Integrative Omics for Biomarker Discovery in Respiratory Infections and Post-Infectious Sequelae

Bioinformatics and multi-omics are transforming the study of respiratory and systemic infectious diseases by enabling unprecedented insight into the interactions between microbial pathogens and their hosts. In the era where severe respiratory infections such as sepsis and COVID-19 challenge both acute and chronic care, the integration of transcriptomic, proteomic, metabolomic, and microbiome data allows researchers to unravel how pathogens influence host immunity, drive tissue pathology, and shape patient outcomes. Despite advances, key questions remain regarding the cellular mechanisms of infection, the molecular determinants of host susceptibility and resilience, and the enduring impact of microbial exposures on chronic airway diseases, including COPD, bronchopulmonary dysplasia, and post-acute sequelae such as PASC (long COVID).

Recent studies employing single-cell and bulk multi-omics have shed light on the diversity and dynamics of host-pathogen interactions, identified infection-specific and cross-disease molecular signatures, and revealed new therapeutic vulnerabilities. Computational biology and explainable artificial intelligence (AI) have begun to bridge gaps between data-rich multi-omics assays and actionable clinical insights, enabling diagnostic risk stratification and mechanistic discovery. However, a significant need remains for studies linking omics findings to in vivo functional outcomes, multi-cohort validation of biomarkers, and robust modeling of microbial and host factors in diverse populations and ecological contexts, with focus on on respiratory pathogens.

This Research Topic aims to accelerate discovery and application of bioinformatics and multi-omics approaches to the cellular and infection microbiology of respiratory and systemic infectious diseases. We seek contributions that identify and validate molecular biomarkers, decode host–microbe and microbiome–immune interactions, and advance computational methods for integrating omics with clinical and experimental data. Emphasis will be placed on research providing mechanistic insights into pathogenesis, immune regulation, disease progression, and antimicrobial response in the context of bacteria, viruses, and other pathogenic microorganisms affecting the respiratory system.

To gather further insights in the mechanisms, diagnosis, and prognosis of infectious respiratory diseases through omics-driven approaches, we welcome articles addressing, but not limited to, the following themes:

1. Multi-omics-based discovery of host response biomarkers in acute and chronic respiratory infections
2. Integrative studies of airway, blood, and tissue microbiomes in health and disease
3. Application of explainable AI and computational modeling to unravel host–pathogen dynamics
4. Omics-guided identification of therapeutic targets and antimicrobial response pathways
5. Translational studies linking omics findings to physiology, clinical phenotypes, and post-infectious sequelae (e.g., PASC, COPD, BPD)
6. Comparative and cross-species analyses of zoonotic infections to support One Health perspectives, with a focus on respiratory pathogens
7. Studies that employ cellular or experimental models to validate omics discoveries and mechanisms