Opinion 意见
Evolutionary Rationale for Phages as Complements of Antibiotics
噬菌体与抗生素互补的进化原理
Clara Torres-Barceló1,* and Michael E. Hochberg1,2,*
Clara Torres-Barceló1,* 和 Michael E. Hochberg1,2,*
Trends 发展趋势
The efficacy of new and old antibiotics could be preserved if combined with phages.
如果与噬菌体结合使用，新旧抗生素的功效都能得到保留。
Positive interactions have been observed between antibiotics and lytic phages in controlling bacterial pathogens both in vitro and in vivo.
在体外和体内，都观察到抗生素和溶菌噬菌体在控制细菌病原体方面的良性相互作用。
Phage–antibiotic combinations are capable of targeting multidrug-resis- tant bacteria but their underlying mechanisms remain to be discovered.
噬菌体-抗生素组合能够靶向抗多种药物的细菌，但其基本机制仍有待发现。
Evolutionary biology provides a framework for understanding the interactions between antimicrobial agents and the successful management of bacterial pathogens, their resistance, and their virulence.
进化生物学为理解抗菌剂与成功控制细菌病原体之间的相互作用、它们的抗药性和毒性提供了一个框架。
Antibiotic-resistant bacterial infections are a major concern to public health. Phage therapy has been proposed as a promising alternative to antibiotics, but an increasing number of studies suggest that both of these antimicrobial agents in combination are more effective in controlling pathogenic bacteria than either alone. We advocate the use of phages in combination with antibiotics and present the evolutionary basis for our claim. In addition, we identify compelling challenges for the realistic application of phage–antibiotic combined therapy.
抗生素耐药细菌感染是公共卫生的一个主要问题。噬菌体疗法被认为是抗生素的一种有前途的替代疗法，但越来越多的研究表明，这两种抗菌剂联合使用比单独使用任何一种都能更有效地控制病原菌。我们主张将噬菌体与抗生素结合使用，并提出了我们这一主张的进化基础。此外，我们还指出了噬菌体-抗生素联合疗法在现实应用中面临的严峻挑战。
New Therapeutic Strategies Are Needed
需要新的治疗策略
Infections by antibiotic-resistant pathogens are a serious concern. Conventional methods for finding novel antibiotics are inadequate, with the staggering result being that mortality due to antibiotic resistance is estimated to be about 25 000 persons per year in both the USA and Europe according to the Centers for Disease Control and Prevention (CDC) and its European counterpart the ECDC [1,2]. In many developing countries antibiotic resistance is also a major cause of mortality, and many procedures to control resistance are unfeasible [3,4]. Despite this situation, we continue the search for the Ehrlichian ‘magic bullet’ that will be exempt from the evolution of bacterial resistance and the latter’s spread through horizontal gene transfer to other bacteria, be they pathogenic, commensal, or mutually beneficial. Recent research on antibiotic discovery [5] and the isolation and elucidation of potent DNA gyrase inhibitors [6,7] present new opportunities to control the evolution of bacterial resistance and not make the same errors of the past. But can the potency of existing antibiotics be maintained and the pristine status of future discoveries be conserved? Unless the employment of new antibiotics is carefully managed, bacteria will inevitably evolve resistance [8].
