Genomic insights into emerging South Korean uncommon Orientia tsutsugamushi strains and their value as new surveillance resources.
OBJECTIVES Orientia tsutsugamushi, the causative agent of scrub typhus, shows strain diversity and a highly repetitive genome. In South Korea, strain Boryong predominates, whereas non-Boryong strains remain under-characterized at the whole-genome level. This study performed whole-genome sequencing and comparative genomic analysis of two patient-derived less-common South Korean strains, Chuncheon17-2 and strain Chuncheon17-13. METHODS Archived isolates were reactivated and confirmed by 56-kDa TSA PCR and sequencing. Hybrid sequencing was performed using PacBio HiFi and Illumina platforms. Genomes were annotated and compared using 56-kDa TSA sequence analysis, phylogenetic reconstruction, average nucleotide identity, repeated CDS clustering, annotation-based screening of IS-related CDSs, and whole-genome dot plots. RESULTS Both strains were assembled as single chromosomal contigs and showed highly repetitive genome features. Chuncheon17-2 was related to Je-Cheon by 56-kDa TSA sequence but formed a distinct genome-wide lineage, while Chuncheon17-13 was related to Young-Worl and clustered closer to Ikeda/Kato-related genomes. Dot plots and ANI indicated that neither strain was nearly identical to available genomes. CONCLUSIONS Strain-specific IS-related CDS profiles further suggest that mobile genetic element variation may contribute to genome plasticity. These genomes expand resources for less-common O. tsutsugamushi lineages and support molecular surveillance, diagnostic assay improvement, and future genome-scale studies linking strain diversity with clinical features.