School of Information, Computer, and Communication Technology (ICT), Sirindhorn International Institute of Technology, Thammasat Universitygrid.412434.4, Pathum Thani, Thailand.
National Center for Genetic Engineering and Biotechnologygrid.419250.b (BIOTEC), National Science and Technology Agency (NSTDA), Pathum Thani, Thailand.
Microbiol Spectr. 2022 Feb 23;10(1):e0131121. doi: 10.1128/spectrum.01311-21. Epub 2022 Jan 5.
Actinobacillus pleuropneumoniae causes porcine pleuropneumonia, an important disease in the pig industry. Accurate and sensitive diagnostics such as DNA-based diagnostics are essential for preventing or responding to an outbreak. The specificity of DNA-based diagnostics depends on species-specific markers. Previously, an insertion element was found within an A. pleuropneumoniae-specific gene commonly used for A. pleuropneumoniae detection, prompting the need for additional species-specific markers. Herein, 12 marker candidates highly conserved (99 - 100% identity) among 34 A. pleuropneumoniae genomes (covering 13 serovars) were identified to be A. pleuropneumoniae-specific , as these sequences are distinct from 30 genomes of 13 other and problematic [] species and more than 1700 genomes of other bacteria in the family. Five marker candidates are within the gene, a known A. pleuropneumoniae-specific gene, validating our marker discovery method. Seven other A. pleuropneumoniae-specific marker candidates within the , , , , and genes were validated by polymerase chain reaction (PCR) to be specific to 129 isolates of A. pleuropneumoniae (covering all 19 serovars), but not to four closely related species, four [] species, or seven other bacterial species. This is the first study to identify A. pleuropneumoniae-specific markers through genome mining. Seven novel A. pleuropneumoniae-specific DNA markers were identified by a combination of and molecular methods and can serve as additional or alternative targets for A. pleuropneumoniae diagnostics, potentially leading to better control of the disease. Species-specific markers are crucial for infectious disease diagnostics. Mutations within a marker sequence can lead to false-negative results, inappropriate treatment, and economic loss. The availability of several species-specific markers is therefore desirable. In this study, 12 DNA markers specific to A. pleuropneumoniae, a pig pathogen, were simultaneously identified. Five marker candidates are within a known A. pleuropneumoniae-specific gene. Seven novel markers can be used as additional targets in DNA-based diagnostics, which in turn can expedite disease diagnosis, assist farm management, and lead to better animal health and food security. The marker discovery strategy outlined herein requires less time, effort, and cost, and results in more markers compared with conventional methods. Identification of species-specific markers of other pathogens and corresponding infectious disease diagnostics are possible, conceivably improving health care and the economy.
副猪嗜血杆菌引起猪传染性胸膜肺炎，是养猪业中的一种重要疾病。准确和敏感的诊断方法，如基于 DNA 的诊断方法，对于预防或应对疫情至关重要。基于 DNA 的诊断的特异性取决于物种特异性标记物。此前，在一种常用于副猪嗜血杆菌检测的副猪嗜血杆菌特异性基因内发现了一个插入元件，这促使人们需要更多的物种特异性标记物。在此，在 34 个副猪嗜血杆菌基因组（涵盖 13 个血清型）中鉴定出 12 个高度保守（99-100%同一性）的标记候选物，这些标记候选物是副猪嗜血杆菌特异性的，因为这些序列与 30 个其他和有问题的[]种的 30 个基因组以及家族中的 1700 多个其他细菌基因组不同。5 个标记候选物位于已知的副猪嗜血杆菌特异性基因内，验证了我们的标记发现方法。通过聚合酶链反应（PCR）验证，另外 7 个副猪嗜血杆菌特异性标记候选物位于、、、、和基因内，这些标记候选物针对 129 株副猪嗜血杆菌（涵盖所有 19 个血清型）具有特异性，但对 4 种密切相关的种、4 种[]种或 7 种其他细菌种不具有特异性。这是首次通过基因组挖掘鉴定副猪嗜血杆菌特异性标记物的研究。通过组合基因组挖掘和分子方法鉴定了 7 个新型副猪嗜血杆菌特异性 DNA 标记物，它们可以作为副猪嗜血杆菌诊断的附加或替代靶标，可能有助于更好地控制该疾病。物种特异性标记物对于传染病诊断至关重要。标记物序列内的突变可能导致假阴性结果、不适当的治疗和经济损失。因此，有几个物种特异性标记物是理想的。在这项研究中，同时鉴定了 12 个针对猪病原体副猪嗜血杆菌的 DNA 标记物。5 个标记候选物位于一个已知的副猪嗜血杆菌特异性基因内。7 个新型标记物可作为 DNA 基于诊断的附加靶标，这反过来又可以加快疾病诊断，协助农场管理，并改善动物健康和食品安全。与传统方法相比，本文概述的标记发现策略需要更少的时间、精力和成本，并且产生更多的标记物。鉴定其他病原体的物种特异性标记物和相应的传染病诊断是可能的，可以想象这将改善医疗保健和经济。
