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Hua RQ, Du XD, He X, Gu XB, Xie Y, He R, Xu J, Peng XR, Yang GY. Genetic diversity of Echinococcus granulosus sensu lato in China: Epidemiological studies and systematic review. Transbound Emerg Dis 2022; 69:e1382-e1392. [PMID: 35139582 DOI: 10.1111/tbed.14469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 01/05/2022] [Accepted: 02/01/2022] [Indexed: 11/26/2022]
Abstract
Cystic echinococcosis (CE) is a neglected tropical zoonosis caused by Echinococcus granulosus sensu lato (s.l.) and remains a major public health concern globally. Here, CE isolates (n = 3310) with clearly defined genotypes and geographical origins in China were retrieved through our epidemiological survey (2016-2020) and systematic review (1992-2020). Existing known genotypes of Echinococcus granulosus sensu lato (E. granulosus s.l.) except for G4 have been found in China, particularly on the Tibetan Plateau, where their genetic diversity is unique to that part of the world. According to the systematic review, genetic compositions of E. granulosus s.l. in China were as follows: E. granulosus (G1, G3), 98.3%; Echinococcus ortleppi (G5), 0.1%; Echinococcus intermedius (G6, G7), 1.4%; and Echinococcus canadensis (G8, G10), 0.2%. Specifically, G1 was responsible for 97.7% of infections and characterized by the broadest host ranges and geographic distributions. Our epidemiological results showed a relatively stable genetic composition of E. granulosus s.l. in sheep and yaks from three CE hyperendemic provinces (Xinjiang, Sichuan, Qinghai). A higher proportion of fertile cysts were found in sheep (287/406, 70.7%) than in yaks (28/184, 15.2%). During the past 29 years, 51 cox1 haplotypes of E. granulosus s.l. were endemic in China. The ancestral haplotype (Hap_2) remained the most common haplotype, 12 relatively common haplotypes were endemic and nine newly reported haplotypes were found during the survey. Overall, our results demonstrate that the compulsory immunization of sheep and the pilot EG95 vaccination campaign in yaks are well matched with the current genotypic situation. In addition to yaks, we advocate for more surveillance of CE isolates from pigs, cattle, goats and camels, since their roles in the transmission and reservation of E. granulosus s.l. have been largely ignored in China.
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Affiliation(s)
- Rui-Qi Hua
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, P. R. China
| | - Xiao-Di Du
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, P. R. China
| | - Xue He
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, P. R. China
| | - Xiao-Bin Gu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, P. R. China
| | - Yue Xie
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, P. R. China
| | - Ran He
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, P. R. China
| | - Jing Xu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, P. R. China
| | - Xue-Rong Peng
- Department of Chemistry, College of Life and Basic Science, Sichuan Agricultural University, Ya'an, P. R. China
| | - Guang-You Yang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, P. R. China
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Comparative genomic analysis of Echinococcus multilocularis with other tapeworms. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01120-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Wang HM, Li R, Deng YP, Liu GH, Fu YT. Comparative Mitochondrial Genomic Analysis Robustly Supported That Cat Tapeworm Hydatigera taeniaeformis (Platyhelminthes: Cestoda) Represents a Species Complex. Front Vet Sci 2022; 9:931137. [PMID: 35812880 PMCID: PMC9258744 DOI: 10.3389/fvets.2022.931137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 05/23/2022] [Indexed: 11/13/2022] Open
Abstract
Hydatigera taeniaeformis is one of the most common intestinal tapeworms that has a worldwide distribution. In this study, we sequenced the complete mitochondrial (mt) genome of H. taeniaeformis from the leopard cat (designated HTLC) and compared it with those of H. taeniaeformis from the cat in China (designated HTCC) and Germany (designated HTCG). The complete mt genome sequence of HTLC is 13,814 bp in size, which is 167 bp longer than that of HTCC and is 74 bp longer than that of HTCG. Across the entire mt genome (except for the two non-coding regions), the sequence difference was 3.3% between HTLC and HTCC, 12.0% between HTLC and HTCG, and 12.1% between HTCC and HTCG. The difference across both nucleotide and amino acid sequences of the 12 protein-coding genes was 4.1 and 2.3% between the HTLC and HTCC, 13.3 and 10.0% between the HTLC and HTCG, and 13.8 and 10.6% between the HTCC and HTCG, respectively. Phylogenetic analysis based on concatenated amino acid sequences of 12 protein-coding genes showed the separation of H. taeniaeformis from different hosts and geographical regions into two distinct clades. Our analysis showed that the cat tapeworm H. taeniaeformis represents a species complex. The novel mt genomic datasets provide useful markers for further studies of the taxonomy and systematics of cat tapeworm H. taeniaeformis.
