Major alteration of Lung Microbiome and the Host Reaction in critically ill COVID-19 Patients with high viral load (preprint)

Background Patients with COVID-19 under invasive mechanical ventilation are at higher risk of developing ventilator-associated pneumonia (VAP), associated with increased healthcare costs, and unfavorable prognosis. The underlying mechanisms of this phenomenon have not been thoroughly dissected. Therefore, this study attempted to bridge this gap by performing a lung microbiota analysis and evaluating the host immune responses that could drive the development of VAP.Materials and methods In this prospective cohort study, mechanically ventilated patients with confirmed SARS-CoV-2 infection were enrolled. Nasal swabs (NS), endotracheal aspirates (ETA), and blood samples were collected initially within 12 hours of intubation and again at 72 hours post-intubation. Plasma samples underwent cytokine and metabolomic analyses, while NS and ETA samples were sequenced for lung microbiome examination. The cohort was categorized based on the development of VAP. Data analysis was conducted using RStudio version 4.3.1.Results In a study of 36 COVID-19 patients on mechanical ventilation, significant differences were found in the nasal and pulmonary microbiome, notably in Staphylococcus and Enterobacteriaceae, linked to VAP. Patients with VAP showed a higher SARS-CoV-2 viral load, elevated neutralizing antibodies, and reduced inflammatory cytokines, including IFN-δ, IL-1β, IL-12p70, IL-18, IL-6, TNF-α, and CCL4. Metabolomic analysis revealed changes in 22 metabolites in non-VAP patients and 27 in VAP patients, highlighting D-Maltose-Lactose, Histidinyl-Glycine, and various phosphatidylcholines, indicating a metabolic predisposition to VAP.Conclusions This study reveals a critical link between respiratory microbiome alterations and ventilator-associated pneumonia in COVID-19 patients, with elevated SARS-CoV-2 levels and metabolic changes, providing novel insights into the underlying mechanisms of VAP with potential management and prevention implications.

Reliability and reproducibility of clinical phenotypes developed during the first wave of COVID-19: A validation study in critically ill patients from the second and third wave (preprint)

Background: During the first wave of the COVID-19 pandemic, different clinical phenotypes were published. However, none of them have been validated in subsequent waves, so their current validity is unknown. The aim of the study is to validate the unsupervised cluster model developed during the first pandemic wave in a cohort of critically ill patients from the second and third pandemic waves. Methods: Retrospective, multicentre, observational study of critically ill patients with confirmed COVID-19 disease and acute respiratory failure admitted from 74 Intensive Care Units (ICU) in Spain. To validate our original phenotypes model, we assigned a phenotype to each patient of the validation cohort using the same medoids, the same number of clusters (n= 3), the same number of variables (n= 25) and the same discretisation used in the development cohort. The performance of the classification was determined by Silhouette analysis and general linear modelling. The prognostic models were validated, and their performance was measured using accuracy test and area under curve (AUC)ROC. Results: The database included a total of 2,033 patients (mean age 63[53-92] years, 1643(70.5%) male, median APACHE II score (12[9-16]) and SOFA score (4[3-6]) points. The ICU mortality rate was 27.2%. Although the application of unsupervised cluster analysis classified patients in the validation population into 3 clinical phenotypes. Phenotype A (n=1,206 patients, 59.3%), phenotype B (n=618 patients, 30.4%) and phenotype C (n=506 patients, 24.3%), the characteristics of patients within each phenotype were significantly different from the original population. Furthermore, the silhouette coefficients were close to or below zero and the inclusion of phenotype classification in a regression model did not improve the model performance (accuracy =0.78, AUC=0.78) with respect to a standard model (accuracy = 0.79, AUC=0.79) or even worsened when the model was applied to patients within each phenotype (accuracy = 0.80, AUC 0.77 for Phenotype A, accuracy=0.73, AUC= 0.67 for phenotype B and accuracy= 0.66 , AUC= 0.76 for phenotype C ) Conclusion:  Models developed using machine learning techniques during the first pandemic wave cannot be applied with adequate performance to patients admitted in subsequent waves without prior validation. Trial Registration: The study was retrospectively registered (NCT 04948242) on June 30, 2021

Relationship between corticosteroid administration and incidence of ventilator-associated lower respiratory tract infections in COVID-19 patients: a retrospective multicenter study (preprint)

