DNA metabarcoding of faecal samples is being successfully used to study the foraging niche of species. We assessed the ability of two benchtop high-throughput sequencing (HTS) platforms, to identify a large taxonomic array of food items from domestic cats Felis silvestris catus, including prey and human-related food taxa (pet food and leftovers leaving undetectable solid remains in faeces). Scats from a captive feeding trial (n = 41) and from free-ranging individuals (n = 326) were collected and analysed using a cytb mini-barcode in independent PCR replicates on the Ion PGM and the MiSeq platforms. Outputs from MiSeq were more sensitive and reproducible than those from Ion PGM due to a higher sequencing depth and sequence quality on MiSeq. DNA from intact prey taxa was detected more often (82% of the expected occurrences) than DNA from pet food (54%) and raw fish and meat (31%). We assumed that this variability was linked to different degree of DNA degradation: The Ion PGM detected significantly less human-linked food, birds, field voles, murids and shrews in the field-collected samples than the MiSeq platform. Pooling the replicates from both platforms and filtering the data allowed identification of at least one food item in 87.4% of the field-collected samples. Our DNA metabarcoding approach identified 29 prey taxa, of which 25 to species level (90% of items) including 9 rodents, 3 insectivores, 12 birds and 1 reptile and 33 human-related food taxa of which 23 were identified to genus level (75% of items). Our results demonstrate that using HTS platforms such as MiSeq, which provide reads of sufficiently high quantity and quality, with sufficient numbers of technical replicates, is a robust and non-invasive approach for further dietary studies on animals foraging on a wide range of food items in anthropogenic landscapes.

Echinococcus multilocularis, Toxoplasma gondii and Toxocara spp. are foodborne parasites whose eggs or oocysts are spread in the environment via canid or felid faeces. They can cause infections in humans following the raw consumption of contaminated fruit or vegetables. In this study, their occurrence was investigated by quantitative polymerase chain reaction (qPCR) in 254 carnivore faeces deposited in 94 kitchen gardens of northeastern France that were sampled between two and six times from October 2011 to April 2013. Less than 25% of the sampled kitchen gardens contained more than 75% of the collected faeces. Of the 219 faeces that could be attributed to an emitter, cat accounted for 58%, fox for 32% and dog for 10%. Echinococcus multilocularis was detected in 35%, 11% and 7% of fox, dog and cat faeces, respectively, and Toxocara spp. in 33%, 12% and 5.5% of cat, fox and dog faeces, respectively. Toxoplasma gondii was detected in 2/125 cat faeces and 2/21 dog faeces. The 34 faeces that tested positive for E. multilocularis were found in only 19 out of the 94 sampled kitchen gardens, and the 40 faeces that tested positive for Toxocara spp. were found in 28 of them. Consequently, some kitchen gardens appeared particularly at risk of human exposure to foodborne parasites, including E. multilocularis responsible for alveolar echinococcosis (AE), which is a serious zoonosis. In endemic areas, kitchen garden owners should be informed about the zoonotic risk linked to carnivore faeces deposits and encouraged to set up preventive measures. Echinococcus multilocularis, Toxoplasma gondii et Toxocara spp. sont des parasites transmissibles par l’alimentation dont les œufs ou oocystes sont répandus dans l’environnement avec les fèces de canidés ou félidés. Ils peuvent être responsables d’infections humaines suite à la consommation crue de fruits et légumes contaminés. Leur présence a été recherchée par qPCR dans 254 fèces de carnivores déposées dans 94 potagers du nord-est de la France, échantillonnés deux à six fois entre octobre 2011 et avril 2013. Moins de 25 % de ces potagers contenaient plus de 75 % des fèces collectées. Parmi les 219 fèces pour lesquelles l’émetteur a pu être identifié, 58 % étaient de chat, 32 % de renard et 10 % de chien. Echinococcus multilocularis a été détecté dans 35 %, 11 % et 7 % des fèces de renard, chien et chat respectivement et Toxocara spp. dans 33 %, 12 % et 5.5 % des fèces de chat, renard et chien, respectivement. Toxoplasma gondii a été détecté dans 2/125 fèces de chat et 2/21 fèces de chien. Les 34 fèces testées positives pour E. multilocularis ont été trouvées dans seulement 19 des 94 potagers échantillonnés et les 40 fèces testées positives pour Toxocara spp. dans 28 d’entre eux. En conséquence, certains potagers apparaissent particulièrement à risque d’exposition humaine aux parasites transmissibles par l’alimentation et, notamment, à E. multilocularis responsable de l’échinococcose alvéolaire qui est une grave zoonose. En zone d’endémie, les propriétaires de potagers devraient être informés du risque zoonotique lié au dépôt de fèces de carnivores et encouragés à prendre des mesures de prévention.

