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Background  Contemporary information relating to the prevalence of  Toxoplasma gondii  in humans is lacking for the UK population, with even less information available about the human prevalence of the parasite in Scotland. To address this, two different study groups were used to determine the prevalence and genotypes of  Toxoplasma gondii  in the Scottish population.    Methods  The first study group included serum samples from blood donors ( n  = 3273) over a four-year period (2006–2009) and the second study group comprised of DNA samples extracted from human brains ( n  = 151) over a five-year period (2008–2012). A  T. gondii  IgG ELISA was performed to determine seroprevalence and available sera from individuals who had seroconverted were tested by TgERP ELISA (sporozoite specific antigen). Human brain DNA was tested for  T. gondii  by ITS1 PCR and positives genotyped at the SAG3 and GRA6 loci by PCR-RFLP analysis.    Results  Seroprevalence to  T. gondii  from blood donors was found to be 13.2 % (95 % CI: 11.5–15.1 %). Evidence of seroconversion ( n  = 2) as well as reversion to sero-negative status ( n  = 6) was evident from blood donors who had donated within all four collection periods ( n  = 184). The TgERP ELISA (indicating oocyst infection) was positive for one individual. The molecular detection of  T. gondii  DNA from human brains indicated a prevalence of 17.9 % (95 % CI: 12.1–24.9 %), with genotyping identifying alleles for types I and III. An increase in age was associated with an increase in detection of the parasite within both study groups.    Conclusions  Our research provides current figures for the prevalence of  T. gondii  in Scotland and also shows evidence of seroreversion within the cohort of blood donors. In both study groups there was a correlation between increasing age and an increase in  T. gondii  prevalence, indicating that acquired infection plays an important role within the Scottish population.    Electronic supplementary material  The online version of this article (doi:10.1186/s13071-016-1610-6) contains supplementary material, which is available to authorized users.

The prevalence and genotypic analysis of Toxoplasma gondii from individuals in Scotland, 2006–2012