Phage biology and diversity in Clostridium difficile

艰难梭菌目前是工业化国家与医疗保健相关的感染性腹泻的最常见原因。最近，一种名为NAP1/027的超强毒株出现，并自2001年以来引发了几次疫情。艰难梭菌的流行病学似乎正在迅速演变，尽管近年来对这种病原体进行了深入的研究，但我们对艰难梭菌进化的驱动因素以及可能导致NAP1/027菌株出现的事件知之甚少。此外，最近的研究表明，动物可能是艰难梭菌繁殖的天然宿主，但指定宿主特异性的分子决定因素(例如人类或动物宿主)尚不清楚。前噬菌体，即整合到细菌染色体中的病毒(或噬菌体)，是众所周知的可移动的遗传元件，通过多种方式影响宿主。然而，到目前为止，它们在艰难梭菌中的作用仍然相对未知，尽管已经分离了几个前驱噬菌体。因此，我们的长期目标是评估前驱噬菌体在艰难梭菌生活方式和宿主特异性、遗传多样性、毒力和进化中的作用。为了实现这一目标，我们将描述艰难梭菌分离株中存在的来自人、动物和环境来源的前驱体的特征。将进行全基因组测序和比较前驱体基因组学，这将提供关于前驱体及其宿主(即艰难梭菌)的遗传多样性和进化的重要和新的数据。将研究NAP1/027菌株在溶原性(潜伏噬菌体感染)和活跃噬菌体复制(裂解周期)期间的噬菌体以及细菌基因的表达，这将带来关于噬菌体/病原体/宿主相互作用的重要数据。总之，我们的研究将为人类最致命的病原体之一的遗传多样性和噬菌体在多样性和快速进化中的贡献带来非常新颖的数据和新的见解。我们还相信，噬菌体/病原体相互作用的研究将导致发现新型抗菌剂的细菌靶标。

Clostridium difficile is currently the most frequent cause of healthcare-associated infectious diarrhea in industrialized countries. Recently, a hypervirulent strain, called NAP1/027, has emerged and has caused several outbreaks since 2001. The epidemiology of C. difficile seems to be evolving rapidly and despite intensive research on this pathogen in recent years, we don't know much about factors that drive C. difficile evolution and the events that might have contributed to the emergence of the NAP1/027 strain. Moreover, recent studies suggest that animals might be natural reservoirs for C. difficile propagation, but the molecular determinants specifying host specificity (e.g. human or animal hosts) are unknown. Prophages, i.e. viruses (or phages) integrated into the chromosome of bacteria, are mobile genetic elements well known to affect their host by multiple ways. However, their role in C. difficile has remained relatively unexplored so far, although several prophages have been isolated. Our long-term objective is thus to assess the role of prophages in C. difficile lifestyle and host specificity, genetic diversity, virulence and evolution. To achieve this goal, we will characterize prophages present in C. difficile isolates from human, animal and environmental origin. Whole genome sequencing and comparative prophage genomics will be performed, which will provide important and novel data regarding genetic diversity and evolution of both prophages and their host, i.e. C. difficile. Phage as well as bacterial gene expression during lysogeny (latent prophage infection) and during active phage replication (lytic cycle) will be studied in the NAP1/027 strain, which will bring important data regarding phage/pathogen/host interactions. In summary, our study will bring highly novel data and new insights on the genetic diversity and contribution of phages in the diversity and rapid evolution of one of the most deadly human pathogens. We also believe that phage/pathogen interaction studies will lead to the discovery of bacterial targets for novel antimicrobial agents.