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1. Genetic diversity and phylogeography of the elusive, but epidemiologically importantEchinococcus granulosussensu stricto genotype G3

Author

Houria Zait, Teivi Laurimäe, Sami Simsek, Mohammad Rostami-Nejad, Adriano Casulli, Urmas Saarma, Liina Kinkar, Hossein Mirhendi, Eshrat Beigom Kia, Malik Irshadullah, Steffen Rehbein, Viliam Šnábel, Ibrahim Balkaya, Gérald Umhang, Mitra Sharbatkhori, Antonio Varcasia, Francisco Ponce-Gordo, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia, University of Tartu, Atatürk University School of Medicine, World Health Organization Collaborating Centre for the Epidemiology, Detection and Control of Cystic and Alveolar Echinococcosis, University Hospital Mustapha Alger, Aligarh Muslim University, Golestan University of Medical Sciences, Isfahan University of Medical Sciences, Isfahan University of Medical Sciences [Iran] (MUI), Shahid Beheshti University of Medical Sciences [Tehran] (SBUMS), Shahid Beheshti University, Universidad Complutense de Madrid = Complutense University of Madrid [Madrid] (UCM), Merial GmbH, Tehran University of Medical Sciences (TUMS), Firat University Faculty of Engineering Geology Department, Slovak Academy of Sciences (SAS), Laboratoire de la rage et de la faune sauvage de Nancy (LRFSN), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), and University of Sassari

Subjects
0301 basic medicine, Mitochondrial DNA, Species complex, Genotype, [SDV]Life Sciences [q-bio], DNA, Mitochondrial, 03 medical and health sciences, Mitochondrial genome, Sensu, Echinococcosis, Zoonoses, parasitic diseases, Genetic variation, Animals, Humans, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Genetic variability, Echinococcus granulosus, Phylogeny, Genetic diversity, biology, Genotype G3, Genetic Variation, Bayes Theorem, Bayesian phylogeny, DNA, Helminth, biology.organism_classification, 3. Good health, Cystic echinococcosis, Phylogeography, 030104 developmental biology, Infectious Diseases, Evolutionary biology, Genome, Mitochondrial, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Animal Science and Zoology, Parasitology
Abstract

Cystic echinococcosis (CE) is a severe parasitic disease caused by the species complexEchinococcus granulosussensu lato. Human infections are most commonly associated withE. granulosussensu stricto (s.s.), comprising genotypes G1 and G3. The objective of the current study was to provide first insight into the genetic diversity and phylogeography of genotype G3. Despite the epidemiological importance of the genotype, it has remained poorly explored due to the ambiguity in the definition of the genotype. However, it was recently demonstrated that long sequences of mitochondrial DNA (mtDNA) provide a reliable method to discriminate G1 and G3 from each other. Therefore, we sequenced near-complete mtDNA of 39 G3 samples, covering most of the known distribution range and host spectra of the genotype. The phylogenetic network revealed high genetic variation withinE. granulosus s.s.G3 and while G3 is significantly less prevalent worldwide than G1, the genetic diversity of both of the genotypes is equally high. We also present the results of the Bayesian phylogeographic analysis, which yielded several well-supported diffusion routes of genotype G3 originating from Turkey and Iran, suggesting the Middle East as the origin of the genotype.

Published
2018
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2. Global phylogeography and genetic diversity of the zoonotic tapeworm Echinococcus granulosus sensu stricto genotype G1