抗生素耐药性病原体的感染是一个令人严重关切的问题。根据美国疾病控制与预防中心（CDC）和欧洲疾病控制与预防中心（ECDC）的估计，美国和欧洲每年因抗生素耐药性导致的死亡人数约为 25 000 人[1,2]。在许多发展中国家，抗生素耐药性也是导致死亡的一个主要原因，而许多控制耐药性的方法都不可行[3,4]。尽管如此，我们仍在继续寻找埃希氏 “灵丹妙药”，以避免细菌耐药性的进化以及耐药性通过水平基因转移扩散到其他细菌（无论是致病菌、共生菌还是互利菌）。最近的抗生素发现研究[5]以及强效 DNA 回旋酶抑制剂的分离和阐明[6,7]为控制细菌耐药性的进化和避免重蹈覆辙提供了新的机遇。但是，现有抗生素的效力能否保持，未来发现的抗生素的原始状态能否保持？除非谨慎管理新抗生素的使用，否则细菌将不可避免地产生抗药性[8]。
Evolutionary-rational approaches are currently lacking in antibiotic management and yet have shown considerable potential in application to other diseases. Specifically, combination therapies have an impressive track record in the treatment of diverse illnesses such as cancer, malaria, or HIV, even if certain aggressive therapies are questionable [9]. For example, combinations of general cellular proliferation inhibitors together with more targeted therapies represent important advances in the treatment of many cancers [10]. Likewise, antiretroviral therapies targeting different steps in the HIV life cycle are remarkably successful in reducing viremia and improving patient health [11]. Optimized therapies such as these are derived from advances in the understanding of the biology and pathogenesis of each disease, and knowledge about mechanisms of sensitivity and resistance to rational drug combinations.
目前，抗生素管理缺乏合理的进化方法，但在其他疾病的应用中却显示出相当大的潜力。具体而言，联合疗法在癌症、疟疾或艾滋病等多种疾病的治疗中取得了令人瞩目的成绩，即使某些激进疗法存在疑问[9]。例如，将一般细胞增殖抑制剂与更具针对性的疗法相结合，是治疗许多癌症的重要进展[10]。同样，针对艾滋病毒生命周期不同阶段的抗逆转录病毒疗法在降低病毒血症和改善患者健康方面也取得了显著成功[11]。这些优化疗法源自对每种疾病的生物学和发病机制的深入了解，以及对合理药物组合的敏感性和耐药性机制的认识。
Antibiotic cocktails and combinations with other molecules, such as antimicrobial peptides, are promising alternatives, but may ultimately suffer from some of the same shortcomings as single molecules [12]. By contrast, bacterial viruses (phages) have considerable untapped potential as a complement to antibiotics, not only due to a range of intrinsic differences in their mechanisms of action, but also because of the virtually infinite diversity of phages, their potential to be rapidly ‘trained’ (through serial passages on the ancestral bacterial strain), and their ability to evolve in situ to overcome bacterial resistance [13]. The treatment of bacterial infections could benefit from our extensive knowledge of the genetics and evolution of antibiotic resistance, coupled with a promising alternative therapeutic agent that could act as a powerful enhancer. In this opinion article, we present the multiple advantages of combining these antimicrobials compared to using either independently. We argue that combining phages and antibiotics should be seriously considered as a therapeutic solution to antibiotic-resistant infections, and we provide detailed evolutionary arguments that justify our claim.
鸡尾酒抗生素和与其他分子（如抗菌肽）的组合是很有前途的替代品，但最终可能会出现与单一分子相同的一些缺点[12]。相比之下，细菌病毒（噬菌体）作为抗生素的一种补充，具有相当大的潜力尚待开发，这不仅是因为它们的作用机制存在一系列内在差异，而且还因为噬菌体的多样性几乎是无限的，它们有可能被迅速 “训练”（通过对祖先细菌菌株的连续传代），并有能力在原位进化以克服细菌的抗药性[13]。我们对抗生素耐药性的遗传学和进化有广泛的了解，再加上一种很有希望的替代治疗剂，它可以作为一种强有力的增强剂，从而使细菌感染的治疗受益匪浅。在这篇观点文章中，我们介绍了与单独使用其中一种抗菌剂相比，结合使用这些抗菌剂的多重优势。我们认为，应该认真考虑将噬菌体和抗生素结合起来，作为抗生素耐药性感染的治疗方案，我们还提供了详细的进化论据来证明我们的观点。
Phage Therapy and Hurdles to Its Use
噬菌体疗法及其应用障碍
The origins and employment of phage therapy date back at least a century to Felix d‘Herelle and others [14]. Though not extensively adopted, phage preparations were produced by the Pasteur Institute in France until 1974 and in the USA until the 1990s [15]. Phage therapeutic products have continuously been used in Eastern European countries, notably in the Republic of Georgia, but solid interest slowed outside of the former Soviet Union with the discovery of antibiotics [14]. With decreasing antibiotic discovery and increasing multidrug-resistant bacteria, phages are being reconsidered as alternative therapies for certain types of bacterial pathogens. Phages have received particular attention as substitutes for antibiotics in food safety, agricultural, and farming settings to contain the spread of antibiotic-resistant ‘superbug’ bacteria [16]. Poultry, dogs, dairy products, and processed foods are some examples of the current successful employment of phage therapy (e.g., [17]). For example, in the United States, the FDA has approved commercial phage preparations against common bacterial pathogens such as Listeria monocytogenes and Salmonella to treat ready-to-eat food [18,19].
