Genomic insights into emerging South Korean uncommon Orientia tsutsugamushi strains and their value as new surveillance resources

초록

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 genomescale studies linking strain diversity with clinical features. (c) 2026 The Authors. Published by Elsevier Ltd on behalf of International Society for Infectious Diseases. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/)

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