A panel of five microsatellites as an alternative to mitogenome sequencing for investigating the genetic diversity of Echinococcus granulosus sensu stricto from global to farm scale

@article{umhang2026panel,
  title = {{A panel of five microsatellites as an alternative to mitogenome sequencing for investigating the genetic diversity of Echinococcus granulosus sensu stricto from global to farm scale}},
  author = {Gérald Umhang and Vanessa Bastid and Laura Rinaldi and Paola Pepe and Elena Ciccone and Smaragda Sotiraki and Panagiota Ligda and Myriam Oudni-M'Rad and Selim M'Rad and Samia Lahmar and Yousra Said and Kefiya Elmehatli and Haroon Ahmed and Tetiana Kuzmina and Valentyna Yevstafieva and Sargis Aghayan and Hasmik Gevorgyan and Sami Simsek and Francesco Ponce-Gordo and M.C. Benchikh El Fegoun and Ikhlass El Berbri and Ouafaa Fassi Fihri and Urmas Saarma and Frédéric Grenouillet and Franck Boué and Jaime Aguayo},
  journal = {Infection, Genetics and Evolution},
  year = {2026},
  month = oct,
  doi = {10.1016/j.meegid.2025.105868},
  url = {https://hal.science/hal-05829962v1},
  note = {CC BY-NC-ND},
}

TY  - JOUR
TI  - A panel of five microsatellites as an alternative to mitogenome sequencing for investigating the genetic diversity of Echinococcus granulosus sensu stricto from global to farm scale
AU  - Gérald Umhang
AU  - Vanessa Bastid
AU  - Laura Rinaldi
AU  - Paola Pepe
AU  - Elena Ciccone
AU  - Smaragda Sotiraki
AU  - Panagiota Ligda
AU  - Myriam Oudni-M'Rad
AU  - Selim M'Rad
AU  - Samia Lahmar
AU  - Yousra Said
AU  - Kefiya Elmehatli
AU  - Haroon Ahmed
AU  - Tetiana Kuzmina
AU  - Valentyna Yevstafieva
AU  - Sargis Aghayan
AU  - Hasmik Gevorgyan
AU  - Sami Simsek
AU  - Francesco Ponce-Gordo
AU  - M.C. Benchikh El Fegoun
AU  - Ikhlass El Berbri
AU  - Ouafaa Fassi Fihri
AU  - Urmas Saarma
AU  - Frédéric Grenouillet
AU  - Franck Boué
AU  - Jaime Aguayo
PY  - 2026
DA  - 2026/10/21
JO  - Infection, Genetics and Evolution
DO  - 10.1016/j.meegid.2025.105868
UR  - https://hal.science/hal-05829962v1
AB  - While the molecular identification of Echinococcus granulosus species is essential for surveillance, a detailed investigation of the parasite's genetic diversity would offer a more accurate understanding of its transmission. This may be done by partial or whole mitochondrial genome sequencing, but both cost and time requirements limit routine application. Microsatellites are an alternative approach as they are a rapid, simple, highly discriminative, and low-cost tool. Our research project was designed to obtain a panel of microsatellite targets for population genetic analyses to describe the genetic diversity of E. granulosus sensu stricto (s.s.) at the global to farm scale. A panel of five informative microsatellite loci for population genetic analysis of E. granulosus s.s. was developed and validated. A total of 145 isolates from 11 countries were used to evaluate the panel at the international level. Additionally, 131 samples from sheep and cattle across six regions in southern Italy were analyzed to assess the panel's usefulness at both the regional and farm scale. Population genetics showed high genotypic diversity. Simpson's index gave high values (0.94-0.98) for the expected heterozygosity (0.80 to 0.87). Discriminant analysis of principal components (DAPC) revealed the structure of populations for each country, with Greece distinctly distant from Algeria, Italy, and Tunisia. This was also confirmed by FST values. DAPC further revealed a genetic structure among the farms from the Italian regional sample set, with three different clusters explained by different farming practices. This microsatellite panel can provide data relevant for E. granulosus s.s. population genetics from global to farm scale, making it a low-cost, simple alternative to full mitochondrial genome sequencing for analyzing numerous samples and obtaining a detailed overview of genetic diversity, an input that is useful for cystic echinococcosis control programs.
SN  - 1567-1348
SN  - 1567-7257
ER  -