Prevalence, genetic Diversity and drug-resistance of trypanosomes in Kwale, Taita-taveta, Kajiado, Narok and Turkana counties of Kenya
African animal trypanosomiasis (AAT) is a livestock disease caused by the animal trypanosomes. This disease is known to affect food security in most affected sub-Saharan African countries. In Kenya and in recent years, the ITS1 primers have been commonly used to detect the different species of trypanosomes. However, ITS1 was recently discovered not to detect some known species of trypanosomes such as T. theileri. Hence, to overcome this challenge a combination of use of different specific and generic primers such as ITS1; gGAPDH; partial 28S and partial 18S, ITS1, 5.8S, ITS2 rRNA genes have proven to detect both known and new species of trypanosomes which is what our study sort to detect, to determine the genetic diversity, prevalence and drug resistance of trypanosomes found in Kwale, Taita-taveta, Kajiado, Turkana and Narok  Prevalence by molecular approach; for ITS1 the overall prevalence in the five counties was 3.56%, in Kajiado was 1.33%, Narok 1.67%, Kwale 2.66%, Taita 0.52% and Turkana 10.67%. Nested PCR with ITS-123 and 4 had an overall prevalence of 9.34% and there were more positive trypanosomes detection compared to single ITS1 reactions. In addition, some cases of single infections in ITS1 reactions were detected to be mixed infections with nested ITS-123 and 4. However, there were also some few cases where positive cases were detected using single ITS1 which could not be detected using nested ITS-1234. T. brucei was the most highly detected species in Turkana compared to other species detected within other counties and within Turkana. For nested PCR with gGAPDH, the positive cases detected were less than ITS-123 and 4, however some positive cases detected by gGAPDH could not be detected using ITS-123 and 4 and these include species such as T.evansi. For DpnII digestion two isolates from Kwale showed three bands 248-400bp and 648bp (two bands associated with resistant strains and one band associated with sensitive strain) and three isolates showed two bands 248-400bp (both associated with resistant strain), from Turkana nine isolates showed three bands 248-400bp and 648bp (two bands associated with resistant strains and one band with sensitive strain). In conclusion, genetic diverse species of trypanosomes exist in the 5 endemic counties of Kenya, and there are trypanosome species associated with drug resistance from Kwale and Turkana counties, while some are sensitive to trypanocidal drugs.