Real-Time Whole Genome Sequencing Analysis of Carbapenemase-Producing Organisms in the Non-Outbreak Hospital Setting

项目摘要： 携带碳青霉烯酶的革兰氏阴性菌在世界范围内迅速传播， 健康问题，导致死亡率高达60%。产碳青霉烯酶微生物（CPO）是 由于其日益增加的患病率，其多药耐药（MDR）特征及其 容易在种与种之间传播，甚至在革兰氏阴性菌的不同属之间传播 通过可传递的遗传元件（即转座子、插入序列和质粒）。知识差距： 在美国，对CPO传播的研究一般仅限于暴发环境; 在地方性环境中的传播情况基本上是未知的。此外，研究评估了 碳青霉烯酶一般仅限于肠杆菌科;葡萄糖非发酵菌的作用 (e.g.,假单胞菌属和不动杆菌属）大多被忽略了。我们建议填补这些空白， 通过了解抗生素耐药性的分子机制，并在所有CPO中传播 （肠杆菌科和葡萄糖非发酵菌）在美国的一个地区流行的CPO。这些数据将 在确定如何最好地限制患者之间的CPO传播和指导治疗决策方面至关重要。 为了实现这些目标，我们组建了一个由临床科学家、生物医学工程师和 具有临床微生物学、流行病学、传染病、抗生素等专业知识的生物信息学家 管理，并在新的MinION技术的应用。目的1：确定分子机制 使用全基因组测序在非暴发环境中传播CPO所涉及的传播 （WGS）。目的2：鉴定CPO分离株所携带的所有耐药基因，以将耐药基因连接起来 携带碳青霉烯酶的循环克隆或质粒。目标3：确定是否与 具有特定质粒或克隆的抗性基因可用于准确预测抗生素敏感性 CPO临床分离株的特征。重要性和影响：通过更好地了解 的分子机制的耐药性和传播之间的CPO，我们可以帮助指导治疗和适当的 预防策略，以阻止这些重要病原体在临床环境中的传播。

Project Summary: Gram-negative bacteria harboring carbapenemases are rapidly spreading worldwide and are a significant public health concern, resulting in mortality upwards of 60%. Carbapenemase-producing organisms (CPO) are considered a triple threat due to their increasing prevalence, their multidrug-resistant (MDR) profile, and their ease of transmission from species to species and even among different genera of Gram-negative bacteria through transmissible genetic elements (i.e. transposons, insertion sequences, and plasmids). Knowledge gaps: Studies of CPO transmission in the US have generally been limited to outbreak settings; data regarding transmission in endemic settings are largely unknown. Additionally, studies evaluating transmission of carbapenemases have generally been restricted to Enterobacteriaceae; The role of glucose non-fermenters (e.g., Pseudomonas and Acinetobacter spp.) has mostly been ignored. We propose to fill these gaps in knowledge by understanding the molecular mechanisms of antibiotic resistance and spread amongst all CPO (Enterobacteriaceae and glucose non-fermenters) in a region of the US endemic for CPO. These data will be critical in determining how best to limit CPO transmission between patients and to guide therapeutic decisions. To accomplish these goals, we have assembled a team of clinician-scientists, biomedical engineers, and bioinformaticians with expertise in clinical microbiology, epidemiology, infectious diseases, antibiotic stewardship, and in applications of the novel MinION technology. Aim 1: Determine the molecular mechanisms of spread involved in the dissemination of CPO in a non-outbreak setting using whole genome sequencing (WGS). Aim 2: Identify all antibiotic-resistance genes harbored by the CPO isolates to link the resistance genes to the circulating clones or plasmids harboring carbapenemases. Aim 3: Determine if the association of resistance genes with particular plasmids or clones can be used to accurately predict antibiotic susceptibility profiles of CPO clinical isolates. Significance and Impact: By gaining a better understanding of the complexity of the molecular mechanisms of resistance and spread among CPO, we can help guide therapy and appropriate prevention strategies to halt the spread of these important pathogens within the clinical setting.