Background Ventilator-associated lower respiratory tract infections (VA-LRTI) are  common in patients with severe SARS-CoV-2 pneumonia. The aim of this ancillary analysis of the coVAPid multicenter observational retrospective study is to assess the relationship between corticosteroid adjuvant administration and the incidence of VA-LRTI. MethodsPlanned ancillary analysis of a multicenter retrospective European cohort in 36 ICUs. Adult patients receiving invasive mechanical ventilation for more than 48 hours for a SARS-CoV-2 pneumonia were consecutively included between February and May 2020. VA-LRTI diagnosis required strict definition with clinical, radiological and microbiological documentation. We assessed the association of VA-LRTI with corticosteroid administration using univariate and multivariate cause-specific Cox’s proportional hazard models with adjustment on prespecified confounders.Results 545 patients were included, of whom 191 (35%) received corticosteroids. The proportional hazard assumption for the effect of corticosteroids on the incidence of VA-LRTI was violated (p=0.018) indicating that this effect varied during the ICU stay. We found a lower risk of VA-LRTI for corticosteroid treated patients during the first days in the ICU and an increased risk for longer ICU stay. By modeling the effect of corticosteroids with time dependent coefficients, the association between corticosteroids and the incidence of VA-LRTI was not significant (overall effect p=0.068), with time-dependent hazard ratios (95% confidence interval) of 0.45 (0.18 to 1.10) at day 2, 0.89 (0.62 to 1.27) at day 7, 1.38 (0.99 to 1.92) at day 14 and 1.80 (1.08 to 2.98) at day 21.Conclusions No significant association was found between corticosteroid adjuvant therapy and the incidence of VA-LRTI, although a significant time-varying effect of corticosteroids was identified along the 28-day follow-up. 

Timing of Intubation and ICU Mortality in Covid-19 Patients: A Preplanned Retrospective Analysis of 4198 Critically Ill Patients (preprint)

BackgroundOptimal time to intubate patients with SARS-CoV-2 pneumonia is controversial. Whereas some authors recommend trying noninvasive respiratory support before intubate, others argue that delaying intubation can cause patient-self-induced lung injury and worsen the prognosis. We hypothesized that delayed intubation would increase the risk mortality in COVID-19 patients.MethodsThis preplanned retrospective observational study used prospectively collected data from adult patients with COVID-19 and respiratory failure admitted to 73 intensive care units between February 2020 and March 2021. Patients with limitations on life support and those with missing data were excluded.We collected demographic, laboratory, clinical variables and outcomes.Intubation was classified as 1) Very early: before or at ICU admission; 2) Early: < 24 hours after ICU admission; or 3) Late: ≥24 hours after ICU admission. We compared the early group versus those intubated late, using chi-square tests for categorical variables and the Mann-Whitney U for continuous variables. To assess the relationship between early versus late intubation and mortality, we used multivariable binary logistic regression. Statistical significance was set at p<0.05.Results We included 4198 patients [median age, 63 (54‒71) years; 70.8% male; median SOFA score, 4 (3‒7); median APACHE score, 13 (10‒18)], and median PaO2/FiO2, 131 (100‒190)]; intubation was very early in 2024 (48.2%) patients, early in 928 (22.1%), and late in 441 (10.5%). ICU mortality was 30.2% and median ICU stay was 14 (7‒28) days. Although patients in the late group were younger [62 vs. 64, respectively, p<0.05] and had less severe disease [APACHE II (13 vs. 14, respectively, p<0.05) and SOFA (3 vs. 4, respectively, p<0.05) scores], and higher PaO2/FiO2 at admission (116 vs. 100, respectively, p<0.05), mortality was higher in the late group than in the early group (36.9% vs. 31.6%, p<0.05). Late intubation was independently associated with mortality (OR1.83; 95%CI 1.35‒2.47).ConclusionsDelaying intubation beyond the first 24 hours of admission in patients with COVID-19 pneumonia increases the risk of mortality. Trial registration: The study was retrospectively registered at Clinical-Trials.gov (NCT 04948242) on the 30th June 2021.

ICU-Acquired Pneumonia is a Risk Factor of a Poor Health Post-Covid-19 Syndrome (preprint)

Background: . Some patients who had previously presented with COVID-19 have been reported to develop persistent COVID-19 symptoms. Whilst this information has been adequately recognised and extensively published with respect to non-critically ill patients, less is known about the prevalence and risk factors and characteristics of persistent COVID_19 . On other hand these patients have very often intensive care unit-acquired pneumonia (ICUAP). A second infectious hit after COVID increases the length of ICU stay and mechanical ventilation and could have an influence in the poor health post-Covid 19 syndrome in ICU discharged patients Methods: This prospective, multicentre and observational study was done across 40 selected ICUs in Spain. Consecutive patients with COVID-19 requiring ICU admission were recruited and evaluated three months after hospital discharge. Results: A total of 1,255 ICU patients were scheduled to be followed up at 3 months; however, the final cohort comprised 991 (78.9%) patients. A total of 315 patients developed ICUAP (97% of them had ventilated ICUAP) Patients requiring invasive mechanical ventilation had persistent, post-COVID-19 symptoms than those who did not require mechanical ventilation. Female sex, duration of ICU stay, and development of ICUAP were independent risk factors for persistent poor health post-COVID-19. Conclusions: : Persistent, post-COVID-19 symptoms occurred in more than two-thirds of patients. Female sex, duration of ICU stay and the onset of ICUAP comprised all independent risk factors for persistent poor health post-COVID-19. Prevention of ICUAP could have beneficial effects in poor health post-Covid 19

Severe COVID-19 is characterised by inflammation and immature myeloid cells early in disease progression (preprint)

