In the world, Blastocystis has been reported as the most common eukaryotic microorganism in the intestine of humans and animals, with prevalences even up to 100%, along with Giardia intestinalis, which has been considered the main causal agent of diarrheal pictures in humans, affecting approximately 200 million individuals worldwide. In general, the diagnosis of both microorganisms is frequently based on the observation of typical forms in feces and only at the research level is their typification sought through the use of molecular techniques. In addition, it should be noted that few genes have been used to evaluate their characteristics at the genetic level and that most molecular studies have focused solely on typing and few have included the evaluation of genetic diversity and structure of intra- and inter-group populations. , leaving aside the study of its biology, taxonomy, distribution, zoonotic transmission potential and even obtaining evidence to clarify whether its population structure is sexual or clonal. In Colombia, the situation is not very different from that reported in other countries, mainly those under development, where behavioral, socioeconomic and environmental conditions favor the transmission of some intestinal diseases, and areas with high endemicity tend to increase in genetic variation of these microorganisms, which, possibly, together with the environment of strong competition at the intestinal level, make the expansion to new hosts more feasible and therefore maintain zoonotic transmission, both with domestic and wild animals, fulfilling a fundamental role in the maintenance of epidemiological cycles and making the control and prevention of these infections increasingly difficult. For this reason, this study sought, not only to molecularly detect these microorganisms in different regions of the country, but also to know their circulating genotypes, making a first approach to the molecular epidemiology of these intestinal parasites in the evaluated areas, and later, evaluating the existing diversity at the intra taxa level of both G. intestinalis and Blastocystis, through the analysis of new genetic targets that allowed us to demonstrate great genetic variation, particularly related to possible genetic exchange events in G. intestinalis and intra-Subtype (ST) variation in the case of Blastocystis. The results produced by this thesis allowed: a) to describe a first approximation of the frequency of each of the parasitic microorganisms evaluated, such as Blastocystis, G. intestinalis, Cryptosporidium and the Entamoeba histolytica / dispar / moshkovskii complex in five biogeographic regions of Colombia, suggesting that the Caribbean region has a higher frequency for each of these. Furthermore, thanks to the assemblages of Giardia, the STs of Blastocystis and Cryptosporidium species found, 11 show the possible zoonotic transmission of these microorganisms to humans in some regions of the country, b) show the genetic variability present in G. intestinalis and the intra- and inter-assembly genetic exchange events, by evaluating nine genetic targets and finally c) determining the genetic diversity of Blastocystis and its intra-subtype variation, thanks to the joint use of the ribosomal gene 18s and the metabolic gene sdhA. In conclusion, these results show the great need to continue evaluating the genetic characteristics of these microorganisms, primarily in Colombia, in order to establish more effective control and prevention interventions, and even more so, taking into account that the great diversity found can directly influence in its prevalence, transmission dynamics and virulence. Perhaps, in the near future, the use of genomic analysis of strains isolated from Colombian samples may solve some of the knowledge gaps that remain regarding these microorganisms and their biological characteristics.
