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Background  African trypanosomes are mainly transmitted through the bite of tsetse flies ( Glossina  spp.). The present study investigated the occurrence of pathogenic trypanosomes in tsetse flies and cattle in tsetse fly-infested areas of Northern Cameroon.    Results  Trypanosomes were identified using nested polymerase chain reaction (PCR) analysis of internal transcribed spacer 1 (ITS1) region, both by size estimation and sequencing of PCR products. Apparent density indices recorded in Gamba and Dodeo were 3.1 and 3.6 tsetse flies per trap and day, respectively.  Trypanosoma  prevalence infection rate for the tsetse fly gut (40%) and proboscis (19%) were recorded. Among the flies where trypanosomes were detected in the gut, 41.7% were positive for  T. congolense  and 14.6% for  T. brucei  ssp., whereas in the proboscis 36% harboured  T. congolense  and 62% contained  T. vivax .  T. grayi  was highly prevalent in tsetse fly gut (58%). The most common mixed infections were the combination of  T. congolense  and  T. grayi . Trypanosome prevalence rate in cattle blood was 6%. Among these,  T. vivax  represented 26%,  T. congolense  35%,  T. brucei  ssp. 17% and  T. theileri  17% of the infections. Surprisingly, in one case  T. grayi  was found in cattle. The mean packed cell volume (PCV) of cattle positive for trypanosomes was significantly lower (24.1 ± 5.6%;  P  < 0.05) than that of cattle in which trypanosomes were not detected (27.1 ± 4.9%). Interestingly, the occurrence of  T. theileri  or  T. grayi  DNA in cattle also correlated with low PCV at pathological levels.    Conclusion  This molecular epidemiological study of  Trypanosoma  species in Northern Cameroon revealed active foci of trypanosomes in Dodeo and Gamba. These findings are relevant in assessing the status of trypanosomosis in these regions and will serve as a guide for setting the priorities of the government in the control of the disease.    Electronic supplementary material  The online version of this article (10.1186/s13071-017-2540-7) contains supplementary material, which is available to authorized users.

Molecular screening of tsetse flies and cattle reveal different Trypanosoma species including T. grayi and T. theileri in northern Cameroon