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Studying emerging or neglected pathogens is often challenging due to insufficient information and absence of genetic tools. Dual RNA-seq provides insights into host-pathogen interactions, and is particularly informative for intracellular organisms. Here we apply dual RNA-seq to Orientia tsutsugamushi (Ot), an obligate intracellular bacterium that causes the vector-borne human disease scrub typhus. Half the Ot genome is composed of repetitive DNA, and there is minimal collinearity in gene order between strains. Integrating RNA-seq, comparative genomics, proteomics, and machine learning to study the transcriptional architecture of Ot, we find evidence for wide-spread post-transcriptional antisense regulation. Comparing the host response to two clinical isolates, we identify distinct immune response networks for each strain, leading to predictions of relative virulence that are validated in a mouse infection model. Thus, dual RNA-seq can provide insight into the biology and host-pathogen interactions of a poorly characterized and genetically intractable organism such as Ot.

Original publication




Journal article


Nature communications

Publication Date





Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany.


Cell Line, Animals, Humans, Mice, Orientia tsutsugamushi, Scrub Typhus, Disease Models, Animal, Bacterial Proteins, Interferon Type I, RNA, Bacterial, RNA, Untranslated, Feasibility Studies, Proteomics, Transcription, Genetic, Gene Expression Regulation, Bacterial, Interspersed Repetitive Sequences, Genome, Bacterial, Female, Host-Pathogen Interactions, Neglected Diseases, Human Umbilical Vein Endothelial Cells, Whole Exome Sequencing, RNA-Seq