ml. Samples with values above the ranges were tested again with a 40-fold dilution. All raw data were collected by a data-manager for further analyses in the SAS Software.
Whole blood leukocyte ex vivo stimulation (WBS)
The standardized functional immunoassay QuantiFERON Monitor® (QFM, Qiagen) was used according to the manufacturer’s instructions. Within 3 h after blood sampling, one milliliter of whole blood was incubated at 37 °C for 20 ± 1 h with a QFM LyoSphere containing anti-CD3 T-cell receptor ligand and R848 (TLR7/8 ligand), or without LyoSphere (non-stimulated blood). Plasma was harvested after centrifugation at 4000 rpm for 10 min and stored at −80 °C until use. Whole blood leukocyte production of IFN-γ (IU/ml) upon stimulation was measured using ELISA (Qiagen), and fifteen other analytes using the Human Th9/Th17/Th22 Discovery Luminex® assay (R&D Systems, USA): CD40 ligand, GM-CSF, IL-1β, IL-2, IL-4, IL-5, IL-6, IL-10, IL-12, IL-13, IL-15, IL-17A, IL-33, TNF-α, CCL20. All samples were measured the same day by the same person and using the same kit. Samples with values above the ranges were tested again with further dilution. The cytokine production after stimulation was expressed as the difference of concentrations between plasma from stimulated blood and those from non-stimulated blood.
As a reference, we used samples from 7 control patients included in the Pneumochondrie study (ClinicalTrials.gov NCT03955887) and who underwent QuantiFERON Monitor® assay in the same conditions. The control population consisted of outpatients without fever during the previous 15 days and who underwent bronchoalveolar lavage for a non-infectious condition . Samples were conditioned and measured in the same way as for the LYMPHONIE study.
Data were described according to COVID-19 status (i.e. non-COVID-19 vs COVID-19). Continuous variables were expressed as mean ± standard deviation (SD) or median and inter-quartile range (IQR), according to their distribution, and categorical variables as frequencies and percentage. Univariate comparisons were performed using Student’s test for means, Wilcoxon Mann–Whitney test for medians and IQRs and Chi square test (or Fisher’s exact test when appropriate) for percentages. Cytokines with p < 0.05 were presented by boxplots to visualize potential associations with COVID-19 status.
Principal component analysis (PCA) was used to identify potentially significant patterns of 64 variables: clinical characteristics and outcomes (n = 6), biological findings (n = 13), plasma cytokines (n = 30), cytokine production upon ex vivo stimulation (n = 15). PCA identifies factors, called principal components, that induce the most variation in the overall data . These factors can be expressed as a linear combination of the correlated original variables (OVs). By inversing these formulas, we can express each OV as a linear combination of the factors and coefficients defining these linear combinations are interpreted as correlation coefficients. Moreover, each factor describes a percent of variation in the OVs. The number of factor to retain was determined using the scree plot  and the clinical interpretability of factors . Finally, patients OVs data can be projected on the plans defined by the retained factors, which allows observing patient’s patterns in a two-dimensional plot.
Spearman correlations were computed between cytokines and the most pertinent clinical outcomes associated with Covid-19 status in univariate analyses and PCA patterns. To account for potential confounders, we constructed multivariable linear regressions, with the MV duration as an outcome, for each selected cytokine. adjusted for age, COVID-19 status and either SOFA score (model 1) or PaO2:FiO2 (model 2). The interaction between COVID-19 status and cytokines was systematically tested. Absence of serial correlation and heteroscedasticity were assessed using the DW statistic  and the White test  respectively. The proportion of variance explained by the models was quantified using the R2 coefficient. Measures of association are expressed as mean differences ± standard error (SE). A p-value < 0.05 was considered statistically significant. Analyses were performed using SAS version 9.4 (SAS Institute Inc., Cary, NC, USA).