摘要

    背景：细菌产生的抗生素耐药性是对全球健康的重大威胁。抗生素
抗性基因（ARG）通过多种传播途径分布在不同的细菌种群中，
包括由噬菌体介导的水平基因转移。噬菌体携带的ARG被认为是
特别是由于它们在环境中的持久性，快速的复制速度以及
感染各种细菌宿主。多项采用qPCR和病毒宏基因组学的研究表明，病毒
临床和环境样品中的片段和病毒序列读数带有许多ARG。但是，只有少数
在由元基因组读段组装的病毒重叠群中发现了ARG，其中大多数基因缺乏
有效的抗生素抗性表型。尽管如此，由于病毒宏基因组学的广泛应用，
在从不同环境获得的病毒基因组中不断发现不同类别的ARGs。
因此，由噬菌体编码的ARG的存在和功能仍有待争论。
结果：我们评估了从城市地表水病毒基因组中回收的病毒重叠群中挖掘出的ARG。
数据。在病毒的阅读和重叠群中，多种ARG，包括多粘菌素抗性基因，多药外排蛋白，
鉴定了β-内酰胺酶和β-内酰胺酶。尤其是当e值的宽阈值≤1×e-5并进行查询时
Resfams数据库的覆盖率≥60％，新型β-内酰胺酶blaHRV-1和blaHRVM-1为
成立。这些基因具有独特的序列，形成了不同的A类和B3类β-内酰胺酶进化枝，
分别。包含blaHRV-1和blaHRVM-1和blaHRV-1的大肠杆菌菌株的最低抑菌浓度分析
纯化的HRV-1和HRVM-1的催化动力学表明对青霉素，窄谱和扩谱头孢菌素和碳青霉烯类药物的敏感性降低。这些基因也在细菌基因组中发现，表明
它们是通过积极感染噬菌体而被藏起来的。

    Background: Antibiotic resistance developed by bacteria is a significant threat to global health. Antibiotic
resistance genes (ARGs) spread across different bacterial populations through multiple dissemination routes,
including horizontal gene transfer mediated by bacteriophages. ARGs carried by bacteriophages are considered
especially threatening due to their prolonged persistence in the environment, fast replication rates, and ability to
infect diverse bacterial hosts. Several studies employing qPCR and viral metagenomics have shown that viral
fraction and viral sequence reads in clinical and environmental samples carry many ARGs. However, only a few
ARGs have been found in viral contigs assembled from metagenome reads, with most of these genes lacking
effective antibiotic resistance phenotypes. Owing to the wide application of viral metagenomics, nevertheless,
different classes of ARGs are being continuously found in viral metagenomes acquired from diverse environments.
As such, the presence and functionality of ARGs encoded by bacteriophages remain up for debate.
Results: We evaluated ARGs excavated from viral contigs recovered from urban surface water viral metagenome
data. In virome reads and contigs, diverse ARGs, including polymyxin resistance genes, multidrug efflux proteins,
and β-lactamases, were identified. In particular, when a lenient threshold of e value of ≤ 1×e−5 and query
coverage of ≥ 60% were employed in the Resfams database, the novel β-lactamases blaHRV-1 and blaHRVM-1 were
found. These genes had unique sequences, forming distinct clades of class A and subclass B3 β-lactamases,
respectively. Minimum inhibitory concentration analyses for E. coli strains harboring blaHRV-1 and blaHRVM-1 and
catalytic kinetics of purified HRV-1 and HRVM-1 showed reduced susceptibility to penicillin, narrow- and extendedspectrum cephalosporins, and carbapenems. These genes were also found in bacterial metagenomes, indicating
that they were harbored by actively infecting phages.

    https://link.springer.com/content/pdf/10.1186/s40168-020-00863-4.pdf