E. coli ST131-H30 colonization: defining community and population level antagonism in the gastrointestinal microbiome

 描述(由申请人提供)：大肠杆菌序列类型131(ST131)的一个毒力亚克隆，称为ST131-H30，已成为美国主要的肠外致病大肠杆菌谱系，每年导致数千名患者死亡。多药耐药是ST131-H30的一个特点--包括产生CTX-M-15超广谱β-内酰胺酶(ESBL)--使其临床管理特别具有挑战性。ST131-H30比其他菌株更频繁和持久地定植的能力被认为是其不成比例的负担的重要原因。然而，在我们的初步研究中，我们观察到，尽管长期暴露在家庭中，一些人仍未能感染ST131-H30。这有力地表明，除ST131-H30‘S的固有性状外，其他因素也会影响定殖率。我们知道，在人类胃肠道中，ST131-H30并不是单独生活的，而是作为复杂微生物群落的一个次要组成部分，在其中它可能受到物种间和物种内的激烈竞争。在我们之前对其他身体部位的微生物组研究中，我们观察到共生细菌和机会病原体之间的可预测关系。这导致我们假设GI微生物区系的不同成分，包括产生细菌素的大肠杆菌菌株，可能竞争性地排除ST131-H30。方法：通过对600名参与者(他们将贡献7,000份粪便标本)的持续纵向研究，我们将进行两项病例对照研究，以确定尽管家庭持续接触ST131-H30但仍保持12个月未感染ST131-H30的个人所特有的微生物区系(精英非殖民者)，与持续受到ST131-H30持续殖民12个月的个人(精英殖民者)和在研究期间新感染ST131-H30的个人(收购者)进行比较。我们将使用指示种和决策树分析来确定最能预测对ST131-H30 GI定植耐药的细菌种。该决策模型将使用来自另一项横断面调查的另外300名参与者的粪便微生物区系数据进行验证。为了探索种内竞争，我们将使用体外抑制试验来鉴定对ST131-H30具有拮抗作用的共生大肠杆菌菌株，并将通过使用纵向和横断面队列数据来评估拮抗菌株与ST131-H30排除的相关性来交叉验证体外结果。创新：我们的方法是创新的，它试图定义影响ST131-H30胃肠道定植的机制；它的重点是精英非定殖者；它在正在进行的纵向流行病学研究中对微生物群进行物种间和物种内的调查；以及它的目标是识别对单个毒力大肠杆菌亚克隆具有拮抗作用的共生细菌。这项研究的预期结果是鉴定能够从胃肠道中排除ST131-H30的共生菌。随着新出现的耐药性抵消了我们目前的抗生素机构的有效性，我们必须找到新的方法来防止多重耐药定植病原体的传播。这些结果可能导致新的益生菌策略，以阻断ST131-H30和未来多药耐药定植病原体的传播。

 DESCRIPTION (provided by applicant): A virulent subclone of E. coli sequence type 131 (ST131), called ST131-H30, has become the dominant extraintestinal pathogenic E. coli lineage in the US, where it kills thousands of patients each year. Multidrug resistance is a hallmark of ST131-H30-including production of the CTX-M-15 extended spectrum beta-lactamase (ESBL)-making its clinical management particularly challenging. The ability of ST131-H30 to colonize more frequently and persistently than other strains is thought to be important to its disproportional dis- ease burden. Yet, in our preliminary studies, we have observed that some people fail to become colonized with ST131-H30 despite prolonged household exposure. This strongly suggests that factors other than ST131- H30's intrinsic traits influence colonization. We know that, in the human GI tract, ST131-H30 does not live alone, but rather, as a minor component of a complex microbial community, within which it may be subjected to intense inter- and intra-species competition. In our previous microbiome studies of other body sites, we observed predictable relationships between commensal bacteria and opportunistic pathogens. This led us to hypothesize that distinct components of the GI microbiota, including bacteriocin-producing E. coli strains, may competitively exclude ST131-H30. Approach: By leveraging an ongoing longitudinal study of 600 participants, who will contribute > 7,000 fecal specimens, we will conduct two case-control studies to identify the microbiota unique to individuals who remain free of ST131-H30 for 12 months despite ongoing household exposure to ST131-H30 (elite non-colonizers), as compared to individuals with persistent colonization by ST131-H30 for 12 months (elite colonizers) and individuals who newly acquire ST131-H30 during the study (acquirers). We will identify bacterial species most predictive of resistance to ST131-H30 GI colonization using indicator species and decision tree analysis. The decision model will be validated using fecal microbiota data from an additional 300 participants from another cross-sectional survey. To explore intra-species competition, we will identify commensal E. coli strains antagonistic to ST131-H30 using in vitro inhibition assays, and will cross-validate the in vitro results by assessing the antagonistic strains' association with ST131-H30 exclusion using data from the longitudinal and cross-sectional cohorts. Innovation: Our approach is innovative in attempting to define mechanisms that influence GI colonization with ST131-H30; its focus on elite non-colonizers; its inter- and intra- species investigation of the microbiome within an ongoing longitudinal epidemiologic study; and its goal of identifying commensal bacteria antagonistic to a single virulent E. coli subclone. The expected outcome of this study is to identify commensal bacteria that can exclude ST131-H30 from the GI tract. With emerging resistance neutralizing the effectiveness our current antibiotic armamentarium, we must find new ways to prevent the spread of multidrug-resistant colonizing pathogens. These results could lead to novel, probiotic strategies for interrupting the transmission of ST131-H30 and future multidrug-resistant colonizing pathogens.