East Coast Fever Carrier Status and Theileria parva Breakthrough Strains in Recently ITM Vaccinated and Non-Vaccinated Cattle in Iganga District, Eastern Uganda

East Coast fever (ECF) is a tick-borne disease of cattle that hinders the development of the livestock industry in eastern, central and southern Africa. The ‘Muguga cocktail’ live vaccine, delivered by an infection and treatment method (ITM), remains the only immunisation strategy of controlling ECF. However, there are challenges of the live vaccine inducing ECF carrier status in immunised animals and the possibility of lack of protection from parasite strains that are antigenically different from the vaccine strains. In Uganda, there are insufficient data regarding the ECF carrier status and T. parva genetic diversity in vaccinated and associated non-vaccinated cattle to assess the effectiveness of ITM vaccination. Blood was collected from recently ECF vaccinated (98) and non-vaccinated (73) cattle from Iganga district in Eastern Uganda at 120 days post-vaccination. The p104 gene nested PCR was used to screen for T. parva DNA, 11 minisatellite and 3 microsatellite markers (SSR) were used for genotyping. Two minisatellite markers (MS7 and MS19) were used to determine whether ECF carrier status was due to the T. parva vaccine or local strains. The prevalence of T. parva based on p104 nPCR was 61.2% (60/98) (RR 2.234, 95% CI 1.49–3.35, p-value < 0.001) among recently vaccinated cattle and 27.4% (20/73) (RR 1.00) among associated non-vaccinated cattle. The Muguga cocktail vaccine strains were responsible for carrier status in 10 (58.8%) by MS7 and 11 (64.7%) by MS19 in vaccinated cattle. Genotypes of T. parva with different-sized alleles to the vaccine strains that could be potential ‘breakthroughs’ were detected in 2 (11.8%)) and 4 (23.5%) isolates from vaccinated cattle based on MS7 and MS19 minisatellite markers, respectively. Using 14 SSR markers, T. parva diversity was higher in vaccinated (Na = 2.214, Ne = 1.978, He = 0.465) than associated non-vaccinated (Na = 1.071, Ne = 1.048, He = 0.259) cattle. The principal component analysis (PCA) showed isolates from vaccinated cattle were closely related to those from non-vaccinated cattle. The analysis of molecular variance (AMOVA) revealed high genetic variation (96%) within T. parva isolates from vaccinated and non-vaccinated cattle but low variation (4%) between vaccinated and non-vaccinated cattle. This study reveals the role of ITM in inducing the carrier status and higher T. parva genetic diversity in vaccinated cattle. The low genetic variation between T. parva isolates in both vaccinated and non-vaccinated cattle may be suggestive of the protective role of vaccine strains against genetically related local strains in the study area.