Decoding the microbial bioburden of diabetic foot ulcers: A metagenomic approach

解码糖尿病足溃疡的微生物生物负荷：宏基因组方法

• 批准号: 9062519
• 负责人: Elizabeth Anne Grice
• 金额: $ 51.06万
• 依托单位: UNIVERSITY OF PENNSYLVANIA
• 依托单位国家: 美国
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-05-01 至 2018-02-28
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9062519
• 关键词: Address; Amputation; Antibiotic Resistance; Antibiotic Therapy; Bacteria; Basic Science; Characteristics; Chronic; Clinical; Clinical Research; DNA; Data; Databases; Debridement; Deterioration; Development; Diabetes Mellitus; Diabetic Foot Ulcer; Dimensions; Genes; Genetic; Genomic approach; Genomics; Healed; Health; Infection; Intervention; Investigation; Lead; Longitudinal Studies; Lower Extremity; Measurement; Measures; Metabolic; Metagenomics; Methods; Microbe; Microbial Biofilms; Modeling; Molecular; Morbidity - disease rate; Organism; Osteomyelitis; Outcome; Pathogenicity; Pathway interactions; Patients; Persons; Play; Predictive Value; Quality of life; RNA, Ribosomal, 16S; Recruitment Activity; Research Personnel; Resolution; Role; Science; Sequence Analysis; Shotguns; Skin; Specimen; Statistical Data Interpretation; Streptococcus; Techniques; Testing; Time; Treatment Protocols; Ulcer; Virulence; Virulence Factors; Wound Healing; antimicrobial; base; clinical practice; effective therapy; follow-up; foot; glycemic control; healing; insight; lens; metagenome; metagenomic sequencing; microbial; microbial community; microbiome; microbiota; microorganism; outcome prediction; pathogen; rRNA Genes; reconstruction; treatment effect; treatment strategy; whole genome; wound

 DESCRIPTION (provided by applicant): The role of colonizing and infecting pathogens (wound bioburden) on diabetic foot ulcer (DFU) outcomes remains unclear. Our group has shown that the totality of microorganisms in DFUs measured using high throughput 16S ribosomal RNA (rRNA) gene sequencing, is directly related to: ulcer duration, ulcer depth, and poor glycemic control. However, changes in bioburden over time provided only limited insights into the role of these changes on DFU outcomes. Nonetheless, bioburden may be influencing DFU outcomes, but the specific dimensions of importance may not be discernable using 16S rRNA profiling. Major limitations of this molecular technique include the fact that it does not disclose functional potential of the microbiota and resolution to species or strain level is often impossible. To circumvent these limitations, we will employ whole genome shotgun (WGS) metagenomic sequencing and analysis, a powerful lens for deciphering the functional potential of microbial communities. Our overarching hypothesis is that specific dimensions of the dynamic DFU microbiome are predictive of outcome. Additionally, we hypothesize that different treatment regimens have different effects on the DFU microbiome. We have assembled a multi-disciplinary team of experts to execute the aims of this proposal, with basic science expertise in wound microbiome and metagenomics and clinical and research expertise in DFUs and infection. To test our hypothesis, we will complete the following aims: Aim 1: Determine if pathogenic species/strains and overall microbial diversity of the DFU metagenome are associated with specific DFU outcomes. We will characterize the changes in metagenomes over time for 107 subjects with DFUs recruited from our previous studies, from whom specimens were collected every 2 weeks from presentation to final outcome. We will determine if 1) the presence of specific species or strains of pathogens (e.g. beta-hemolytic Streptococcus); and 2) low microbial diversity are directly associated with lower rates of healing or infection-related complications (i.e., ulcer deterioration, osteomyelitis or amputation). Aim 2: Determine if pathogenicity genes in the DFU metagenome are associated with specific DFU outcomes. We will examine the presence and relative abundance of genes conferring 1) biofilm-formation potential, 2) antibiotic resistance and, 3) virulence factors, to determine if they are association with lower rates of healing and infection-related complications. Aim 3: Determine the effects of aggressive sharp debridement and antibiotic treatment on the DFU metagenome. This is the first longitudinal study of the role of the DFU microbiome on DFU outcomes using WGS metagenomic sequencing as well as the first to examine the impact of two commonly employed antimicrobial interventions on the DFU metagenome.

 描述（由申请人提供）：定植和感染病原体（伤口生物负载）对糖尿病足溃疡 (DFU) 结果的作用仍不清楚。我们的小组已经表明，使用高通量 16S 核糖体 RNA (rRNA) 测量 DFU 中的微生物总数。基因测序与：溃疡持续时间、溃疡深度和血糖控制不良直接相关，然而，随着时间的推移，生物负荷的变化只能对这些因素的作用提供有限的了解。然而，生物负载可能会影响 DFU 结果，但使用 16S rRNA 分析可能无法辨别重要的具体维度，该分子技术的主要局限性包括它没有揭示微生物群的功能潜力和分辨率。为了规避这些限制，我们将采用全基因组鸟枪法（WGS）宏基因组测序和分析，这是解读微生物群落功能潜力的强大镜头。动态 DFU 微生物组的特定维度可以预测结果。此外，我们还追求不同的治疗方案对 DFU 微生物组有不同的影响。我们组建了一个多学科专家团队来执行该提案的基本目标。伤口微生物组和宏基因组学方面的科学专业知识以及 DFU 和感染方面的临床和研究专业知识 为了检验我们的假设，我们将完成以下目标： 目标 1：确定致病物种/菌株以及总体微生物多样性。 DFU 宏基因组与特定的 DFU 结果相关。我们将描述从我们之前的研究中招募的 107 名 DFU 受试者的宏基因组随时间的变化，从出现到最终结果，每两周采集一次样本。我们将确定是否 1)特定种类或菌株的病原体（例如β-溶血性链球菌）的存在；2）微生物多样性低与较低的治愈率或感染相关并发症直接相关（即溃疡恶化、骨髓炎或截肢） 目标 2：确定 DFU 宏基因组中的致病基因是否与特定的 DFU 结果相关。我们将检查赋予 1) 生物膜形成潜力、2) 抗生素的基因的存在和相对丰度。耐药性和 3) 毒力因子，以确定它们是否相关 目标 3：确定积极锐性清创和抗生素治疗对 DFU 宏基因组的影响 这是第一个使用 WGS 宏基因组测序来研究 DFU 微生物组对 DFU 结果的作用的纵向研究。以及第一个研究两种常用抗菌干预措施对 DFU 宏基因组的影响。