Transcriptomic profiling of Yersinia enterocolitica O:3 and O:8 reveals serotype-specific expression differences leading to largely different YstA toxin levels

The enteric pathogen Yersinia enterocolitica is a the most common gram-negative zoonotic pathogen that causes a variety of gut-associated diseases named yersiniosis ranging from enteritis, watery diarrhea, mesenteric lymphadenitis to post infectious extraintestinal sequelae such as reactive arthritis human yersiniosis. The species Y. enterocolitica comprises a diverse group of about 70 serotypes of which only 11 are harmful to humans. Among the pathogenic strains are the highly mouse-virulent 1B/O:8 strains (YeO:8). This bioserotype, in particular YeO:8 strain 8081v has been used to study the pathogenesis of Y. enterocolitica using mouse infection models. However, by far the most frequent cause of human yersiniosis in Europe and Japan (>90%) is Y. enterocolitica bioserotype O:3 (YeO:3), which is also frequently found in pigs and pork products. In this study a comparative RNA-seq-based transcriptomic approach was used to identify serotype/isolate-specific differences in the transcriptome of the isolates YeO:8 8081v and YeO:3 Y1 under infection-relevant conditions. This strategy allowed the generation of the first in-depth single-nucleotide resolution transcriptome of Y. enterocolitica, revealed major differences in the temperature- and growth phase-dependent expression profiles, and led to the discovery of changes that modulate transcripts levels of important virulence-relevant traits. Additionally a comprehensive map of transcriptional start sites for Y. enterocolitica was generated using cDNA libraries based on samples enriched for primary transcripts. Overall design: RNA of Y. enterocolitica Y1 (YeO:3) and 8081v (YeO:8) from in vitro cultures

肠道致病菌小肠结肠炎耶尔森菌（Yersinia enterocolitica）是最为常见的革兰氏阴性人畜共患病致病菌，可引发多种名为耶尔森菌病（yersiniosis）的肠道相关疾病，病症谱系涵盖肠炎、水样腹泻、肠系膜淋巴结炎，乃至反应性关节炎等感染后肠外后遗症，最终引发人类耶尔森菌病。该菌种包含约70种血清型的多样化类群，其中仅11种对人类具有致病性。致病菌株中包含高小鼠毒力的1B/O:8血清型菌株（YeO:8），其中特定生物血清型YeO:8菌株8081v，已被用于借助小鼠感染模型研究小肠结肠炎耶尔森菌的致病机制。然而，截至目前，欧洲与日本地区人类耶尔森菌病的最常见致病原（占比超90%）为小肠结肠炎耶尔森菌生物血清型O:3（YeO:3），该菌株也频繁存在于猪及猪肉制品中。
本研究采用基于RNA测序（RNA-seq）的比较转录组学方法，旨在鉴定感染相关条件下，YeO:8菌株8081v与YeO:3菌株Y1的转录组中血清型/分离株特异性差异。该策略首次获得了小肠结肠炎耶尔森菌高深度单核苷酸分辨率转录组图谱，揭示了温度和生长阶段依赖的基因表达谱的显著差异，并发现了可调控重要毒力相关性状转录水平的变化。此外，本研究基于富集初级转录本的样本构建互补DNA（cDNA）文库，绘制了小肠结肠炎耶尔森菌的全面转录起始位点图谱。
实验整体设计：采集体外培养的小肠结肠炎耶尔森菌Y1（YeO:3）与8081v（YeO:8）的总RNA。