Weill Institute for Neurosciences, University of California, San Francisco, CA, 94158, USA.
Department of Neurology, University of California, San Francisco, CA, 94158, USA.
Sci Rep. 2021 Aug 20;11(1):16994. doi: 10.1038/s41598-021-95804-y.
Modern day large-scale, high-density farming environments are inherently susceptible to viral outbreaks, inadvertently creating conditions that favor increased pathogen transmission and potential zoonotic spread. Metagenomic sequencing has proven to be a useful tool for characterizing the microbial burden in both people, livestock, and environmental samples. International efforts have been successful at characterizing pathogens in commercial farming environments, especially swine farms, however it is unclear whether the full extent of microbial agents have been adequately captured or is representative of farms elsewhere. To augment international efforts we performed metagenomic next-generation sequencing on nine swine slurry and three environmental samples from a United States of America (U.S.A.) farm operation, characterized the microbial composition of slurry, and identified novel viruses. We assembled a remarkable total of 1792 viral genomes, of which 554 were novel/divergent. We assembled 1637 Picobirnavirus genome segments, of which 538 are novel. In addition, we discovered 10 new viruses belonging to a novel taxon: porcine Statoviruses; which have only been previously reported in human, macaques, mouse, and cows. We assembled 3 divergent Posaviruses and 3 swine Picornaviruses. In addition to viruses described, we found other eukaryotic genera such as Entamoeba and Blastocystis, and bacterial genera such as Listeria, Treponema, Peptoclostridium and Bordetella in the slurry. Of these, two species Entamoeba histolytica and Listeria monocytogenes known to cause human disease were detected. Further, antimicrobial resistance genes such as tetracycline and MLS (macrolide, lincosamide, streptogramin) were also identified. Metagenomic surveillance in swine fecal slurry has great potential for novel and antimicrobial resistant pathogen detection.
现代大规模、高密度的养殖环境天生容易受到病毒爆发的影响，无意中创造了有利于病原体传播和潜在人畜共患病传播的条件。宏基因组测序已被证明是一种有用的工具，可用于描述人和牲畜以及环境样本中的微生物负担。国际上的努力已经成功地对商业养殖环境中的病原体进行了特征描述，特别是在养猪场，但尚不清楚是否已经充分捕获了全部微生物剂，或者是否代表了其他农场的情况。为了加强国际努力，我们对美国一个养猪场的 9 个猪粪浆和 3 个环境样本进行了宏基因组下一代测序，对粪浆的微生物组成进行了特征描述，并鉴定了新的病毒。我们总共组装了 1792 个病毒基因组，其中 554 个是新的/不同的。我们组装了 1637 个 Picobirnavirus 基因组片段，其中 538 个是新的。此外，我们还发现了 10 种属于新分类群的新病毒：猪 Statoviruses；以前仅在人类、猕猴、老鼠和牛中报告过。我们组装了 3 个不同的 Posaviruses 和 3 个猪正粘病毒。除了描述的病毒外，我们还在粪浆中发现了其他真核生物属，如 Entamoeba 和 Blastocystis，以及细菌属，如 Listeria、Treponema、Peptoclostridium 和 Bordetella。其中，两种已知会引起人类疾病的物种 Entamoeba histolytica 和 Listeria monocytogenes 被检测到。此外，还鉴定了四环素和 MLS（大环内酯类、林可酰胺类、链阳性菌素类）等抗生素耐药基因。猪粪浆中的宏基因组监测具有发现新的和抗生素耐药病原体的巨大潜力。
