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BackgroundPCR-based screenings on the presence of diarrhoea-causing intestinal protist species are limited in Zambia, resulting in inaccurate current prevalence and epidemiological data. Sensitive PCR-based methods are particularly well suited for detecting subclinical infections in apparently healthy carriers.MethodologyIn this prospective cross-sectional study, we investigated the occurrence of the most common intestinal protists in an apparently healthy paediatric population (5-18 years) in Lusaka Province, Zambia. We collected single stool samples (n = 256) and epidemiological questionnaires on demographics, behavioural habits, drinking water and toilet access from participating children. We used PCR for the initial screening of samples for the presence of intestinal protist species and Sanger and next-generation sequencing for genotyping. We conducted statistical analyses to assess the association of the gathered variables with an increased likelihood of the investigated pathogens.Principal findingsBlastocystis sp. was the most prevalent intestinal protist found (37.9%, 97/256; 95% CI: 31.9-44.1), followed by Giardia duodenalis (30.9%, 79/256; 95% CI: 25.3-36.90), Entamoeba dispar (13.3%, 34/256; 95% CI: 9.4-18.1), and Cryptosporidium spp. (4.3%, 11/256, 95% CI: 2.2-7.6). Entamoeba histolytica was not detected. Based on Sanger sequencing results, subtypes ST2 (44.3%, 43/97), ST1 (35.1%, 34/97), and ST3 (20.6%, 20/97) were identified within Blastocystis sp. and assemblages B (71.0%), A+B (16.1%), and A (12.9%) within G. duodenalis. Cryptosporidium parvum (81.8%) and C. hominis (18.2%) were the only two Cryptosporidium species found. Living in the Kafue District was positively associated with higher infection rates by G. duodenalis and Blastocystis sp. Schoolchildren living in Chongwe District were more likely to be infected by Cryptosporidium spp.Conclusions/significanceIntestinal protist infection/colonization is a common finding in apparently healthy children in Lusaka Province, Zambia. Asymptomatic carriers may play an underestimated role as spreaders of gastrointestinal parasitic infections. This study improves our current understanding of the epidemiology of diarrhoea-causing protists in Zambia and sub-Saharan Africa and indicates that the role of asymptomatic carriers of gastrointestinal parasites in transmission should be further explored.

Rickettsia asembonensis is a flea-related Rickettsia with unknown pathogenicity to humans. We detected R. asembonensis DNA in 2 of 1,153 human blood samples in Zambia. Our findings suggest the possibility of R. asembonensis infection in humans despite its unknown pathogenicity.