Clinical Report: Genomic Analysis of Novel Orientia tsutsugamushi Strains

Background

Scrub typhus, caused by Orientia tsutsugamushi, is endemic in the Asia-Pacific region, including South Korea, and can be difficult to distinguish clinically from other acute febrile infections. The organism has substantial antigenic and genomic diversity. Although the 56-kDa TSA gene is useful for routine strain assignment, single-gene typing may not capture genome-wide relationships, structural variation, or repeat-associated features.

Data Highlights

Whole-genome sequencing was performed on two patient-derived South Korean isolates, Chuncheon17-2 and Chuncheon17-13. Their circular chromosomes contained 1,978,471 and 2,349,610 base pairs, respectively. The 56-kDa TSA gene linked Chuncheon17-2 with Je-Cheon and Chuncheon17-13 with Young-Worl, although neither was identical to its corresponding reference sequence. Neither isolate had an average nucleotide identity above 99.5% with any available genome.

Key Findings

• Both isolates had highly repetitive genomes and were genomically distinct from currently available O. tsutsugamushi genomes.

• Core-genome analysis placed Chuncheon17-13 near Ikeda and Kato, whereas Chuncheon17-2 formed a distinct genome-wide lineage.

• The genome-wide relationships differed from those identified through 56-kDa TSA analysis, showing that single-gene typing does not always reflect broader phylogeny.

• Primer-template mismatches may have contributed to incomplete conventional Sanger sequencing, but amplification efficiency was not experimentally evaluated.

• Repeat-associated and insertion-sequence–related profiles differed among strains, although their biological significance remains undetermined.

Clinical Implications

Whole-genome sequencing can complement 56-kDa TSA genotyping by providing broader information for molecular surveillance and diagnostic evaluation of uncommon or poorly represented lineages. Negative or partial results obtained with affected 56-kDa TSA primers should be interpreted cautiously. The findings should not be interpreted as evidence of increased virulence because virulence and clinical severity were not assessed.

Conclusion

Genomic characterization identified Chuncheon17-2 and Chuncheon17-13 as distinct South Korean strains and expanded the available resources for less-common O. tsutsugamushi lineages. The sequences support future genomic surveillance, diagnostic evaluation, and studies integrating genomic variation with clinical data.

Related Resources & Content

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