*Article* **Comparative Performance of Eight PCR Methods to Detect** *Cryptosporidium* **Species**

**Damien Costa 1,2,3,\*, Louise Soulieux 1, Romy Razakandrainibe 2,3, Louise Basmaciyan 4,5, Gilles Gargala 1,2,3, Stéphane Valot 4,5, Frédéric Dalle 4,5 and Loic Favennec 1,2,3**


**Abstract:** Diagnostic approaches based on PCR methods are increasingly used in the field of parasitology, particularly to detect *Cryptosporidium*. Consequently, many different PCR methods are available, both "in-house" and commercial methods. The aim of this study was to compare the performance of eight PCR methods, four "in-house" and four commercial methods, to detect *Cryptosporidium* species. On the same DNA extracts, performance was evaluated regarding the limit of detection for both *C. parvum* and *C. hominis* specificity and the ability to detect rare species implicated in human infection. Results showed variations in terms of performance. The best performance was observed with the FTD® Stool parasites method, which detected *C. parvum* and *C. hominis* with a limit of detection of 1 and 10 oocysts/gram of stool respectively; all rare species tested were detected (*C. cuniculus, C. meleagridis, C. felis, C. chipmunk*, and *C. ubiquitum*), and no cross-reaction was observed. In addition, no cross-reactivity was observed with other enteric pathogens. However, commercial methods were unable to differentiate *Cryptosporidium* species, and generally, we recommend testing each DNA extract in at least triplicate to optimize the limit of detection.

**Keywords:** *Cryptosporidium*; PCR; detection; diagnosis; sensitivity; specificity
