As sequencing technologies advance genome studies are becoming a basic tool for studying an organism, and with more genomes available comparative genomics is maturing into a powerful tool for biological research. This thesis demonstrates the strength of a comparative genomics approach on a group of understudied eukaryotes, the diplomonads. Diplomonads are a group of single cell eukaryotic flagellates living in oxygen-poor environments. Most diplomonads are intestinal parasites, like the well-studied human parasite Giardia intestinalis. There are seven different G. intestinalis assemblages (genotypes) affecting different hosts, and it’s under debate whether these are one species. A genome-wide study of three G. intestinalis genomes from different assemblages reveals little inter-assemblage sexual recombination, supporting that the different G. intestinalis assemblages are genetically isolated and thus different species. A genomic comparison between the fish parasite S. salmonicida and G. intestinalis reveals genetic differences reflecting differences in their parasitic lifestyles. There is a tighter transcriptional regulation and a larger metabolic reservoir in S. salmonicida, likely adaptations to the fluctuating environments it encounters during its systemic infection compared to G. intestinalis which is a strict intestinal parasite. The S. salmonicida genome analysis also discovers genes involved in energy metabolism. Some of these are experimentally shown to localize to mitochondrion-related organelles in S. salmonicida, indicating that they possess energy-producing organelles that should be classified as hydrogenosomes, as opposed to the mitosomes in G. intestinalis. A transcriptome analysis of the free-living Trepomonas is compared with genomic data from the two parasitic diplomonads. The majority of the genes associated with a free-living lifestyle, like phagocytosis and a larger metabolic capacity, are of prokaryotic origin. This suggests that the ancestor of the free-living diplomonad was likely host-associated and that the free-living lifestyle is a secondary adaptation acquired through horizontal gene transfers.  In conclusion, this thesis uses different comparative genomics approaches to broaden the knowledge on diplomonad diversity and to provide more insight into how the lifestyle differences are reflected on the genetic level. The bioinformatics pipelines and expertise gained in these studies will be useful in other projects in diplomonads and other organismal groups.

Introducción. El estado nutricional de los individuos es considerado un valioso indicador del estado de salud de la población, así como también del accionar de factores socio-económicos y ambientales. Objetivos: Analizar la relación entre el estado nutricional, las enteroparasitosis y las condiciones socioambientales en niños de Aristóbulo del Valle, Misiones. Métodos. Estudio antropométrico transversal y parasitológico en niños de ambos sexos y entre 6 a 11 años de escuelas públicas del Municipio de Aristóbulo del Valle. Para el análisis de desnutrición se utilizó como referencia CDC/NCHS y para exceso de peso IOTF. El análisis parasitológico se realizó mediante la toma de muestras seriadas de materia fecal y escobillado anal. El relevamiento de las condiciones socio-ambientales se realizó mediante encuestas estructuradas. Resultados. El estado nutricional indicó mayor desnutrición crónica (7,5%) que global y aguda y mayor sobrepeso (9,8%) respecto a obesidad. Los niños presentaron alto porcentaje de parasitismo (86%) y las especies más prevalentes fueron Blastocystis hominis, Enterobius vermicularis y Giardia lamblia. La mayoría de las familias de estos niños habitaban viviendas de chapa y madera, con limitado acceso a servicios públicos, altos niveles de desempleo y padres con un nivel educativo básico. / Introduction: The study of the growth and nutritional status of the individuals is considered an important sign of the population health, as well as the action of socio-economic and environmental factors. Objectives: To analyze the relationship among the nutritional status, enteroparasitoses and socio-environmental conditions in children from Aristóbulo del Valle, Misiones. Methods: A cross-sectional anthropometrical and parasitological study was made in children from both sexes between 6 to 11 years old of public school from Municipality of Aristóbulo del Valle. NCHS was employed as reference in the analysis of undernutrition, and IOTF for the excess of weight. The parasitological analysis was realized by faecal samples and anal brushes. Socio-environmental conditions were evaluated through structured interviews. Results: The nutritional status indicated higher chronic undernutrition (7.5%) than underweight and wasting, and higher overweight than obesity (9.8%). Children showed high percentage of parasitism (86%) and Blastocystis hominis, Enterobius vermicularis and Giardia lamblia were the more prevalent species. Most families of these children live in precarious constructions made out of wood and/or masonry, with limited access to public services, high unemployment levels and a basic educational level of parents. Conclusions: The results obtained indicate the impact of the socio-economic, educational and sanitary impairment, in the children health from a sector Aristóbulo del Valle population, that entails to the coexistence of undernutrition, overweight and parasitic infections.

