Gastrointestinal Nematode Diversity in Kenyan Cattle at Wildlife-Livestock Interfaces: A Deep Amplicon Sequencing Approach
Background: Gastrointestinal nematodes cause significant economic impacts on livestock production worldwide. Comprehensive information on their epidemiology is crucial for successful and effective control. In Africa, very little data is available on the true diversity of circulating gastrointestinal nematodes (GIN), as most of the studies to date have mainly relied on faecal egg counts and larvae morphology, which tend to focus on diagnosis of particular species and have limited resolution. Our aims were to estimate the diversity of GIN and to assess the use of deep amplicon based sequencing tools for use in an African setting where culture to L3 stage is challenging. Methods: We investigated the diversity of Clade V nematode infections in adult cattle and their calves at a livestock/wildlife interface, using next-generation deep amplicon sequencing based on internal transcribed spacer-2, nemabiome metabarcoding. The study was carried out dam and calf pairs, at the Ol Pejeta wildlife conservancy, Kenya, using faecal, first-stage larvae (L1) and third-stage larvae (L3) samples to determine the gastrointestinal nematode species composition in individual animals. Results: Nemabiome analysis confirmed the presence of eight GIN species in 29 cattle which were predominantly infected by Cooperia curticei, Cooperia pectinata, Cooperia punctata, Haemonchus placei, Haemonchus contortus, Trichostrongylus axei, Teladorsagia circumcincta and Trichostrongylus colubriformis. The majority (77.4%) of samples were co-infected with more than one species. Our results demonstrated calves had higher infection rates than dams and exhibited more diverse nematode communities early in life. Additionally, faeces and L1 larvae provide a robust resource for studying GIN diversity, and they can be used as reliable DNA sources in tropical regions, rather than relying on the more labour-intensive and time-consuming culturing to L3 larvae stage.
Background: Gastrointestinal nematodes cause significant economic impacts on livestock production worldwide. Comprehensive information on their epidemiology is crucial for successful and effective control. In Africa, very little data is available on the true diversity of circulating gastrointestinal nematodes (GIN), as most of the studies to date have mainly relied on faecal egg counts and larvae morphology, which tend to focus on diagnosis of particular species and have limited resolution. Our aims were to estimate the diversity of GIN and to assess the use of deep amplicon based sequencing tools for use in an African setting where culture to L3 stage is challenging. Methods: We investigated the diversity of Clade V nematode infections in adult cattle and their calves at a livestock/wildlife interface, using next-generation deep amplicon sequencing based on internal transcribed spacer-2, nemabiome metabarcoding. The study was carried out dam and calf pairs, at the Ol Pejeta wildlife conservancy, Kenya, using faecal, first-stage larvae (L1) and third-stage larvae (L3) samples to determine the gastrointestinal nematode species composition in individual animals. Results: Nemabiome analysis confirmed the presence of eight GIN species in 29 cattle which were predominantly infected by Cooperia curticei, Cooperia pectinata, Cooperia punctata, Haemonchus placei, Haemonchus contortus, Trichostrongylus axei, Teladorsagia circumcincta and Trichostrongylus colubriformis. The majority (77.4%) of samples were co-infected with more than one species. Our results demonstrated calves had higher infection rates than dams and exhibited more diverse nematode communities early in life. Additionally, faeces and L1 larvae provide a robust resource for studying GIN diversity, and they can be used as reliable DNA sources in tropical regions, rather than relying on the more labour-intensive and time-consuming culturing to L3 larvae stage.