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

• 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
• 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

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) 物种，特别是耐碳青霉烯类肺炎克雷伯菌 (CRKP)，在全球范围内被视为“紧急威胁”病原体。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，随着时间的推移，多样性会不断发展，目前尚不清楚由特定细菌的克隆但遗传多样性菌株引起的血流感染的频率，因为临床和研究实验室通常对阳性培养物中的单个菌落进行表征。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 个菌落进行了证明，10 名患者中有 8 名的血流感染是由克隆内的、遗传多样性的 CRK 引起的，包括具有非同义的菌株。核心基因组中的单核苷酸多态性、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。来自 2 名患者的遗传变异株在小鼠血流感染期间表现出显着的毒力差异。我们在这项研究中的目的是表征遗传和变异株。从我们医院患者的基线和纵向血培养中恢复的 CRK 菌株的表型多样性，表明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，我们将确定导致基线和复发血流的 CRK 菌株的多样性遗传。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，我们将确定来自每个阳性培养物的遗传上不同的菌株的抗生素敏感性和其他感染。对于优先染色，我们将评估小鼠血流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。我们将测量在患者中观察到多样性的基因的同基因、实验室创建的突变体和互补菌株（例如编码 CPS 的菌株），以及质粒策划和非策划的菌株。这项研究的结果将证实 CRK 阳性血液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决定性遗传因素。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。

项目成果

Within-Host Genotypic and Phenotypic Diversity of Contemporaneous Carbapenem-Resistant Klebsiella pneumoniae from Blood Cultures of Patients with Bacteremia.

菌血症患者血培养中同时期碳青霉烯类耐药肺炎克雷伯菌的宿主内基因型和表型多样性。

• 发表时间: 2022-12-20
• 影响因子: 6.4
• 作者: Cheng, Shaoji;Fleres, Giuseppe;Chen, Liang;Liu, Guojun;Hao, Binghua;Newbrough, Anthony;Driscoll, Eileen;Shields, Ryan K;Squires, Kevin M;Chu, Ting;Kreiswirth, Barry N;Nguyen, M Hong;Clancy, Cornelius J
• 通讯作者: Clancy, Cornelius J