Agriculture is key to New Zealand�s economy with land-use conversions in response to market forces occurring regularly. Recently, high-intensity dairy farming has replaced low-density livestock farming, often degrading surrounding waterways. Of particular concern is that dairy cattle can be a source of the parasite Giardia, which in humans is a common cause of gastrointestinal infection. Thus, this thesis evaluated whether dairy farm conversions posed significant consequences for public health. First I examined the prevalence of Giardia in calves in a rapidly intensifying dairying region of New Zealand. A total of 1190 faecal samples were collected from calves one to seven weeks old during two spring calving seasons and screened by direct immunofluorescent microscopy. Giardia cysts were detected in 31% of samples. To evaluate the potential risk that this environmental source of Giardia posed to the human population, molecular genotyping was used to compare forty Giardia strains isolated from calves with thirty isolates from humans collected in the same region and period. Sequencing the β-giardin gene, Giardia duodenalis assemblages A and B were identified from both hosts, with genotype comparisons revealing substantial overlap of identical genotypes for both assemblages, implying zoonotic transmission. Environmental agencies routinely promote the planting of streamside edges to decrease nonpoint pollution from dairy farms entering waterways. However, current methods for tracking pathogens across farmland and into waterways via surface runoff are limited and typically have been developed using artificially created landscapes. Furthermore, no studies have investigated how Giardia moves across the landscape in farm surface runoff. I developed a field-based tracking method specific for Giardia and used this technique to compare the ability of recently planted vegetation strips with bare soil strips cleared of vegetation at decreasing pathogen concentrations; a typical scenario when planting barriers to reduce waterway contamination. A spike containing a bromide tracer and inactivated Giardia cysts was applied in drip-irrigated surface runoff, with one-minute samples collected from the bottom of the plot. A significant treatment effect was identified for Giardia, with 26% fewer detected in runoff from the planted strip, highlighting the immediate benefit of vegetation planting in removing pathogens. Next I evaluated the effects of four riparian treatments on Giardia runoff: exotic pasture grass and weeds growing in the absence of cattle grazing due to fencing, in comparison to monocultural plantings of three New Zealand native grassland species. Runoff experiments were performed after planting, both prior to and following the main summer growing season. Bromide recovery was high from all four treatments (54 - 99%), with no significant treatment effects. By comparison, Giardia recovery was low (1 - 13%). Prior to summer, two native species reduced Giardia in runoff more than the pasture grass/weed treatment which was almost vegetation-free at this time. After summer, Giardia recoveries were uniformly lower in all treatments. These results demonstrate that after one growing season, fencing waterways produces riparian buffers, via the growth of exotic pasture plants released from grazing, that decrease pathogen concentrations in surface runoff to concentrations indistinguishable from native plantings. Given infectious organisms are known to be in the environment, it is important to assess the risk these pose to human populations. Findings from this research can be used to improve currently available risk-assessment models for Giardia transmission from infected dairy animals via water to humans.

