09.12.2023
Vet. Sci. 2023, 10, 690.
A comprehensive review published in Veterinary Sciences highlights key developments, limitations, challenges, and potential future applications of Next-Generation Sequencing (NGS) in avian medicine and poultry meat production. The article specifically explores the application of NGS technology for the detection of microbial agents in avian clinical samples. NGS offers rapid genetic characterization of host pathogens, contrasting with RT-PCR, which has the dual disadvantage of providing no genetic information on the identified agent and being sensitive to mutations at the primer or probe sites used for the tests. NGS can be employed in clinical diagnosis and veterinary surveillance through two main approaches: direct-targeted NGS (tNGS) and direct-non-targeted NGS (ntNGS).
1. Direct-Targeted NGS (tNGS): tNGS is a rapid and sensitive method for precisely characterizing suspected agents. It enables precise genetic characterization of host pathogens, facilitating healthy production and identifying genetic changes in RNA viruses threatening poultry health. tNGS provides cost-effective alternatives, potentially replacing classical diagnostic methods like real-time PCR (RT-PCR) as the first line of diagnostics. It offers high specificity, compatibility with various clinical samples, and the generation of nearly complete infection profiles, encompassing viruses, bacteria, fungi, and parasites.
2. Direct-Non-Targeted NGS (ntNGS): ntNGS (also known as random NGS) of nucleic acids in diagnostic samples can characterize complex infections more rapidly than traditional diagnosis, leading to more effective prevention and control of poultry diseases. ntNGS is evolving as a powerful tool for farm-animal diagnostics, identifying and genetically characterizing multiple agents simultaneously in each sample (mixed infections).
Both tNGS and ntNGS have the potential to become preferred diagnostic methodologies, replacing traditional approaches, and thereby improving poultry production and enhancing veterinary surveillance.
The richness of information provided by sequencing is evident in the rapid, specific genotypic, and virulence information offered by NGS nucleotide sequences.
NGS serves as a potent tool for actively surveilling poultry farms, providing information beneficial for flock management and selecting more specific vaccines.
The comprehensive review by Claudio Afonso & Anna Afonso outlines the promising future of NGS-based diagnostics for the avian industry, emphasizing the necessity for standard operating procedures and professional training in bioinformatics. The potential for AI to automate data processing and management is also discussed. Overall, the article provides insights into advancements, challenges, and future developments in avian NGS-based technology for diagnostic purposes.
