First Insight into Strongylid Nematode Diversity and Anthelmintic Treatment Effectiveness in Beef Cattle in the Czech Republic Explored by HTS Metagenomics

Abstract

Parasitic diseases and mitigation of their effects play an important role in the health management of grazing livestock worldwide, with gastrointestinal strongylid nematodes being of prominent importance. These helminths typically occur in complex communities, often composed of species from numerous strongylid genera. Detecting the full diversity of strongylid species in non-invasively collected faecal samples is nearly impossible using conventional methods. In contrast, high-throughput amplicon sequencing (HTS) can effectively identify co-occurring species. During the four-year project, we collected and analysed faecal samples from beef cattle on more than 120 farms throughout the Czech Republic. Strongylids were the predominant nematodes, detected in 56 % of the samples, but at a low level of infection. The apparent limitations in identifying strongylid taxa prompted this pilot study on a representative group of samples testing positive for strongylids using Illumina ITS-2 HTS metabarcoding. The most widespread genera parasitizing Czech cattle were Ostertagia (O. ostertagi) and Oesophagostomum spp., followed by Trichostrongylus and Cooperia, while Bunostomum, Nematodirus and Chabertia were present only in a minority. The comparative samples from Romania were dominated by Haemonchus placei. In two selected farms, strongylid communities shifted after anthelmintic treatment with ivermectin, suggesting possible resistance of Cooperia and Ostertagia.

Keywords: Cattle, strongylid nematodes, resistance, anthelmintic treatment