PT  - JOURNAL ARTICLE
AU  - Bozena Mika-Gospodorz
AU  - Suparat Giengkam
AU  - Alexander J. Westermann
AU  - Jantana Wongsantichon
AU  - Willow Kion-Crosby
AU  - Suthida Chuenklin
AU  - Loo Chien Wang
AU  - Piyanate Sunyakumthorn
AU  - Radoslaw Sobota
AU  - Selvakumar Subbian
AU  - Jörg Vogel
AU  - Lars Barquist
AU  - Jeanne Salje
TI  - Dual RNA-seq provides insight into the biology of the neglected intracellular human pathogen <em>Orientia tsutsugamushi</em>
AID  - 10.1101/743641
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 743641
4099  - http://biorxiv.org/content/early/2019/08/24/743641.short
4100  - http://biorxiv.org/content/early/2019/08/24/743641.full
AB  - Emerging and neglected pathogens pose challenges as their biology is frequently poorly understood, and genetic tools often do not exist to manipulate them. Organism agnostic sequencing technologies offer a promising approach to understand the molecular processes underlying these diseases. Here we apply dual RNA-seq to Orientia tsutsugamushi (Ot), the obligate intracellular causative agent of 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, we investigated the transcriptional architecture of Ot, including operon structure and non-coding RNAs, and found evidence for wide-spread post-transcriptional antisense regulation. We compared the host response to two clinical isolates and identified distinct immune response networks that are up-regulated in response to each strain, leading to predictions of relative virulence which were confirmed in a mouse infection model. Thus, dual RNA-seq can reveal the biology and host-pathogen interactions of a poorly characterized and genetically intractable organism such as Ot.