Molecular diversity of <i>Enterocytozoon bieneusi</i> (microsporidia) among children, adolescents, and young women in poor-resource settings in southern Madagascar

Microsporidia are obligate intracellular eukaryotic parasites, phylogenetically related to fungi, and are recognised causes of significant morbidity in humans. They are opportunistic pathogens of particular concern in HIV-infected and other immunocompromised populations. In this study, the occurrence and genetic diversity of microsporidian infections (Enterocytozoon bieneusi and Encephalitozoon spp.) were investigated in socially vulnerable populations from disadvantaged areas in southern Madagascar. Epidemiological questionnaires were used to collect demographic data and potential risk factors. Faecal samples (n = 436) from 318 children and adolescents (7-21 years), 57 young mothers (16-21 years), and 61 of their infants (0-5 years) were collected and analysed using molecular methods (PCR and Sanger sequencing). Only E. bieneusi infections were detected, with an overall prevalence of 3.0% (95% CI: 1.6-5.0). The highest prevalence was observed in young mothers (3.5%; 95% CI: 0.4-12.1), nearly followed by infants (3.3%; 95% CI: 0.4-11.4). Genotyping of E. bieneusi was successfully performed in 11 of the 13 positive samples, identifying five known genotypes (A, CAF1, D, PigEBITS7, and Type IV) and one novel genotype, designated HhMdEb1. The most frequently detected genotypes were A and CAF1. All genotypes identified, including the novel genotype, belong to Group 1, which is characterised by low host specificity and high zoonotic potential. The detection of genotypes commonly associated with animal hosts suggests both zoonotic and anthroponotic transmission pathways. These findings underscore the need to implement integrated control strategies within the framework of the 'One Health' approach.