Introduction
Kawasaki disease (KD) is an acute pediatric vasculitis of unknown etiology, with growing interest in the role of host–microbiota interactions. This study aimed to characterize the nasopharyngeal microbiota in KD patients compared with children with mild upper respiratory viral infections and healthy controls, while also exploring associated epidemiological, clinical, and microbiological factors.

Methods
Nasopharyngeal samples were collected from 238 patients and subjected to 16S rRNA gene sequencing targeting the V3–V4 region. A total of 233 samples met the inclusion criteria (45 KD, 84 viral controls, and 104 healthy controls). Bioinformatic analyses were performed using QIIME 2 (v2025.4) and R (v4.4.2). Sequence quality control and denoising were conducted with DADA2, and taxonomic classification was performed using the Greengenes2 database (v2024.09). Downstream analyses included alpha and beta diversity, differential abundance testing, and unsupervised clustering.

Results
Significant differences in the diversity and composition of the nasopharyngeal microbiota were observed in KD patients compared with both control groups. KD samples exhibited greater richness but lower evenness, suggesting communities dominated by a few amplicon sequence variants (ASVs). Beta-diversity analyses confirmed significant compositional separation from controls. KD samples showed a higher mean relative abundance of Corynebacterium and Dolosigranulum, and a lower abundance of Streptococcus and Moraxella_651924 compared with controls. Several ASVs displayed group-specific associations, with ASV45 (Corynebacterium propinquum) strongly associated with KD. Additionally, KD cases exhibited reduced Streptococcus pneumoniae carriage as determined by real-time PCR. No taxa were associated with clinical factors. Partitioning Around Medoids (PAM) clustering identified seven clusters, including one KD-enriched cluster (12 cases) characterized by high Dolosigranulum/Corynebacterium abundance and a lower incidence of vaginal delivery.

Discussion
Children with KD exhibited a distinct nasopharyngeal microbiota compared with children with viral respiratory infections and healthy controls. ASV45 (Corynebacterium propinquum) was strongly associated with KD. Unsupervised clustering revealed a KD-enriched cluster with elevated Dolosigranulum and Corynebacterium abundance. Interestingly, this cluster showed lower incidence of vaginal delivery, a relationship previously described in the literature and warranting further investigation. Overall, these findings support a potential role of airway microbiota in KD pathobiology. Larger, multicenter studies are needed to validate these associations and explore underlying mechanisms.