Cryptosporidium spp., Giardia intestinalis, and Blastocystis sp. under one health: prevalence, risks, and transmission dynamics in diverse habitats and potential impacts in the gut microbiome

Intestinal parasites are of significance in disease, especially in relevance to diarrhoea and its subsequent burden. Diarrhoea is one of the main causes of death worldwide, even though the majority of cases are preventable and even treatable. This issue is particularly significant in developing countries where poor sanitation and limited access to clean water is a major problem. Additionally, the proximity of humans to livestock and wild animals is prevalent in these areas, leading to increased transmission between hosts and their shared environments. Therefore, the implementation of One Health principles, which consider various hosts in infection and transmission, is crucial. Given the presence of poor hygiene and sanitation in rural settings in low- and middle-income countries (LMICs) in Africa and Asia, investigating One Health is important for prevention purposes, especially considering the wider host range and higher prevalence of diarrhoea in LMICs. Therefore, studying One Health in the context of intestinal parasites, such as Cryptosporidium spp., Blastocystis sp., Giardia intestinalis, and Entamoeba histolytica is beneficial. These intestinal parasites can play a significant role in causing diarrhoea. They also infect a wide range of hosts. Additionally, they can be found in environmental settings due to their high resistance when in cyst form. Examining the presence of the clinical and veterinary important Cryptosporidium species, Cryptosporidium parvum, in aquaculture is another key aspect to consider in transmission studies. For example, fish can serve as a food source, so emphasising the importance of proper management and cooking of fish can act as a crucial point in disease prevention work. More research is needed on intestinal parasites and their transmission. Moreover, studying them in relation to the bacterial composition of the human gut is vital. However, due to constraints in obtaining human samples, such as a prolonged ethical approval requirement period, exploring alternative avenues becomes necessary. With easier access to samples from non-human primates (NHP) and their close genetic proximity to humans, investigating them not only becomes more accessible but also facilitates comparisons and theoretical extrapolations for human health. Therefore, examining their microbiomes can provide valuable insights into human intestinal health. With this knowledge, this thesis aimed to investigate the presence of the intestinal parasites Cryptosporidium spp., Blastocystis sp., G. intestinalis, and E. histolytica, in a variety of hosts in rural and slum areas of Algeria, Bangladesh, and Uganda and analyse the gut microbiome of wild chimpanzees in relation to the presence/absence of these intestinal parasites. To investigate the prevalence and the transmission of these specific intestinal parasites, I focused on studying human- and animal hosts, as well as their shared environment. 11 The first part of this thesis included sample collection in Algeria from humans, livestock, and environmental as well as aquaculture (more specifically fish). This involved sampling from both humans and animals residing within the same households, along with environmental samples taken from within or around the households, such as soil and water. In total, 218 samples were collected from 39 different households, consisting of 66 human samples and 135 animal samples. Additionally, environmental samples included five water samples and twelve soil samples. The investigation aimed to detect the presence of the intestinal parasites, Cryptosporidium spp., G. intestinalis, E. histolytica, and Blastocystis sp. Furthermore, 68 faecal samples from camels (Camelus dromedarius) and five environmental samples were collected from within a camel farm. Cryptosporidium was detected in humans, various animals, and environmental samples. This included the presence of C. bovis, C. andersoni, C. ryanae and C. parvum (subtypes IIaA18G2R1, IIaA17G2R1, IIaA15G2R1 IIaA14G1R1, IIaA13G1R1 IIdA19G1, and IdA16G1b). Moreover, Blastocystis ST1-ST3, ST5-ST7, ST10, ST14-ST15, ST21, ST23-ST26 and ST30, as well as G. intestinalis B and E was also detected in human, animal, and environmental samples. In addition to the previous sampling efforts, fish samples were included to investigate the presence of the zoonotic C. parvum. These fish specimens were obtained from the Mediterranean Sea as well as local rivers, and dams in Algeria. For this study, 860 different fish species were collected, with Cryptosporidium present in 173 of them. Molecular analysis revealed the detection of zoonotic C. parvum IIaA16G2R1 and IIaA17G2R1 in Sparus aurata. The subsequent phase of my PhD research involved sampling in Bangladesh, mirroring parts of the approach taken in Algeria. This sampling consisted of sixteen human samples, 32 soil samples, and 54 animal samples from various households. The animal samples encompassed both free-ranging animals and animals residing within specific households. The samples were collected from households in a slum region within the city of Mymensingh. Analysis revealed the presence of Blastocystis ST1-ST3, ST7, ST10, ST23-ST25, as well as C. bovis, C. meleagridis, C. bailey, and C. parvum (IIaA17G2R2 and IIaA15G2R1) and G. intestinalis assemblage B, detected in human, animal, and soil. In the final phase of my PhD research, the focus shifted to examining the presence of intestinal parasites in chimpanzees (Pan troglodytes) residing in the Budongo Forest in Uganda. A total of 150 stool samples were collected. This included longitudinal sampling, allowing for collection from the same chimpanzee at different intervals. Additional information was also available, such as chimpanzee communities, age, gender, and family relationships. These enabled comparisons of intestinal parasite infections not only within individual hosts but also between different chimpanzees within the reserve. Moreover, analysis of the gut microbiome and consideration of the potential alteration of gut microbial composition due to 12 intestinal parasitic infections were conducted. Intestinal parasites that were detected in the sampled chimpanzees included Blastocystis sp., specifically ST1, ST2, and ST3, as well as C. parvum, subtypes IIaA17G2R1, IIaA18G2R1, and IIaA15G2R1, C. hominis IfA12G2, and C. felis. G. intestinalis assemblage B was also detected. With the identification of identical sequences between hosts, a possible transmission between chimpanzees was illustrated, and even possible migration beyond their communities. The microbiome analysis in chimpanzees revealed Firmicutes, Actinobacteria, and Bacteroidetes as predominant phyla, with Olsenella being the most prevalent genus. Additionally, the microbiome analysis provided insights into the bacterial composition, but it did not reveal any significant differences between the groups included in this project, such as infections, age, gender, and community. However, variations in abundance were observed. Overall, my thesis emphasises the need for a holistic One Health approach, encompassing wild animals, humans, livestock, and their shared environment. Further exploration of the microbiome and its interactions with intestinal parasites across these interconnected systems is essential for comprehensively understanding and addressing health challenges.