A longitudinal two-year survey of the prevalence of trypanosomes in domestic cattle in Ghana by massively parallel sequencing of barcoded amplicons

BackgroundAnimal African Trypanosomiasis (AAT) is one of the most economically important diseases affecting livestock productivity in sub-Saharan Africa. The disease is caused by a broad range of Trypanosoma spp., infecting both wild and domesticated animals through cyclical and mechanical transmission. This study aimed to characterize trypanosomes present in cattle at regular intervals over two years in an AAT endemic and a non-endemic region of Ghana. Methodology/Principal findingsGroups of cattle at Accra and Adidome were selected based on their geographical location, tsetse fly density, prevalence of trypanosomiasis and the breed of cattle available. Blood for DNA extraction was collected at approximately four to five-week intervals over a two-year period. Trypanosome DNA were detected by a sensitive nested PCR targeting the tubulin gene array and massively parallel sequencing of barcoded amplicons. Analysis of the data was a semi-quantitative estimation of infection levels using read counts obtained from the sequencing as a proxy for infection levels. Majority of the cattle were infected with multiple species most of the time [190/259 (73%) at Adidome and 191/324 (59%) at Accra], with T. vivax being the most abundant. The level of infection and in particular T. vivax, was higher in Adidome, the location with a high density of tsetse flies. The infection level varied over the time course, the timings of this variation were not consistent and in Adidome it appeared to be independent of prophylactic treatment for trypanosome infection. Effect of gender or breed on infection levels was insignificant. Conclusions/SignificanceMost cattle were infected with low levels of several trypanosome species at both study sites, with T. vivax being the most abundant. The measurements of infection over time provided insight to the importance of the approach in identifying cattle that could suppress trypanosome infection over an extended time and may serve as reservoir. Author summaryCattle are of economic importance in sub-Saharan Africa as they fulfil multiple roles, ranging from draught power, to providing manure, milk, and meat. However, Animal African Trypanosomiasis (AAT) diseases in cattle affect productivity and food security in most African countries. In Ghana, bovine trypanosomiasis has been detected in few cross-sectional studies by molecular methods. To get a better understanding of the disease, a longitudinal study showing natural trypanosome infection over the life of cattle will be applicable. To explore this issue, the study determined the nature of trypanosome infection in cattle in farm settings in Ghana over two years, a period similar to that used in beef production, by massively parallel amplicon sequencing. The study provided a description of the prevalence over two years and showed that the cattle were infected with multiply species most of the time and the level of infection varied but was low most of the time. The longitudinal study allowed the identification of one individual able to supress infection far more effectively than other members of the herd and this is crucial in implementing control measures in the infected area.