Species diversity and risk factors of gastrointestinal nematodes in smallholder dairy calves in Kenya
Gastrointestinal nematodes (GIN) are of major concern in dairy farming, particularly in smallholder systems, because of their impact on the health of the calves and later on their productivity. These infections often occur as co-infections, which can complicate their prevention and treatment. The ai...
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Frontiers Media S.A.
2025-08-01
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| Series: | Frontiers in Veterinary Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fvets.2025.1588350/full |
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| author | Sylvia Cheptoo Sylvia Cheptoo Erhan Yalcindag Lina González Gordon Benson Rukwaro Benson Rukwaro Joseph Samuel Kimatu Joseph Samuel Kimatu Joseph Wasonga Joseph Wasonga Benedict E. Karani Gideon Ndambuki Susan Migeni Jesse Kagai Linus Eric Kiprotich Nelson Saya Deepali Vasoya Getrude Nangekhe Justus Onguso Grace Mungai Barend Mark Bronsvoort Elizabeth Anne Jessie Cook |
| author_facet | Sylvia Cheptoo Sylvia Cheptoo Erhan Yalcindag Lina González Gordon Benson Rukwaro Benson Rukwaro Joseph Samuel Kimatu Joseph Samuel Kimatu Joseph Wasonga Joseph Wasonga Benedict E. Karani Gideon Ndambuki Susan Migeni Jesse Kagai Linus Eric Kiprotich Nelson Saya Deepali Vasoya Getrude Nangekhe Justus Onguso Grace Mungai Barend Mark Bronsvoort Elizabeth Anne Jessie Cook |
| author_sort | Sylvia Cheptoo |
| collection | DOAJ |
| description | Gastrointestinal nematodes (GIN) are of major concern in dairy farming, particularly in smallholder systems, because of their impact on the health of the calves and later on their productivity. These infections often occur as co-infections, which can complicate their prevention and treatment. The aim of this study was to conduct fecal egg counts (FEC), genetically identify GIN species, assess species diversity, and identify associated risk factors for GIN infections in dairy calves. Fecal samples were collected from 532 dairy calves across 289 small holder dairy farms. Species identification was achieved through deep amplicon sequencing of the Internal Transcribed Spacer-2 rDNA locus (ITS-2) of first-stage larvae (L1). The mean eggs per gram (EPG) was 62.0 ± 93.0. Most of the calves 64.2% had low-intensity infections (<50 EPG), 28.6% had medium-intensity infections (50–200 EPG), and 7.2% had high-intensity infections (>200 EPG). Next Generation Sequencing analysis identified nine GIN species, with Cooperia punctata (27.8%), Haemonchus placei (26.3%), and Haemonchus contortus (23.6%) being the most prevalent. Co-infections were common, accounting for 69.5% of all infections, with two (40.1%), three (26.9%), and four-species combinations (19.8%) predominating. Male calves showed a significant association with both increased FEC and smaller heart girth, while FEC decreased with age. H. placei and C. punctata were associated with increased FEC, whereas Ostertagia ostertagi (14.5%) and Trichostrongylus colubriformis (8.0%) were associated with decreased heart girth. Calves managed under pasture systems had higher odds of co-infection. This study reveals that GIN infections are highly prevalent in dairy calves, with co-infections being common, and that GIN burden is significantly influenced by calf age, sex, and management system. The Nemabiome tool offers a promising approach to assessing GIN burden and guiding the selection of anthelmintic protocols as part of sustainable farming strategies in tropical regions. |
| format | Article |
| id | doaj-art-ee52cb850eee46d7a394c42252273f50 |
| institution | DOAJ |
| issn | 2297-1769 |
| language | English |
| publishDate | 2025-08-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Veterinary Science |
| spelling | doaj-art-ee52cb850eee46d7a394c42252273f502025-08-20T03:04:02ZengFrontiers Media S.A.Frontiers in Veterinary Science2297-17692025-08-011210.3389/fvets.2025.15883501588350Species diversity and risk factors of gastrointestinal nematodes in smallholder dairy calves in KenyaSylvia Cheptoo0Sylvia Cheptoo1Erhan Yalcindag2Lina González Gordon3Benson Rukwaro4Benson Rukwaro5Joseph Samuel Kimatu6Joseph Samuel Kimatu7Joseph Wasonga8Joseph Wasonga9Benedict E. Karani10Gideon Ndambuki11Susan Migeni12Jesse Kagai13Linus Eric Kiprotich14Nelson Saya15Deepali Vasoya16Getrude Nangekhe17Justus Onguso18Grace Mungai19Barend Mark Bronsvoort20Elizabeth Anne Jessie Cook21Jomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi, KenyaCentre for Tropical Livestock Genetics and Health (CTLGH), International Livestock Research Institute (ILRI), Nairobi, KenyaCentre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh, United KingdomCentre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh, United KingdomCentre for Tropical Livestock Genetics and Health (CTLGH), International Livestock Research Institute (ILRI), Nairobi, KenyaDepartment of Veterinary Pathology, Microbiology and Parasitology, The University of Nairobi, Nairobi, KenyaCentre for Tropical Livestock Genetics and Health (CTLGH), International Livestock Research Institute (ILRI), Nairobi, KenyaDepartment of Public