A Compact Closed Genome of Orientia tsutsugamushi from Hainan Island, China Provides a TA763_A Reference and Reveals Repeat-Driven Remodeling

Scrub typhus, caused by the obligate intracellular bacterium Orientia tsutsugamushi (O. tsutsugamushi), remains a major public-health concern in the Asia–Pacific region. Genome-wide inference is complicated by extensive repetitive DNA and frequent genome rearrangement. We isolated O. tsutsugamushi HMU_001 from a scrub typhus patient on Hainan Island, China. Intracellular morphology was examined and replication was quantified in endothelial cells. Using long-read sequencing with short-read polishing, we generated a closed circular genome and performed standardized comparative analyses across all available complete O. tsutsugamushi genomes. HMU_001 assembled as a 1,895,724 bp genome and, among the 17 complete genomes analyzed in this study, represented the most compact genome. Repeats comprised 873,550 bp (46.08%) and included 72 RAGE loci (4 relatively complete) and 283 insertion sequences (54 intact). Repeat content varied widely and largely explained genome size differences. A core-gene phylogeny resolved four clades with partial geographic structure, while tsa56 genotypes were only partly congruent with it. Genome synteny was generally limited across strains but markedly higher among the closest relatives, consistent with ongoing rearrangement. HMU_001 expands representation of complete O. tsutsugamushi genomes by adding a TA763_A lineage strain from a high-incidence island setting. Comparative analyses support a model in which repeat proliferation and decay drive genome evolution and structural remodeling.