The rates and routes of transmission of multidrug resistant Klebsiella clones and genes into the clinic from environmental sources.

多重耐药克雷伯氏菌克隆和基因从环境来源传播到诊所的速率和途径。

• 批准号: MR/R00241X/1
• 负责人: Edward Feil
• 金额: $ 51.71万
• 依托单位: University of Bath
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2017
• 资助国家: 英国
• 起止时间: 2017 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=MR%2FR00241X%2F1
• 关键词: rates; routes; transmission; multidrug; resistant

Recent years have seen a dramatic global increase of strains of bacteria that pose a high risk in health care settings due to broad resistance to a wide range of antibiotics.Our research project will concentrate on Klebsiella pneumoniae (Klebsiella), a leading cause of multidrug resistant hospital-acquired infections globally, particularly among neonates, the elderly and immunosuppressed patients, with reported mortality rates upwards of 50%. It is also responsible for an increasing burden due to community-acquired invasive infections, which can lead to pyogenic liver abscess, pneumonia, and meningitis. In addition to causing disease, Klebsiella is an ecological generalist and can be carried asymptomatically in the intestinal tract, skin, nose, and throat of healthy individuals, and can thrive in a range of arthropod, bird or plant hosts (including crops and trees) and environmental niches such as water and soil. It can also cause invasive disease in several animal species, and it is a common cause of mastitis in dairy herds.In order to control the spread of Klebsiella through targeted surveillance and intervention policies it is necessary to identify the sources of emergent community and health-care associated infection from the interlinked and varied niches encompassing "the environment". Environmental prevalence data provides a critical baseline, but is not always sufficient to inform on public health policy. For instance, the observation that gulls frequently harbour Klebsiella is, by itself, insufficient to guide policy on managing gull populations, as direct transmission to humans remains very difficult to demonstrate. However, if, say, water were to be identified as a major Klebsiella reservoir with frequent transmission to and from the clinic, this might in turn impact on waste water treatment procedures. Similarly, if cockroaches are found to be associated with Klebsiella this should lead to increased pest control both in hospitals and in the community. To address this, we will take samples in order to identify Klebsiella from multiple clinical, community, agricultural, veterinary and environmental settings. Then we will use a novel approach based on whole genome sequencing to provide a much more efficient means to understand ecological adaptation, the distribution of resistance and virulence genes in the bacteria, and to identify key environmental settings from which these Klebsiella bacterial clones emerge. This approach will involve sequencing multiple colonies of bacteria simultaneously in order to detect a wider sample of genes present within a given sample. We will build a comprehensive, data-driven, model of adaptation, diversification, gene flow and transmission dynamics between all relevant ecological and clinical compartments. This will then pave the way for the development of targeted disease management strategies.

近年来，全球范围内对多种抗生素产生广泛耐药性的高风险细菌菌株急剧增加，我们的研究项目将集中在肺炎克雷伯菌（Klebsiella pneumoniae，Klebsiella），这是全球范围内多重耐药医院获得性感染的主要原因，特别是在新生儿、老年人和免疫抑制患者中，报告的死亡率超过50%。它也是由于社区获得性侵入性感染造成的负担增加的原因，这可能导致化脓性肝脓肿，肺炎和脑膜炎。除了引起疾病，克雷伯氏菌是一种生态通才，可以在健康个体的肠道，皮肤，鼻子和喉咙中无症状地携带，并且可以在一系列节肢动物，鸟类或植物宿主（包括作物和树木）和环境小生境（如水和土壤）中茁壮成长。克雷伯氏菌还可在多种动物中引起侵袭性疾病，是奶牛乳房炎的常见病因。为了通过有针对性的监测和干预政策控制克雷伯氏菌的传播，有必要从“环境”中相互关联和不同的小生境中确定紧急社区和卫生保健相关感染的来源。环境流行率数据提供了一个关键的基线，但并不总是足以为公共卫生政策提供信息。例如，关于海鸥经常携带克雷伯氏菌的观察结果本身不足以指导管理海鸥种群的政策，因为直接传播给人类仍然很难证明。然而，如果，比如说，水被确定为一个主要的克雷伯氏菌水库与频繁的传播进出诊所，这可能反过来影响废水处理程序。同样，如果发现蟑螂与克雷伯氏菌有关，这将导致医院和社区增加害虫控制。为了解决这个问题，我们将采取样本，以确定克雷伯氏菌从多个临床，社区，农业，兽医和环境设置。然后，我们将使用一种基于全基因组测序的新方法，提供一种更有效的手段来了解生态适应，细菌中抗性和毒力基因的分布，并确定这些克雷伯氏菌属细菌克隆出现的关键环境设置。这种方法将涉及同时对多个细菌菌落进行测序，以便检测给定样品中存在的更广泛的基因样品。我们将建立一个全面的，数据驱动的，适应，多样化，基因流动和所有相关的生态和临床分区之间的传输动态模型。这将为制定有针对性的疾病管理战略铺平道路。

项目成果

Rapid statistical methods for inferring intra- and inter-hospital transmission of nosocomial pathogens from whole genome sequence data

从全基因组序列数据推断医院内和医院间病原体传播的快速统计方法

• DOI: 10.1101/442319
• 发表时间: 2018
• 作者: Aspbury M

Genome of Superficieibacter maynardsmithii, a novel, antibiotic susceptible representative of Enterobacteriaceae.

• DOI: 10.1093/g3journal/jkab019
• 发表时间: 2021-02-09
• 期刊: G3 (Bethesda, Md.)
• 作者: Batisti Biffignandi G;Gibbon MJ;Corbella M;Thorpe HA;Merla C;Castelli M;Kallonen T;Pegrum K;Brisse S;Corander J;Marone P;Feil EJ;Sassera D
• 通讯作者: Sassera D

Rapid Genomic Characterization and Global Surveillance of Klebsiella Using Pathogenwatch.

• DOI: 10.1093/cid/ciab784
• 发表时间: 2021-12-01
• 期刊: Clinical infectious diseases : an official publication of the Infectious Diseases Society of America
• 作者: Argimón S;David S;Underwood A;Abrudan M;Wheeler NE;Kekre M;Abudahab K;Yeats CA;Goater R;Taylor B;Harste H;Muddyman D;Feil EJ;Brisse S;Holt K;Donado-Godoy P;Ravikumar KL;Okeke IN;Carlos C;Aanensen DM;NIHR Global Health Research Unit on Genomic Surveillance of Antimicrobial Resistance
• 通讯作者: NIHR Global Health Research Unit on Genomic Surveillance of Antimicrobial Resistance

PIRATE: A fast and scalable pangenomics toolbox for clustering diverged orthologues in bacteria

PIRATE：一种快速且可扩展的泛基因组学工具箱，用于对细菌中不同的直向同源物进行聚类

• DOI: 10.1101/598391
• 发表时间: 2019
• 作者: Bayliss S

One Health drivers of antibacterial resistance: Quantifying the relative impacts of human, animal and environmental use and transmission.

• DOI: 10.1016/j.onehlt.2021.100220
• 发表时间: 2021-06
• 期刊: One health (Amsterdam, Netherlands)
• 作者: Booton RD;Meeyai A;Alhusein N;Buller H;Feil E;Lambert H;Mongkolsuk S;Pitchforth E;Reyher KK;Sakcamduang W;Satayavivad J;Singer AC;Sringernyuang L;Thamlikitkul V;Vass L;OH-DART Study Group;Avison MB;Turner KME
• 通讯作者: Turner KME