Occurrence, Diversity and Risk Factors of Parasitic Gastrointestinal Nematodes in Smallholder Dairy Calves from Nandi County, Kenya

Gastrointestinal nematodes (GIN) are of major importance in dairy farming, particularly in smallholder systems, because of their impact on calf health and productivity. Most of these infections occur as coinfections. While several studies have investigated GIN infections in cattle, many have relied on microscopy that may not accurately identify mixed infections or species level. To address this limitation, molecular techniques, such as deep amplicon sequencing, have emerged as powerful tools for characterizing GIN communities and identifying mixed infections. In this article, we present results for a cross-sectional study on 289 smallholder dairy farms with 532 calves, in Kenya from September to December 2023. Fresh fecal samples were collected and Fecal Egg Count(FEC) conducted using Salt floatation cuvette method. Identification of nematode species was conducted by deep amplicon sequencing of Internal Transcribed spacer-2 rDNA locus of first stage larvae. Generalized mixed-effects models were used to identify risk factors associated with FEC, Heart girth as an indicator of weight and coinfections. Nine GIN species were detected, with Cooperia punctata , Haemonchus placei , and Haemonchus contortus being the most prevalent. A high proportion (69.5%) of infections were coinfections. Sex and age were significantly associated with both FEC and heart girth. H.placei and C.punctata were significantly associated with FEC while O.ostertagi and T.colubriformis were associated with Hearth girth. Management and breed were significantly associated with coinfections. The result of this study shows that deep amplicon sequencing can accurately identify GIN species of dairy calves, particularly in cases of coinfections.