Abstract 摘要
The global rise of antibiotic resistance in bacterial pathogens and the waning efficacy of antibiotics urge consideration of alternative antimicrobial strategies. Phage therapy is a classic approach where bacteriophages (bacteria-specific viruses) are used against bacterial infections, with many recent successes in personalized medicine treatment of intractable infections. However, a perpetual challenge for developing generalized phage therapy is the expectation that viruses will exert selection for target bacteria to deploy defenses against virus attack, causing evolution of phage resistance during patient treatment. Here we review the two main complementary strategies for mitigating bacterial resistance in phage therapy: minimizing the ability for bacterial populations to evolve phage resistance and driving (steering) evolution of phage-resistant bacteria toward clinically favorable outcomes. We discuss future research directions that might further address the phage-resistance problem, to foster widespread development and deployment of therapeutic phage strategies that outsmart evolved bacterial resistance in clinical settings.
细菌病原体对抗生素的耐药性在全球范围内不断上升，抗生素的疗效也在不断减弱，这促使人们考虑采用其他抗菌策略。噬菌体疗法是利用噬菌体（细菌特异性病毒）抗击细菌感染的经典方法，最近在治疗顽固性感染的个性化医疗方面取得了许多成功。然而，开发通用噬菌体疗法面临的一个长期挑战是，病毒会对目标细菌进行选择，使其采取防御措施抵御病毒攻击，从而导致患者在治疗过程中产生噬菌体抗药性。在此，我们回顾了在噬菌体疗法中减轻细菌耐药性的两种主要互补策略：最大限度地降低细菌种群进化出噬菌体耐药性的能力，以及推动（引导）耐噬菌体细菌向临床上有利的结果进化。我们讨论了未来可能进一步解决噬菌体抗药性问题的研究方向，以促进治疗性噬菌体策略的广泛开发和应用，从而在临床环境中战胜已进化的细菌抗药性。
Keywords 关键词
antibiotic, phage therapy, phage-resistant bacteria, evolutionary trade-offs
抗生素、噬菌体疗法、抗噬菌体细菌、进化权衡
1. INTRODUCTION 1.引言
Widespread use of small molecule antibiotics in medicine and agriculture has exerted strong selection for bacterial species to evolve multi-drug resistance (MDR), prompting a global public-health antibiotic-resistance crisis (1–3). Worse, new antibiotics are discovered and developed at a slow pace (4), causing novel antibiotic development to lag significantly behind the emergence of MDR pathogens: bacteria resistant to multiple antibiotic classes (5). Although antibiotics still save countless lives each year, their waning potency for treating certain infections raises concerns that we are entering a postantibiotic era (6) and manifests the urgent need to develop new strategies (7, 8).
小分子抗生素在医药和农业领域的广泛使用，对细菌物种产生了强烈的选择作用，使其进化出多重耐药性（MDR），引发了全球公共卫生领域的抗生素耐药性危机（1-3）。更糟糕的是，新抗生素的发现和开发速度缓慢（4），导致新型抗生素的开发大大落后于 MDR 病原体的出现：对多种抗生素类产生耐药性的细菌（5）。尽管抗生素每年仍能挽救无数人的生命，但其治疗某些感染的效力正在减弱，这不禁让人担心我们正在进入后抗生素时代（6），并表明迫切需要开发新的策略（7、8）。
A promising alternative is the use of bacteriophages (phages), viruses that specifically target bacterial cells. In phage therapy, lytic phages are administered to patients to target and kill the bacterial pathogen(s) causing an infection (9–12). Phages present many advantages over traditional antibiotics: They are highly specific for their hosts, reducing off-target bacterial killing; phages are the most abundant biological entities on Earth, providing an enormous reservoir for phage therapy; they can self-amplify and disseminate in the body to encounter susceptible bacteria; phages are generally regarded as safe, based on extremely rare cases of toxicity in animals and patients (13); and finally, phages often target different bacterial mechanisms than antibiotics, possibly minimizing evolution of cross-resistance (14–16).
一种很有前景的替代方法是使用噬菌体（phage），即专门针对细菌细胞的病毒。在噬菌体疗法中，给病人注射溶解性噬菌体，靶向杀死引起感染的细菌病原体（9-12）。与传统抗生素相比，噬菌体具有许多优势：噬菌体对宿主具有高度特异性，减少了对细菌的非靶向杀伤；噬菌体是地球上最丰富的生物实体，为噬菌体疗法提供了巨大的资源库；在宿主体内，噬菌体可以进行自主复制并散播，从而寻找到易感细菌；噬菌体被普遍认为是安全的，因为在动物和患者中发生毒性的病例极为罕见（13）；最后，噬菌体通常针对的细菌机制与抗生素不同，可能最大限度地减少交叉耐药性的演变（14- 16）。
Despite the promising therapeutic potential of phages, phage therapy presents several limitations that are yet to be addressed (14–16). Two of the most significant obstacles to developing generalized phage therapy (beyond personalized treatment) are phage specificity or phages with narrow host range, and the emergence of phage-resistant bacteria. Mitigating the latter is the focus of this review. Like antibiotics, lytic phages impose strong selective pressures on their hosts, to evolve resistance and prevent virus attack. Selection and enrichment of phage-resistant genotypes in the target bacterial population might result in therapy failure. Hence, it is crucial that in modern development of phage-based treatments, phages and therapeutic strategies are carefully designed to mitigate evolution of phage resistance. Here, we begin by reviewing the various mechanisms that bacteria employ to resist phage attack.
尽管噬菌体具有良好的治疗潜力，但噬菌体疗法也存在一些局限性，有待解决（14-16）。噬菌体特异性或噬菌体宿主范围狭窄以及抗噬菌体细菌的出现是开发通用噬菌体疗法（超越个性化治疗）的两个最大障碍。减少后者是本综述的重点。与抗生素一样，溶菌噬菌体也会对宿主施加强大的选择性压力，使其产生抗药性并防止病毒攻击。目标细菌群中噬菌体抗性基因型的选择和富集可能导致治疗失败。因此，在开发基于噬菌体的现代疗法时，必须精心设计噬菌体和治疗策略，以减少噬菌体抗药性的进化。在此，我们首先回顾一下细菌抵抗噬菌体攻击的各种机制。