Distinguishing Echinococcus granulosus sensu stricto genotypes G1 and G3 with confidence: A practical guide

Liina Kinkar (1) , Teivi Laurimäe (1) , Gerardo Acosta-Jamett (2) , Vanessa Andresiuk (3) , Ibrahim Balkaya (4) , Adriano Casulli (5) , Robin Gasser (6) , Luis Miguel González (7) , Karen Haag (8) , Houria Zait (9) , Malik Irshadullah (10) , Abdul Jabbar (6) , David Jenkins (11) , Maria Teresa Manfredi (12) , Hossein Mirhendi (13) , Selim M'Rad (14) , Mohammad Rostami-Nejad (15) , Myriam Oudni-M'Rad (14) , Nora Beatriz Pierangeli (16) , Francisco Ponce-Gordo (17) , Steffen Rehbein (18) , Mitra Sharbatkhori (19) , Eshrat Beigom Kia (20) , Sami Simsek (21) , Silvia Viviana Soriano (16) , Hein Sprong (22) , Viliam Šnábel (23) , Gérald Umhang (24) , Antonio Varcasia (25) , Urmas Saarma (1)

1 Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
2 Universidad Austral de Chile
3 FCEyN - Facultad de Ciencias Exactas y Naturales [Buenos Aires]
4 Atatürk University School of Medicine
5 World Health Organization Collaborating Centre for the Epidemiology, Detection and Control of Cystic and Alveolar Echinococcosis
6 Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne
7 ISC - Instituto de Salud Carlos III [Madrid]
8 UFRGS - Universidade Federal do Rio Grande do Sul [Porto Alegre]
9 University Hospital Mustapha Alger
10 Aligarh Muslim University
11 Charles Sturt University [Australia]
12 UNIMI - Università degli Studi di Milano = University of Milan
13 Isfahan University of Medical Sciences
14 UM - Université de Monastir - University of Monastir
15 SBUMS - Shahid Beheshti University of Medical Sciences [Tehran]
16 UNCOMA - Universidad Nacional del Comahue [Neuquén]
17 UCM - Universidad Complutense de Madrid = Complutense University of Madrid [Madrid]
18 Kathrinenhof Research Center
19 Golestan University of Medical Sciences
20 IUMS - Iran University of Medical Sciences [Tehran, Iran]
21 University of Firat
22 Centre for Infectious Disease Control Netherlands
23 SAS - Slovak Academy of Sciences
24 LRFSN - Laboratoire de la rage et de la faune sauvage de Nancy
25 UNISS - Università degli Studi di Sassari = University of Sassari [Sassari]

Cystic echinococcosis (CE), a zoonotic disease caused by tapeworms of the species complex Echinococcus granulosus sensu lato, represents a substantial global health and economic burden. Within this complex, E. granulosus sensu stricto (genotypes G1 and G3) is the most frequent causative agent of human CE. Currently, there is no fully reliable method for assigning samples to genotypes G1 and G3, as the commonly used mitochondrial cox1 and nad1 genes are not sufficiently consistent for the identification and differentiation of these genotypes. Thus, a new genetic assay is required for the accurate assignment of G1 and G3. Here we use a large dataset of near-complete mtDNA sequences (n = 303) to reveal the extent of genetic variation of G1 and G3 on a broad geographical scale and to identify reliable informative positions for G1 and G3. Based on extensive sampling and sequencing data, we developed a new method, that is simple and cost-effective, to designate samples to genotypes G1 and G3. We found that the nad5 is the best gene in mtDNA to differentiate between G1 and G3, and developed new primers for the analysis. Our results also highlight problems related to the commonly used cox1 and nad1. To guarantee consistent identification of G1 and G3, we suggest using the sequencing of the nad5 gene region (680 bp). This region contains six informative positions within a relatively short fragment of the mtDNA, allowing the differentiation of G1 and G3 with confidence. Our method offers clear advantages over the previous ones, providing a significantly more consistent means to distinguish G1 and G3 than the commonly used cox1 and nad1.

Keywords: Cystic echinococcosis; Echinococcus granulosus sensu stricto; Genotype identification; Mitochondrial markers; The nad5 gene

Domains: Life Sciences [q-bio]; Veterinary medicine and animal Health; Parasitology

Liina Kinkar, Teivi Laurimäe, Gerardo Acosta-Jamett, Vanessa Andresiuk, Ibrahim Balkaya, et al.. Distinguishing Echinococcus granulosus sensu stricto genotypes G1 and G3 with confidence: A practical guide. Infection, Genetics and Evolution, 2018, 64, pp.178-184. ⟨10.1016/j.meegid.2018.06.026⟩. ⟨anses-03413319⟩