Clinical Scorecard: Genomic Analysis of Novel Orientia tsutsugamushi Strains from South Korea and Their Potential Role in Surveillance Efforts

At a Glance

Key Highlights

• Boryong predominates in South Korea, whereas several non-Boryong strains remain undercharacterized at the whole-genome level.

• The study generated whole-genome sequences for two uncommon, patient-derived strains: Chuncheon17-2 and Chuncheon17-13.

• The 56-kDa TSA gene linked Chuncheon17-2 with Je-Cheon and Chuncheon17-13 with Young-Worl, but genome-wide analyses revealed different relationships.

• Whole-genome sequencing provides information on phylogenetic relationships, genome structure, and repeat-associated features that single-gene typing cannot fully capture.

• Strain-dependent differences in experimental virulence and disease severity have been suggested, but this study did not assess virulence or clinical severity.

Guideline-Based Recommendations

Diagnosis

• Eschar formation can support clinical diagnosis, but clinical findings alone cannot identify the infecting strain or its relationship to other lineages.

• The article does not provide formal diagnostic guidelines.

Management

• The 56-kDa TSA gene remains useful for preliminary strain identification and routine genotyping.

• Whole-genome sequencing can provide additional genomic context for uncommon or poorly represented strains.

Monitoring & Follow-up

• Expand genomic surveillance of less-common circulating lineages and evaluate primer conservation across a broader collection of O. tsutsugamushi genomes.

• Interpret negative or partial results obtained with affected 56-kDa TSA primers cautiously.

Risks

• Single-gene typing may not fully represent genome-wide relationships.

• Primer-template mismatches may contribute to weak, incomplete, or potentially false-negative results for divergent strains, although amplification efficiency was not experimentally evaluated.

Patient & Prescribing Data

The study analyzed two archived, deidentified isolates obtained from patients with scrub typhus in South Korea in 2017. Detailed clinical records, travel histories, and individual patient information were unavailable. The study did not evaluate treatment or prescribing practices.

Clinical Best Practices

• Use 56-kDa TSA sequencing for preliminary strain identification and routine genotyping.

• Use whole-genome sequencing to resolve broader phylogenetic relationships, structural variation, and repeat-associated features.

• Interpret partial or negative PCR results cautiously when primer-template mismatches may be present.

• Avoid inferring virulence or clinical severity from genomic relatedness alone.

Related Resources & Content

• Kang H, Choi Y-J, Oh C, et al. Phylogeographic diversity of Orientia tsutsugamushi strains from clinical isolates in South Korea. Epidemiol Infect. 2026;154:e14.

• Park S-W, Lee C, Kwak Y, et al. Antigenic drift of Orientia tsutsugamushi in South Korea as identified by sequence analysis of a 56-kDa protein-encoding gene. Am J Trop Med Hyg. 2010;83(4):930–935.

• Choi YJ, Lee IY, Song HJ, et al. Geographical distribution of Orientia tsutsugamushi strains in chiggers from three provinces in Korea. Microbiol Immunol. 2018;62(9):547–553.

• Cho N-H, Kim H-R, Lee J-H, et al. Orientia tsutsugamushi genome reveals massive proliferation of conjugative type IV secretion system and host-cell interaction genes. Proc Natl Acad Sci U S A. 2007;104(19):7981–7986.

• Nakayama K, Yamashita A, Kurokawa K, et al. The whole-genome sequencing of the obligate intracellular bacterium Orientia tsutsugamushi revealed massive gene amplification during reductive genome evolution. DNA Res. 2008;15(4):185–199.

• Nakayama K, Kurokawa K, Fukuhara M, et al. Genome comparison and phylogenetic analysis of Orientia tsutsugamushi strains. DNA Res. 2010;17(5):281–291.

• Batty EM, Chaemchuen S, Blacksell S, et al. Long-read whole-genome sequencing and comparative analysis of six strains of the human pathogen Orientia tsutsugamushi. PLoS Negl Trop Dis. 2018;12(6):e0006566.

• Minahan NT, Yen T-Y, Guo Y-LL, Shu P-Y, Tsai K-H. Concatenated ScaA and TSA56 surface antigen sequences reflect genome-scale phylogeny of Orientia tsutsugamushi: An analysis including two genomes from Taiwan. Pathogens. 2024;13(4):299.