Abstract
Next generation sequencing (NGS) can be applied to identify and characterize the entire set of microbes within a sample. However, this platform does not provide a morphological context or specific association between the viral or bacterial sequences detected and the histological lesions. This limitation has generated uncertainty whether the sequences identified by NGS are actually contributing or not for the clinical outcome. Although in situ hybridization (ISH) and immunohistochemistry (IHC) can be used to detect pathogens in tissue samples, only ISH has the advantage of being rapidly developed in a context of an emerging disease, especially because it does not require development of specific primary antibodies against the target pathogen. Based on the sequence information provided by NGS, ISH is able to check the presence of a certain pathogen within histological lesions, by targeting its specific messenger RNA, helping to build the relationship between the pathogen and the clinical outcome. In this mini review we have compiled results of the application of NGS-ISH to the investigation of challenging diagnostic cases or emerging pathogens in pigs, that resulted in the detection of porcine circovirus type 3, porcine parvovirus type 2, Senecavirus A, and Mycoplasma hyorhinis.
Highlights
The U.S swine industry has evolved from small independent farming operations to integrated large systems [1]
Next-generation sequencing has been recently used to detect nucleotide sequences in challenging diagnostic cases, Next generation sequencing (NGS)-in situ hybridization (ISH): Diagnosis of Emerging Diseases of Swine but it does not provide morphological context that would allow the association of a specific viral sequences with the histological lesions
In situ hybridization assay allows the detection of nucleotide sequences in histological sections without requiring the development of such antibodies
Summary
The U.S swine industry has evolved from small independent farming operations to integrated large systems [1]. Next-generation sequencing has been recently used to detect nucleotide sequences in challenging diagnostic cases, NGS-ISH: Diagnosis of Emerging Diseases of Swine but it does not provide morphological context that would allow the association of a specific viral sequences with the histological lesions. When dealing with an emerging disease, production of a sensible and specific antibody and the optimization of the immunohistochemistry protocol can take several months, delaying effective actions to control a particular emerging disease This mini-review focuses on the development and application of a new platform of diagnostics that combine next-generation sequencing and in situ hybridization for investigating unsolved diagnostic cases in swine. The association of NGS and ISH has been extremely advantageous to overcome those limitations (Figure 1)
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