Pharyngeal Microenvironment Associated with Human Rhinovirus Infection in Children: Insights from Metatranscriptomic Sequencing

Human rhinovirus (HRV) is one of the most common causes of acute low respiratory tract infections (ALRTIs) in children and adults resulting in significant alterations in host gene expression and respiratory tract microbiome composition. We sought to clarify HRV prevalence features in children in Wuhan, and investigate interactions between HRV and host in pharynx microenvironment. A total of 1,790 samples were collected from children with ALRTI between September 2021 and September 2023 and screened for HRV infections using qPCR and targeted next-generation sequencing (tNGS). Among all samples, 47 positive samples, 29 healthy control and 27 HRV-negative ALRTI samples were analyzed by meta-transcriptomic sequencing to compare the microbiota dynamics, gene expression and antimicrobial resistance genes (ARGs) profile of infected and healthy individuals. The analysis revealed an HRV positive rate of 13.8%, with HRV-A and HRV-C strains being more dominant than HRV-B in Wuhan. Microbial diversity was significantly higher in HRV-positive samples, with specific genera such as Haemophilus, Neisseria, and Streptococcus being more abundant. There were 22,321 differentially expressed genes (DEGs) identified in the HRV patients. Enrichment analysis showed that these DEGs were associated with alterations in host responses, including modulations in immune activation and cellular processes. The identified ARGs conferred resistance to 18 distinct classes of antibiotics, with these ARGs being more prevalent in healthy individuals compared to those infected with HRV. Procrustes analysis demonstrated significant concordance between pharyngeal microbial community composition and ARG profiles, while co-occurrence network analysis identified strong associations between Pseudomonadota and ARGs conferring resistance to multiple antibiotic classes. HRV infection was associated with distinct shifts in pharyngeal microbial communities and host transcriptional responses. Collectively, these findings suggest that variation in the pharyngeal microbiome is closely linked to variation in resistome composition.