<i>In vivo</i> transcriptomes of <i>Streptococcus suis</i> reveal genes required for niche-specific adaptation and pathogenesis

<i>Streptococcus suis</i> is a Gram-positive bacterium and a zoonotic pathogen residing in the nasopharynx or the gastrointestinal tract of pigs with a potential of causing life-threatening invasive disease. It is endemic in the porcine production industry worldwide, and it is also an emerging human pathogen. After invasion, the pathogen adapts to cause bacteremia and disseminates to different organs including the brain. To gain insights in this process, we infected piglets with a highly virulent strain of <i>S. suis</i>, and bacterial transcriptomes were obtained from blood and different organs (brain, joints, and heart) when animals had severe clinical symptoms of infection. Microarrays were used to determine the genome-wide transcriptional profile at different infection sites and during growth in standard growth medium <i>in vitro</i>. We observed differential expression of around 30% of the Open Reading Frames (ORFs) and infection-site specific patterns of gene expression. Genes with major changes in expression were involved in transcriptional regulation, metabolism, nutrient acquisition, stress defenses, and virulence, amongst others, and results were confirmed for a subset of selected genes using RT-qPCR. Mutants were generated in two selected genes, and the encoded proteins, i.e., NADH oxidase and MetQ, were shown to be important virulence factors in coinfection experiments and <i>in vitro</i> assays. The knowledge derived from this study regarding <i>S. suis</i> gene expression <i>in vivo</i> and identification of virulence factors is important for the development of novel diagnostic and therapeutic strategies to control <i>S. suis</i> disease.

猪链球菌（Streptococcus suis）是一种革兰氏阳性细菌（Gram-positive bacterium），亦是一种人畜共患病原体（zoonotic pathogen），可定植于猪的鼻咽部或胃肠道，具备引发致命侵袭性疾病的潜力。该菌在全球养猪产业中呈地方性流行，同时也是一种新兴的人类致病菌。病原体入侵宿主后，会适应体内环境引发菌血症（bacteremia），并播散至包括大脑在内的多个器官。为深入解析这一致病过程，我们使用高毒力猪链球菌菌株感染仔猪，待仔猪出现严重感染临床症状时，采集血液及大脑、关节、心脏等不同器官的样本，获取细菌转录组数据。我们通过基因芯片（Microarrays）分析了不同感染位点以及体外（in vitro）标准培养基培养条件下的全基因组转录谱。研究发现，约30%的开放阅读框（Open Reading Frames，ORFs）存在差异表达，且呈现感染位点特异性的基因表达模式。表达发生显著变化的基因涉及转录调控、代谢、营养获取、应激防御及毒力等多个功能类别，我们通过RT-qPCR对部分筛选得到的基因进行了表达验证。我们构建了两个靶基因的突变体，其编码的NADH氧化酶（NADH oxidase）与MetQ蛋白，经共感染试验及体外（in vitro）实验证实为重要的毒力因子。本研究获得的猪链球菌体内（in vivo）基因表达数据及毒力因子鉴定结果，可为开发防控猪链球菌病的新型诊断与治疗策略提供重要理论支撑。