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Toxoplasma gondii is a protozoan parasite that uses felids as definitive hosts and warm-blooded animals as intermediate hosts. While the dispersal of T. gondii infectious oocysts from land to coastal waters has been well documented, transmission routes to pelagic species remain puzzling. We used the modified agglutination test (MAT titre ≥ 10) to detect antibodies against T. gondii in sera collected from 1014 pelagic seabirds belonging to 10 species. Sampling was carried out on eight islands of the Western Indian Ocean: Reunion and Juan de Nova (colonized by cats), Cousin, Cousine, Aride, Bird, Europa and Tromelin islands (cat-free). Antibodies against T. gondii were found in all islands and all species but the great frigatebird. The overall seroprevalence was 16.8% [95% CI: 14.5%-19.1%] but significantly varied according to species, islands and age-classes. The low antibody levels (MAT titres = 10 or 25) detected in one shearwater and three red-footed booby chicks most likely resulted from maternal antibody transfer. In adults, exposure to soils contaminated by locally deposited oocysts may explain the detection of antibodies in both wedge-tailed shearwaters on Reunion Island and sooty terns on Juan de Nova. However, 144 adults breeding on cat-free islands also tested positive. In the Seychelles, there was a significant decrease in T. gondii prevalence associated with greater distances to cat populations for species that sometimes rest on the shore, i.e. terns and noddies. This suggests that oocysts carried by marine currents could be deposited on shore tens of kilometres from their initial deposition point and that the number of deposited oocysts decreases with distance from the nearest cat population. The consumption of fishes from the families Mullidae, Carangidae, Clupeidae and Engraulidae, previously described as T. gondii oocyst-carriers (i.e. paratenic hosts), could also explain the exposure of terns, noddies, boobies and tropicbirds to T. gondii. Our detection of antibodies against T. gondii in seabirds that fish in the high sea, have no contact with locally contaminated soils but frequent the shores and/or consume paratenic hosts supports the hypothesis of an open-sea dispersal of T. gondii oocysts by oceanic currents and/or fish.

Dermacentor is Europe's second most important tick genus. It comprises two species: Dermacentor reticulatus, which has a more northerly range, and Dermacentor marginatus, which is typically found in Mediterranean regions. In France, especially in the east, the presence of Dermacentor remains understudied. Leveraging projects on Ixodes ricinus, we identified high-risk ecosystems for Dermacentor ticks. Both species were present, but D. reticulatus was dominant (96.3 %), always coexisting with Ixodes, at densities reaching 30.3 questing adults/100 m² in Bas-Rhin. This species was found to thrive in wet meadows, alluvial forests, and lakes, where wild boars (Sus scrofa) are common. Among domestic animals, dogs and horses were the preferred hosts. Regarding human pathogens, we focused on the circulation of rickettsiae responsible for tick-borne lymphadenopathy. Acarological risk varied by region, with Rickettsia raoultii being the most prevalent bacterial species in all the departments, whereas Rickettsia slovaca was rarer and present only in 2 Bas-Rhin nature reserves. At the peak of tick activity, up to 18.7 % of Dermacentor adult ticks carried R. raoultii. In the studied region, D. reticulatus is the only known vector of these potentially pathogenic microorganisms.