The evolutionary emergence of multidrug resistant bacterial pathogens

细菌感染中抗生素耐药性的增加是对现代医学的严重威胁，因此了解为什么一些细菌对多种抗生素产生耐药性，而另一些细菌却没有，对微生物学家、医生和兽医来说是一个重要的挑战。致病性大肠杆菌是全球最常见的血液和尿液感染原因，被世界卫生组织认定为全球最大的健康威胁。在致病性大肠杆菌中，抗生素耐药性与获得额外的DNA环有关，这种DNA环被称为质粒，携带几种不同的抗生素抗性基因。并不是所有的大肠杆菌菌株都能维持这样的质粒，这可能是因为获得质粒通常非常昂贵，因为质粒携带的基因会干扰细菌细胞的运作。我们的工作使我们假设大肠杆菌菌株之间的这种差异是由于不同菌株调节其基因表达的方式不同，从而使一些菌株能够减轻质粒对细胞造成的破坏。在这个项目中，我们将在实验室中使用进化实验和尖端测序技术来测试这个想法。我们收集了一组无质粒的大肠杆菌菌株，它们的近亲在自然界中通常携带抗生素抗性质粒。首先，我们将比较获得质粒的成本和两种菌株提供的抗生素耐药性水平。我们预测，在通常不携带质粒的菌株中，成本会更高。其次，我们将通过测量两种菌株表达基因的模式来比较获得质粒对细胞造成的破坏。我们预测，在通常不携带质粒的菌株中，获得质粒对细胞造成的破坏将更大，而且这将随着我们携带质粒的成本而增加。第三，我们将在实验室中实验进化携带质粒的细菌，实时观察自然选择如何补偿获得质粒的成本。我们预测，进化后的细菌将在调节基因开启或关闭的调节因子中获得新的突变，以减轻携带质粒对细胞造成的破坏，并且在通常携带质粒的菌株中，这一过程将更快更有效。第四，我们将测试在实验进化过程中观察到的突变如何影响有质粒和没有质粒的细胞中基因的表达，以了解进化允许细菌维持质粒的分子机制。这个项目将推进我们对大肠杆菌的致病菌株如何以及为什么对抗生素具有高度耐药性的进化的基本理解。在未来，这种见解可以帮助我们在潜在的超级细菌出现之前识别它们，或者为药物提供新的靶点，迫使细菌失去抗生素抗性质粒，使它们对常规治疗敏感。

Increasing antibiotic resistance in bacterial infections is a serious threat to modern medicine, so understanding why some bacteria become resistant to multiple antibiotics whereas others do not is an important challenge for microbiologists, doctors and vets. In pathogenic E. coli - the most common cause of blood and urine infections worldwide and recognised by the World Health Organisation as a top global health threat - antibiotic resistance is associated with gaining extra loops of DNA called plasmids that carry several different antibiotic resistance genes. Not all E. coli strains seem to be able to maintain such plasmids, which is probably because gaining plasmids is typically very costly because the genes the plasmids carry interfere with the workings of the bacterial cell. Our work has led us to hypothesise that this variation between strains of E. coli is due to differences in how the various strains regulate the expression of their genes allowing some to mitigate for the disruption caused to the cell by the plasmid. In this project we will test this idea in the laboratory using evolution experiments and cutting-edge sequencing technology. We have gathered together a collection of plasmid-free E. coli strains whose close relatives do typically carry antibiotic resistance plasmids in nature. First, we will compare the costs of acquiring a plasmid and the level of antibiotic resistance provided in both types of strain. We predict that costs will be higher in strains that don't typically carry plasmids. Second, we will compare the disruption caused to the cell by acquiring a plasmid in both types of strain by measuring patterns of how they express their genes. We predict that disruption to the cell caused by gaining the plasmid will be greater in strains that don't typically carry plasmids, and that this will scale with the costs we measure of carrying the plasmid. Third, we will experimentally evolve bacteria carrying plasmids in the lab to observe in real time how natural selection compensates for the cost of acquiring a plasmid. We predict that evolved bacteria will gain new mutations in regulators that turn genes on or off, to mitigate the disruption to the cell caused by carrying a plasmid, and that this process will be faster and more efficient in strains that typically carry plasmids. Fourth, we will test how the mutations observed during experimental evolution affect the expression of genes in cells with and without plasmids, to understand the molecular mechanisms by which evolution allows bacteria to maintain plasmids. This project will advance our fundamental understanding of how and why pathogenic strains of E. coli that are highly resistant to antibiotics evolve. In future this insight could help us to identify potential superbugs before they emerge, or suggest novel targets for drugs that force bacteria to lose their antibiotic resistance plasmids making them susceptible to conventional treatments.