Author

Ibrahim Balkaya, Houria Zait, Viliam Šnábel, Teivi Laurimäe, Sami Simsek, Robin B. Gasser, Maria Teresa Manfredi, Francisco Ponce-Gordo, Luis Miguel González, Selim M’rad, Gerardo Acosta-Jamett, Abdul Jabbar, Steffen Rehbein, Mitra Sharbatkhori, Liina Kinkar, Karen Luisa Haag, Hein Sprong, Myriam Oudni-M’rad, Vanessa Andresiuk, David Jenkins, Antonio Varcasia, Eshrat Beigom Kia, Adriano Casulli, Gérald Umhang, Mohammad Rostami-Nejad, Joke van der Giessen, Urmas Saarma, Hossein Mirhendi, Silvia Viviana Soriano, Malik Irshadullah, Nora Beatriz Pierangeli, Institute of Ecology and Earth Sciences [Tartu], University of Tartu, Universidad Austral de Chile, Laboratorio de Zoonosis Parasitarias (FCEyN, UNMdP), Atatürk University School of Medicine, World Health Organization Collaborating Centre for the Epidemiology, Detection and Control of Cystic and Alveolar Echinococcosis, Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Centre for Infectious Disease Control Netherlands, National Institute for Public Health and the Environment [Bilthoven] (RIVM), Instituto de Salud Carlos III [Madrid] (ISC), Universidade Federal do Rio Grande do Sul [Porto Alegre] (UFRGS), University Hospital Mustapha Alger, Aligarh Muslim University, Charles Sturt University [Australia], Tehran University of Medical Sciences (TUMS), Università degli Studi di Milano [Milano] (UNIMI), Isfahan Neurosciences Research Center, Alzahra Research Institute, Isfahan University of Medical Sciences, Université de Monastir - University of Monastir (UM), Shahid Beheshti University of Medical Sciences [Tehran] (SBUMS), Shahid Beheshti University, Comahue National University, Universidad Complutense de Madrid = Complutense University of Madrid [Madrid] (UCM), Kathrinenhof Research Center, Merial GmbH, Golestan University of Medical Sciences, University of Firat, Slovak Academy of Sciences (SAS), Laboratoire de la rage et de la faune sauvage de Nancy (LRFSN), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), University of Sassari, This work was supported by institutional research funding (IUT20-32) from the Estonian Ministry of Education and Research, and the Estonian Doctoral School of Ecology and Environmental Sciences. RBG’s recent research has been supported by the Australian Research Council (ARC), the National Health and Medical Research Council (NHMRC) of Australia, Yourgene Bioscience (Taiwan), Melbourne Water Corporation (Australia) and The University of Melbourne (Australia)., European Project: 602051,EC:FP7:HEALTH,FP7-HEALTH-2013-INNOVATION-1,HERACLES(2013), Università degli Studi di Milano = University of Milan (UNIMI), Universidad Nacional del Comahue [Neuquén] (UNCOMA), and Università degli Studi di Sassari = University of Sassari [Sassari] (UNISS)

Subjects
0301 basic medicine, Genotype, [SDV]Life Sciences [q-bio], 030231 tropical medicine, 03 medical and health sciences, Global phylogeography, 0302 clinical medicine, Mitochondrial genome, Echinococcosis, Zoonoses, Genetic variation, parasitic diseases, Animals, Humans, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Genetic variability, Echinococcus granulosus, Genetic diversity, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, biology, Molecular epidemiology, Phylogenetic tree, Genetic Variation, DNA, Helminth, biology.organism_classification, Livestock domestication, Phylogeography, Cystic echinococcosis, 030104 developmental biology, Infectious Diseases, Evolutionary biology, Parasitology, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie
Abstract

International audience; Echinococcus granulosus sensu stricto (s.s.) is the major cause of human cystic echinococcosis worldwide and is listed among the most severe parasitic diseases of humans. To date, numerous studies have investigated the genetic diversity and population structure of E. granulosus s.s. in various geographic regions. However, there has been no global study. Recently, using mitochondrial DNA, it was shown that E. granulosus s.s. G1 and G3 are distinct genotypes, but a larger dataset is required to confirm the distinction of these genotypes. The objectives of this study were to: (i) investigate the distinction of genotypes G1 and G3 using a large global dataset; and (ii) analyse the genetic diversity and phylogeography of genotype G1 on a global scale using near-complete mitogenome sequences. For this study, 222 globally distributed E. granulosus s.s. samples were used, of which 212 belonged to genotype G1 and 10 to G3. Using a total sequence length of 11,682 bp, we inferred phylogenetic networks for three datasets: E. granulosus s.s. (n = 222), G1 (n = 212) and human G1 samples (n = 41). In addition, the Bayesian phylogenetic and phylogeographic analyses were performed. The latter yielded several strongly supported diffusion routes of genotype G1 originating from Turkey, Tunisia and Argentina. We conclude that: (i) using a considerably larger dataset than employed previously, E. granulosus s.s. G1 and G3 are indeed distinct mitochondrial genotypes; (ii) the genetic diversity of E. granulosus s.s. G1 is high globally, with lower values in South America; and (iii) the complex phylogeographic patterns emerging from the phylogenetic and geographic analyses suggest that the current distribution of genotype G1 has been shaped by intensive animal trade.

Published
2018
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3. Distinguishing Echinococcus granulosus sensu stricto genotypes G1 and G3 with confidence: A practical guide

