The evolutionary ecology of plasmid-mediated horizontal gene transfer in the hospital sink drain ecosystem

机会性病原体中的抗菌素耐药性(AMR)是现代医学面临的一大新威胁。一个难以治疗的机会性感染的世界既影响了感染的直接负担，也影响了如果选择性手术变得过于危险对生活质量的更广泛影响。当细菌从他们的邻居那里获得被称为质粒的DNA片段时，通常会出现AMR。质粒传播可能发生在感染环境之外，也不需要抗生素的选择，因此许多条件致病菌在有机会引起感染之前，就在它们的正常栖息地获得了AMR。然而，细菌携带质粒的能力可能会有所不同，某些物种或菌株比其他物种或菌株更善于携带和传播质粒。因此，在细菌群落的背景下了解质粒生物学对于预测和控制机会性病原体的AMR至关重要。医院病房的水槽是发生临床影响的AMR的关键栖息地。细菌通过水滴和气溶胶从汇上扩散，基因组监测表明汇是AMR爆发的点源。洗涤槽通常靠近高抗菌剂使用环境，这可能提供抗药性细菌的来源，而感染可能提供危险病原体的来源。汇维持着强大、持久的多物种生物膜，这有利于促进质粒传播的密切相互作用。接收器也经常用化学物质处理，这些化学物质既可以直接触发质粒结合，也可以选择与AMR一起携带消毒剂抗性的质粒。然而，在支持动物模型的AMR研究中，病房水池独特的生态系统经常被忽视。在这个项目中，我将直接研究汇微生物生态系统中质粒传播的进化和生态驱动因素。我将把重点放在铜绿假单胞菌上--这是一种常见的汇居民，是机会性感染的主要原因，也是AMR研究的“关键优先事项”(世界卫生组织，2017)，因为如果没有有效的抗生素，假单胞菌感染可能很难控制。我之前对假单胞菌的工作发现并表征了一个广泛的导致AMR的质粒家族，但我也表明，假单胞菌携带质粒的能力在不同物种和菌株之间存在很大差异。在这项工作的基础上，我将在这里测试这一假设，即一些假单胞菌充当质粒库，推动AMR向汇排水生态系统中的病原体传播。我有四个目标：1.利用创新的元基因组学，通过追踪整个社区的质粒转移，探索真实世界医院病房下水道中的质粒传播，并确定这些模式是如何受到化学消毒的影响的。2.通过测试不同物种和菌株在获得新质粒时的反应，研究假单胞菌的质粒库的生物学。3.通过确定与跨越近100个菌株的质粒运输相关的基因组变化，调查质粒库的进化。4.确定质粒库在实验的汇水池群落中的作用，并测量它们对AMR持久性的贡献。此外，这些实验将建立AMR在优先病原体AMR中出现的生态特征在与感染相关的环境栖息地。在这个过程中，该项目将揭示质粒-细菌相互作用和微生物生态学的一般原理，这些原理将为未来限制AMR出现的干预措施提供信息。

Antimicrobial resistance (AMR) in opportunistic pathogens represents a major emerging threat to modern medicine. A world of difficult-to-treat opportunistic infections impacts health outcomes both in terms of the direct burden of infections, and the broader effects on quality of life if elective procedures become too dangerous. AMR often emerges when bacteria acquire pieces of DNA known as plasmids from their neighbours. Plasmid transmission can occur outside of an infection setting and without antibiotic selection, so many opportunistic pathogens acquire AMR in their normal habitats before they have the chance to cause infection. However, the ability of bacteria to carry plasmids can vary, with some species or strains better at carrying and spreading plasmids than others. Understanding plasmid biology in the context of bacterial communities is therefore crucial to predicting and controlling AMR in opportunistic pathogens.Sinks on hospital wards are a key habitat in which clinically-impactful AMR emergence can occur. Bacteria are dispersed from sinks by droplets and aerosols, and genomic surveillance has implicated sinks as point sources of AMR outbreaks. Sinks are often located close to high antimicrobial usage environments, which can provide a source of resistant bacteria, and to infections, which can provide a source of dangerous pathogens. Sinks sustain robust, long-lasting multispecies biofilms, which favour close interactions that promote plasmid transmission. Sinks are also frequently treated with chemicals that can act both as a direct trigger of plasmid conjugation and select for plasmids that carry disinfectant resistance alongside AMR. However, the unique ecosystem of the ward sink has often been overlooked in studies of AMR in favour of animal models. In this project I will directly investigate the evolutionary and ecological drivers of plasmid transmission in the sink microbial ecosystem. I will focus on Pseudomonas aeruginosa - a common inhabitant of sinks, a major cause of opportunistic infection, and a 'critical priority' for AMR research (World Health Organisation, 2017) because without effective antibiotics, Pseudomonas infections can be very difficult to control.My previous work with Pseudomonas identified and characterised a widespread family of plasmids responsible for AMR, but I have also shown that the ability of Pseudomonas to carry plasmids varies widely between different species and strains. Building on this work, here I will test the hypothesis that some Pseudomonas act as plasmid 'reservoirs', driving transmission of AMR to pathogens in the sink drain ecosystem. I have four objectives:1.Explore plasmid transmission in real-world sinks on an experimental hospital ward and determine how these patterns are affected by chemical disinfection, using innovative metagenomics that can track plasmid transfer across whole communities.2.Investigate the biology of Pseudomonas plasmid 'reservoirs' by testing how different species and strains respond when they acquire a new plasmid.3.Investigate how plasmid reservoirs evolve, by determining the genome changes associated with plasmid carriage across almost 100 strains.4.Determine the role of plasmid 'reservoirs' in experimental sink drain communities, and measure their contribution to AMR persistence.Together these experiments will establish the ecological features of AMR emergence in a priority pathogen, in an infection-relevant environmental habitat. In the process, this project will reveal general principles of plasmid-bacterial interactions and microbial ecology that will inform future interventions to limit AMR emergence.