A multi-level genomic and spatial analysis of MRSA transmission

MRSA 传播的多层次基因组和空间分析

• 批准号: 10581576
• 负责人: Kyle Jeanne Popovich
• 金额: $ 53.86万
• 依托单位: RUSH UNIVERSITY MEDICAL CENTER
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-03-11 至 2025-02-28
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10581576
• 关键词: African American; Area; Back; Bacteremia; Caring; Censuses; Chicago; Cities; Clinical; Communities; Community Networks; Community based prevention; County; Data; Data Set; Disparity; Epidemic; Epidemiology; Funding; Genetic; Genomics; Geographic Locations; Hospitals; Household; Illicit Drugs; Imprisonment; Individual; Infection; Infection prevention; Interruption; Intervention; Jail; Knowledge; Medical; Modeling; Molecular Epidemiology; Movement; Neighborhoods; Patients; Phenotype; Phylogenetic Analysis; Population; Prevention; Proxy; Public Health; Public Hospitals; Research; Risk; Risk Factors; Role; Sexually Transmitted Diseases; Site; Spatial Distribution; Staphylococcus aureus infection; Testing; Time; Trees; Underserved Population; Urban Community; acquired factor; care seeking; community intervention; community setting; community transmission; cooking; data integration; design; genome sequencing; genomic data; genomic epidemiology; high risk; housing instability; illicit drug use; innovation; lonely individuals; methicillin resistant Staphylococcus aureus; opioid epidemic; pathogen; recidivism; residence; simulation; social contact; transmission process; urban area; whole genome

Project Summary (REWRITTEN) Community-associated methicillin-resistant S. aureus (CA-MRSA) is a major problem in urban areas, with illicit drug use, incarceration, unstable housing, and geographic area of residence each being associated with CA- MRSA risk. Using genomic sequencing, we have previously demonstrated that community networks may facilitate the spread of MRSA outside of households, and epidemiologic exposures, including residence in a high detainee release area, may serve as the basis for linkages between individuals colonized or infected with genetically similar MRSA strains. The extent to which jails facilitate MRSA transmission, both during incarceration and to the community at large, is unknown. Our preliminary data demonstrate a high proportion of individuals enter the jail already colonized with MRSA and jails then provide an opportunity for at-risk individuals to intermingle which may promote further spread of MRSA. As urban jails are characterized by high turnover and high recidivism, we speculate the jails may be one of the major drivers of MRSA spread from and back into urban communities. Despite the demonstrated risk associated with community settings, studies examining infection prevention for MRSA have been conducted almost exclusively in hospitals. It is unknown if transmission dynamics and risk factors for acquisition of MRSA in the community are the same as those that drive transmission in hospitals. Prior studies of sexually transmitted diseases have demonstrated that interventions in urban jails can have significant downstream benefits in the community and provide an opportunity to intervene with a difficult-to-reach population that often lacks access to medical care. We believe this type of intervention could be extended to MRSA and that molecular epidemiologic analysis would help to design and maximize the benefits of a community intervention. Funds are requested to examine the genomic epidemiology of MRSA in an urban community and to identify and characterize epicenters for MRSA spread. We will use existing MRSA clinical cultures from 2008-2018 and integrate genomic data from these isolates with geocoding, epidemiologic, detainee release, and US census data to test whether there are geographic areas at highest risk for MRSA spread. We will use spatial transmission modeling to identify rates of MRSA transmission within and between community areas and to test hypothetical interventions. The proposal has three aims: (1) Characterize the movement of MRSA over time to identify if there is differential risk for spread in various community areas, (2) Determine if community MRSA strains are genomically related to MRSA strains isolated from individuals incarcerated at the jail, and (3) Identify hotspots of MRSA spread in the community using population genomics modeling. This innovative project will be the first to track the spread of MRSA in a large urban area, with results highlighting populations and community areas that may be the best targets for prevention efforts. Because the study will explore well-documented disparities with CA-MRSA, our findings will be generalizable to other underserved populations, underscoring the public health importance.

项目摘要（重写） 社区相关的耐甲氧西林金黄色葡萄球菌 (CA-MRSA) 是城市地区的一个主要问题，非法 吸毒、监禁、不稳定的住房和居住的地理区域均与 CA- MRSA 风险。使用基因组测序，我们之前已经证明社区网络可以 促进 MRSA 在家庭之外的传播以及流行病学暴露，包括居住在 被拘留者高释放区，可以作为被殖民或感染的个人之间联系的基础 基因相似的 MRSA 菌株。监狱促进 MRSA 传播的程度，无论是在 监禁和整个社区都不得而知。我们的初步数据显示比例很高 的人进入已经感染 MRSA 的监狱，监狱为高危人群提供了机会 个体之间的混合可能会促进 MRSA 的进一步传播。由于城市监狱的特点是人员素质高 人员流动率和高累犯率，我们推测监狱可能是 MRSA 传播的主要驱动力之一 回到城市社区。尽管已证明存在与社区环境相关的风险，但研究 MRSA 感染预防检查几乎全部在医院进行。未知是否 社区中感染 MRSA 的传播动态和风险因素与那些相同 医院中的驱动传输。先前对性传播疾病的研究表明， 对城市监狱的干预可以给社区带来显着的下游效益，并提供 对难以接触到的、往往无法获得医疗服务的人群进行干预的机会。我们相信 这种类型的干预措施可以扩展到 MRSA，分子流行病学分析将有助于 设计并最大限度地发挥社区干预的效益。需要资金来检查基因组 城市社区 MRSA 的流行病学，并确定和描述 MRSA 传播的震中。 我们将使用 2008-2018 年现有的 MRSA 临床培养物，并整合这些分离株的基因组数据 使用地理编码、流行病学、被拘留者释放和美国人口普查数据来测试是否存在地理差异 MRSA 传播风险最高的地区。我们将使用空间传输模型来识别 MRSA 的比率 社区内部和社区之间的传播并测试假设的干预措施。该提案有 三个目标：(1) 描述 MRSA 随时间的移动特征，以确定是否存在不同的传播风险 在各个社区区域，(2) 确定社区 MRSA 菌株是否与 MRSA 在基因组上相关 从监狱中被监禁的人中分离出的菌株，以及 (3) 确定 MRSA 在监狱中传播的热点 社区使用群体基因组学模型。这个创新项目将是第一个追踪病毒传播的项目 大城市地区的 MRSA，结果突出显示可能是最好的人口和社区区域 预防工作的目标。由于该研究将探索与 CA-MRSA 之间有据可查的差异，我们 研究结果将推广到其他服务不足的人群，强调公共卫生的重要性。