Author

Gerardo Acosta-Jamett, Karen Luisa Haag, Viliam Šnábel, Myriam Oudni-M’rad, David Jenkins, Houria Zait, Nora Beatriz Pierangeli, Steffen Rehbein, Robin B. Gasser, Liina Kinkar, Teivi Laurimäe, Antonio Varcasia, Sami Simsek, Gérald Umhang, Vanessa Andresiuk, Hein Sprong, Abdul Jabbar, Silvia Viviana Soriano, Francisco Ponce-Gordo, Mohammad Rostami-Nejad, Eshrat Beigom Kia, Hossein Mirhendi, Malik Irshadullah, Adriano Casulli, Ibrahim Balkaya, Urmas Saarma, Maria Teresa Manfredi, Selim M’rad, Luis Miguel González, Mitra Sharbatkhori, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia, University of Tartu, Universidad Austral de Chile, Facultad de Ciencias Exactas y Naturales [Buenos Aires] (FCEyN), Universidad de Buenos Aires [Buenos Aires] (UBA), Atatürk University School of Medicine, World Health Organization Collaborating Centre for the Epidemiology, Detection and Control of Cystic and Alveolar Echinococcosis, Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Instituto de Salud Carlos III [Madrid] (ISC), Universidade Federal do Rio Grande do Sul [Porto Alegre] (UFRGS), University Hospital Mustapha Alger, Aligarh Muslim University, Charles Sturt University [Australia], Università degli Studi di Milano [Milano] (UNIMI), Isfahan University of Medical Sciences, Isfahan University of Medical Sciences [Iran] (MUI), Université de Monastir - University of Monastir (UM), Shahid Beheshti University of Medical Sciences [Tehran] (SBUMS), Shahid Beheshti University, Comahue National University, Universidad Complutense de Madrid = Complutense University of Madrid [Madrid] (UCM), Kathrinenhof Research Center, Merial GmbH, Golestan University of Medical Sciences, Iran University of Medical Sciences [Tehran, Iran] (IUMS), University of Firat, Centre for Infectious Disease Control Netherlands, National Institute for Public Health and the Environment [Bilthoven] (RIVM), Slovak Academy of Sciences (SAS), Laboratoire de la rage et de la faune sauvage de Nancy (LRFSN), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), and University of Sassari

Subjects
0301 basic medicine, Microbiology (medical), Mitochondrial DNA, Species complex, Genotype, [SDV]Life Sciences [q-bio], Genomics, Biology, Mitochondrial markers, Microbiology, Genome, 03 medical and health sciences, Sensu, Echinococcosis, parasitic diseases, Genetic variation, Genetics, Animals, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Echinococcus granulosus, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Genes, Helminth, Phylogeny, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, Echinococcus granulosus sensu stricto, Geography, The nad5 gene, 030108 mycology & parasitology, biology.organism_classification, 3. Good health, Cystic echinococcosis, Phylogeography, Infectious Diseases, Genes, Mitochondrial, Genotype identification, Evolutionary biology, Genome, Mitochondrial
Abstract

International audience; 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.

Published
2018
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4. Multicenter evaluation of Neurelec Digisonic implant reliability

Author

RADULESCU, Luminita, COZMA, Sebastian, NIEMCZYK, Casimir, Guevara, Nicolas, GAHIDE, Ivan, ECONOMIDES, John, Lavieille, Jean-Pierre, Meller, Renaud, Bebear, Jean-Pierre, RADAFY, Emilien, Bordure, Philippe, DJENNAOUI, Djamel, Truy, Eric, ENT Department Rehabilitation Hospital, University of Medicine and Pharmacy 'Grigore T.Popa' Iasi (UMF lasi), ENT Department, University Hospital Banacha, Hôpital Pasteur [Nice] (CHU), General Children's hospital Aghia Sophia, Laboratoire de Biomécanique Appliquée (LBA UMR T24), Aix Marseille Université (AMU)-Université Gustave Eiffel, Aix-Marseille Université - Faculté de médecine (AMU MED), Aix Marseille Université (AMU), Hôpital Pellegrin, CHU Bordeaux [Bordeaux]-Groupe hospitalier Pellegrin, Centre hospitalier universitaire de Nantes (CHU Nantes), University Hospital Mustapha Alger, Centre de recherche en neurosciences de Lyon - Lyon Neuroscience Research Center (CRNL), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre de recherche en neurosciences de Lyon (CRNL), and Université de Lyon-Université de Lyon-Université Jean Monnet [Saint-Étienne] (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract

Over the past decade, the adoption of universal hearing screening in newborns has led to earlier detection of hearing problems and significant lowering of the age of first cochlear implantation. As a consequence, recipients are now expected to keep their cochlear implants (CIs) for a longer period of time. Comprehensive longitudinal information on CI reliability is essential for device choice. The aim of this study was to assess the reliability (in children and adults) of the latest generation of the Digisonic® SP CI launched in 2006 by Neurelec. Failure rate (FR) and cumulative survival rate (CSR) for a 5-year period were calculated. This survey is a multicenter retrospective study. A questionnaire was sent to nine CI centers requesting information about patients implanted with Neurelec Digisonic® SP CIs. FR and CSR over a 5-year period were calculated on this group. Collaborating centers collected data on 672 patients (362 children and 310 adults) implanted between March 2006 and March 2011. The overall rate of explantation was 2.23 % (15 cases): six devices were explanted due to device failure (0.89 %) and nine were explanted for medical reasons (1.34 %). Four patients were lost to follow-up. The CSR at 5 years was 98.51 % on all patients, 98.48 % for children and 98.57 % for adults. FR was 0.97 % for adults and 0.83 % for children. This first independent study that assesses FR and CSR on the current generation of Digisonic® SP CI represents an important resource that can help clinicians and patients during their device choice.

Published
2013
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