Genomic variation in epidemic carbapenem-resistant K.pneumoniae

流行性耐碳青霉烯类肺炎克雷伯菌的基因组变异

• 批准号: 9035583
• 负责人: Liang Chen
• 金额: $ 23.85万
• 依托单位: RBHS-NEW JERSEY MEDICAL SCHOOL
• 依托单位国家: 美国
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-01-01 至 2017-12-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9035583
• 关键词: Accounting; Antibiotic Resistance; Antibiotics; Antigens; Automobile Driving; Bacteremia; Bacteria; Biological; Biological Assay; Centers for Disease Control and Prevention (U.S.); Characteristics; Chromosome Structures; Chromosomes; Clinical; Data; Development; Diagnostic; Diagnostic tests; Disease; Effectiveness; Epidemic; Epidemiology; Future; Generations; Genes; Genetic; Genetic Recombination; Genetic Variation; Genome; Genomics; Goals; Hospitals; Human; Hybrids; Immune response; Immunity; Immunocompromised Host; In Vitro; Infection; Inherited; Klebsiella pneumonia bacterium; Lead; Measures; Mobile Genetic Elements; Modeling; Molecular Evolution; Molecular Genetics; Morbidity - disease rate; Multi-Drug Resistance; Nosocomial Infections; Operon; Other Genetics; Plasmids; Polysaccharides; Public Domains; Recombinants; Recording of previous events; Resistance; Role; Serum; Source; Streptococcus pneumoniae; Surface Antigens; Testing; Therapeutic; United States; Vaccines; Variant; Virulence; Virulence Factors; Virulent; antimicrobial; capsule; carbapenem resistance; carbapenem-resistant Enterobacteriaceae; carbapenemase; combat; comparative genomics; driving force; gene synthesis; genetic variant; genome sequencing; genomic variation; in vivo; in vivo Model; mortality; mouse model; neutrophil; novel; novel therapeutics; pathogen; pathogenic bacteria; pressure; public health relevance; resistant strain; success; transmission process; whole genome

 DESCRIPTION (provided by applicant) Carbapenem-resistant Enterobacteriaceae (CRE), especially Klebsiella pneumoniae carbapenemase (KPC)- producing K. pneumoniae (KPC-Kp), have emerged as a significant hospital-acquired pathogen causing considerable morbidity and mortality in the United States and worldwide. Strikingly, a large majority of KPC-Kp isolates belong to a single sequence type, ST258. However, the molecular evolution of this epidemic clone is still very poorly understood and the genetic factors contributing to its epidemiological success remain unknown. Recent comparative genomic studies indicate that Kp ST258 strains are undergoing significant diversification in both plasmid and chromosome structures, especially at the K-antigen encoded capsular polysaccharides synthesis (cps) gene operons. Similar to what has been described in other pathogenic bacteria (e.g. Streptococcus pneumoniae), the recombination of cps-harboring region appears to be a major driving force in the genetic diversification in ST258. To date, we have found six different cps operons (cps-1 to -6) in Kp ST258 strains and identified several ST258 associated blaKPC-harboring plasmids. Notably, our preliminary data showed the variations in ST258 clades (different cps groups) are not limited to the cps regions, but also involve multiple loci that harbor genes contributing to colonization, resistance and virulence. One significant concern is that this epidemic clone may acquire enhanced virulence via chromosomal recombination and/or plasmid transfer, evolving as a highly virulent, multidrug resistant (HV-MDR) strain and further complicating current efforts to battle this crisis. Alarmingly, our preliminary results showed that certain "new" Kp ST258 clades (i.e. harboring novel cps operons) had higher virulence in comparison to strains from other circulating clades. Thus, we hypothesize that variable chromosomal regions and/or acquired plasmids alter host-pathogen interactions that may lead to the emergence of strains of enhanced virulence. Our objective is to identify these genomic factors and plasmid contents, and characterize their biological role associated with ST258 virulence, and examine plasmid transmissibility. In this application, we will investigate the extent to which genetic recombination has influenced genetic variation in Kp ST258. Through whole genome sequencing (WGS) of representative Kp isolates from different cps groups (cps-1 to cps-6) as well as their putative donor strains (unique STs that are likely the source of the cps replacement in ST258), we will systematically evaluate both large and small scale genomic variations in this epidemic clone and elucidate their molecular evolution history (Aim 1). Next, by using in vitro and in vivo models, we will investigate whether recombination that results in replacement of capsule-encoding machinery as well as other biologically important loci results in the emergence of HV-MDR clades (Aim 2a). In addition, we will test the hypothesis that ST258 genetic background has higher transfer efficiency and stability for KPC plasmids, which may partly explain the success of this KPC epidemic clone (Aim 2b). The results generated in this study will yield a wealth of information regarding the content and characteristics of Kp genomic variations and will likely identify novel virulence factors. The identification of genomic variations that impact the disease-causing potential of Kp strains will provide potential diagnostic and therapeutic solutions.

