Genomic characterisation of multidrug-resistant septicaemia-causing Klebsiella pneumoniae to inform patient care and infection control

引起多重耐药败血症的肺炎克雷伯菌的基因组特征可为患者护理和感染控制提供信息

• 批准号: 2893013
• 金额: --
• 依托单位: University of Edinburgh
• 依托单位国家: 英国
• 项目类别: Studentship
• 财政年份: 2023
• 资助国家: 英国
• 起止时间: 2023 至 无数据
• 项目状态: 未结题
• 来源: https://gtr.ukri.org/projects?ref=studentship-2893013
• 关键词: Genomic; characterisation; multidrug; resistant; septicaemia

Antimicrobial resistance (AMR) is global health crisis. Klebsiella pneumoniae, a Gram-negative bacteria, that are resistant to carbapenems (part of the last-line drugs for difficult-to-treat infections) are on the World Health Organization's list of critically resistant pathogens. They contribute to many healthcare-associated infections and are associated with increased mortality and morbidity. This is partly due to their ability to rapidly become systemic from the initial infection site, but also because they can share resistance genes on mobile genetic elements, such as plasmids, leading them to rapidly spread AMR to other Gram-negative species. This can lead to failed antimicrobial therapy and negative patient outcomes, especially in cases where rapid administration of the correct antibiotics is crucial, such as sepsis. These plasmids can also carry genes that aid in environmental survival, regulate virulence factors and confer multidrug resistance. Plasmid acquisition can, therefore, change the bacterial phenotype and alter disease severity and patient outcomes. Thus, it is important to understand the mechanisms of plasmid evolution to be able to predict changes in virulence and risk of plasmid spread. In this project, we will employ long-read sequencing to analyse the genomes of clinical isolates of K. pneumoniae where it caused sepsis in patients. We aim to understand why some strains caused fatal infections while others did not. Bioinformatic analyses will be employed to identify both chromosomal and plasmid-borne AMR genes, virulence factors and error-prone polymerases that may lead to mutations. This will be complemented by phenotypic assessments such as survival within phagocytic cells and antimicrobial susceptibility to understand the differences in patient outcomes. Environmental survival in the presence of disinfectants, desiccated conditions and adherence to surfaces will be investigated to assess environmental survival and spread as fomites. We will also set up long-term cultures in the presence of sub-inhibitory concentrations of antibiotics to evaluate the role of error-prone polymerases in carbapenemase evolution, enzymes that inactivate Beta-lactam antibiotics. This will be supported by frequent sequencing and phenotypic characterisation to identify genetic mutations and changes in phenotypic expression. We will also conduct inter- and intra-species plasmid transfer and associated changes in phenotypes to plasmid-free strains in gut bacteria. These investigations will result in an understanding how whole-genome sequencing can influence patient treatment outcomes, manage pathogen and plasmid spread and inform infection control practices and surveillance of resistant pathogens in healthcare settings. This should aid in the development of new strategies to combat the spread of plasmids and resistant pathogens.

抗菌素耐药性(AMR)是全球性的健康危机。肺炎克雷伯氏菌是一种革兰氏阴性细菌，对碳青霉烯类(治疗难治感染的最后一线药物的一部分)具有耐药性，被列入世界卫生组织的严重耐药病原体名单。它们导致许多与医疗保健相关的感染，并与死亡率和发病率的增加有关。这在一定程度上是因为它们有能力从最初的感染部位迅速成为全身性的，但也因为它们可以在可移动的遗传元件上共享抗药性基因，如质粒，导致它们将AMR迅速传播给其他革兰氏阴性物种。这可能导致抗菌治疗失败和患者的负面结果，特别是在快速给予正确的抗生素至关重要的情况下，如败血症。这些质粒还可以携带有助于环境生存、调节毒力因子和产生多药耐药性的基因。因此，获取质粒会改变细菌的表型，改变疾病的严重程度和患者的预后。因此，了解质粒进化的机制，以便能够预测毒力的变化和质粒传播的风险是很重要的。在这个项目中，我们将使用长阅读测序来分析导致患者败血症的肺炎克雷伯菌临床分离株的基因组。我们的目标是了解为什么一些菌株会导致致命的感染，而另一些菌株则不会。生物信息学分析将用于识别染色体和质粒携带的AMR基因、毒力因子和可能导致突变的容易出错的聚合酶。这将得到表型评估的补充，例如吞噬细胞内的存活率和抗菌素敏感性，以了解患者预后的差异。将调查在消毒剂存在、干燥条件和表面附着情况下的环境生存情况，以评估环境生存和作为混合菌群传播。我们还将建立长期培养，在存在亚抑制浓度的抗生素的情况下，评估容易出错的聚合酶在碳青霉烯酶进化中的作用，碳青霉烯酶是使β-内酰胺类抗生素失活的酶。这将得到频繁测序和表型特征的支持，以确定表型表达的遗传突变和变化。我们还将进行物种间和物种内的质粒转移和相关的表型变化，以使肠道细菌中的无质粒菌株。这些研究将使人们了解全基因组测序如何影响患者的治疗结果，管理病原体和质粒的传播，并为医疗保健环境中的感染控制做法和耐药病原体的监测提供信息。这应该有助于制定新的战略，以抗击质粒和耐药病原体的传播。