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Human enteric pathogens circulation in the Bogotá region and its impact on the health of vulnerable communities

Abstract : Acute gastroenteritis affect between a quarter and a half of people in the World each year. They are responsible for significant morbidity, mortality and healthcare costs. Their direct or indirect transmissions via water, food, air or inert surfaces depend on their aetiology (viral, bacterial or parasitic) and the local context. Bogotá and its region have several specificities: wastewater are often discharged into rivers without or after primary treatment only, the deposit in landfill of toilet papers and diapers soiled by excrement, and the low consumption of fruits and vegetables largely restricted to a handful of relatively cheap products that may be irrigated by surface freshwaters heavily contaminated with faeces. Our PhD aimed to assess the fluxes of some human enteric pathogens in the region of Bogotá and to try to relate these fluxes to the population health. The PhD combined three contributions. First, a method for culturing the human norovirus has been developed using isolated mouse intestinal villi as a cell model exhibiting the full diversity of intestinal epithelial cells. Several concentrations of trypsin were tested to activate noroviruses; the method was applied to faecal and environmental samples. Second, contamination with E. coli and some human enteric pathogens was monitored in water (landfill leachate, runoff water, river, irrigation water, drinking water), leafy vegetables eaten raw (chards) and air (above a landfill, in rural areas, in urban areas) in the Bogotá region. Third, the impact of socioeconomic contexts and individual practices (food, hygiene and health) on cases of acute gastroenteritis was assessed from surveys carried out in one district of Bogotá and analysed by various tools (principal component analysis, modelling …). We have shown that mouse isolated intestinal villi allow the infection and replication of human norovirus. The virus has to be activated with trypsin and has an average replicative cycle of 10 h. Villi are efficient in obtaining abundant biological material and are ideal for studying the biological activity of norovirus or for generating antibodies. They made it possible to see infectious noroviruses not detected by molecular method in several faeces and environmental samples; almost all samples positive by molecular method or immunodot-blot contain infectious noroviruses. At the regional level, the discharges of wastewater in the Bogotá and Balsillas rivers and in Tres Esquinas march contaminate the irrigation network of La Ramada area in the northwest of Bogotá with E. coli and potentially human enteric pathogens. Chards harvested in this area were heavily contaminated, in contrast to other growing areas. Their contamination evolved from their production to their purchase in nearby stores, washings increasing or decreasing their contamination, and handling on the merchant's stalls increasing contamination. The air was often contaminated with E. coli and Shigella spp.; it was not possible to detect a particular contribution of the Doña Juana landfill in pathogen aerosolization. The presence of Shigella spp. was observed in parallel in more than half of the stools of people with diarrhoea. Surveys have shown that the annual frequency of acute gastroenteritis decreases with increasing age; it seemed less common in households with elderly people, possibly due to stricter food hygiene practices. A transmission model of acute gastroenteritis distinguishing contamination from outside the households and contaminations between people in the same households did not show significant differences between neighbourhoods. Used to simulate numerical experiments, it suggests working on much higher numbers of surveys.
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José Jordan Lozano. Human enteric pathogens circulation in the Bogotá region and its impact on the health of vulnerable communities. Agricultural sciences. Université d'Avignon; Universidad nacional de Colombia, 2020. English. ⟨NNT : 2020AVIG0359⟩. ⟨tel-03464118⟩

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