摘要

       抗生素耐药性是全球范围内迅速增长的卫生保健问题，会导致许多疾病和死亡。细菌可以通过由移动遗传元件介导的水平转移获得抗生素抗性基因 (ARG)，其中噬菌体在其在自然环境中传播的作用尚未明确解决。从宏基因组研究中，我们发现在原噬菌体中发现的预测 ARG 的平均比例 (0-0.0028%) 低于游离病毒中存在的比例 (0.001-0.1%)。来自猪肠道病毒的 β-内酰胺酶占预测基因的 0.10%。总体而言，在环境中，与病毒相关的 ARG 分布与人类活动密切相关，并且观察到的低 dN/dS 比率主张对病毒携带的 ARG 进行负选择。我们的网络方法表明，病毒与假定的病原体（肠杆菌目和弧菌科）有关，并且被认为是 ARG 转移中的关键载体，类似于质粒。因此，这些 ARG 然后可以在比细菌基因组中包含的那些更大的时空尺度上传播，从而允许时间延迟的遗传交换。

       Antibiotic resistance is a rapidly growing health care problem globally and causes many illnesses and deaths. Bacteria can acquire antibiotic resistance genes (ARGs) by horizontal transfer mediated by mobile genetic elements, where the role of phages in their dissemination in natural environments has not yet been clearly resolved. From metagenomic studies, we showed that the mean proportion of predicted ARGs found in prophages (0–0.0028%) was lower than those present in the free viruses (0.001–0.1%). Beta-lactamase, from viruses in the swine gut, represented 0.10 % of the predicted genes. Overall, in the environment, the ARG distribution associated with viruses was strongly linked to human activity, and the low dN/dS ratio observed advocated for a negative selection of the ARGs harbored by the viruses. Our network approach showed that viruses were linked to putative pathogens (Enterobacterales and vibrionaceae) and were considered key vehicles in ARG transfer, similar to plasmids. Therefore, these ARGs could then be disseminated at larger temporal and spatial scales than those included in the bacterial genomes, allowing for time-delayed genetic exchanges.

https://www.nature.com/articles/s41396-019-0478-9