Bozena Mika-GospodorzSuparat GiengkamAlexander J. WestermannJantana WongsantichonWillow Kion-CrosbySuthida ChuenklinLoo Chien WangPiyanate SunyakumthornRadoslaw M. SobotaSelvakumar SubbianJörg VogelLars BarquistJeanne SaljeHelmholtz-Institut für RNA-basierte InfektionsforschungA-Star, Institute of Molecular and Cell BiologyArmed Forces Research Institute of Medical Sciences, ThailandMahidol UniversityJulius-Maximilians-Universität WürzburgNuffield Department of MedicineRutgers UniversityState University of New Jersey2020-08-252020-08-252020-12-01Nature Communications. Vol.11, No.1 (2020)204117232-s2.0-85087419564https://repository.li.mahidol.ac.th/handle/123456789/57667© 2020, The Author(s). 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.Mahidol UniversityBiochemistry, Genetics and Molecular BiologyChemistryPhysics and AstronomyArticleSCOPUS10.1038/s41467-020-17094-8