**2. Final Considerations**

kind of study enables the identification of relapses, drug-resistant pathogens, and clinically distinct variants, as investigated in protozoan parasites such as Leishmania [45, 63] and Plasmodium [64, 65]. The geographical dissemination of microorganisms can also be charac‐ terized by microsatellites studies [66, 67] helping in the characterization of transmission

Domestic and sylvatic animal sources of pathogenic microorganisms infecting human, with or without clinical outcomes according to genetic variants, can also be investigated by genotyping. Toxoplasmosis, an example of a zoonosis, is caused by *Toxoplasma gondii*, a protozoan parasite with high genetic variability, from the apicomplexa group. Attempts to identify genetic variants associated to specific animal hosts or clinical outcome fail; however, it is possible to identify the source of parasite infection by genotyping with the use of multilocus PCR and RFLP [68]. Using this methodology, a study on German patients revealed that ocular, cerebral, and systemic toxoplasmosis presented predominance of *T. gondii* from lineage type II, the same genotype found in parasite oocysts isolated from cats of the same geographic region [69]. The prevalence of *T. gondii* lineages presents specific regional distribution, being highly variable in South America [70], where the parasites are isolated from domestic and wild animals, including chiropterans [71]. Based on these studies, it is possible to recognize several potential parasite intermediate hosts and map the risk areas for toxoplasmosis transmission. Chaga's disease caused by *Trypanosoma cruzi*, a protozoan parasite from the kinetoplastida group, is also an excellent example of eco-epidemiologic study using genotyping. Parasites are transmitted naturally to humans by the exposure of abraded skin to feces of triatomine bugs, and they circulate in the wild in different sylvatic animals and triatomine species. There are six principal genetic variants or discrete typing units of *T. cruzi* determined by multilocus PCR, RFLP, and sequencing analysis, associated to geographical distribution and transmission cycles [72-74]. The association of the outcome of Chaga's disease and specific parasite geno‐ types is still controversial; however, comparative investigation of *T. cruzi* genotypes in human infections, sylvatic bugs, and animal reservoirs, in rural areas near forest, which is common in

South America, can reveal potential vectors and animal sources of infection.

made for influenza vaccine recommendation each year.

The most effective means to control an infectious disease is a vaccine, which is still not available for malaria, trypanosomiasis (Chaga's disease, sleeping sickness, leishmaniasis), and most of arboviruses (dengue fever, chikungunya fever, etc.). The genetic variability of infectious agents, a rapid genomic evolution in case of viruses, and several escape mechanisms from host immune system selected along parasite–host interactions constitutes intricate drawbacks for vaccine development. The problem of genetic prompt variability of virus genome can be circumvented by systematic sequencing during epidemic periods such as the one successfully

Influenza vaccine is composed of attenuated viruses produced in eggs, every year, following the virus strain recommendation by World Health Organization, after monitoring genetic variation in the gene encoding the surface protein hemagglutinin due to its antigenic properties (http://www.who.int/influenza/vaccines/virus/recommendations/201502\_recommenda‐

*1.2.3. Disease control and vaccines*

patterns which can be used for control strategies.

66 Nucleic Acids - From Basic Aspects to Laboratory Tools

Economic and social impact of infectious diseases should be considered worldwide, princi‐ pally in developing countries, including necessity of medical care, vector control, people morbidity with loss of working hours, and reduced tourism in affected areas. The increase in population, high people mobility, and the lack of an effective vaccine against the most disseminated infectious diseases, such as dengue fever, malaria, tripanosomiasis, etc., make these human threats an important public health concern. Nucleic acid technologies have been contributing to the knowledge of infectious disease transmission, distribution, clinical manifestations, and progression, helping in its control and management. Several examples are discussed in this chapter, and hopefully, it will stimulate readers to investigate these micro‐ biological intricacies and magnificent parasite–host interactions, more profoundly.
