A metagenomic assessment of viral contamination on fresh parsley plants irrigated with fecally tainted river water
A metagenomic assessment of viral contamination on fresh parsley plants irrigated with fecally tainted river water
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DOI：
10.1016/j.ijfoodmicro.2017.06.001
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发表时间：
2017-09-18
影响因子：
5.4
通讯作者：
Girones, R.
中科院分区：
文献类型：
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作者：
Fernandez-Cassi, X.;Timoneda, N.;Girones, R.
尽管实施了微生物质量立法以提高食品安全，但微生物食源性疾病仍经常报告。在所有的微生物病原体中，病毒是引起食源性疾病暴发的最重要病原体。开发和应用新一代测序技术来检测新鲜农产品中的病毒污染物是一个尚未探索的领域，可以研究可能通过食用受污染食物经粪-口途径传播的病毒种群。为了推进这片有前途的土地，欧芹在受控条件下种植和生长，并使用受污染的河水灌溉。利用宏基因组学技术对污染灌溉水和欧芹叶片的病毒进行了研究。为了解决由于样品操作、文库制备和其他来源而导致的可能污染，使用营养液灌溉的欧芹植物作为阴性对照。同时，使用相同的方法分析了用于植物灌溉的河水中存在的病毒。根据样品，可以分配占测序总读数2.4%至74.88%的病毒分类单位。在河水中检测到的大多数病毒读段与植物病毒科Tymoviridae（66.13%）和Virgaviridae（14.45%）以及噬菌体病毒科Myoviridae（5.70%）、Siphoviridae（5.06%）和Microviridae（2.89%）相关。不到1%的病毒读段与感染人类的病毒家族相关，包括腺病毒科、呼肠孤病毒科、小核糖核酸病毒科和星状病毒科的成员。在欧芹植物表面上，检测到的大部分病毒读段被分配到双链病毒科（Dicistroviridae）（41.52%）。检测到与重要病毒病原体相关的序列，如戊型肝炎病毒、来自A和B种的几种小核糖核酸病毒以及人痘病毒和GIV诺如病毒。在欧芹植物中发现的病毒序列的高度多样性表明，对粪便污染的食物进行灌溉可能在病毒家族的广泛多样性传播中发挥作用。这一发现强化了这样一种观点，即避免食源性病毒性疾病的最佳方法是引入良好的田间灌溉和生产实践。已经鉴定了与小核糖核酸病毒科相关并且与肝炎病毒科远缘的新菌株。然而，仅检测到病毒基因组并不一定表明存在感染或疾病发展的风险。因此，进一步的研究对于将样本中病毒宏基因组的检测与感染风险相关联至关重要。还迫切需要开发新的方法来提高当前下一代测序（NGS）技术在食品安全领域中的灵敏度。
Microbial food-borne diseases are still frequently reported despite the implementation of microbial quality legislation to improve food safety. Among all the microbial agents, viruses are the most important causative agents of food-borne outbreaks. The development and application of a new generation of sequencing techniques to test for viral contaminants in fresh produce is an unexplored field that allows for the study of the viral populations that might be transmitted by the fecal-oral route through the consumption of contaminated food. To advance this promising field, parsley was planted and grown under controlled conditions and irrigated using contaminated river water. Viruses polluting the irrigation water and the parsley leaves were studied by using metagenomics. To address possible contamination due to sample manipulation, library preparation, and other sources, parsley plants irrigated with nutritive solution were used as a negative control. In parallel, viruses present in the river water used for plant irrigation were analyzed using the same methodology. It was possible to assign viral taxons from 2.4 to 74.88% of the total reads sequenced depending on the sample. Most of the viral reads detected in the river water were related to the plant viral families Tymoviridae (66.13%) and Virgaviridae (14.45%) and the phage viral families Myoviridae (5.70%), Siphoviridae (5.06%), and Microviridae (2.89%). Less than 1% of the viral reads were related to viral families that infect humans, including members of the Adenoviridae, Reoviridae, Picornaviridae and Astroviridae families. On the surface of the parsley plants, most of the viral reads that were detected were assigned to the Dicistroviridae family (41.52%). Sequences related to important viral pathogens, such as the hepatitis E virus, several picornaviruses from species A and B as well as human sapoviruses and GIV noroviruses were detected. The high diversity of viral sequences found in the parsley plants suggests that irrigation on fecally-tainted food may have a role in the transmission of a wide diversity of viral families. This finding reinforces the idea that the best way to avoid food-borne viral diseases is to introduce good field irrigation and production practices. New strains have been identified that are related to the Picornaviridae and distantly related to the Hepeviridae family. However, the detection of a viral genome alone does not necessarily indicate there is a risk of infection or disease development. Thus, further investigation is crucial for correlating the detection of viral metagenomes in samples with the risk of infection. There is also an urgent need to develop new methods to improve the sensitivity of current Next Generation Sequencing (NGS) techniques in the food safety area.