Divergent biological pathways distinguish community-acquired pneumonia from COVID-19 despite similar plasma cytokine profiles
Bibliographic record
Abstract
BACKGROUND: Pulmonary infections, ranging from mild respiratory issues to severe multiorgan failure, pose a major global health threat. The immune response in community-acquired pneumonia (CAP) and COVID-19 influences disease severity and outcomes, but molecular pathogenesis differs across pathogens. Comparisons of plasma cytokine profiles between CAP and COVID-19 are limited. Analyzing these profiles with machine learning and bioinformatics could reveal subtle patterns and improve our understanding of immune responses in both conditions. METHODS: We conducted a novel case-control study to profile cytokine levels in patients with CAP and COVID-19. Age- and sex-matched cohorts included 39 patients with CAP, 39 with COVID-19, and 20 healthy controls. We measured 384 plasma cytokine levels using proximity extension assays and analyzed differences between cohorts with conventional statistical methods, bioinformatics and machine learning. RESULTS: Median ages of the cohorts were comparable (P = 0.797). COVID-19 patients exhibited a higher prevalence of hematologic disease (P = 0.047), increased corticosteroid use (P = 0.040), and reduced antibiotic use (P = 0.012). Clinical outcomes, including mortality, ICU admission, invasive mechanical ventilation, renal replacement therapy, acute respiratory distress syndrome, and acute kidney injury, were similar between groups. Both cohorts showed comparable absolute circulating cytokine profiles but distinct profiles relative to healthy controls. Machine learning identified a model of twelve cytokines that distinguished CAP from COVID-19 with a classification accuracy of 0.71 (SD 0.20). Gene ontology and enrichment analysis revealed differences in cytosolic and nuclear functions, intracellular signaling, stress responses, and cell cycle processes between patient cohorts and healthy controls. Enriched GO pathways showed that CAP pathways were positively associated with leukocyte counts and ARDS development, while COVID-19 pathways were negatively associated with ARDS and positively with platelet counts. CONCLUSIONS: This case-control study provides insights into cytokine profiles related to CAP and COVID-19 pathogenesis. Although absolute circulating cytokine levels showed no significant differences between the groups, machine learning identified a model of twelve proteins that effectively distinguished the cohorts. Gene ontology and enrichment analyses also revealed distinct dysregulated pathways with differing associations with clinical variables in each cohort. These findings underscore the complexity and variability of cytokine responses in pulmonary infections.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.010 | 0.251 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.001 | 0.002 |
| Science and technology studies | 0.002 | 0.002 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.001 | 0.004 |
| Research integrity | 0.000 | 0.003 |
| Insufficient payload (model declined to judge) | 0.001 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one teacher head, not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".