Targeted sequence capture of Orientia tsutsugamushi DNA from chiggers and humans

Scrub typhus is a febrile disease caused by Orientia tsutsugamushi, transmitted by larval stage Trombiculid mites (chiggers), whose primary hosts are small mammals. The phylogenomics of O. tsutsugamushi in chiggers, small mammals and humans remains poorly understood. To combat the limitations imposed by the low relative quantities of pathogen DNA in typical O. tsutsugamushi clinical and ecological samples, along with the technical, safety and cost limitations of cell culture, a novel probe-based target enrichment sequencing protocol was developed. The method was designed to capture variation among conserved genes and facilitate phylogenomic analysis at the scale of population samples. A whole-genome amplification step was incorporated to enhance the efficiency of sequencing by reducing duplication rates.

恙虫病（Scrub typhus）是由恙虫病东方体（Orientia tsutsugamushi）引发的发热性疾病，其传播媒介为幼虫期恙螨（Trombiculid mites，chiggers），小型哺乳动物为该病原体的主要宿主。目前学界对恙螨、小型哺乳动物及人体内恙虫病东方体的系统基因组学（phylogenomics）研究仍较为匮乏。鉴于临床与生态样本中恙虫病东方体的病原体DNA相对含量较低，且细胞培养存在技术、安全及成本层面的局限性，研究人员开发了一种新型基于探针的目标富集测序（probe-based target enrichment sequencing）方案。该方案旨在捕获保守基因间的变异，以支持群体样本规模下的系统基因组学分析。方案中加入了全基因组扩增（whole-genome amplification）步骤，通过降低测序重复率来提升测序效率。