Non-Invasive Wildlife Disease Surveillance Using Real Time PCR Assays: The Case of the Endangered Galemys pyrenaicus Populations from the Central System Mountains (Extremadura, Spain)

Abstract

The Iberian desman (Galemys pyrenaicus) is a small semi-aquatic mammal that inhabits mountainous areas from the centre to the north of the Iberian Peninsula and the Pyrenees and is listed as endangered because it has suffered a serious decline. Since 1960, only three species of digeneans (Omphalometra flexuosa, Maritrema pyrenaica and Mathovius galemydis) and two nematodes (Aonchotheca galemydis and Paracuaria hispanica) have been reported from the desman, but no further information on health status and no data from Extremadura has been available. The aim of our study was to characterise the diversity and distribution of parasites and microbiomes of desmans in different areas of the Central System of Extremadura. Between 2019 and 2021 we collected 238 fecal samples and one tissue (intestine) sample that was obtained from a dead desman. DNA templates were processed by commercial or customised real-time PCR using TaqMan probes. Representative data were obtained for Cryptosporidium spp., Omphalometra spp., Eimeria spp., Salmonella spp., Staphylococcus spp. and Leptospira spp. Omphalometra spp. was studied using a newly developed PCR test. The screening of the dead desman allowed us to obtain, for the first time, a partial sequence of the 18SrDNA. This study is the most complete study of the desman, allowing us to identify parasites and the microbiome in populations of G. pyrenaicus using non-invasive sampling.

Keywords: Central System Mountains; Galemys pyrenaicus; Omphalometra flexuosa; insectivores; non-invasive; pathogens; real time PCR.

Figure 1

Map locating the three districts with Iberian desman populations in the north of Extremadura.

Figure 2

Phylogenetic tree resulting from Maximum Likelihood analysis of 28S rDNA alignment of representative plagiorhioidean and microphalloidean taxa showing the position of Omphalometra spp. from the Pyrenean desman sequenced in our study. The family Omphalometridae is indicated by the shaded rectangle. Numbers above internodes indicate bootstrap support values. Only values >50% are shown. The scale bar indicates the number of substitutions per site.