摘要
      从不同种类的食物中分离出的病毒DNA中已鉴定出抗生素抗性基因（ARGs），但对其起源知之甚少。在这项研究中，从先前报道携带ARGs的食物样本中分析了21种病毒，包括肉类（家禽、小牛肉和猪肉）、鱼类（地中海、大西洋、冷冻、养殖和贝类）和蔬菜（生菜、黄瓜和菠菜）。Kraken对重叠群的分类显示，在所有病毒群中，有很大比例的未分类重叠群（43.7–98.2%）。只有0.05-7.1%的重叠群被鉴定为病毒，其中91%以上属于不同的噬菌体家族，其中Podophages和Siphophages最为普遍。根据VirSorter的研究，贝类的病毒群数量最多，其次是菠菜。菠菜病毒群还包括PHASTER鉴定的数量最多的噬菌体序列。病毒中细菌基因的大量存在，包括16S rRNA基因，归因于细菌基因组片段的噬菌体包装，因为在病毒衣壳外没有发现细菌DNA。在不同的病毒群中检测16S rRNA基因可以鉴定不同的噬菌体细菌宿主。所确定的三个主要基因功能组与代谢、解毒/抗性有关，最重要的是与生物合成有关。通过qPCR对病毒中的各种ARG进行定量，最常见的是β-内酰胺酶，尤其是blaTEM。Prokka和CARD对病毒群中ARG多样性的分析揭示了各种抗性相关基因，而ResFinder的一项更严格的搜索在所有食物病毒群中鉴定了blaTEM，在大西洋鱼-1和刺突鱼-2中鉴定了blaOXA，在莴苣-1中鉴定了oqxB，在刺突鱼2中鉴定了dfr。ARGs在食物病毒中的存在表明细菌DNA通过转导机制动员。因此，噬菌体颗粒对抗性的转导可能有助于沿着食物链出现抗性菌株，应予以监测。
Abstract
Antibiotic resistance genes (ARGs) have been identified in viral DNA isolated from different kinds of food, but little is known about their origin. In this study, twenty-one viromes were analyzed from samples of food previously reported to carry ARGs, including meat (poultry, veal, and pork), fish (Mediterranean, Atlantic, frozen, farmed and shellfish) and vegetables (lettuce, cucumber, and spinach). Classification of the contigs by Kraken revealed a large percentage of unclassified contigs (43.7–98.2%) in all the viromes. Only 0.05–7.1% of the contigs were identified as viral and of these, more than 91% belonged to different bacteriophage families, Podophages and Siphophages being the most prevalent. According to VirSorter, the largest number of viral contigs were derived from viromes of shellfish, followed by spinach. Spinach viromes also included the largest number of phage sequences identified by PHASTER. The abundant presence of bacterial genes in the viromes, including 16S rRNA genes, was attributed to the phage packaging of the bacterial genome fragments, as no bacterial DNA was found outside the viral capsids. The detection of 16S rRNA genes in the different viromes allowed diverse phage bacterial hosts to be identified. The three major functional groups of genes determined were related to metabolism, detoxification/resistance, and above all, biosynthesis. Various ARGs were quantified in the viromes by qPCR, the most prevalent being β-lactamases, particularly blaTEM. Analysis of ARG diversity in the viromes by Prokka and CARD revealed various resistance-related genes, whereas a more restrictive search by ResFinder identified blaTEM in all the food viromes, blaOXA in Atlantic fish-1 and spinach-2, oqxB in lettuce-1, and dfr in spinach-2. The presence of ARGs in the food viromes points to bacterial DNA mobilization by transduction mechanisms. Transduction of resistances by phage particles may therefore contribute to the emergence of resistant strains along the food chain and should be monitored.

https://www.sciencedirect.com/science/article/pii/S0963996922003994