Novel Pediatric TB Diagnostics using Host and Microbial Biomarkers

/SUMMARY Tuberculosis (TB) is a leading cause of death in children worldwide, with children contributing to an estimated 14% of global TB deaths and 96% of these deaths being undiagnosed. Children <5 years old have the highest risk of severe disease and mortality and are the most challenging to diagnose, mainly due to paucibacillary disease, non-specific symptoms, and difficulty in expectorating sputum. Innovative and non-sputum-based diagnostic TB tests for this group are needed to reduce childhood TB mortality. Multiple host transcriptomic signatures in blood have been identified for diagnosing pediatric TB, although most have not met the WHO criteria for a pediatric diagnostic test. Transcriptomics on upper airway samples has been used to identify diagnostic biomarkers and study disease pathophysiology for respiratory infections and chronic inflammatory lung conditions. However, no transcriptomic studies are using these specimens for TB. Profiling the upper airway also enables the parallel study of the respiratory microbiome, which has been shown to differ amongst adults with TB disease compared to healthy controls. However, the diagnostic potential of specific microbial communities and their interplay with the host is unexplored in children. With the initial pathogen-host encounter in pulmonary TB occurring in the upper respiratory tract, we hypothesize that detection of host gene expression and the microbiome in the oropharynx and nasal cavity could be used to develop novel diagnostic tests for TB, with the added advantage of using non-invasive and easy to collect specimens. Using already collected samples from two ongoing studies, we propose to perform total RNA-sequencing on nasal brushings and oral swabs collected from children <5 years old with signs and/or symptoms of TB in Uganda (n=150). We will be the first to develop pediatric TB disease diagnostic biomarkers based on detecting upper respiratory tract host gene expression profiles, microbial activity, or a combination. We will also compare our identified nasal and oral host biomarkers to blood host biomarkers to determine how changes in the upper airway reflect those previously found in blood. Finally, we will explore interactions between microbial composition and host gene and pathway expression, increasing our understanding of how microbial communities may influence the host immune response to TB in the upper airways. If successful, our findings will justify larger R01-level studies to validate biomarkers across independent, geographically distinct cohorts for TB diagnosis, as well as mechanistic longitudinal studies focused on investigating causal links between the immune response and the microbiome. Project Number: 1R21AI197168-01 | Fiscal Year: 2026 | NIH Institute/Center: National Institute of Allergy and Infectious Diseases (NIAID) | Principal Investigator: William Johnson | Institution: RUTGERS BIOMEDICAL AND HEALTH SCIENCES, Newark, NJ | Award Amount: $210,302 | Activity Code: R21 | Study Section: Population based Research in Infectious Disease Study Section[PRID] View on NIH RePORTER: https://reporter.nih.gov/project-details/1R21AI19716801