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

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.

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Publication Details

Journal
Infection Genetics and Evolution
Published
2025-12-19
DOI
https://doi.org/10.1016/j.meegid.2025.105868
Primary Topic
Parasitic infections in humans and animals
Type
article
Field-Weighted Citation Impact
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article

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

Παναγιώτα Λίγδα, Yousra Saïd, Sargis A. Aghayan, Paola Pepe et al.
Infection Genetics and Evolution
Parasitic infections in humans and animals
article

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

Παναγιώτα Λίγδα, Yousra Saïd, Sargis A. Aghayan, Paola Pepe, M.C. Benchikh El Fegoun, Urmas Saarma, Laura Rinaldi, Myriam Oudni-M’rad, Frédéric Grenouillet, Gérald Umhang, V. Yevstafieva, Hasmik Gevorgyan, Sami Şimşek, Jaime Aguayo, Smaragda Sotiraki, Ouafaa Fassi Fihri, Francisco Ponce‐Gordo, Ikhlass El Berbri, Vanessa Bastid, Elena Ciccone, Тetiana А. Kuzmina, Franck Boué, Samia Lahmar, S. Ben Mrad, Haroon Ahmad, Kefiya Elmehatli
article en

Abstract

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.

Infection Genetics and EvolutionVol. 137
Universidad Complutense de Madrid (ES), University Frères Mentouri Constantine 1 (DZ), Centre National de la Recherche Scientifique (FR), Fırat University (TR), COMSATS University Islamabad (PK), University of Monastir (TN), Regione Campania (IT), Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (FR), Scientific Center of Zoology and Hydroecology (AM), Laboratoire Chrono-Environnement (FR), Poltava State Agrarian University (UA), Centre for Research and Technology Hellas (GR), Département Santé des Plantes et Environnement (FR), Agence Nationale de Sécurité Sanitaire de l’Alimentation, de l’Environnement et du Travail (FR), I.I. Schmalhausen Institute of Zoology (UA), Institut Agronomique et Vétérinaire Hassan II (MA), Ministry of Agriculture (TN), University of Tartu (EE), University of Naples Federico II (IT), Manouba University (TN), Université de Franche-Comté (FR)
Openalex Percentile: Top 43%
Parasitic infections in humans and animals
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