Individual genotyping of red fox field stools from the analysis of 14 microsatellite targets and one sex marker and the research of Echinococcus multilocularis DNA presence.

Individual genotyping of red fox stools sampled on the field, from the analysis of 14 microsatellite targets (AHT121, AHT137, C01.424, INU055, AHTh171, C08.618, CPH2, FH2010, C04.140, CXX0279, FH2848, REN169O18, CPH11, FH2457) and one sex marker (K9-AMELO). Em(+): Echinococcus multilocularis DNA detection in faeces, qPCRVv: qPCR for Vulpes Vulpes DNA detection on part of the CytB gene (Knapp et al., 2016) and Cq values, ND: no data. First the fox faeces were identified using a host faecal qPCR technique from total copro-DNA extracts, as previously described (Knapp et al., 2016).

The study was conducted from March 2017 to January 2020 in a grassland area of 3.18 Km² in the village of Les Alliés (006°26’46”E, 46°56’53”N, Fig. 1) in eastern France, at an average altitude of 971 m above sea level.

The QIAmp Fast DNA Stool kit (Qiagen, Hilden, Germany) was used to extract genomic DNA from faecal samples.
Fragment size analyses were performed to obtained allele size quantification for the 14 microsatellites and the sex marker, by using a SeqStudio Genetic Analyzer (Applied Biosystems, Foster City, CA). Genetic profiles were determined using the Microsatellite Analysis module available on the Thermo Fisher cloud (https://apps.thermofisher.com/editor-web/#/app/app-microsatellites-web).
Copro-DNA extracts from foxes were tested for the presence of E. multilocularis (Em(+)) using a specific E. multilocularis-qPCR, as previously described.

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