Enhancing the E. coli Plasmid Genome Database and the Tools for its Effective Use

禽致病性大肠杆菌（APEC）引起的大肠杆菌病是一种严重危害我国养禽业的经济性疾病。 此外，有证据表明，APEC，污染零售家禽，可能是一个食源性E。大肠杆菌引起的尿路感染和其他肠道外疾病。 尽管APEC的重要性，很少有人知道这种生物体的能力，导致疾病，抵抗治疗，并坚持在环境中的机制。 然而，科学家们最近报告说，质粒在APEC中广泛存在，可能是APEC致病型的定义特征。 质粒是染色体外DNA分子，在“细菌性行为”期间经常在细菌之间转移。 APEC质粒已被证明具有许多使E.大肠杆菌能引起疾病并抵抗抗生素和重金属，如用作消毒剂的那些。 这些质粒的可传播性及其在家禽生产环境和零售家禽中的APEC中的普遍存在表明，这些质粒可以作为其他细菌病原体（包括引起人类疾病的病原体）的“疾病增强”基因的储存库。 不幸的是，科学家对质粒对疾病的贡献的理解受到缺乏完整质粒基因组序列和研究质粒的工具不足的阻碍。 本研究试图通过提供已知最常见的APEC质粒的高质量序列，培训新一代质粒序列分析科学家，以及开发新的大肠杆菌，来解决这些问题。大肠杆菌质粒基因组数据库工具，可广泛用于分析大肠杆菌。coli质粒。 该项目的直接目标是获得7种最常见的APEC质粒的完整注释的基因组序列。这些序列将实现高通量功能基因组研究，加速对大肠杆菌病发病机制的假设驱动研究，并深入了解这些质粒和质粒转移在塑造APEC和其他昂贵和致命病原体基因组中的作用。 据认为，拟议的研究将使人们能够更好地了解如何在未来控制质粒转移，以改善动物，人类和环境健康。 具体来说，研究人员将：1）构建7种APEC质粒的基因组文库，并对每种质粒进行8倍覆盖率的随机鸟枪测序; 2）组装序列草案，关闭序列缺口，并解决歧义; 3）注释所有质粒基因组，并将其与已知序列进行比较; 4）在密西西比州立大学培训生物信息学和基因组学的学生; 5）向生产者、家禽兽医、家禽健康研究人员和其他对大肠杆菌病预防和治疗、质粒以及质粒转移对APEC和其他细菌病原体致病能力和耐药性发展的影响感兴趣的科学家传播本项目的信息和材料。

Avian pathogenic Escherichia coli (APEC) cause colibacillosis, an economically devastating disease, which has major impact on this country's poultry industry. Also, there is evidence that APEC, contaminating retail poultry, may be a food-borne source of E. coli causing urinary tract infections and other extraintestinal diseases in human beings. Despite the importance of APEC, little has been known about the mechanisms underlying this organism's abilities to cause disease, resist therapy, and persist in the environment. However, scientists have recently reported that plasmids are widespread among APEC and may be the defining trait of the APEC pathotype. Plasmids are extrachromosomal DNA molecules that are frequently transferred among bacteria during "bacterial sex". APEC plasmids have been shown to possess many of the genes which enable E. coli to cause disease and resist antibiotics and heavy metals, such as those used as disinfectants. The transmissibility of these plasmids and their ubiquity among APEC in the poultry production environment and on retail poultry suggest that these plasmids could serve as a reservoir of "disease-enhancing" genes for other bacterial pathogens, including those causing disease in humans. Unfortunately, scientists' understanding of plasmids' contributions to disease have been hindered by the lack of complete plasmid genomic sequences available and the inadequacies of the tools with which plasmids can be studied. The present study seeks to remedy these problems by providing high quality sequences of the most common APEC plasmids known, training a new generation of scientists in plasmid sequence analysis, and development of a new E. coli Plasmid Genome Database tool that is available for widespread use for analysis of E. coli plasmids. The immediate objective of this project is to obtain fully annotated genomic sequences of 7 of the most commonly occurring APEC plasmids. These sequences will enable high-throughput functional genomic investigations, accelerate hypothesis-driven research on the pathogenesis of colibacillosis, and provide insight into the role of these plasmids and plasmid transfer in sculpting the genome of APEC and other costly and deadly pathogens. It is thought that the proposed study will enable better understanding of how plasmid transfer can be controlled in the future to the betterment of animal, human, and environmental health. Specifically, the investigators will: 1) construct genomic libraries of 7 APEC plasmids and conduct random shotgun sequencing of each to 8-fold coverage; 2) assemble the draft sequences, close sequence gaps, and resolve ambiguities; 3) annotate all plasmid genomes and compare them to known sequences; 4) train students at Mississippi State University in bioinformatics and genomics; and 5) disseminate information and materials from this project to producers, poultry veterinarians, poultry health researchers, and other scientists with interests in colibacillosis prevention and treatment, plasmids, and the effects of plasmid transfer on development of disease-causing ability and antimicrobial resistance among APEC and other bacterial pathogens.