Health, Pharmacology and Toxicology, The University of Nairobi, Nairobi, KenyaCentre for Tropical Livestock Genetics and Health (CTLGH), International Livestock Research Institute (ILRI), Nairobi, KenyaDepartment of Community Health, Amref International University (AMIU), Nairobi, KenyaCentre for Tropical Livestock Genetics and Health (CTLGH), International Livestock Research Institute (ILRI), Nairobi, KenyaCentre for Tropical Livestock Genetics and Health (CTLGH), International Livestock Research Institute (ILRI), Nairobi, KenyaCentre for Tropical Livestock Genetics and Health (CTLGH), International Livestock Research Institute (ILRI), Nairobi, KenyaMazingira Centre, International Livestock Research Institute (ILRI), Nairobi, KenyaMazingira Centre, International Livestock Research Institute (ILRI), Nairobi, KenyaMazingira Centre, International Livestock Research Institute (ILRI), Nairobi, KenyaUK Dementia Research Institute at University of Edinburgh, Edinburgh, United KingdomCentre for Tropical Livestock Genetics and Health (CTLGH), International Livestock Research Institute (ILRI), Nairobi, KenyaJomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi, KenyaJomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi, KenyaCentre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh, United KingdomCentre for Tropical Livestock Genetics and Health (CTLGH), International Livestock Research Institute (ILRI), Nairobi, KenyaGastrointestinal nematodes (GIN) are of major concern in dairy farming, particularly in smallholder systems, because of their impact on the health of the calves and later on their productivity. These infections often occur as co-infections, which can complicate their prevention and treatment. The aim of this study was to conduct fecal egg counts (FEC), genetically identify GIN species, assess species diversity, and identify associated risk factors for GIN infections in dairy calves. Fecal samples were collected from 532 dairy calves across 289 small holder dairy farms. Species identification was achieved through deep amplicon sequencing of the Internal Transcribed Spacer-2 rDNA locus (ITS-2) of first-stage larvae (L1). The mean eggs per gram (EPG) was 62.0 ± 93.0. Most of the calves 64.2% had low-intensity infections (<50 EPG), 28.6% had medium-intensity infections (50–200 EPG), and 7.2% had high-intensity infections (>200 EPG). Next Generation Sequencing analysis identified nine GIN species, with Cooperia punctata (27.8%), Haemonchus placei (26.3%), and Haemonchus contortus (23.6%) being the most prevalent. Co-infections were common, accounting for 69.5% of all infections, with two (40.1%), three (26.9%), and four-species combinations (19.8%) predominating. Male calves showed a significant association with both increased FEC and smaller heart girth, while FEC decreased with age. H. placei and C. punctata were associated with increased FEC, whereas Ostertagia ostertagi (14.5%) and Trichostrongylus colubriformis (8.0%) were associated with decreased heart girth. Calves managed under pasture systems had higher odds of co-infection. This study reveals that GIN infections are highly prevalent in dairy calves, with co-infections being common, and that GIN burden is significantly influenced by calf age, sex, and management system. The Nemabiome tool offers a promising approach to assessing GIN burden and guiding the selection of anthelmintic protocols as part of sustainable farming strategies in tropical regions.https://www.frontiersin.org/articles/10.3389/fvets.2025.1588350/fullgastrointestinal nematodesdeep amplicon sequencingrisk factorco-infectionsdairy calvesKenya |
| spellingShingle | Sylvia Cheptoo Sylvia Cheptoo Erhan Yalcindag Lina González Gordon Benson Rukwaro Benson Rukwaro Joseph Samuel Kimatu Joseph Samuel Kimatu Joseph Wasonga Joseph Wasonga Benedict E. Karani Gideon Ndambuki Susan Migeni Jesse Kagai Linus Eric Kiprotich Nelson Saya Deepali Vasoya Getrude Nangekhe Justus Onguso Grace Mungai Barend Mark Bronsvoort Elizabeth Anne Jessie Cook Species diversity and risk factors of gastrointestinal nematodes in smallholder dairy calves in Kenya Frontiers in Veterinary Science gastrointestinal nematodes deep amplicon sequencing risk factor co-infections dairy calves Kenya |
| title | Species diversity and risk factors of gastrointestinal nematodes in smallholder dairy calves in Kenya |
| title_full | Species diversity and risk factors of gastrointestinal nematodes in smallholder dairy calves in Kenya |
| title_fullStr | Species diversity and risk factors of gastrointestinal nematodes in smallholder dairy calves in Kenya |
| title_full_unstemmed | Species diversity and risk factors of gastrointestinal nematodes in smallholder dairy calves in Kenya |
| title_short | Species diversity and risk factors of gastrointestinal nematodes in smallholder dairy calves in Kenya |
| title_sort | species diversity and risk factors of gastrointestinal nematodes in smallholder dairy calves in kenya |
| topic | gastrointestinal nematodes deep amplicon sequencing risk factor co-infections dairy calves Kenya |
| url | https://www.frontiersin.org/articles/10.3389/fvets.2025.1588350/full |
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