Abstract
Tsetse flies are major vectors of trypanosomes in Sub-Saharan Africa, posing risks to livestock and human health. This study investigated the diversity, distribution, and infection rates of tsetse species, as well as the genetic diversity of drug resistance-associated trypanosome strains in Kenya. Flies were collected from Kwale, Taita-Taveta, Kajiado, Narok, and Turkana counties between November 2024 and February 2025. DNA analyses targeting rRNA and transporter genes (TbAT/P2, E6M6, DMT, TcoAde2) identified infections and resistance-associated mutations among 4693 sampled flies. Apparent density was highest in Kwale (101.52 flies/trap/day) and lowest in Turkana (1.18). Species distribution varied by county, with Kwale dominated by G. pallidipes, G. austeni, and G. brevipalpis; Taita-Taveta G. pallidipes, and G. brevipalpis; Kajiado G. pallidipes and G. longipennis; Narok G. pallidipes, G. brevipalpis, G. swynnertoni, and G. longipennis; and Turkana only G. pallidipes. Trypanosoma congolense was most prevalent, especially in Kwale, while T. brucei was common in Kajiado and Kwale. G. brevipalpis, G. austeni, and G. pallidipes showed higher infection risks. Drug resistance-associated T. congolense strains were found in Kwale and Taita-Taveta, with TcoAde2 and E6M6 gene diversity linked to Kenyan isolates. These findings highlight the need for targeted control of high-risk tsetse species and drug-resistant trypanosomes in Kenya.