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Zhao L, Nielsen R, Korneliussen TS. distAngsd: Fast and accurate inference of genetic distances for Next Generation Sequencing data. Mol Biol Evol 2022; 39:6596627. [PMID: 35647675 PMCID: PMC9234764 DOI: 10.1093/molbev/msac119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Commonly used methods for inferring phylogenies were designed before the emergence of high throughput sequencing and can generally not accommodate the challenges associated with noisy, diploid sequencing data. In many applications, diploid genomes are still treated as haploid through the use of ambiguity characters; while the uncertainty in genotype calling - arising as a consequence of the sequencing technology - is ignored. In order to address this problem we describe two new probabilistic approaches for estimating genetic distances: distAngsd-geno and distAngsd-nuc, both implemented in a software suite named distAngsd. These methods are specifically designed for next generation sequencing data, utilize the full information from the data, and take uncertainty in genotype calling into account. Through extensive simulations, we show that these new methods are markedly more accurate and have more stable statistical behaviors than other currently available methods for estimating genetic distances - even for very low depth data with high error rates.
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Affiliation(s)
- Lei Zhao
- Section for Geogenetics, Globe Institute, University of Copenhagen, Oster Voldgade 5-7, 1350 Kobenhavn K
| | - Rasmus Nielsen
- Section for Geogenetics, Globe Institute, University of Copenhagen, Oster Voldgade 5-7, 1350 Kobenhavn K.,Departments of Integrative Biology and Statistics 3040 Valley Life Sciences Building 3140 Berkeley, CA 94720-3140
| | - Thorfinn Sand Korneliussen
- Section for Geogenetics, Globe Institute, University of Copenhagen, Oster Voldgade 5-7, 1350 Kobenhavn K
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Bobes RJ, Estrada K, Rios-Valencia DG, Calderón-Gallegos A, de la Torre P, Carrero JC, Sanchez-Flores A, Laclette JP. The Genomes of Two Strains of Taenia crassiceps the Animal Model for the Study of Human Cysticercosis. Front Cell Infect Microbiol 2022; 12:876839. [PMID: 35619649 PMCID: PMC9128525 DOI: 10.3389/fcimb.2022.876839] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 04/12/2022] [Indexed: 12/13/2022] Open
Abstract
Human cysticercosis by Taenia solium is the major cause of neurological illness in countries of Africa, Southeast Asia, and the Americas. Publication of four cestode genomes (T. solium, Echinococcus multilocularis, E. granulosus and Hymenolepis microstoma) in the last decade, marked the advent of novel approaches on the study of the host-parasite molecular crosstalk for cestode parasites of importance for human and animal health. Taenia crassiceps is another cestode parasite, closely related to T. solium, which has been used in numerous studies as an animal model for human cysticercosis. Therefore, characterization of the T. crassiceps genome will also contribute to the understanding of the human infection. Here, we report the genome of T. crassiceps WFU strain, reconstructed to a noncontiguous finished resolution and performed a genomic and differential expression comparison analysis against ORF strain. Both strain genomes were sequenced using Oxford Nanopore (MinION) and Illumina technologies, achieving high quality assemblies of about 107 Mb for both strains. Dotplot comparison between WFU and ORF demonstrated that both genomes were extremely similar. Additionally, karyotyping results for both strains failed to demonstrate a difference in chromosome composition. Therefore, our results strongly support the concept that the absence of scolex in the ORF strain of T. crassiceps was not the result of a chromosomal loss as proposed elsewhere. Instead, it appears to be the result of subtle and extensive differences in the regulation of gene expression. Analysis of variants between the two strains identified 2,487 sites with changes distributed in 31 of 65 scaffolds. The differential expression analysis revealed that genes related to development and morphogenesis in the ORF strain might be involved in the lack of scolex formation.
