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（由适用提供）：殖民和感染病原体（伤口生物负责）对糖尿病足溃疡（DFU）结局的作用尚不清楚。我们的小组表明，使用高吞吐量16S核糖体RNA（RRNA）基因测序测量的DFU中的微生物的总体与：溃疡持续时间，溃疡深度和低血糖控制直接相关。但是，随着时间的流逝，生物负责人的变化仅提供了对这些变化对DFU结果的作用的有限见解。但是，BioBurden可能会影响DFU结果，但是使用16S rRNA分析可能无法辨别重要性的特定维度。该分子技术的主要局限性包括以下事实：它没有披露微生物群的功能潜力，而分辨率为物种或应变水平是不可能的。为了避免这些局限性，我们将采用整个基因组shot弹枪（WGS）元基因组测序和分析，这是一种强大的镜头，用于破译微生物群落的功能潜力。我们的总体假设是动态DFU微生物组的特定维度可以预测结果。此外，我们假设不同的治疗方案对DFU微生物组具有不同的影响。我们已经组建了一个由专家组成的多学科团队，以执行该提案的目标，并在伤口微生物组和元基因组学方面具有基础科学专业知识以及DFUS和DFUS感染方面的临床和研究专业知识。为了检验我们的假设，我们将完成以下目的：目标1：确定DFU元基因组的致病物种/菌株和整体微生物多样性是否与特定的DFU结果有关。我们将表征107名受试者随着时间的推移的变化，从我们以前的研究中募集了DFU，每2个每2个都收集了标本，我们将确定是否存在1）是否存在特定物种或病原体的菌株（例如β-溶血性链球菌）； 2）低微生物多样性与较低的愈合或感染相关并发症（即溃疡定义，骨髓炎或截肢）直接相关。 AIM 2：确定DFU元基因组中的致病性基因是否与特定的DFU结果有关。我们将检查基因会议的存在和相对丰度1）生物膜形成潜力，2）抗生素耐药性和3）病毒因素，以确定它们是否是关联 愈合率较低和与感染有关的并发症。 AIM 3：确定侵略性尖锐调试和抗生素处理对DFU元基因组的影响。这是对DFU微生物组对DFU结果的作用的首次纵向研究，使用WGS元基因组测序，也是第一个研究两种常用的抗菌干预对DFU麦吻合组的影响。