Giardia intestinalis is an anaerobic parasite, that colonizes the small intestine of humans and other vertebrate hosts. This cosmopolitan parasite, which causes diarrhoea, is transmitted by contaminated water or food via a resistant stage, the cyst. The encystation process involves a number of events that lead to a complete reconstruction of the cell into the form of infectious cyst. The aim of this work was to visualize these modifications in vivo by means of enzymatic labelling of proteins. For the purposes of this work, enzymatic tags Y-FAST and HaloTag were chosen, as they enable visualizing live cells under anaerobic conditions. Chimeric protein constructs were created to visualize the dynamics of the encystation vesicles, the structures of endoplasmic reticulum, the adhesive disc and mitosis. Using the developed constructs, we successfully followed the dynamics of the encystation vesicles and the adhesive disc in vivo. Finally, this work has provided novel molecular tools, which will be used to follow the overall redesign of the parasite cell during encystation.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Giardia duodenalis is one of the main causative agents of diarrhea worldwide, being transmitted by oral-fecal route. Giardiasis is usually self-limiting in immunocompetent individuals, indicating the presence of effective host defense mechanisms. The objective of that study was to determine the prepatent period and to evaluate the kinetics of elimination of cysts and the immune response humoral systemic (IgA, IgG1, IgG2a, IgM, IgE) and intestinal secretory (IgA) in gerbils (Meriones unguiculatus) inoculated, experimentally, with different doses of trophozoites of Giardia duodenalis, in the primary infection, reinfection, immunosuppression and reinfection/immunosuppression. We used 48 animals, 6-8 weeks old, distributed in 5 groups inoculated with different doses of trophozoites of G. duodenalis (101, 102, 103, 104 and 105) and a group control. Coproparasitology exams were carried out, daily, using the method of fluctuation in zinc sulfate 33%, to determine the prepatent period and the kinetics of elimination of cysts. Weekly, blood collections for retro-orbital puncture were performed and samples of feces were processed for obtaining of faecal extracts. In the 45th day after inoculation, the animals of each group were redistributed in 4 subgroups and submitted to the reinfection, immunosuppression or reinfection/immunosuppression. It was verified that all the gerbils inoculated with different trophozoites doses were susceptible to the primary infection, with prepatent period between 9 and 13 days. The reinfected animals didn't eliminate cysts and the immunosuppressed or reinfected/immunosuppressed again they presented recrudescence of the infection. The production of antibodies was induced by the parasite, although the systemics antibodies just reflect the stimulation of the immune response for G. duodenalis, since they don't act in the elimination of the parasite. In the reinfection it was observed fast production of both serum and secretory antibodies and the immunossuppressed animals they presented smaller levels of responsible antibodies for the control of the infection. Fecal IgA showed increase in the titles in the period in that absence of cysts was verified in the feces, could be correlated with the control of the giardiasis in this experimental model. / Giardia duodenalis é um dos principais agentes causadores de diarréia em todo o mundo, sendo transmitido por via oro-fecal. A giardíase é, usualmente, auto-limitante em indivíduos imunocompetentes, indicando a presença de mecanismos efetivos de defesa do hospedeiro. O objetivo desse estudo foi determinar o período pré-patente e avaliar a cinética de eliminação de cistos e a resposta imune humoral sistêmica (IgA, IgG1, IgG2a, IgM, IgE) e secretora intestinal (IgA) em gerbils (Meriones unguiculatus) inoculados, experimentalmente, com diferentes doses de trofozoítos de Giardia duodenalis, na infecção primária, reinfecção, imunossupressão e reinfecção/imunossupressão. Foram utilizados 48 animais, com idade entre 6 e 8 semanas, distribuídos em 5 grupos inoculados com diferentes doses de trofozoítos de G. duodenalis (101, 102, 103, 104 e 105) e um grupo controle. Exames coproparasitológicos foram realizados, diariamente, utilizando método de flutuação em sulfato de zinco a 33%, para determinar o período pré-patente e a cinética de eliminação de cistos. Semanalmente, coletas sanguíneas por punção