School of Food and Agriculture, University of Maine, Maine, USA.
Wisconsin Cooperative Wildlife Research Unit, Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Wisconsin, USA.
Microb Genom. 2024 Mar;10(3). doi: 10.1099/mgen.0.001214.
With emerging infectious disease outbreaks in human, domestic and wild animal populations on the rise, improvements in pathogen characterization and surveillance are paramount for the protection of human and animal health, as well as the conservation of ecologically and economically important wildlife. Genomics offers a range of suitable tools to meet these goals, with metagenomic sequencing facilitating the characterization of whole microbial communities associated with emerging and endemic disease outbreaks. Here, we use metagenomic sequencing in a case-control study to identify microbes in lung tissue associated with newly observed pneumonia-related fatalities in 34 white-tailed deer () in Wisconsin, USA. We identified 20 bacterial species that occurred in more than a single individual. Of these, only was found to substantially differ (in number of detections) between case and control sample groups; however, this difference was not statistically significant. We also detected several bacterial species associated with pneumonia and/or other diseases in ruminants (, , , , ); however, these species did not substantially differ between case and control sample groups. On average, we detected a larger number of bacterial species in case samples than controls, supporting the potential role of polymicrobial infections in this system. Importantly, we did not detect DNA of viruses or fungi, suggesting that they are not significantly associated with pneumonia in this system. Together, these results highlight the utility of metagenomic sequencing for identifying disease-associated microbes. This preliminary list of microbes will help inform future research on pneumonia-associated fatalities of white-tailed deer.
随着人类、家养和野生动物群体中新发传染病的爆发不断增加，提高病原体特征描述和监测水平对于保护人类和动物健康以及保护具有生态和经济重要性的野生动物至关重要。基因组学提供了一系列合适的工具来实现这些目标，其中宏基因组测序有助于对与新发和地方性疾病爆发相关的整个微生物群落进行特征描述。在这里，我们在一项病例对照研究中使用宏基因组测序来鉴定与美国威斯康星州 34 头白尾鹿（）新观察到的肺炎相关死亡相关的肺部组织中的微生物。我们鉴定出 20 种细菌物种，这些物种存在于多个个体中。其中，只有 在病例和对照组之间的数量上存在显著差异；然而，这种差异没有统计学意义。我们还检测到几种与肺炎和/或反刍动物其他疾病相关的细菌物种（、、、、）；然而，这些物种在病例和对照组之间没有显著差异。平均而言，我们在病例样本中检测到的细菌物种数量多于对照组，这支持了多微生物感染在该系统中的潜在作用。重要的是，我们没有检测到病毒或真菌的 DNA，这表明它们与该系统中的肺炎没有显著关联。总之，这些结果突出了宏基因组测序在鉴定与疾病相关的微生物方面的实用性。这个初步的微生物清单将有助于为未来研究白尾鹿肺炎相关死亡提供信息。
