Absence of measurable quantities of Candida auris and Cryptococcus spp. in the gut microbiota of Ghanaian individuals with and without HIV infection as confirmed by applying multiple real-time PCR assays

<b>Introduction</b>. Fungal infections are relevant health risks for individuals with acquired immunodeficiency in the resource-limited tropics, but available surveillance data are scarce. For <i>Candida auris</i> and <i>Cryptococcus</i> spp., the evolution from environmental reservoirs to human pathogens causing life-threatening diseases is currently discussed as a public health concern in the context of climate change and limited treatment options.<b>Gap statement</b>. Uncovering the gastrointestinal tract as an epidemiological niche of fungi emerging from the environment into individuals for whom fungal infections are not diagnosed.<b>Aim</b>. To contribute to data on the local epidemiology of <i>C. auris</i> and <i>Cryptococcus</i> spp. in Western African Ghana by analysing gastrointestinal samples of Ghanaian individuals.<b>Methodology</b>. Four real-time PCR assays targeting <i>C. auris</i> and five real-time PCR assays targeting <i>Cryptococcus</i> spp. were applied with stool samples of 875 non-age-stratified Ghanaian HIV patients and 30 Ghanaian control individuals without known HIV infection. Also, 664 samples from Ghanaian children under 2 years of age were investigated. The true abundance of the target micro-organism was considered as unlikely in the case of one or fewer positive signals, likely in the case of two to three positive signals and highly likely in the case of four or more positive signals per sample in the real-time PCR assays.<b>Results</b>. The combined application of sensitive, target-specific real-time PCR assays indicates that neither <i>C. auris</i>, <i>Cryptococcus neoformans</i> complex nor <i>Cryptococcus gattii</i> complex were part of the gut microbiota of Ghanaian individuals with or without HIV infection.<b>Conclusion</b>. Despite the significant disease burden from these pathogens in immunosuppressed Ghanaian individuals, detection from gastrointestinal samples was unlikely, which should be taken into account when discussing screening strategies for these fungi of public health concern. In contrast, the detection of these fungi from such samples should not routinely be considered as commensal colonization flora.