PDF(Pubmed)
Abstract：
Swine influenza A virus (swIAV) plays an important role in porcine respiratory infections. In addition to its ability to cause severe disease by itself, it is important in the multietiological porcine respiratory disease complex. Still, to date, no comprehensive diagnostics with which to study polymicrobial infections in detail have been offered. Hence, veterinary practitioners rely on monospecific and costly diagnostics, such as Reverse Transcription quantitative PCR (RT-qPCR), antigen detection, and serology. This prevents the proper understanding of the entire disease context, thereby hampering effective preventive and therapeutic actions. A new, nanopore-based, metagenomic diagnostic platform was applied to study viral and bacterial profiles across 4 age groups on 25 endemic swIAV-infected German farms with respiratory distress in the nursery. Farms were screened for swIAV using RT-qPCR on nasal and tracheobronchial swabs (TBS). TBS samples were pooled per age, prior to metagenomic characterization. The resulting data showed a correlation between the swIAV loads and the normalized reads, supporting a (semi-)quantitative interpretation of the metagenomic data. Interestingly, an in-depth characterization using beta diversity and PERMANOVA analyses allowed for the observation of an age-dependent interplay of known microbial agents. Also, lesser-known microbes, such as porcine polyoma, parainfluenza, and hemagglutinating encephalomyelitis viruses, were observed. Analyses of swIAV incidence and clinical signs showed differing microbial communities, highlighting age-specific observations of various microbes in porcine respiratory disease. In conclusion, nanopore metagenomics were shown to enable a panoramic view on viral and bacterial profiles as well as putative pathogen dynamics in endemic swIAV-infected herds. The results also highlighted the need for better insights into lesser studied agents that are potentially associated with porcine respiratory disease. IMPORTANCE To date, no comprehensive diagnostics for the study of polymicrobial infections that are associated with porcine respiratory disease have been offered. This precludes the proper understanding of the entire disease landscape, thereby hampering effective preventive and therapeutic actions. Compared to the often-costly diagnostic procedures that are applied for the diagnostics of porcine respiratory disease nowadays, a third-generation nanopore sequencing diagnostics workflow presents a cost-efficient and informative tool. This approach offers a panoramic view of microbial agents and contributes to the in-depth observation and characterization of viral and bacterial profiles within the respiratory disease context. While these data allow for the study of age-associated, swIAV-associated, and clinical symptom-associated observations, it also suggests that more effort should be put toward the investigation of coinfections and lesser-known pathogens (e.g., PHEV and PPIV), along with their potential roles in porcine respiratory disease. Overall, this approach will allow veterinary practitioners to tailor treatment and/or management changes on farms in a quicker, more complete, and cost-efficient way.
摘要：
猪甲型流感病毒(swIAV)在猪呼吸道感染中起重要作用。除了它本身引起严重疾病的能力，它在多病因猪呼吸道疾病复合体中很重要。尽管如此，到目前为止,没有提供详细研究多微生物感染的全面诊断。因此，兽医从业者依赖于单一特异性和昂贵的诊断，如逆转录定量PCR（RT-qPCR），抗原检测,和血清学。这阻碍了对整个疾病背景的正确理解，从而阻碍了有效的预防和治疗行动。一个新的,基于纳米孔的，应用宏基因组诊断平台研究了25个地方性感染swIAV的德国农场的4个年龄组的病毒和细菌谱,这些农场在托儿所出现呼吸窘迫.使用RT-qPCR在鼻和气管支气管拭子（TBS）上筛选农场的swIAV。按年龄收集TBS样本，在宏基因组表征之前。结果数据显示SwIAV负载和归一化读数之间的相关性，支持宏基因组数据的(半)定量解释。有趣的是,使用β多样性和PERMANOVA分析的深入表征允许观察已知微生物制剂的年龄依赖性相互作用。此外，鲜为人知的微生物，比如猪多发性瘤，副流感,和血凝性脑脊髓炎病毒，被观察到。对SwIAV发病率和临床体征的分析显示出不同的微生物群落，强调猪呼吸道疾病中各种微生物的年龄特异性观察。总之,纳米孔宏基因组学被证明能够全景图病毒和细菌谱以及地方性swIAV感染的畜群中假定的病原体动力学。结果还强调需要更好地了解较少研究的可能与猪呼吸道疾病相关的药物。重要性迄今为止，没有提供与猪呼吸道疾病相关的多微生物感染研究的全面诊断。这妨碍了对整个疾病景观的正确理解，从而阻碍了有效的预防和治疗行动。与目前应用于猪呼吸道疾病诊断的通常昂贵的诊断程序相比，第三代纳米孔测序诊断工作流程提供了一种经济高效且信息丰富的工具.这种方法提供了微生物制剂的全景视图，并有助于在呼吸道疾病背景下深入观察和表征病毒和细菌谱。虽然这些数据允许年龄相关的研究，SwIAV相关，和临床症状相关的观察，它还表明，应该对共感染和鲜为人知的病原体进行更多的调查(例如，PHEV和PPIV)，以及它们在猪呼吸道疾病中的潜在作用。总的来说,这种方法将使兽医从业者能够更快地调整农场的治疗和/或管理变化，更完整,和成本有效的方式。