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Affiliation(s)
- Raúl J. Bobes
- Biomedical Research Institute, Universidad Nacional Autónoma de México, CDMX, Mexico
| | - Karel Estrada
- Biotechnology Institute, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | | | | | - Patricia de la Torre
- Biomedical Research Institute, Universidad Nacional Autónoma de México, CDMX, Mexico
| | - Julio C. Carrero
- Biomedical Research Institute, Universidad Nacional Autónoma de México, CDMX, Mexico
| | - Alejandro Sanchez-Flores
- Biotechnology Institute, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
- *Correspondence: Juan P. Laclette, ; Alejandro Sanchez-Flores,
| | - Juan P. Laclette
- Biomedical Research Institute, Universidad Nacional Autónoma de México, CDMX, Mexico
- *Correspondence: Juan P. Laclette, ; Alejandro Sanchez-Flores,
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Cháves-González LE, Morales-Calvo F, Mora J, Solano-Barquero A, Verocai GG, Rojas A. What lies behind the curtain: Cryptic diversity in helminth parasites of human and veterinary importance. CURRENT RESEARCH IN PARASITOLOGY & VECTOR-BORNE DISEASES 2022; 2:100094. [PMID: 35800064 PMCID: PMC9253710 DOI: 10.1016/j.crpvbd.2022.100094] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 05/28/2022] [Accepted: 06/07/2022] [Indexed: 11/17/2022]
Abstract
Parasite cryptic species are morphologically indistinguishable but genetically distinct organisms, leading to taxa with unclear species boundaries. Speciation mechanisms such as cospeciation, host colonization, taxon pulse, and oscillation may lead to the emergence of cryptic species, influencing host-parasite interactions, parasite ecology, distribution, and biodiversity. The study of cryptic species diversity in helminth parasites of human and veterinary importance has gained relevance, since their distribution may affect clinical and epidemiological features such as pathogenicity, virulence, drug resistance and susceptibility, mortality, and morbidity, ultimately affecting patient management, course, and outcome of treatment. At the same time, the need for recognition of cryptic species diversity has implied a transition from morphological to molecular diagnostic methods, which are becoming more available and accessible in parasitology. Here, we discuss the general approaches for cryptic species delineation and summarize some examples found in nematodes, trematodes and cestodes of medical and veterinary importance, along with the clinical implications of their taxonomic status. Lastly, we highlight the need for the correct interpretation of molecular information, and the correct use of definitions when reporting or describing new cryptic species in parasitology, since molecular and morphological data should be integrated whenever possible. Cryptic diversity has been described in helminths of human and animal importance. Cryptic species are morphologically indistinguishable but genetically distinct organisms. These entities emerge by different evolutionary and speciation mechanisms. Analysis of molecular and morphological data is needed for cryptic species delimitation. Cryptic diversity may affect pathogenicity, virulence and drug resistance of helminths.
