Abstract
Orientia tsutsugamushi is an intracellular α-proteobacterium which resides in trombiculid mites, and is the causative agent of scrub typhus in East Asia. The genome sequence of this species has revealed an unprecedented number of repeat sequences, most notably of the genes encoding the conjugative properties of a type IV secretion system (T4SS). Although this observation is consistent with frequent intragenomic recombination, the extent of homologous recombination (gene conversion) in this species is unknown. To address this question, and to provide a protocol for the epidemiological surveillance of this important pathogen, we have developed a multilocus sequence typing (MLST) scheme based on 7 housekeeping genes (gpsA, mdh, nrdB, nuoF, ppdK, sucD, sucB). We applied this scheme to the two published genomes, and to DNA extracted from blood taken from 84 Thai scrub typhus patients, from 20 cultured Thai patient isolates, 1 Australian patient sample, and from 3 cultured type strains. These data demonstrated that the O. tsutsugamushi population was both highly diverse [Simpson's index (95% CI) = 0.95 (0.92–0.98)], and highly recombinogenic. These results are surprising given the intracellular life-style of this species, but are broadly consistent with results obtained for Wolbachia, which is an α-proteobacterial reproductive parasite of arthropods. We also compared the MLST data with ompA sequence data and noted low levels of consistency and much higher discrimination by MLST. Finally, twenty-five percent of patients in this study were simultaneously infected with multiple sequence types, suggesting multiple infection caused by either multiple mite bites, or multiple strains co-existing within individual mites.
Highlights
Scrub typhus is a zoonotic disease endemic in Southeast Asia caused by Orientia tsutsugamushi, a Gram-negative obligate intracellular coccobacillus
Despite the importance of this pathogen, little is known of the population diversity or the role of homologous recombination in driving the microevolution of this species
The rickettsial infectious disease caused by the obligate intracellular bacterium Orientia tsutsugamushi, is endemic across the Asia Pacific region
Summary
Scrub typhus is a zoonotic disease endemic in Southeast Asia caused by Orientia tsutsugamushi, a Gram-negative obligate intracellular coccobacillus. The number of new cases in East Asia has been estimated at approximately one million per year [1]. It is transmitted by the bite of larval stages of trombiculid mites (‘‘Chiggers’’; Leptotrombidium spp.), which more typically feed on small rodents. Disease severity and manifestations vary widely from asymptomatic to fatal, and show marked geographical differences, with reported fatality rates in the pre-antibiotic era ranging from 3% in Taiwan to 40% in Japan [2] It is not known whether these geographical differences reflect genetic variation in the bacteria, the host, or both. Strains of O. tsutsugamushi are typically distinguished serologically on the basis of the 56 kDaouter membrane protein encoded by ompA, which is known to be highly polymorphic within the natural population
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