retro-orbital foram realizadas e amostras de fezes foram processadas para obtenção de extratos fecais. No 45º dia após inoculação, os animais de cada grupo foram redistribuídos em 4 subgrupos e submetidos à reinfecção, imunossupressão ou reinfecção/imunossupressão. Verificou-se que todos os gerbils inoculados com diferentes doses de trofozoítos mostraram-se susceptíveis à infecção primária, com período pré-patente entre 9 e 13 dias. Os animais reinfectados não voltaram a eliminar cistos e os imunossuprimidos ou reinfectados/imunossuprimidos apresentaram recrudescência da infecção. A produção de anticorpos foi induzida pelo parasito, embora os sistêmicos apenas reflitam a estimulação da resposta imune por G. duodenalis, já que não atuam na eliminação do parasito. Na reinfecção foi observada rápida produção de anticorpos séricos e secretores e os animais imunossuprimidos apresentaram baixos níveis de anticorpos responsáveis pelo controle da infecção. A IgA fecal mostrou aumento nos títulos no período em que se verificou ausência de cistos nas fezes, podendo estar correlacionada com o controle da giardíase neste modelo experimental. / Mestre em Imunologia e Parasitologia Aplicadas

Giardia duodenalis é um protozoário entérico de distribuição mundial responsável por causar a giardíase em uma grande variedade de mamíferos, incluindo os humanos. É considerada uma espécie complexa, no qual os isolados podem ser classificados em sete agrupamentos genéticos distintos apesar de serem morfologicamente indistinguíveis. O presente trabalho teve como objetivo avaliar a variabilidade genotípica de isolados de G. duodenalis provenientes de humanos naturalmente infectados, residentes em cidades do litoral de São Paulo, na Baixada Santista. A caracterização molecular de 43 isolados pelo seqüenciamento parcial de genes codificadores da enzima glutamato-desidrogenase (gdh) e da proteína beta-giardina (bg) mostrou que o assemblage B da G. duodenalis é o mais freqüente na região litorânea, ocorrendo em 53,5% (n=23) das amostras, sendo o assemblage A identificado em 34,8% (n=15). A maioria das seqüências obtidas pelo gene gdh se mostrou polimórfica, caracterizada por picos duplos de nucleotídeos em algumas posições em cromatograma e quando a análise dos dois genes foi combinada cinco isolados apresentaram identidades diferentes. A esses fenômenos duas explicações são atribuídas, infecção mista ou heterozigose de seqüência alélica. As análises filogenéticas mostraram que o gene bg é mais conservado que o gene gdh, não sendo capaz de discriminar os sub-agrupamentos que constituem os Assemblages do parasita. Com base nos resultados apresentados podemos concluir que a participação de genótipos zoonóticos é relevante na epidemiologia das giardíases nos indivíduos residentes das cidades litorâneas do estado de São Paulo e que estudos de caracterização molecular da G. duodenalis são indispensáveis para melhor conhecimento da epidemiologia desta infecção. / Giardia duodenalis is an enteric protozoa of global distribution responsible for causing giardiasis in a wide range of mammals including humans. Is considered complex specie in which the isolates can be classified in different genetic groups despite to be morphologically indistinguishable. The purpose of this study was evaluating the genetic variability of G. duodenalis isolates from humans naturally infected residents in the coast cities of Sao Paulo, in Baixada Santista. The molecular characterization of 43 isolates using the gene encoding glutamate-desidrogenasi enzyme (gdh) and beta-giardin protein (bg) showed that the assemblage B is the most common in the coast region, occurring in 53.5% (n=23) samples, the assemblage A was identified in 34.8% (n=15). Most sequences obtained by the gdh gene showed polymorphism, characterized for double peaks of nucleotides in some chromatogram positions and when the analysis of two genes was combined five isolates were differently identified. For this phenomena can be attributed two explanations, mixed infections or heterozygosis allelic sequence. The phylogenetic analysis showed that bg gene is more conserved than gdh gene, not being able to discriminate the sub-groups of parasite assemblages. Based on the presented results we can conclude the participation of zoonotic genotypes is important in the epidemiology of giardiasis in residents of the coast cities of Sao Paulo state and molecular characterization studies of G. duodenalis are essential for better understanding the epidemiology of this infection.

