Investigation of Parasitic Infection in Crocodile Lizards (Shinisaurus crocodilurus) Using High-Throughput Sequencing

SIMPLE SUMMARY: To explore unexplained crocodile lizard deaths, we analyzed fecal samples from crocodile lizards at the Daguishan and Luokeng nature reserves using high-throughput sequencing to investigate parasitic infections in this endangered species. The present study reported the occurrence of parasitic infection in wild and captive crocodile lizards, with a total parasitic infection rate of 33.33% (23/69). Different influencing factors (populations and regions) were analyzed, and significant differences were found. The results indicate that captive crocodile lizards were more susceptible to parasitic diseases than wild crocodile lizards. In addition, only Cryptosporidium infection varied by geographical location, with crocodile lizards from Daguishan showing higher susceptibility to Cryptosporidium infestation. From a disease prevention perspective, these findings have great significance for crocodile lizard conservation. ABSTRACT: The highly endangered crocodile lizard (Shinisaurus crocodilurus) continues to be impacted by disease, especially in captive breeding populations. In this paper, based on high-throughput sequencing, we investigated parasitic infections in captive and wild crocodile lizard populations in the Daguishan National Nature Reserve and Guangdong Luokeng Shinisaurus crocodilurus National Nature Reserve. The results show that the overall parasitic infection rate in crocodile lizards was 33.33% (23/69). Four parasite genera were detected, including Eimeria, Cryptosporidium, Nematopsis, and Acanthamoeba, with infection rates of 15.94% (11/69), 17.39% (12/69), 7.25% (5/69), and 4.35% (3/69), respectively. Significant differences in the infection rate were found between the different parasite species (χ(2) = 8.54, p < 0.05, chi-squared test). The parasitic infection rates in the captive and wild populations were 39.29% (22/56) and 7.69% (1/13), respectively, which were significantly different (p < 0.05, Fisher’s exact test). However, no significant differences in the infection rates of the four parasite genera were found between the captive and wild populations (p > 0.05, Fisher’s exact test). The parasitic infection rates in Daguishan and Luokeng were 34.09% (15/44) and 32.00% (8/25), respectively, which were not significantly different (p > 0.05, Fisher’s exact test). However, significant differences in terms of species were found in the two reserves (p < 0.01, Fisher’s exact test). Only Cryptosporidium infection showed a significant difference between the two regions (p < 0.01, Fisher’s exact test). Our results suggest that captive crocodile lizards are more susceptible to parasitic diseases than wild crocodile lizards and that Cryptosporidium infection varies by geographical region. This study provides basic information about the parasites of endangered crocodile lizards, as well as a reference for disease control and conservation.