| Summary: | <i>Entamoeba gingivalis</i> is a parasitic protist that resides in the oral cavity. Although <i>E. gingivalis</i> has been frequently detected in individuals with periodontitis, its precise role in this context remains to be established, since <i>E. gingivalis</i> is also regularly found in healthy individuals. Sequence data on <i>E. gingivalis</i> are still scarce, with only a limited number of sequences available in public databases. In this study, a diagnostic PCR protocol was established in order to obtain a first impression on the prevalence of <i>E. gingivalis</i> in Austria and enable a differentiation of isolates by targeting the variable internal transcribed spacer regions. In total, 59 voluntary participants were screened for <i>E. gingivalis</i> and almost 50% of the participants were positive, with a significantly higher prevalence of participants with self-reported gingivitis. Moreover, in addition to the established subtypes ST1 and ST2, a potentially new subtype was found, designated ST3. 18S DNA sequencing and phylogenetic analyses clearly supported a separate position of ST3. Interestingly, subtype-specific PCRs revealed that, in contrast to ST2, ST3 only occurred in association with ST1. ST2 and ST1/ST3 were more often associated with gingivitis; however, more data will be necessary to corroborate this observation.
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