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Affiliation(s)
- Luis Enrique Cháves-González
- Laboratory of Helminthology, Centro de Investigación en Enfermedades Tropicales, University of Costa Rica, San José, Costa Rica
| | - Fernando Morales-Calvo
- Laboratory of Helminthology, Centro de Investigación en Enfermedades Tropicales, University of Costa Rica, San José, Costa Rica
| | - Javier Mora
- Laboratory of Helminthology, Centro de Investigación en Enfermedades Tropicales, University of Costa Rica, San José, Costa Rica
| | - Alberto Solano-Barquero
- Laboratory of Helminthology, Centro de Investigación en Enfermedades Tropicales, University of Costa Rica, San José, Costa Rica
| | - Guilherme G. Verocai
- Department of Veterinary Pathobiology, Texas A&M University, College of Veterinary Medicine and Biomedical Sciences, College Station, TX, USA
| | - Alicia Rojas
- Laboratory of Helminthology, Centro de Investigación en Enfermedades Tropicales, University of Costa Rica, San José, Costa Rica
- Corresponding author. Twitter icon
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Lightowlers MW, Gasser RB, Hemphill A, Romig T, Tamarozzi F, Deplazes P, Torgerson PR, Garcia HH, Kern P. Advances in the treatment, diagnosis, control and scientific understanding of taeniid cestode parasite infections over the past 50 years. Int J Parasitol 2021; 51:1167-1192. [PMID: 34757089 DOI: 10.1016/j.ijpara.2021.10.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 10/06/2021] [Accepted: 10/07/2021] [Indexed: 02/07/2023]
Abstract
In the past 50 years, enormous progress has been made in the diagnosis, treatment and control of taeniid cestode infections/diseases and in the scientific understanding thereof. Most interest in this group of parasites stems from the serious diseases that they cause in humans. It is through this lens that we summarize here the most important breakthroughs that have made a difference to the treatment of human diseases caused by these parasites, reduction in transmission of the taeniid species associated with human disease, or understanding of the parasites' biology likely to impact diagnosis or treatment in the foreseeable future. Key topics discussed are the introduction of anti-cestode drugs, including benzimidazoles and praziquantel, and the development of new imaging modalities that have transformed the diagnosis and post-treatment monitoring of human echinococcoses and neurocysticercosis. The availability of new anti-cestode drugs for use in dogs and a detailed understanding of the transmission dynamics of Echinococcus granulosus sensu lato have underpinned successful programs that have eliminated cystic echinococcosis in some areas of the world and greatly reduced the incidence of infection in others. Despite these successes, cystic and alveolar echinococcosis and neurocysticercosis continue to be prevalent in many parts of the world, requiring new or renewed efforts to prevent the associated taeniid infections. Major advances made in the development of practical vaccines against E. granulosus and Taenia solium will hopefully assist in this endeavour, as might the understanding of the parasites' biology that have come from an elucidation of the nuclear genomes of each of the most important taeniid species causing human diseases.
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Affiliation(s)
- Marshall W Lightowlers
- Department of Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, 250 Princes Highway, Werribee, Victoria 3030, Australia.
| | - Robin B Gasser
- Department of Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Andrew Hemphill
- Institute of Parasitology, Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Länggassstrasse 122, 3012 Bern, Switzerland
| | - Thomas Romig
- University of Hohenheim, Parasitology Unit, Emil-Wolff-Strasse 34, 70599 Stuttgart, Germany
| | - Francesca Tamarozzi
- Department of Infectious Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, 37024 Negrar di Valpolicella, Verona, Italy
| | - Peter Deplazes
- Institute of Parasitology, Vetsuisse, and Medical Faculty, University of Zürich, Zürich, Switzerland
| | - Paul R Torgerson
- Section of Epidemiology, Vetsuisse Faculty, University of Zürich, Zürich, Switzerland
| | - Hector H Garcia
- Infectious Diseases Laboratory Research-LID, Faculty of Science and Philosophy, Alberto Cazorla Talleri, Universidad Peruana Cayetano Heredia, Lima, Perú; Cysticercosis Unit, Instituto Nacional de Ciencias Neurológicas, Lima, Perú
| | - Peter Kern
- Ulm University Hospital, Division of Infectious Diseases, Albert-Einstein-Allee 23, 89081 Ulm, Germany
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Kamenetzky L, Maldonado LL, Cucher MA. Cestodes in the genomic era. Parasitol Res 2021; 121:1077-1089. [PMID: 34665308 DOI: 10.1007/s00436-021-07346-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 10/10/2021] [Indexed: 12/20/2022]
Abstract
The first cestode genomes were obtained by an international consortium led by the Wellcome Sanger Institute that included representative institutions from countries where the sequenced parasites have been studied for decades, in part because they are etiological agents of endemic diseases (Argentina, Uruguay, Mexico, Canada, UK, Germany, Switzerland, Ireland, USA, Japan, and China). After this, several complete genomes were obtained reaching 16 species to date. Cestode genomes have smaller relative size compared to other animals including free-living flatworms. Moreover, the features genome size and repeat content seem to differ in the two analyzed orders. Cyclophyllidean species have smaller genomes and with fewer repetitive content than Diphyllobothriidean species. On average, cestode genomes have 13,753 genes with 6 exons per gene and 41% GC content. More than 5,000 shared cestode proteins were accurately annotated by the integration of gene predictions and transcriptome evidence being more than 40% of these proteins of unknown function. Several gene losses and reduction of gene families were found and could be related to the extreme parasitic lifestyle of these species. The application of cutting-edge sequencing technology allowed the characterization of the terminal sequences of chromosomes that possess unique characteristics. Here, we review the current status of knowledge of complete cestode genomes and place it within a comparative genomics perspective. Multidisciplinary work together with the implementation of new technologies will provide valuable information that can certainly improve our chances to finally eradicate or at least control diseases caused by cestodes.
