Preliminary Genomic Data on Five Orientia tsutsugamushi Strains Isolated in Vellore, India

Orientia tsutsugamushi, the causative agent of scrub typhus, can be isolated in Vero or L929 cells and has a small genome (2-2.5 Mb). However, genome assembly is challenging due to the presence of host DNA contamination and a high proportion of repeat regions (up to 51%). Current global data includes 11 fully annotated genomes, with none from India. Here, we present the first whole-genome sequences of O. tsutsugamushi strains circulating within India.

Five O. tsutsugamushi strains were cultured in Vero cells and confirmed by 47 kDa real-time PCR. Genomic DNA was extracted after removal of host DNA and sequencing libraries were prepared. Whole-genome sequencing was performed using the PacBio Sequel II system in CCS/HiFi mode. The raw reads were assembled using Flye, and genome completeness was assessed with QUAST and BUSCO. Annotation was performed using the NCBI PGAP pipeline and comparative genome analysis by Roary. Phylogenetic analyses were performed using both the complete 56-kDa gene and whole-genome sequences to assess genetic relationships among O. tsutsugamushi strains.

We report five complete (circular) genomes of O. tsutsugamushi. Genome sizes range from 2.1 to 2.4 Mb. The total number of predicted genes falls between 2,379 and 2,715, with an average of 1,824 coding genes and 613 pseudogenes. Repeat regions ranged from 55% to 59%, corresponding to total lengths of approximately 1.2-1.44 Mb. All five genomes have been submitted to NCBI GenBank (Accession Numbers: CP166954-58). Phylogenetic analysis based on the full-length 56 kDa gene revealed that two strains belong to the Karp genogroup, two to Kato, and one to TA763.

This study presents the first whole-genome sequencing data of O. tsutsugamushi from India. Comprehensive phylogenomic studies, particularly to elucidate evolutionary dynamics and potential recombination events, will provide further information.