**5. Conclusions**

Recent epidemiology confirms that cryptosporidiosis is common worldwide in both immunocompetent and immunocompromised individuals. Diagnostic approaches are still mainly based on microscopy; however, PCR-based methods are increasingly used for routine diagnosis. The performance of PCR methods is variable and needs to be evaluated. In this study, based on PCR analysis of the same DNA extracts, we compared the performance of eight commonly used methods according to limit of detection (for both *C. hominis* and *C. parvum*), specificity, and rare species identification. All eight methods were able to detect *C. parvum* and *C. hominis* with a limit of detection of 1000 oocysts/gram of stool, but only one method (FTD®) was able to detect one and ten oocysts/gram for *C. parvum* and *C. hominis*, respectively. Specificity was satisfactory for each tested method. Six of the eight methods were able to detect rare species implicated in human infection.

**Author Contributions:** Conceptualization: D.C., R.R., L.F. and F.D.; methodology: D.C. and L.S.; investigation: D.C. and L.S.; supervision: D.C., L.F. and F.D.; writing—original draft preparation: D.C.; writing—review: G.G., S.V., L.B., L.F., R.R. and F.D. All authors have read and agreed to the published version of the manuscript.

**Funding:** The authors gratefully thank Santé Publique France for their funding of CNR-LE cryptosporidiosis activities.

**Institutional Review Board Statement:** Not applicable.

**Informed Consent Statement:** Not applicable.

**Data Availability Statement:** Not applicable.

**Acknowledgments:** The authors are grateful to Nikki Sabourin-Gibbs, Rouen University Hospital, for her help in editing the manuscript.

**Conflicts of Interest:** The authors declare no conflict of interest.

#### **References**

