Evolution of KPC-K pneumoniae that persist in patients on prolonged antibiotics

长期服用抗生素的患者体内持续存在的 KPC-K 肺炎的演变

• 批准号: 8823883
• 负责人: CORNELIUS J CLANCY
• 金额: $ 22.47万
• 依托单位: UNIVERSITY OF PITTSBURGH AT PITTSBURGH
• 依托单位国家: 美国
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-12-01 至 2016-11-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8823883
• 关键词: Abdominal Infection; Acute; Anabolism; Antibiotic Resistance; Antibiotics; Antimicrobial Resistance; Attenuated; Bacteremia; Bacteria; Biological Assay; Biological Markers; Blood Circulation; Carbapenems; Cessation of life; Clinical; Colistin; Complementarity Determining Regions; Data; Databases; Development; Diagnostic tests; Environment; Epidemiology; Evolution; Exhibits; Extreme drug resistant tuberculosis; Gene Expression; Gene Expression Profile; Genes; Genetic; Genetic Heterogeneity; Genome; Goals; Heterogeneity; Hospitals; Individual; Infection; Intra-abdominal; Iron; Klebsiella pneumonia bacterium; Lead; Link; Lipopolysaccharides; Measures; Molecular; Mus; Mutation; Outcome; Pathogenesis; Patients; Pharmacy facility; Plasmids; Process; Production; Recurrence; Relative (related person); Resistance; Resources; Sampling; Septic Shock; Staining method; Stains; Stress; Symptoms; Testing; Time; Transplant Recipients; Treatment Protocols; Vaccine Therapy; Virulence; Virulent; antimicrobial; antimicrobial drug; attenuation; base; biobank; biological adaptation to stress; capsule; carbapenem resistance; carbapenemase; clinical investigation; colistin resistance; doripenem; fitness; functional genomics; genetic evolution; genetic makeup; in vitro Assay; in vivo; insight; killings; microbial; mortality; mouse model; mutant; novel diagnostics; pathogen; porin; predictive marker; pressure; public health relevance; research study; resistant strain; response; stem; therapeutic vaccine; transcriptome sequencing; treatment response

 DESCRIPTION (provided by applicant): Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae (KPC-Kp) have emerged as major pathogens, causing extensively drug resistant infections with crude mortality rates that can exceed 50%. Since 2008, we have maintained a biorepository of >700 KPC-Kp strains from our center, linked to clinical and pharmacy databases. We have shown that outcomes among patients with KPC-Kp bacteremia and intra- abdominal infections (IAI) range from acute death due to septic shock, to rapid cure, to recurrent or persistent infections that have lasted for more than a year. As is true at most U.S centers, KPC-Kp sequence type 258 (ST258) strains predominate among our patients. Our preliminary data demonstrate that ST258, KPC-Kp strains that are clonal by conventional molecular epidemiologic criteria exhibit significant genetic heterogeneity, including in antimicrobial resistance repertoire, porin function and within the chromosomal hypervariable region. Longitudinal strains from individual patients with persistent infections become increasingly resistant to antimicrobial agents, and have mutations in genes involved in lipopolysaccharide and capsule biosynthesis, iron transport, stress responses and other processes. Our major goal in this project is to identify the genetic bases by which KPC-Kp strains cause persistent infections. We hypothesize that persistence stems, at least in part, from the development of further antimicrobial resistance and attenuation of virulence by strains in response to treatment regimens and the stresses of in vivo environments. Our objectives are to comprehensively define genetic differences among ST258, KPC-Kp strains causing persistent infections, characterize the genetic evolution of strains during persistent infections, and correlate these results with antimicrobial resistance, virulence and gene expression in vivo. To achieve these objectives, we will pursue two specific aims. In aim 1, we will test longitudinally-collected ST258, KPC-Kp strains from patients with persistent infections for the emergence of resistance to the combination of doripenem and colistin (our front- line treatment regimen) during time-kill assays in vitro, and relative virulence during intra-abdominal infections of mice. Based on preliminary data, we anticipate that last longitudinal strains will be more resistant to doripenem-colistin and less acutely virulent than first longitudinal strains. In aim 2, we will perform whole genome and plasmid sequencing on ST258, KPC-Kp strains, use RNA-Seq to define transcriptomes in mice during IAIs, and create mutant strains to verify that genes identified by sequencing and RNA-Seq contribute to resistance and virulence. We anticipate that our results will afford insights into mechanisms by which KPC-Kp strains adapt to treatment and environmental pressures during infections. This project will generate new hypotheses about resistance and pathogenic mechanisms, and identify targets for the development of novel diagnostics, therapeutics, vaccines, and predictive markers for treatment responses.

 描述（由申请人提供）：产生肺炎克雷伯菌碳青霉烯酶（KPC）的肺炎克雷伯菌（KPC-Kp）已成为主要病原体，主要引起耐药性感染，粗死亡率可超过 50% 自 2008 年以来，我们一直认为。我们中心拥有超过 700 种 KPC-Kp 菌株的生物储存库，与临床和药学数据库相连，我们已经证明了 KPC-Kp 患者的结果。菌血症和腹腔内感染 (IAI) 的范围从感染性休克导致的急性死亡到快速治愈，再到持续一年以上的复发或持续感染，KPC-Kp 序列类型 258 是如此。 (ST258) 菌株在我们的患者中占主导地位，我们的初步数据表明，通过传统分子流行病学克隆的 ST258、KPC-Kp 菌株表现出显着的遗传异质性，包括在持续感染个体患者的抗菌药物耐药性、孔蛋白功能和纵向菌株对抗菌药物的耐药性越来越强，并且涉及脂多糖和荚膜生物合成、铁转运、应激反应和其他过程的基因发生突变。该项目的主要目标是确定 KPC-Kp 菌株引起持续性感染的遗传基础，我们努力证明持续性至少部分源于此。菌株对治疗方案和体内环境应激的进一步耐药性的发展和毒力减弱我们的目标是全面定义引起持续感染的 ST258、KPC-Kp 菌株之间的遗传差异，表征菌株的遗传进化。为了实现这些目标，我们将在目标 1 中实现纵向收集的两个具体目标。来自持续感染患者的 ST258、KPC-Kp 菌株，在体外时间杀灭试验中出现对多尼培南和粘菌素（我们的一线治疗方案）组合的耐药性，以及在小鼠腹内感染期间的相对毒力。 根据初步数据，我们预计最后的纵向菌株将比第一个纵向菌株对多尼培南粘菌素具有更强的耐药性，并且毒性较小。在目标 2 中，我们将对 ST258、KPC-Kp 菌株进行全基因组和质粒测序，使用 RNA。 -Seq 定义 IAI 期间小鼠的转录组，并创建突变株以验证通过测序和 RNA-Seq 鉴定的基因是否有助于耐药性和毒力。该项目将产生关于耐药性和致病机制的新假设，并确定开发新型诊断、治疗、疫苗和治疗反应预测标记的目标。