 描述（由申请人提供） 耐碳青霉烯类肠杆菌科 (CRE)，尤其是产肺炎克雷伯菌碳青霉烯酶 (KPC) 的肺炎克雷伯菌 (KPC-Kp)，已成为一种重要的医院获得性病原体，在美国和全世界造成相当大的发病率和死亡率。引人注目的是，绝大多数 KPC-Kp 分离株属于单一序列类型 ST258。然而，人们对这种流行性克隆的分子进化仍然知之甚少，导致其流行病学成功的遗传因素仍然未知。最近的比较基因组研究表明，Kp ST258 菌株在质粒和染色体结构方面正在经历显着的多样化，特别是在 K 抗原编码的荚膜多糖合成 (cps) 基因操纵子上。与其他病原菌（例如肺炎链球菌）中所描述的类似，cps 携带区域的重组似乎是 ST258 遗传多样化的主要驱动力。迄今为止，我们在 Kp ST258 菌株中发现了 6 个不同的 cps 操纵子（cps-1 至 -6），并鉴定了几个 ST258 相关的 blaKPC 携带质粒。值得注意的是，我们的初步数据显示 ST258 进化枝（不同 cps 组）的变异不仅限于 cps 区域，还涉及多个位点，这些位点含有有助于定植、抗性和毒力的基因。一个重要的担忧是，这种流行性克隆可能通过染色体重组和/或质粒转移获得增强的毒力，演变成一种高毒力、多重耐药（HV-MDR）菌株，并使当前应对这一危机的努力进一步复杂化。令人震惊的是，我们的初步结果表明，某些“新”Kp ST258 分支（即携带新的 cps 操纵子）与其他流行分支的菌株相比具有更高的毒力。因此，我们假设可变染色体区域和/或获得性质粒改变宿主-病原体相互作用，可能导致毒力增强菌株的出现。我们的目标是鉴定这些基因组因子和质粒内容，并表征它们与 ST258 毒力相关的生物学作用，并检查质粒的传播性。在此应用中，我们将研究基因重组对 Kp ST258 遗传变异的影响程度。通过对来自不同 cps 组（cps-1 至 cps-6）的代表性 Kp 分离株及其假定的供体菌株（可能是 ST258 中 cps 替代来源的独特 ST）进行全基因组测序（WGS），我们将系统地评估该流行克隆中的大规模和小规模基因组变异，并阐明其分子进化历史（目标 1）。接下来，通过使用体外和体内模型，我们将研究导致胶囊编码机制以及其他生物学重要位点替换的重组是否导致 HV-MDR 进化枝的出现（目标 2a）。此外，我们将测试 ST258 遗传背景对 KPC 质粒具有更高的转移效率和稳定性的假设，这可能部分解释了该 KPC 流行克隆的成功（目标 2b）。本研究产生的结果将产生有关 Kp 基因组变异的内容和特征的大量信息，并可能识别新的毒力因子。影响 Kp 菌株致病潜力的基因组变异的鉴定将提供潜在的诊断和治疗解决方案。