权益分类	功能权益	普通用户	{{item.name}}会员
{{category.name}}	{{benefitItem.name}}

Polyclonality of carbapenem resistant Enterobacteriaceae bloodstream infections

碳青霉烯类耐药肠杆菌科细菌血流感染的多克隆性

基本信息

批准号：
10301365
负责人：
CORNELIUS J CLANCY
金额：
$ 20.46万
依托单位：
UNIVERSITY OF PITTSBURGH AT PITTSBURGH
依托单位国家：
美国
项目类别：
财政年份：
2020
资助国家：
美国
起止时间：
2020-11-12 至 2023-10-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10301365
关键词：
Antibiotic Resistance Antibiotic Therapy Antibiotic susceptibility Antibiotics Attenuated Bacteremia Bacteria Blood Blood Circulation Cessation of life Clinical Microbiology Clinical Research Complement Data Exhibits Failure Foundations Gastrointestinal tract structure Gene Deletion Gene Mutation Gene Targeting Genes Genetic Genetic Determinism Genetic Variation Genome Genotype Hospitals Human Hyperviscosity In Vitro Individual Infection Intravenous Investigation Klebsiella Klebsiella Infections Klebsiella pneumoniae Laboratory Research Laboratory Study Measures Meropenem Mining Mus Mutation Outcome Outcome Measure Pathogenesis Patients Pattern Phagocytosis Phenotype Phylogenetic Analysis Phylogeny Plasmids Polysaccharides Population Recurrence Recurrent disease Resistance Sepsis Serum Siderophores Single Nucleotide Polymorphism Site Stains Symbiosis Testing Time Tissues Treatment Failure VDAC1 gene Variant Virulence Virulence Factors antibiotic tolerance bacterial resistance beta-Lactamase carbapenem resistance carbapenem-resistant Enterobacteriaceae carbapenemase clinically significant follow-up genetic variant gut colonization individual patient insight mortality mutant novel opportunistic pathogen pathogen research study resistant Klebsiella pneumoniae response treatment response whole genome

项目摘要

Carbapenem resistant Klebsiella (CRK) species, in particular carbapenem resistant Klebsiella pneumoniae (CRKP), are recognized as “urgent threat” pathogens globally. Bloodstream and other serious Klebsiella infections, including those due to CRK, usually are caused by a strain that colonizes the gastrointestinal (GI) tract. Emerging whole genome sequence (WGS) data show that the GI tract is colonized by clonal bacterial populations, in which genetic diversity develops over time. It is unknown how often bloodstream infections are caused by clonal but genetically diverse strains of a given bacterium, since clinical and research laboratories generally characterize a single colony from positive cultures. In preliminary studies, we performed WGS on 10 colonies from the first CRK-positive blood culture of 10 randomly selected patients. We demonstrated that bloodstream infections in 8 of 10 patients were caused by intraclonal, genetically diverse CRK, including strains with non-synonymous single nucleotide polymorphisms in the core genome, chromosomal gene deletions, insertions and other mutations, and plasmid or plasmid-borne gene loss. Genotypically distinct CRK strains exhibited significant differences in antibiotic susceptibility, capsular polysaccharide (CPS) content, and other virulence-associated phenotypes. Genetic variant strains from 2 patients displayed significant differences in virulence during bloodstream infections of mice. Our objectives in this study are to characterize the genetic and phenotypic diversity of CRK strains recovered from baseline and longitudinal blood cultures of patients in our hospital and to implicate specific genes, plasmids and mutations in antibiotic resistance and virulence. In specific aim 1, we will determine genetic diversity of CRK strains causing baseline and recurrent bloodstream infections by performing WGS, plasmid sequencing, and analyses of core genome phylogeny and gene mutations for individual colonies selected from positive blood cultures. For genetically distinct strains from each positive culture, we will determine antibiotic susceptibility and other phenotypes in vitro. For prioritized stains, we will assess antibiotic responses and virulence during mouse bloodstream infections. In specific aim 2, we will validate the impact of specific genes, plasmids and mutations on antibiotic treatment responses and virulence. We will infect mice intravenously with isogenic, lab-created mutant and complemented strains for genes in which diversity was observed in patients (e.g., those encoding CPS), and plasmid-curated and non-curated strains. We will measure outcomes in mice treated and not treated with antibiotics. Results from this study will affirm the extent and type of genetic diversity in CRK-positive blood cultures, afford new insights into CRK strain dynamics during bloodstream infections, and identify novel genetic determinants of antibiotic treatment responses and virulence. Insights gathered here will form a foundation for investigations of genetic diversity during bloodstream and other infections by non-CR Klebsiella and other bacteria, and for mechanistic studies of CRK genes or gene targets that dampen antibiotic responses and promote pathogenesis.

耐碳青霉烯类克雷伯菌（CRK），特别是耐碳青霉烯类肺炎克雷伯菌（CRKP），在全球范围内被认为是“紧急威胁”病原体。血液感染和其他严重的克雷伯氏菌感染，包括 CRK 引起的感染，通常是由定植于胃肠道 (GI) 的菌株引起的。新出现的全基因组序列（WGS）数据表明，胃肠道被克隆细菌群体定殖，其中遗传多样性随着时间的推移而发展。由于临床和研究实验室通常从阳性培养物中表征单个菌落，因此尚不清楚特定细菌的克隆但遗传多样性菌株引起血流感染的频率。在初步研究中，我们对 10 名随机选择的患者的第一个 CRK 阳性血培养物中的 10 个菌落进行了全基因组测序 (WGS)。我们证明，10 名患者中有 8 名的血流感染是由克隆内遗传多样性 CRK 引起的，包括核心基因组中具有非同义单核苷酸多态性的菌株、染色体基因缺失、插入和其他突变，以及质粒或质粒携带的基因丢失。基因型不同的 CRK 菌株在抗生素敏感性、荚膜多糖 (CPS) 含量和其他毒力相关表型方面表现出显着差异。 2名患者的基因变异株在小鼠血流感染过程中表现出显着的毒力差异。我们在这项研究中的目的是表征从我们医院患者的基线和纵向血培养中恢复的 CRK 菌株的遗传和表型多样性，并揭示抗生素耐药性和毒力中的特定基因、质粒和突变。在具体目标 1 中，我们将通过对从阳性血培养物中选择的单个菌落进行全基因组测序、质粒测序以及核心基因组系统发育和基因突变分析，确定导致基线和复发性血流感染的 CRK 菌株的遗传多样性。对于来自每个阳性培养物的遗传上不同的菌株，我们将在体外确定抗生素敏感性和其他表型。对于优先染色，我们将评估小鼠血液感染期间的抗生素反应和毒力。在具体目标 2 中，我们将验证特定基因、质粒和突变对抗生素治疗反应和毒力的影响。我们将用实验室创建的同基因突变体和互补菌株静脉内感染小鼠，其中在患者中观察到基因多样性（例如，编码 CPS 的菌株），以及质粒策划和非策划菌株。我们将测量接受抗生素治疗和未接受抗生素治疗的小鼠的结果。这项研究的结果将证实 CRK 阳性血培养物中遗传多样性的程度和类型，为血流感染期间 CRK 菌株动态提供新的见解，并确定抗生素治疗反应和毒力的新遗传决定因素。这里收集的见解将为研究非 CR 克雷伯氏菌和其他细菌的血流和其他感染过程中的遗传多样性以及抑制抗生素反应和促进发病机制的 CRK 基因或基因靶标的机制研究奠定基础。