Soil amended with manure has been implicated as a source of produce contamination leading to foodborne gastrointestinal-disease outbreaks. While current composting guidelines require temperatures ≥ 55°C for 3 days to destroy bacterial pathogens, these requirements have not been evaluated for all pathogens. Investigation of parasite survival in manure required development of a flow cytometry method integrating the cell-impermeant viability dye SytoX for simultaneous quantification and viability assessment of Cryptosporidium and Giardia oocysts/cysts. Further studies will be required to apply this method to investigate thermal reduction in parasites. Studies conducted with bacterial pathogens indicated that E. coli O157:H7 survived longer than other pathogens at 50°C to 55°C. Listeria monocytogenes survived significantly better in chicken manure compared to cow manure at 50°C to 55°C. Results suggest composting guidelines are adequate for bacterial pathogen reduction; however, testing for E. coli O157 along with Salmonella may increase confidence in compost safety.

PhD (Microbiology) / Department of Microbiology / Background: Diarrheal diseases have a major effect on human health, Globally; it is second only to pneumonia as a leading cause of death among children under five. They are due to a variety of infectious and non-infectious agents; including Entamoeba spp. Entamoeba histolytica is an invasive enteric protozoan parasite that causes amebiasis. Amebiasis is frequent in communities without clean water and poor sanitation, which include low-income South African populations in Giyani and Pretoria. In these populations, the amount of diarrhea caused by Entamoeba histolytica inclusive of all ages, sexes and HIV status is uncertain. Diagnosis of the parasite is usually by microscopy. However, microscopy lacks sensitivity and specificity, therefore it is not reliable. Fortunately, molecular diagnostic tests have been developed to detect different Entamoeba species in humans. It is known that the parasite E. histolytica causes asymptomatic and symptomatic diseases. However, the transition from colonization to disease is still unclear. While parasite and host factors, as well as environmental conditions influence the infection outcome, there is currently no clear explanation of wide variation in the presentation of the disease. This could suggest that there are other factors affecting the disease outcome. A better understanding of these factors as well as their role in disease remains target objectives of modern scientists and it will definitely help in the fight against the disease. In spite of the emerging evidence that the host microbiome, parasite burden and the inflammatory response contribute to the virulence of E. histolytica, their roles have never been defined in developing regions such as Giyani and Pretoria. In addition, the present study hypothesized that co-infections with E. histolytica and secretion of extracellular vesicles/exosomes have a significant impact on the virulence of E. histolytica. Little has been explored or elucidated about responses triggered by other enteropathogens/ameba interplay that could be important in the induction of tissue invasion and disease and also how E. histolytica/enteropathogens interplay in these infections has not been determined. Therefore, the knowledge of this interplay could help in understanding how this modifies disease manifestations by modulating pathogen virulence and the host response. The use of secretion systems is an essential biological process exploited by pathogenic microorganisms to promote survival and spread of the pathogen, which in turn exacerbate the infection. The study of extracellular vesicles (EVs) released by pathogens is a new and exciting field that may realistically contribute to a better understanding of the pathogenic process of E. histolytica and provide alternate control strategies. Aim and objective of the study: The overall aim of the study was to determine the impact of enteric pathogens and secreted extracellular vesicles on amebic virulence and the outcome of infection. This aim was addressed in through a series of six primary objectives, which were: a. To investigate the distribution and prevalence of protozoan parasites in South Africa. b. To investigate novel species of Entamoeba circulating in the South African population. ix c. To elucidate the impact of gut microbiota and immune response during amebic infection. d. To determine the role of Entamoeba histolytica macrophage inhibitory factor (EhMIF) during