Poulle, M.-L. | bioRxiv Science

bioRxiv2024

Detection of Echinococcus spp. and other taeniid species in lettuces and berries: two international multicenter studies from the MEmE project

Cystic and alveolar echinococcosis are severe zoonotic diseases characterized by long asymptomatic periods lasting months or years. Viable Echinococcus eggs released into the environment through the feces of canids can infect humans through accidental ingestion via hand-to-mouth contact or consumption of contaminated food or water. Both Echinococcus multilocularis and Echinococcus granulosus sensu lato are considered as foodborne parasites. However, when considering possible pathways of human infection, it appears that food and water-borne related variables do not significantly increase the risk of infection. Providing evidence-based data for the presence of DNA and, potentially, eggs in fresh produce is crucial in understanding foodborne transmission of Echinococcus spp. to humans. Two multicenter and multicountry studies were conducted within the One Health EJP framework to estimate the proportion of lettuces and berries contaminated by E. multilocularis, E. granulosus s.l., and other taeniid DNAs from 12 European countries, Tunisia and Pakistan. A total of 1,117 lettuces, 300 strawberries and 130 blueberries samples were collected and analyzed by washing, sequential sieving and real-time PCRs. Echinococcus multilocularis DNA was detected in 1.2% (7/570) of samples tested from the seven European endemic areas and in 2% (2/100) from Pakistan. In the five European endemic countries for E. granulosus s.l., E. granulosus sensu stricto DNA was identified in 1.3% of lettuces (9/695). The proportion of lettuces contaminated by E. granulosus sensu stricto DNA was 12% (9/75) in Tunisia and 4% (4/100) in Pakistan. Regarding berries, E. multilocularis DNA was detected in 5.4% of strawberries (n=11/202), 7.3% of blueberries (6/82) from the seven European endemic countries and 56% of blueberries (14/25) from Pakistan. High contamination rates of E. granulosus s.s were found outside of Europe, with 12.0% in blueberries (3/25) from Pakistan and 81.3%. DNA in strawberries (13/16) from Tunisia. The total contamination rate of all taeniid species DNA in lettuces (5.3%; 59/1,117) and berries (12.1%; 58/480) suggests that the transfer of taeniid eggs from carnivore feces to food is not uncommon. Although we assume that eggs are the source of the DNA detected in this study, the viability of such eggs is unknown. The detection of Echinococcus species in lettuces and berries suggests a potential risk of foodborne human infection. The relative contribution of this risk remains to be estimated. Further studies on food and environmental contamination are necessary to cover different epidemiological contexts and social habits, leading to a better understanding of human infections by Echinococcus eggs.

microbiology↗

bioRxiv2018

Evaluating metabarcoding to analyse diet composition of species foraging in anthropogenic landscapes using Ion Torrent and Illumina sequencing

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 duplicates 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.

molecular biology↗