Extracting relevant predictive variables for COVID-19 severity prognosis: An exhaustive comparison of feature selection techniques.

With the COVID-19 pandemic having caused unprecedented numbers of infections and deaths, large research efforts have been undertaken to increase our understanding of the disease and the factors which determine diverse clinical evolutions. Here we focused on a fully data-driven exploration regarding which factors (clinical or otherwise) were most informative for SARS-CoV-2 pneumonia severity prediction via machine learning (ML). In particular, feature selection techniques (FS), designed to reduce the dimensionality of data, allowed us to characterize which of our variables were the most useful for ML prognosis. We conducted a multi-centre clinical study, enrolling n = 1548 patients hospitalized due to SARS-CoV-2 pneumonia: where 792, 238, and 598 patients experienced low, medium and high-severity evolutions, respectively. Up to 106 patient-specific clinical variables were collected at admission, although 14 of them had to be discarded for containing ⩾60% missing values. Alongside 7 socioeconomic attributes and 32 exposures to air pollution (chronic and acute), these became d = 148 features after variable encoding. We addressed this ordinal classification problem both as a ML classification and regression task. Two imputation techniques for missing data were explored, along with a total of 166 unique FS algorithm configurations: 46 filters, 100 wrappers and 20 embeddeds. Of these, 21 setups achieved satisfactory bootstrap stability (⩾0.70) with reasonable computation times: 16 filters, 2 wrappers, and 3 embeddeds. The subsets of features selected by each technique showed modest Jaccard similarities across them. However, they consistently pointed out the importance of certain explanatory variables. Namely: patient's C-reactive protein (CRP), pneumonia severity index (PSI), respiratory rate (RR) and oxygen levels -saturation Sp O2, quotients Sp O2/RR and arterial Sat O2/Fi O2-, the neutrophil-to-lymphocyte ratio (NLR) -to certain extent, also neutrophil and lymphocyte counts separately-, lactate dehydrogenase (LDH), and procalcitonin (PCT) levels in blood. A remarkable agreement has been found a posteriori between our strategy and independent clinical research works investigating risk factors for COVID-19 severity. Hence, these findings stress the suitability of this type of fully data-driven approaches for knowledge extraction, as a complementary to clinical perspectives.

Bacteraemic pneumococcal pneumonia and SARS-CoV-2 pneumonia: differences and similarities.

OBJECTIVE: To analyse differences in clinical presentation and outcome between bacteraemic pneumococcal community-acquired pneumonia (B-PCAP) and sSvere Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) pneumonia. METHODS: This observational multi-centre study was conducted on patients hospitalized with B-PCAP between 2000 and 2020 and SARS-CoV-2 pneumonia in 2020. Thirty-day survival, predictors of mortality, and intensive care unit (ICU) admission were compared. RESULTS: In total, 663 patients with B-PCAP and 1561 patients with SARS-CoV-2 pneumonia were included in this study. Patients with B-PCAP had more severe disease, a higher ICU admission rate and more complications. Patients with SARS-CoV-2 pneumonia had higher in-hospital mortality (10.8% vs 6.8%; P=0.004). Among patients admitted to the ICU, the need for invasive mechanical ventilation (69.7% vs 36.2%; P<0.001) and mortality were higher in patients with SARS-CoV-2 pneumonia. In patients with B-PCAP, the predictive model found associations between mortality and systemic complications (hyponatraemia, septic shock and neurological complications), lower respiratory reserve and tachypnoea; chest pain and purulent sputum were protective factors in these patients. In patients with SARS-CoV-2 pneumonia, mortality was associated with previous liver and cardiac disease, advanced age, altered mental status, tachypnoea, hypoxaemia, bilateral involvement, pleural effusion, septic shock, neutrophilia and high blood urea nitrogen; in contrast, ≥7 days of symptoms was a protective factor in these patients. In-hospital mortality occurred earlier in patients with B-PCAP. CONCLUSIONS: Although B-PCAP was associated with more severe disease and a higher ICU admission rate, the mortality rate was higher for SARS-CoV-2 pneumonia and deaths occurred later. New prognostic scales and more effective treatments are needed for patients with SARS-CoV-2 pneumonia.

Are airways structural abnormalities more frequent in children with recurrent lower respiratory tract infections?

UNLABELLED: We report bronchoscopic changes observed in children with recurrent lower airways infections (RLAI) and findings in control children undergoing bronchoscopy for causes other than RLAI. PATIENTS AND METHODS: Retrospective case-control cohorts study. The clinical records of children who had fiberoptic bronchoscopy (FB) for a history of RLAI without any known underlying disorder between 2007 and 2013 and of control children who required FB for other causes were reviewed. Clinical features, bronchospic findings and bronchoalveolar lavage (BAL) results were assessed. RESULTS: Cases were 62 (32 female) children aged 5 years (1-12) and controls 29 children aged 4.5 years (0.5-14). Airway malacia was observed in 32 (52%) vs. 4 (13%) (p = 0.001), profuse respiratory secretions in 34(55%) vs. 6 (20%) (p = 0.007). Endobronchial obstruction: 4 (6.4%) and tracheobronchomegaly were observed only in cases. In cases with profuse respiratory secretions there was a higher prevalence of airways malacia: 64.7% vs. 35.7% (p = 0.04) and of positive BAL cultures: 45.5% vs. 13.3% (p = 0.04). Isolated organisms in cases were non-typable Haemophilus influenzae and Streptococcus pneumoniae most frequently. Pneumocystiis jirovecii, Staphylococcus aureus, and Streptococcus mitis were isolated in controls. CONCLUSIONS: Half of the children with RLAI had tracheo and/or bronchomalacia, their frequency being in keeping with previous reports and far higher than that observed in controls. It was associated with profuse respiratory secretions and with a higher frequency of positive BAL cultures mostly for non typable H. influenzae and S. pneumoniae which were not isolated in controls.

Hereditary pulmonary alveolar proteinosis. Could it be triggered by Mycoplasma pneumoniae pneumonia?

We present a three-year-old girl with respiratory failure due to hereditary pulmonary alveolar proteinosis caused by abnormal alpha chain of the granulocyte-macrophage colony-stimulating factor receptor. Both the patient and an asymptomatic seven-year-old sister were homozygous for the same mutation in CSF2RA. We speculate that the Mycoplasma pneumoniae pneumonia might have triggered the clinical presentation. While a good response to serial partial lung lavage was noticed, the ultimate outcome is uncertain.