Next-generation sequencing technologies for helminth diagnostics and surveillance in ruminants: shifting diagnostic barriers.

Helminth infections are unavoidable in outdoor grazing systems, but must be managed and controlled effectively as they lead to significant production losses and welfare issues. Control has typically relied on a small number of broad-spectrum anthelmintics, but resistance is now widespread and threatens the sustainability of farming. Detection of anthelmintic resistance (AR) has long relied on microscopy-based tests which lack sensitivity and do not offer species-specific information. Next-generation sequencing (NGS) has revolutionized our understanding of the genetic basis of AR in recent years. This has now facilitated the development of improved sequencing-based molecular diagnostics which now can offer for the first time multidrug and multispecies detection in a single assay. Helminth infections in grazing ruminants are a major issue for livestock farming globally, but are unavoidable in outdoor grazing systems and must be effectively managed to avoid deleterious effects to animal health, and productivity. Next-generation sequencing (NGS) technologies are transforming our understanding of the genetic basis of anthelmintic resistance (AR) and epidemiological studies of ruminant gastrointestinal parasites. They also have the potential to not only help develop and validate molecular diagnostic tests but to be directly used in routine diagnostics integrating species-specific identification and AR into a single test. Here, we review how these developments have opened the pathway for the development of multi-AR and multispecies identification in a single test, with widespread implications for sustainable livestock farming for the future. [ABSTRACT FROM AUTHOR]