Quantifying Antibiotic Resistance Evolution in Clinically-Relevant Microbes

当我们用发现或设计的药物治疗受感染的患者时，经常会观察到耐药性，这些药物通常是以高昂的成本发现或设计的，目的是治愈他们的传染病。例如，这种情况发生在艾滋病毒患者、疟疾患者身上，或者当致病微生物，如大肠杆菌，进入某人的血液时。癌症可能很快就会对我们扔给他们的化疗药物产生抗药性，这都是因为进化。在一种新药推出后，我们可能需要数年的时间才能看到临床耐药的确认，而许多抗生素的典型时间尺度是十年。不幸的是，这阻止了制药公司寻找新的抗生素分子。毕竟，他们为什么要花10年的时间，花费巨大的成本，试图用一种在市场上只有10年盈利的药物来治愈疾病？有趣的是，肿瘤患者的耐药性出现的时间要短得多，有时是在化疗开始后的几个月内，这取决于所使用的药物、肿瘤类型和患者个人。那么，为什么我们不应该在抗生素上观察到类似的现象呢？事实上，我们确实观察到了，我们现在看到的数据集显示，细菌病原体可以在单个患者体内进化出抗药性，因为这种细菌的DNA在短短几周甚至几天内发生了变化；这项建议引用了2015年的一项研究(Blair等人，PNAS)，在该研究中，在20周的时间里，对血液传播的沙门氏菌感染的抗生素耐药性进行了逐周追踪，从而导致患者死亡。这项全基因组测序研究使用了一系列旨在实时跟踪进化的计算机和物理模拟技术，非常准确地展示了感染的耐药性是如何通过改变沙门氏菌种群内各种蛋白质的表达水平和结构而迅速变化的。在不到一周的时间里，沙门氏菌种群产生的外排蛋白的数量翻了一番，而且，它现在产生的流出蛋白质比最初的更好，感染沙门氏菌。排出的蛋白质被用来从沙门氏菌细胞内泵出抗生素，以防止抗生素击中目标，因此它们停止工作，但这只是被发现的与治疗期间发生的耐药性变化相关的多种机制之一。值得一提的是“质粒”，即由不同微生物物种传播到地球上的DNA环路，对一系列抗生素产生耐药性。鉴于这些，如果不采取措施缓解如此快速的进化，我们未来应对微生物感染的能力似乎处于极其危险的状态。但我们能做些什么呢？重要的是，2015年的研究暗示了可能性。它表明，细菌对某些抗生素变得敏感，因为它们增加了对其他抗生素的耐药性；换句话说，在治疗过程中出现了交叉或附带敏感性。因此，有时，人们可以使用一种抗生素，然后再使用另一种抗生素。这并不奇怪，这是一个已经在临床上试验过的幽门螺杆菌感染的想法，但除此之外几乎没有什么，所以我们现在需要找到新的交叉敏感性。我们还需要将抗生素结合到新型鸡尾酒中的新方法，其中一些也在这里提出。我声称，通过利用现代工具对实验室中受到抗生素影响的微生物进行数学建模和数据分析，通过观察它们的反应，我们可以发现它们防御中的薄弱环节，这将帮助临床医生设计新的疗法，并为制药公司提供在其分析管道中使用的新方法。事实上，这种情况现在正在发生&我正在寻求资金，以继续我的小组在这项任务中的努力。

Drug resistance is often observed when we treat infected patients with drugs that were discovered,or designed, usually at great cost, with the express purpose of curing people of their infectious disease.This happens, for example, to HIV patients, malaria sufferers or when a pathogenic microbe, like E. coli, finds its way into someone's bloodstream. Cancers can soon become resistant to the chemotherapeutic agents we throwat them too, & all because of evolution.The evolutionary march towards drug resistance can take time. It can be years, ordecades, after the introduction of a new drug before we see confirmation of clinical resistance to it anda ten-year timescale is thought typical of many antibiotics. Unfortunately, this stops pharmaceutical companies fromseeking new antibiotic molecules. After all, why should they spend 10 years, at great cost, seeking to curea disease with a pill that is profitable in the marketplace for only 10 more years?Intriguingly, drug resistance in tumours is seen in patients on a much shorter timescale,sometimes within months of the start of chemotherapy, depending on the drug used, the tumourtype, and on the individual patient. So why should we not observe a similar phenomenon for antibiotics?In fact, we do, & we are now seeing the emergence of datasets showing that bacterial pathogenscan evolve resistance within individual patients because of changes to the DNA of that bacteriumin a matter of mere weeks, even days; & it can be lethal.This proposal cites a 2015 study (Blair et al, PNAS) whereby resistance to antibiotic treatment in ablood-borne Salmonella infection was traced, week-by-week, over a 20-week period, whereupon the patient died.That whole-genome sequencing study, using a range of computer and physical modelling techniquesdesigned to track evolution in real time, showed very precisely how the resistance profile of the infection quicklychanged by altering expression levels and structures of a variety of proteins within the Salmonella population.Within a week the population had doubled the amount of efflux protein it was making, moreover, it was now making even better efflux proteins than the original, infecting Salmonella. The efflux proteins are used to pump the antibiotics from inside Salmonella cells to prevent the antibiotic from hitting its target, so they stop working, but this was just one of a variety of mechanisms identified that were shown to correlate with the changes in drug resistance that took place during treatment.It is important to mention 'plasmids', loops of DNA that are disseminated across the planet by differentmicrobial species that provide resistance to a range of antibiotics, given these, it seems our future ability to deal with microbial infection sits in a terribly parlous state if something is not done to mitigate such rapid evolution. But what can be done?Importantly, the 2015 study hints at possibilities. It shows that bacteria become susceptible to someantibiotics as they increase resistance to others; in other words there are cross- or collateral-sensitivities that emergeduring treatment. So, sometimes, one could use one, and then another antibiotic. This is not outlandish, it is anidea that has been trialled in the clinic for Helicobacter pylori infections, but little else, so we now need to findnovel cross sensitivities. We also need new ways of combining antibiotics into novel cocktails, & some of those areproposed here too.I claim that by bringing to bear modern tools of mathematical modelling and data analysis on microbes thatare subjected to antibiotics in the laboratory, by observing how they respond, we can find weak spotsin their defences that will help clinicians design new therapies & give pharma companies newmethodologies to use within their analysis pipelines. Indeed, this is happening now & I am seeking funding to continue the efforts of my group in this task.