amebic infection. e. To investigate the impact of co-infections on the outcome of amebiasis. f. To determine the presence of secreted extracellular vesicles/exosomes in Entamoeba histolytica. Brief methodology and results: A modified and validated Taqman qPCR assay (with taqman probes and genus specific primers) was used for amplification and target detection. This assay was used to investigate the distribution and prevalence of protozoan parasites (Cryptosporidium spp and Giardia lamblia) in South Africa, the assay was considered superior for this project because it is more sensitive than conventional PCR and it can be used to detect multiple infection targets. This assay allows fast, accurate, and quantitative detection of a broad spectrum of enteropathogens and is well suited for surveillance or clinical purposes. A total of 484 stool samples collected from diarrheal and non-diarrheal patients from rural and urban communities of South Africa were studied. The overall prevalence of parasites (Giardia lamblia and Cryptosporidium spp) in rural and urban patients were found to be 49% (112/227) and 21% (54/257) respectively (p= < 0.0001). The distribution of specific pathogens in rural areas was Cryptosporidium spp (20%) and Giardia lamblia (14%). Our findings showed no significant difference in parasitic infections between gender and the age of the participants (Chapter 3). The discovery of novel species is of great importance to human health. We have recently discovered stools positive for Entamoeba organisms by microscopy but PCR negative for known Entamoeba species. This led to the hypothesis that novel species of Entamoeba are present in the South African population. A comprehensive assay was used which included probes to identify Entamoeba bangladeshi from diarrheal and non-diarrheal participants. A sensitive qPCR assays and amplicon sequencing was used to detect Entamoeba spp, Prevotella copri and Enterobacteriaceae. Interestingly, E. bangladeshi was identified in the South African population. Entamoeba was present in 27% (E. histolytica 8.5% (41/484), E. dispar 8% (38/484), and E. bangladeshi 4.75% (23/484) E. moshkovskii was not detected in the present study. We were also able to observe changes in the host microbiome and the parasite burden associated with E. histolytica infections in S. African diarrhea cases versus asymptomatic controls but not with E. bangladeshi or E. dispar. In E. histolytica positive samples the level of both parasite and P. copri were lower in non-diarrheal samples (p=0.0034) (Chapter 4). There is accumulating evidence that the inflammatory response contributes to injury. Little is known about the key parasite mediators of host mucosal immunopathology. This study hypothesized that migration inhibitory factor (MIF) mediates the destructive host inflammatory response seen in amebic colitis. To determine the role of EhMIF during amebic infection, we used a genetic approach to test the effect of EhMIF on mucosal inflammation. We found that EhMIF induces IL-8 secretion from intestinal epithelial cells. Mice treated with antibodies that specifically block EhMIF had reduced chemokine expression and neutrophil infiltration in the mucosa. In addition to antibody-mediated neutralization, mice infected with parasites overexpressing EhMIF had increased chemokine expression, neutrophil influx and mucosal damage. We also found that the concentration of EhMIF correlated with the level of intestinal inflammation in persons with intestinal amebiasis. Together, our results reveal a novel parasite mediator of mucosal inflammation and support MIF homologs as potential immunomodulatory targets (Chapter 5). To investigate the impact of co-infections on the outcome of amebiasis, we analyzed the co-occurence of E. histolytica with other enteropathogens known to cause diarrheal infections, such as Shigella/EIEC (IpaH), Campylobacter (cadf), Enterotoxigenic E. coli (STh), Norovirus GII and Adenovirus (Hexon). The results were compared with those obtained with E. histolytica that were not interacted with enteropathogens and with E. histolytica interacted with enteropathogens. The impact of multiple infections on the outcome of the infection was compared between nondiarrheal and diarrheal stool samples. It was found that co-infections with two pathogens were associated with diarrhea compared to single infections. Moreover, Norovirus GII, Campylobacter (Cadf) and co-infections were associated with diarrhea in the study population. This study did not show any significant impact of pathogens