Identification of Potential Vectors and Species Density of Tsetse Fly, Prevalence, and Genetic Diversity of Drug-Resistant Trypanosomes in Kenya

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 (<i>TbAT/P2</i>, <i>E6M6</i>, <i>DMT</i>, <i>TcoAde2</i>) 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 <i>G. pallidipes</i>, <i>G. austeni</i>, and <i>G. brevipalpis</i>; Taita-Taveta <i>G. pallidipes</i>, and <i>G. brevipalpis</i>; Kajiado <i>G. pallidipes</i> and <i>G. longipennis</i>; Narok <i>G. pallidipes</i>, <i>G. brevipalpis</i>, <i>G. swynnertoni</i>, and <i>G. longipennis</i>; and Turkana only <i>G. pallidipes</i>. <i>Trypanosoma congolense</i> was most prevalent, especially in Kwale, while <i>T. brucei</i> was common in Kajiado and Kwale. <i>G. brevipalpis</i>, <i>G. austeni</i>, and <i>G. pallidipes</i> showed higher infection risks. Drug resistance-associated <i>T. congolense</i> strains were found in Kwale and Taita-Taveta, with <i>TcoAde2</i> and <i>E6M6</i> 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.