2. Mechanisms of Phage Resistance in Bacteria
2.细菌的噬菌体抗药性机制
Phages and bacteria have likely coevolved for over 3 billion years. Strong evolutionary selection pressure by phage predation is thought to be responsible for an impressive, growing list of bacterial defense mechanisms that span various stages of the phage infection cycle (17–19). The stages of lytic phage replication in bacteria include phage binding to receptor(s) on the cell surface; subverting cell metabolism to achieve transcription/translation of phage-encoded genes; and cell lysis (death), which releases progeny virus particles that can repeat this cycle (Figure 1).
噬菌体和细菌可能已经共同进化了 30 多亿年。噬菌体捕食带来的强大进化选择压力被认为是细菌防御机制不断增加的原因，这些机制跨越了噬菌体感染周期的各个阶段（17-19）。噬菌体在细菌中的溶解复制阶段包括：噬菌体与细胞表面的受体结合；破坏细胞新陈代谢，实现噬菌体编码基因的转录/翻译；细胞裂解（死亡），释放出可重复这一循环的后代病毒粒子（图 1）。
As a proximate defense strategy, bacteria can prevent phage entry to the cell by altering surface phage receptors such as bacterial lipopolysaccharides (LPS), outer membrane proteins, cell-wall teichoic acids, and appendages such as flagella and pili (20, 21) (Figure 1). Bacteria can evolve to modify these receptors via spontaneous mutations or by phase variation, which permits alternative expression of genes for surface-exposed structures (22). Also, receptors can be shielded from phage binding via proteins or polysaccharide capsules that cover the cell surface. A recent study shows that capsular types of Klebsiella pneumoniae clinical isolates are the main determinants of phage host range when viruses attack these bacteria (23). Furthermore, bacterial populations can avoid lytic phage infection by capitalizing on the protective shield of a biofilm, a population or community of bacteria enclosed in a self-produced exopolysaccharide matrix that adheres to a biotic or abiotic surface (24).
作为一种近似防御策略，细菌可以通过改变表面噬菌体受体（如细菌脂多糖（LPS）、外膜蛋白、细胞壁茶酸盐以及鞭毛和纤毛等附属物）来阻止噬菌体进入细胞（20，21）（图 1）。细菌可以通过自发突变或相变来改变这些受体，从而允许表面暴露结构基因的替代表达 ( 22)。此外，受体还可以通过覆盖细胞表面的蛋白质或多糖胶囊来阻挡噬菌体的结合。最近的一项研究表明，肺炎克雷伯菌临床分离株的胶囊类型是病毒攻击这些细菌时噬菌体宿主范围的主要决定因素（23）。此外，细菌种群可以利用生物薄膜的保护屏障来避免溶解性噬菌体的感染，生物薄膜是一种封闭在自身产生的外多糖基质中的细菌种群或群落，粘附在生物或非生物表面上（24）。
If a phage manages to adsorb to the cell surface and successfully injects its genetic material (RNA or DNA) into the cell, bacteria can deploy defense mechanisms that prevent phage replication by targeting and degrading the phage nucleic acid (18) (Figure 1). These defenses are analogous to both innate and adaptive immune systems in eukaryotes. Innate immunity comprises restriction-modification (R-M) systems and other related mechanisms, such as BREX (bacteriophage exclusion) and DISARM (defense islands system associated with R-M). These defenses rely on recognition of DNA modifications to discriminate between bacterial DNA and foreign DNA (18). By contrast, adaptive immunity in bacteria can occur via CRISPR-Cas systems that recognize and cleave specific phage DNA or RNA sequences, which match short phage-derived DNA sequences (CRISPR spacers) in the host genome that reflect previous interactions with similar phages (25, 26).
如果噬菌体成功吸附到细胞表面并将其遗传物质（RNA 或 DNA）成功注入细胞，细菌就会部署防御机制，通过靶向和降解噬菌体核酸来阻止噬菌体的复制 ( 18)（图 1）。这些防御机制类似于真核生物的先天性免疫系统和适应性免疫系统。先天免疫包括限制-修饰（R-M）系统和其他相关机制，如 BREX（噬菌体排斥）和 DISARM（与 R-M 相关的防御岛系统）。这些防御机制依靠识别 DNA 修饰来区分细菌 DNA 和外来 DNA ( 18)。相比之下，细菌的适应性免疫可通过 CRISPR-Cas 系统实现，该系统可识别并切割特定的噬菌体 DNA 或 RNA 序列，这些序列与宿主基因组中的噬菌体衍生 DNA 短序列（CRISPR spacers）相匹配，后者反映了先前与类似噬菌体的相互作用 ( 25, 26)。
Should intracellular phage replication proceed to later stages, bacteria can deploy additional defenses (Figure 1), such as abortive infection (Abi) systems and the newly discovered form of Abi, CBASS (cyclic oligonucleotide-based antiphage signaling system) (27, 28). Abi systems are activated when phage-specific components are detected within an infected cell. Once activated, Abi systems induce cell death or arrest bacterial metabolism to halt the phage replication cycle (18).
如果细胞内的噬菌体复制进入后期阶段，细菌可以部署额外的防御措施（图 1），如中止感染（Abi）系统和新发现的 Abi 形式–CBASS（基于环状寡核苷酸的抗噬菌体信号系统）（27，28）。当被感染细胞内检测到噬菌体特异性成分时，Abi 系统就会被激活。一旦激活，Abi 系统就会诱导细胞死亡或阻止细菌新陈代谢，从而停止噬菌体的复制循环（18）。
Unlike chemical antibiotics, phages are capable of evolving their own strategies to circumvent the bacterial resistance mechanisms they encounter when infecting bacterial cells. Phages can evolve to use a different receptor (29) and encode antidefense proteins to inactivate nucleic acid–targeting defense mechanisms (R-M and CRISPR-Cas defense systems) (18), among other counter-defense strategies (30–35).
与化学抗生素不同，噬菌体能够进化出自己的策略，以规避它们在感染细菌细胞时遇到的细菌抗药性机制。噬菌体可以进化出不同的受体（29），并编码抗防御蛋白，使核酸靶向防御机制（R-M 和 CRISPR-Cas 防御系统）失活（18），以及其他反防御策略（30-35）。
Next, we briefly discuss the occurrence of phage-resistant bacteria and the prevalence of bacterial resistance mechanisms when pathogenic bacteria are challenged with phage in laboratory conditions, animal models, and more importantly clinical settings.
接下来，我们将简要讨论在实验室条件、动物模型以及更重要的临床环境中，当致病菌受到噬菌体挑战时，噬菌体抗性细菌的出现以及细菌抗性机制的普遍性。