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

机会致病菌的抗微生物药物耐药性（AMR）是现代医学面临的一个主要新威胁。一个难以治疗的机会性感染的世界，在感染的直接负担和如果选择性手术变得过于危险对生活质量的更广泛影响方面，都会影响健康结果。当细菌从它们的邻居那里获得被称为质粒的DNA片段时，抗菌素耐药性就会出现。质粒传播可以在感染环境之外发生，并且没有抗生素选择，因此许多机会性病原体在有机会引起感染之前在其正常栖息地获得抗菌素耐药性。然而，细菌携带质粒的能力各不相同，有些物种或菌株比其他物种或菌株更擅长携带和传播质粒。因此，了解细菌群落背景下的质粒生物学对于预测和控制机会致病菌的抗菌素耐药性至关重要。医院病房的水槽是可能发生具有临床影响的抗菌素耐药性的关键栖息地。细菌通过飞沫和气溶胶从水槽中扩散，基因组监测表明水槽是抗菌素耐药性暴发的点源。洗涤池通常位于高抗菌素使用环境附近，这可能成为耐药细菌的来源，并可能成为危险病原体的来源。水槽维持了坚固、持久的多物种生物膜，有利于促进质粒传播的密切相互作用。水槽也经常使用化学物质进行处理，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，在抗菌素耐药性研究中，病房库的独特生态系统往往被忽视，而倾向于动物模型。在这个项目中，我将直接研究质粒在汇微生物生态系统中传播的进化和生态驱动因素。我将重点关注铜绿假单胞菌——一种常见的水槽居民，是机会性感染的主要原因，也是抗菌素耐药性研究的“关键优先事项”（世界卫生组织，2017年），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研究鉴定并描述了一个广泛存在的导致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差异很大。在这项工作的基础上，我将在这里验证一个假设，即一些假单胞菌充当质粒“储存库”，推动抗菌素耐药性向汇排生态系统中的病原体传播。我有四个目标：1。探索在实验医院病房的真实水槽中的质粒传播，并确定这些模式如何受到化学消毒的影响，使用创新的宏基因组学，可以跟踪整个社区的质粒转移。通过测试不同的物种和菌株在获得新的质粒时的反应，研究假单胞菌质粒“储存库”的生物学。通过测定近100个菌株中与质粒携带相关的基因组变化，研究质粒储存库是如何进化的。确定质粒“储存库”在实验汇排群落中的作用，并测量它们对抗菌素耐药性持久性的贡献。这些实验将共同确定在与感染相关的环境栖息地中，在优先病原体中出现的抗菌素耐药性的生态特征。在此过程中，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，这将为未来的干预措施提供信息，以限制AMR的出现。

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.