SARS-CoV-2 infection causes a wide spectrum of disease severity. Immune changes associated with severe disease include pro-inflammatory cytokine production and expansion of immature myeloid populations. The relative importance of the immunological changes in driving progression to severe disease remain poorly understood. We aimed to identify and rank clinical and immunological features associated with progression to severe COVID-19. We sought to use tests available in an on-site diagnostic hospital laboratory to identify an immunological signature for severe disease development which could be detected prior to peak severity thereby allowing initiation of therapeutic interventions. We used univariate and multivariate analysis, including unbiased machine learning, to investigate the relationships between clinical and demographic characteristics, inflammatory markers, and leukocyte immunophenotypes with progression to severe disease in 108 patients and to rank these in importance. A combination of four features (elevated levels of interleukin-6 and C-reactive protein, coupled with reduced monocyte HLA-DR expression and reduced neutrophil CD10 expression), were strongly predictive of severe disease with an average prediction score of 0.925. HighlightsO_LISevere COVID-19 can be predicted by a combination of emergency myelopoiesis (CD10-neutrophils and HLA DR-monocytes) and inflammation (raised IL-6 and CRP) C_LIO_LIThese changes can be identified from tests carried out prior to peak illness severity in a diagnostic laboratory C_LIO_LIThis predictive model was derived from a cohort of patients with a wide range of ages, frailty and COVID-19 severity C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=191 HEIGHT=200 SRC="FIGDIR/small/21262953v1_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@16c6947org.highwire.dtl.DTLVardef@73ba2corg.highwire.dtl.DTLVardef@1c3dd82org.highwire.dtl.DTLVardef@3a48f_HPS_FORMAT_FIGEXP M_FIG C_FIG

A Differential Therapeutic Consideration for use of Corticosteroids According to Established COVID-19 Clinical Phenotypes in Critically Ill Patients (preprint)

Background: The steroids are currently used as standard treatment for severe COVID-19. However, the evidence is weak. Our aim is to determine if the use of corticosteroids was associated with Intensive Care Unit (ICU) mortality among whole population and pre-specified clinical phenotypes.Methods: A secondary analysis derived from multicenter, observational study of adult critically ill patients with confirmed COVID-19 disease admitted to 63 ICUs in Spain. Three phenotypes were derived by non-supervised clustering analysis from whole population and classified as (A: severe, B: critical and C: life-threatening). The primary outcome was ICU mortality. We performed a Multivariate analysis after propensity score full matching (PS), Cox proportional hazards (CPH), Cox covariate time interaction (TIR), Weighted Cox Regression (WCR) and Fine-Gray analysis(sHR) to assess the impact of corticosteroids on ICU mortality according to the whole population and distinctive patient clinical phenotypes. Results:  A total of 2,017 patients were analyzed, 1171(58%) with corticosteroids. After PS, corticosteroids were shown not to be associated with ICU mortality (OR:1.0,95%CI:0.98-1.15). Corticosteroids were administered in 298/537(55.5%) patients of “A” phenotype and their use was not associated with ICU mortality (HR=0.85[0.55-1.33]). A total of 338/623(54.2%) patients in “B” phenotype received corticosteroids. The CPH (HR =0.65 [0.46-0.91]) and TIR regression (1- 25 day tHR=0.56[0.39-0.82] and >25 days tHR=1.53[1.03-7.12]) showed a biphasic effect of corticosteroids due to proportional assumption violation. No effect of corticosteroids on ICU mortality was observed when WCR was performed (wHR=0.72[0.49-1.05]). Finally, 535/857(62.4%) patients in “C” phenotype received corticosteroids. The CPH (HR=0.73[0.63-0.98]) and TIR regression (1- 25 day tHR=0.69[ 0.53-0.89] and >25 days tHR=1.30[ 1.14-3.25]) showed a biphasic effect of corticosteroids and proportional assumption violation. However, wHR (0.75[0.58-0.98]) and sHR (0.79[0.63-0.98]) suggest a protective effect of corticosteroids on ICU mortality.     Conclusion: Our finding warns against the widespread use of corticosteroids in all critically ill patients with COVID-19 at moderate-high dose. Only patients with the highest severity could benefit from steroid treatment although this effect on clinical outcome was minimized during ICU stay. 

Longitudinal analysis of COVID-19 patients shows age-associated T cell changes independent of ongoing ill-health (preprint)

The trajectory of immunological and inflammatory changes following acute COVID-19 infection are unclear. We investigate immunological changes in convalescent COVID-19 and interrogate their potential relationships with persistent symptoms, termed long COVID . We performed paired immunophenotyping at initial SARS-CoV-2 infection and convalescence (n=40, median 68 days) and validated findings in 71 further patients at median 101 days convalescence. Results were compared to 40 pre-pandemic controls. Fatigue and exercise tolerance were assessed and investigated their relationship with convalescent results. We demonstrate persistent expansion of intermediate monocytes, effector CD8+, activated CD4+ and CD8+ T cells, and reduced naïve CD4+ and CD8+ T cells at 68 days, with activated CD8+ T cells remaining increased at 101 days. Patients >60 years also demonstrate reduced naïve CD4+ and CD8+ T cells and expanded activated CD4+ T cells at 101 days. Ill-health, fatigue, and reduced exercise tolerance were common but were not associated with immunological changes. Graphical Abstract