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Affiliation(s)
- Laura Kamenetzky
- iB3, Instituto de Biociencias, Departamento de Fisiología Y Biología Molecular Y Celular, Facultad de Ciencias Exactas Y Naturales, Universidad de Buenos Aires, Biotecnología y Biología traslacional, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina.
| | - Lucas L Maldonado
- Department of Microbiology, School of Medicine, University of Buenos Aires, Buenos Aires, Argentina.,Institute of Research On Microbiology and Medical Parasitology (IMPaM, UBA-CONICET), University of Buenos Aires, Buenos Aires, Argentina
| | - Marcela A Cucher
- Department of Microbiology, School of Medicine, University of Buenos Aires, Buenos Aires, Argentina.,Institute of Research On Microbiology and Medical Parasitology (IMPaM, UBA-CONICET), University of Buenos Aires, Buenos Aires, Argentina
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Cucher MA, Ancarola ME, Kamenetzky L. The challenging world of extracellular RNAs of helminth parasites. Mol Immunol 2021; 134:150-160. [PMID: 33773158 DOI: 10.1016/j.molimm.2021.03.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 02/26/2021] [Accepted: 03/06/2021] [Indexed: 01/08/2023]
Abstract
In the last years, cell free or extracellular RNAs (ex-RNAs) have emerged as novel intercellular messengers between animal cells, including pathogens. In infectious diseases, ex-RNAs represent novel players in the host-pathogen and pathogen-pathogen interplays and have been described in parasitic helminths from the three major taxonomic groups: nematodes, trematodes and cestodes. Altogether, it is estimated that approximately 30 percent of the world's population is infected with helminths, which cause debilitating diseases and syndromes. Ex-RNAs are protected from degradation by encapsulation in extracellular vesicles (EV), or association to proteins or lipoproteins, and have been detected in the excretion/secretion products of helminth parasites, with EV as the preferred extracellular compartment under study. EV is the generic term used to describe a heterogenous group of subcellular membrane-bound particles, with varying sizes, biogenesis, density and composition. However, recent data suggests that this is not the only means used by helminth parasites to secrete RNAs since ex-RNAs can also be found in EV-depleted samples. Furthermore, the use of pathogen ex-RNAs as biomarkers promise the advent of new diagnostic tools though this field is still in early stages of exploration. In this review, we summarize current knowledge of vesicular and non-vesicular ex-RNAs secretion in helminth parasites, their potential as biomarkers and the evidence of their role in parasite and host reciprocal communication, together with unanswered questions in the field.
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Affiliation(s)
- Marcela A Cucher
- Department of Microbiology, School of Medicine, University of Buenos Aires, Buenos Aires, Argentina; Institute of Research on Microbiology and Medical Parasitology (IMPaM, UBA-CONICET), University of Buenos Aires, Buenos Aires, Argentina.
| | - María Eugenia Ancarola
- Department of Microbiology, School of Medicine, University of Buenos Aires, Buenos Aires, Argentina; Institute of Research on Microbiology and Medical Parasitology (IMPaM, UBA-CONICET), University of Buenos Aires, Buenos Aires, Argentina
| | - Laura Kamenetzky
- Laboratorio de Genómica y Bioinformática de Patógenos, iB3
- Instituto de Biociencias, Biotecnología y Biología traslacional, Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
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