co-infecting with E. histolytica on the outcome of amebic infection (Chapter 6). The presence of secreted extracellular vesicles/Exosomes in Entamoeba histolytica was determined by using the Pathogenic ameba strains (HM-1:IMSS or HM-1:IMSS (Sub-strain-US) from petri’s lab to purify exosomes using the commercially available kit to isolate exosomes (total exosomes isolation kit). Our study for the first time revealed that E. histolytica does secrete Evs. This finding increases the appreciation that all organisms are likely to secrete these EVs (Chapter 7). However, the impact of these EVs on the pathogenesis of E. histolytica needs further investigations. Conclusion: This study has contributed significantly to our knowledge on infectious diarrhea and the diversity of Entamoeba species by providing new data on the rate and prevalence of Entamoeba diarrheal infections and their distribution in the South African population. Our study describes for the first time the presence of E. bangladeshi in the South African population. Furthermore, our results reveal a novel parasite mediator of mucosal inflammation and support MIF homologs as potential immunomodulatory targets. This study also, for the first time revealed that E. histolytica does secrete EVs. The results from this work will undoubtedly open an exciting research to establish a deeper understanding of the function and role of these vesicles in amebic infection. We encourage public health interventions like health education programs and improvement of sanitation and hygiene in these populations. Molecular diagnostics should be used for specific diagnostic in clinical settings. / NRF

SNARE proteins play essential role in most membrane fusions taking place in eukaryotic cell. They are responsible for all fusions that occur across endocytic and secretory pathways. Apart from these processes stand mitochondria and plastids. Fusion of these organelles is directed by specific protein machineries. In this work we review up-to-date information on SNARE mediated membrane fusion and fusion of outer and inner mitochondrial membranes with an emphasis on situation in flagellated protozoan parasite Giradia intestinalis. It was suggested that one of typical SNARE protein in Giardia (GiSec20) is localised to its highly reduced mitochondria called mitosomes. This protein is also essential for surviving of Giardia trophozoites. In this work we show that mitosomal localization of Gisec20 is caused by episomal expression however the protein is localised to endoplasmic reticulum under physiological conditions. Using GFP tag we were able to characterize its targeting signal which showed to be localised in transmembrane domain of GiSec20. This signal targets the protein to mitosomes of G. intestinalis and S. cerevisiae, respectively. Mitosomal localization was prevented by adding 3'UTR to gene sequence and its episomal expression. This suggests existence of targeting mechanism based on information...

Amoebic dysenteri is a problem in developing countries and is caused by Entamoeba histolytica (E. histolytica) with symptoms such as diarrhea, vomiting and in worse case extra intestinal manifestation. Currently there are difficulties to diagnose E. histolytica infections in developing countries because PCR requires advanced and expensive and microscopy cannot distinguish E. histolytica from other harmless species of amoebas. The aim of this study was therefore to develop loop-mediated isothermal amplification (LAMP), which is similar to PCR but is performed at a single temperature and amplifies the target gene in less than an hour. LAMP was also compared to real time PCR. With a commercial kit, DNA were extracted from cultivated trophozoites and for the LAMP reaction, a colorimetric mastermix and six primers were used designed from 18S small subunit ribosomal RNA gene. With phenol red positive LAMP reactions showed a color change from pink to yellow and negative LAMP reactions remained pink. The sensitivity of LAMP for detection of E. histolytica was determined to be 80 pg/µl, which was ten times less sensitive than real time-PCR. The method was also shown to work on trophozoites with no DNA extraction and no non-specific amplifications were seen with DNA from G. lamblia, which showed some specificity. LAMP proved to be sensitive and easy to work with, but requires tightly closed tubes to avoid contamination and false positive results. To develop and evaluate the method LAMP for detection of E. histolytica, more studies are needed, including clinical samples and optimization.