Innovative approaches for gastrointestinal nematode identification and resistance surveillance: Transitioning molecular diagnostics from the confines of research to the expanse of the field

Abstract

Livestock industries globally face a critical challenge in managing gastrointestinal nematodes due to escalating drug resistance. This issue is particularly severe in Australia, where internal parasites impose an annual economic burden of AUD $785 million on livestock producers. With no new anthelmintic prospects and the inevitable onset of resistance, deploying existing anthelmintics sustainably becomes crucial. However, the industry's reliance on traditional copromicroscopic techniques hampers progress, highlighting a global need for advanced diagnostic tools, widespread surveillance, and tangible demonstrations of efficacy to pave the way for sustainable approaches in gastrointestinal nematode control. This thesis aimed to develop and validate innovative molecular approaches for improved nematode identification and resistance surveillance. The first method, FECPAKG2 egg nemabiome metabarcoding, uses a digital faecal egg counting platform for direct identification from faeces, showing results comparable to gold standard methods and enabling sample transport without a cold chain. The second method, mixed amplicon metabarcoding, provides comprehensive drug resistance surveillance in Haemonchus spp., detecting single nucleotide polymorphisms for multiple drug classes. Findings revealed the LEV-resistant S168T mutation in Haemonchus spp. populations from Australian sheep and goats, with a prevalence rarely exceeding 16%, and widespread benzimidazole resistance, affirming levamisole's efficacy in New South Wales. Practical application within a mixed farming system identified wild ruminants as potential reservoirs of anthelmintic resistance. The early emergence of LEV-resistant S168T post-LEV introduction in cattle underscores the urgency of addressing resistance. The outcomes of this thesis are crucial for informed decision-making, emphasising the essential role of molecular diagnostics in sustainable gastrointestinal nematode control in global livestock industries.