The aetiology and pathogenesis of bovine respiratory disease (BRD) are complex and involve the interplay of infectious agents, management and environmental factors. Previous studies of BRD focused on ante-mortem samples from the upper respiratory tract and identified several unconventional viruses. The lung, however, is the primary location where significant BRD lesions are usually found and is a common post-mortem diagnostic specimen. In this study, results of high-throughput virome sequencing, bacterial culture, targeted real-time PCR and histological examination of 130 bovine pneumonic lungs from western Canadian cattle were combined to explore associations of microorganisms with different types of pneumonia. Fibrinous bronchopneumonia (FBP) was the predominant type of pneumonia (46.2%, 60/130) and was associated with the detection of Mannheimia haemolytica. Detection of Histophilus somni and Pasteurella multocida was associated with suppurative bronchopneumonia (SBP) and concurrent bronchopneumonia and bronchointerstitial pneumonia (BP&BIP), respectively. Sixteen viruses were identified, of which bovine parvovirus 2 (BPV2) was the most prevalent (11.5%, 15/130) followed by ungulate tetraparvovirus 1 (UTPV1, 8.5%, 11/130) and bovine respiratory syncytial virus (BRSV, 8.5%, 11/130). None of these viruses, however, were significantly associated with a particular type of pneumonia. Unconventional viruses such as influenza D virus (IDV) and bovine rhinitis B virus (BRBV) were detected, although sparsely, consistent with our previous findings in upper respiratory tract samples. Taken together, our results show that while virus detection in post-mortem lung samples is of relatively little diagnostic value, the strong associations of H. somni and M. haemolytica with SBP and FBP, respectively, indicate that histopathology can be useful in differentiating bacterial aetiologies.

中文翻译：

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来自加拿大西部的牛呼吸道疾病的肺病毒，细菌学和组织病理学发现。

牛呼吸道疾病（BRD）的病因和发病机制很复杂，涉及传染原，管理和环境因素之间的相互作用。BRD的先前研究集中于上呼吸道的死前样本，并鉴定了几种非常规病毒。然而，肺是通常发现明显的BRD病变的主要位置，并且是死后诊断的常见标本。在这项研究中，高通量病毒测序，细菌培养，实时荧光定量PCR和来自加拿大西部牛群的130头牛肺部肺的组织学检查结果相结合，探讨了微生物与不同类型肺炎的相关性。纤维化支气管肺炎（FBP）是肺炎的主要类型（46.2％，60/130），并与溶血曼海姆菌有关。化脓性支气管肺炎（SBP）和并发性支气管肺炎和支气管间质性肺炎（BP＆BIP）分别与Somni Histophilus和多杀性巴斯德氏菌相关。鉴定出16种病毒，其中牛细小病毒2（BPV2）最为流行（11.5％，15/130），其次是有蹄类四细病毒1（UTPV1，8.5％，11/130）和牛呼吸道合胞病毒（BRSV，8.5％） ，11/130）。但是，这些病毒均与特定类型的肺炎没有显着相关。尽管稀疏地检测到非常规病毒，例如D型流感病毒（IDV）和牛B型鼻炎病毒（BRBV），与我们先前在上呼吸道样本中的发现一致。在一起