噬菌体疗法的起源和应用至少可以追溯到 Felix d’Herelle 等人的一个世纪之前 [14]。噬菌体制剂虽未被广泛采用，但法国巴斯德研究所一直生产到 1974 年，美国也一直生产到 20 世纪 90 年代[15]。噬菌体治疗产品一直在东欧国家，特别是格鲁吉亚共和国使用，但随着抗生素的发现，前苏联以外的国家对噬菌体治疗产品的兴趣逐渐减弱[14]。随着抗生素发现的减少和耐多药细菌的增加，噬菌体正被重新考虑作为某些类型细菌病原体的替代疗法。在食品安全、农业和养殖业中，噬菌体作为抗生素的替代品受到特别关注，以遏制耐抗生素 “超级细菌 “的传播 [16]。家禽、狗、乳制品和加工食品是目前噬菌体疗法成功应用的一些例子（如 [17]）。例如，在美国，食品及药物管理局已经批准了针对李斯特菌和沙门氏菌等常见细菌病原体的商业噬菌体制剂，用于治疗即食食品[18,19]。
Leading among the factors that explain limited phage employment are the often variable and poorly understood results on their efficacy and their high specificity compared to general-spectrum antibiotics [14,20]. Phage therapy requires an accurate identification of the bacterial pathogen and in vitro examination of its sensitivity to the available phages [15,20]. However, perhaps the most important hurdle is the lack of a specific regulatory framework that considers individualized therapies, or uncertainties for the pharmaceutical industry based on the difficulty of registering intellectual patents for phage preparations [20,21]. Moreover, despite the promise that phages could replace antibiotics in certain situations, there are very few controlled large-scale clinical studies on their safety and efficacy. Biocontrol Ltd reported the first regulated efficacy trial of phage therapy targeting chronic otitis caused by antibiotic-resistant Pseudomonas aeruginosa in 2009 in the UK, showing significant improvement in patients [22]. Current clinical studies like Phagoburn, a European initiative to evaluate the treatment of drug-resistant infections of burn wounds, or funding calls such as those by the Gates Foundation, highlight phage therapy as a central objective for future research [23] (http://gcgh.grandchallenges.org/challenge/addressing-newborn-and-infant-gut-health-through-bacteriophage-mediated-microbiome).
导致噬菌体使用受限的主要因素是，噬菌体的疗效和特异性与普通抗生素相比往往不尽相同，而且人们对噬菌体的疗效和特异性知之甚少[14,20]。噬菌体疗法需要准确识别细菌病原体，并在体外检测其对可用噬菌体的敏感性 [15,20]。然而，最重要的障碍可能是缺乏考虑个体化疗法的具体监管框架，或制药业因难以注册噬菌体制剂的知识专利而面临不确定性 [20,21]。此外，尽管噬菌体有望在某些情况下取代抗生素，但有关其安全性和有效性的大规模临床对照研究却寥寥无几。2009 年，英国生物控制有限公司（Biocontrol Ltd）报告了针对耐抗生素铜绿假单胞菌引起的慢性中耳炎的噬菌体疗法的首次受控疗效试验，结果显示患者病情明显好转 [22]。目前的临床研究，如欧洲评估烧伤伤口耐药感染治疗的倡议 Phagoburn，或盖茨基金会的资助呼吁，都强调噬菌体疗法是未来研究的核心目标[23]（http://gcgh.grandchallenges.org/challenge/addressing-newborn-and-infant-gut-health-through-bacteriophage-mediated-microbiome ）。