Bacterial Resistance to Phages
细菌对噬菌体的抗药性
Bacteria can develop resistance to phage therapy through spontaneous mutations, acquisition of restriction–modification (RM) systems, adaptive immunity via the clustered regular interspaced short palindromic repeat-associated (CRISPR-Cas) system, plasmids, temperate genes, and mobile genetic islands (that can carry genes coding for resistance to antibiotics).30,31 These mechanisms can be used by a bacterium to target different steps in the phage life cycle, including phage attachment, penetration, replication, and host cell lysis.30 Prominent resistance phenotypes are noticed as a result of distinct resistance mechanisms. There are different prominent resistance phenotypes depending on whether the resistance is partial or complete, the fitness cost associated with resistance, and whether the mutation can be countered by a mutation in the infecting phage.32
细菌可通过自发突变、获得限制性修饰（RM）系统、通过簇状规则间隔短回文重复相关（CRISPR-Cas）系统的适应性免疫、质粒、温带基因和移动基因岛（可携带抗生素抗性编码基因）对噬菌体疗法产生抗药性。细菌可利用这些机制来针对噬菌体生命周期中的不同步骤，包括噬菌体附着、穿透、复制和宿主细胞裂解。 30 突出的抗药性表型是不同抗药性机制的结果。根据抗性是部分还是完全、与抗性相关的适应成本以及感染噬菌体中的突变是否能抵消突变，有不同的突出抗性表型。 32
Spontaneous bacterial mutation results in the emergence of phage resistance and phage–bacterium co-evolution,33 which may lead to phage resistance by modifying phage-associated receptors on the bacterial surface. Importantly, such alterations may be associated with reduced fitness relative to non-resistant strains.34 When mutation occurs in bacterial lipopolysaccharides, or when the bacterium undergoes impaired growth as a result of mutations in genes involved in essential cell function, phage-resistant bacteria may become less virulent.35
细菌的自发突变导致了噬菌体抗药性的出现和噬菌体-细菌的共同进化， 33 这可能会通过改变细菌表面的噬菌体相关受体而导致噬菌体抗药性。重要的是，相对于非抗性菌株而言，这种改变可能与适应性降低有关。 34 当细菌脂多糖发生突变，或当细菌因涉及细胞基本功能的基因发生突变而导致生长受阻时，噬菌体抗性细菌的毒性可能会降低。 35
Bacterial RM systems, which are often called primitive immune systems in bacteria, are ubiquitous.36 They are important defense mechanisms against invading phage genomes. They consist of two contrary enzymatic activities: a restriction endonuclease (REase) and a methyltransferase (MTase). The mechanism of bacterial RM systems in defense is through recognition of the methylation status of invading phage genomes. Methylated sequences are recognized as self, while sequences on the invading phage genome lacking methylation are recognized as foreign and are cleaved by the REase. The role of REase is to recognize and cleave non-self-nucleic acid sequences at specific sites, while the role of MTase activity is to ensure identification of self and foreign nucleic acids, by transferring methyl groups to the same specific nucleic acid sequence within the bacterial genome.37
细菌 RM 系统通常被称为细菌的原始免疫系统，无处不在。它们是抵御噬菌体基因组入侵的重要防御机制。它们由两种相反的酶活性组成：限制性内切酶（REase）和甲基转移酶（MTase）。细菌 RM 系统的防御机制是识别入侵噬菌体基因组的甲基化状态。甲基化序列被识别为自身序列，而入侵噬菌体基因组上缺乏甲基化的序列被识别为外来序列，并被 REase 分解。REase 的作用是识别并切割特定位点的非自身核酸序列，而 MTase 活性的作用则是通过将甲基转移到细菌基因组内相同的特定核酸序列上，确保识别自身核酸和外来核酸。 37
CRISPRs regulate the adaptive immunity of bacteria. Bacteria can develop adaptive immunity against phages by acquiring a unique bit of the phages’ DNA CRISPR-Cas machinery, called spacers, from prior exposure or infection. Bacterial adaptive immunity against phages is different from other defense mechanisms because bacteria are able to recognize prior infections by storing pieces of phage DNA (spacers) in their own DNA to neutralize future infections. Surprisingly, bacteria can not only recognize prior infections by using CRISPR-Cas, but also transfer this experience to future generations.38
CRISPR调节细菌的适应性免疫。细菌可以通过从先前的接触或感染中获得噬菌体 DNA CRISPR-Cas 机制的独特片段（称为间隔物），从而对噬菌体产生适应性免疫。细菌对噬菌体的适应性免疫不同于其他防御机制，因为细菌能够通过在自身 DNA 中储存噬菌体 DNA 片段（间隔物）来识别先前的感染，从而中和未来的感染。令人惊讶的是，细菌不仅能通过使用CRISPR-Cas识别先前的感染，还能将这种经验传递给后代。 38
Bacterial mobile genetic elements may promote bacterial resistance to phage therapy. They are responsible for the horizontal transfer of phage-resistant bacterial genes among bacteria. For instance, phage resistance-conferring conjugative plasmids can disseminate quickly both within and between bacterial species by expressing mating-pair complexes that are physically in close proximity.39 Regardless of antibiotic selection, antibiotic resistance plasmids survive in abundance in bacterial populations because plasmids cause minimal bacterial fitness cost. In any case, if there is a fitness cost, it will be balanced rapidly by mutation in the phage or bacteria, or in both.40,41 Phages that specifically bind to the mating-pair complex encoded by conjugative, drug resistance-conferring plasmids have the potential to limit the spread of antibiotic resistance-conferring plasmids.
细菌移动遗传因子可能会促进细菌对噬菌体疗法产生抗药性。它们是细菌间噬菌体抗性基因水平转移的罪魁祸首。例如，具有噬菌体抗药性的共轭质粒可以通过表达物理上接近的配对复合物，在细菌物种内部和之间迅速传播。无论抗生素选择如何，抗生素抗性质粒都能在细菌种群中大量存活，因为质粒造成的细菌健康代价最小。在任何情况下，如果存在适应成本，它都会通过噬菌体或细菌或两者的突变而迅速得到平衡。 40 41 专门与共轭抗药性质粒编码的配对复合物结合的噬菌体有可能限制抗生素抗药性质粒的传播。