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Dubey JP, Thompson PC, Fournet V, Hill DE, Zarlenga D, Gamble HR, Rosenthal BM. Over a century of progress on Trichinella research in pigs at the United States Department of Agriculture: Challenges and solutions. Food Waterborne Parasitol 2024; 36:e00239. [PMID: 39247629 PMCID: PMC11378942 DOI: 10.1016/j.fawpar.2024.e00239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 07/11/2024] [Accepted: 07/22/2024] [Indexed: 09/10/2024] Open
Abstract
Trichinellosis, caused by 13 species/subspecies/genotypes in the nematode genus Trichinella, is a worldwide zoonosis. In the United States, trichinellosis was of historical and economic significance because of European restrictions on the import of U.S. pork. Before the advent of effective protective measures, most cases of trichinellosis were derived from consumption of undercooked or inadequately processed, infected pork. Research conducted at the United States Department of Agriculture (USDA) since 1891, and policies established by USDA regulatory agencies, have helped to reduce Trichinella infections in commercially raised domestic pigs to negligible levels. Here, we review the history of this scientific progress, placing special emphasis on research conducted at the USDA's Beltsville Agricultural Research Center.
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Affiliation(s)
- Jitender P Dubey
- United States Department of Agriculture, Agricultural Research Service, Beltsville Agricultural Research Center, Animal Parasitic Diseases Laboratory, Beltsville, MD 20705-2350, USA
| | - Peter C Thompson
- United States Department of Agriculture, Agricultural Research Service, Beltsville Agricultural Research Center, Animal Parasitic Diseases Laboratory, Beltsville, MD 20705-2350, USA
| | - Valsin Fournet
- United States Department of Agriculture, Agricultural Research Service, Beltsville Agricultural Research Center, Animal Parasitic Diseases Laboratory, Beltsville, MD 20705-2350, USA
| | - Dolores E Hill
- United States Department of Agriculture, Agricultural Research Service, Beltsville Agricultural Research Center, Animal Parasitic Diseases Laboratory, Beltsville, MD 20705-2350, USA
| | - Dante Zarlenga
- United States Department of Agriculture, Agricultural Research Service, Beltsville Agricultural Research Center, Animal Parasitic Diseases Laboratory, Beltsville, MD 20705-2350, USA
| | - H Ray Gamble
- United States Department of Agriculture, Agricultural Research Service, Beltsville Agricultural Research Center, Animal Parasitic Diseases Laboratory, Beltsville, MD 20705-2350, USA
| | - Benjamin M Rosenthal
- United States Department of Agriculture, Agricultural Research Service, Beltsville Agricultural Research Center, Animal Parasitic Diseases Laboratory, Beltsville, MD 20705-2350, USA
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Karadjian G, Bilska-Zając E, Bahn P, Py JS, Johne A, Gassilloud B, Różycki M, Cencek T, Mayer-Scholl A, Vallée I. Species identification of Trichinella originated from various host and different geographical location by MALDI-TOF. Exp Parasitol 2020; 213:107890. [PMID: 32272128 DOI: 10.1016/j.exppara.2020.107890] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 03/24/2020] [Accepted: 03/31/2020] [Indexed: 12/17/2022]
Abstract
The foodborne zoonotic nematode Trichinella spp. can cause human trichinellosis when raw or undercooked contaminated meat is ingested. To date, twelve Trichinella species/genotypes have been described. According to EU regulation any Trichinella larvae detected during mandatory routine examinations need to be identified at a species level by a competent laboratory. Currently, Trichinella species identification is performed using molecular biology tools such as multiplex PCR, PCR-sequencing or PCR-RFLP. These techniques require high level of skills for good interpretation of the results. Due to its rapidness and ease of use a matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) protocol was previously developed for the identification of Trichinella species. Using this method, spectra from different Trichinella species and strains were acquired allowing to generate new Main Spectra (MSP). Finally a new MSP database from Trichinella spp. Samples of different countries (France, Germany and Poland), including field samples, was generated. Comparing the different main spectra, Trichinella worms were identified at the species level and differences in the genetic diversities within the different species are discussed. In conclusion, using the previously described method on field samples is a reliable, rapid, easy-to-use and cheap tool for Trichinella species identification. The new Trichinella database could be incremented with new samples. It constitutes a tool, which could be used as an alternative method to replace the actual molecular methods for Trichinella species identification.
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Affiliation(s)
- Gregory Karadjian
- JRU BIPAR, ANSES, Alfort National Veterinary School, INRA, Animal Health Laboratory, 14 Rue Pierre et Marie Curie, 94701, Maisons-Alfort Cedex, France.
| | - Ewa Bilska-Zając
- Department of Parasitology and Invasive Diseases, National Veterinary Research Institute in Pulawy, Al. Partyzantow 57, 24-100, Pulawy, Poland.
| | - Peter Bahn
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Jean-Sébastien Py
- ANSES, Nancy Laboratory for Hydrology, Water Microbiology Unit, MALDI-TOF Platform, Nancy, France
| | - Anette Johne
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Benoit Gassilloud
- ANSES, Nancy Laboratory for Hydrology, Water Microbiology Unit, MALDI-TOF Platform, Nancy, France
| | - Mirosław Różycki
- Department of Parasitology and Invasive Diseases, National Veterinary Research Institute in Pulawy, Al. Partyzantow 57, 24-100, Pulawy, Poland
| | - Tomasz Cencek
- Department of Parasitology and Invasive Diseases, National Veterinary Research Institute in Pulawy, Al. Partyzantow 57, 24-100, Pulawy, Poland
| | - Anne Mayer-Scholl
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Isabelle Vallée
- JRU BIPAR, ANSES, Alfort National Veterinary School, INRA, Animal Health Laboratory, 14 Rue Pierre et Marie Curie, 94701, Maisons-Alfort Cedex, France
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Li TT, Tang B, Bai X, Wang XL, Luo XN, Yan HB, Zhu HF, Jia H, Liu XL, Liu MY. Development of genome-wide polymorphic microsatellite markers for Trichinella spiralis. Parasit Vectors 2020; 13:58. [PMID: 32046770 PMCID: PMC7014596 DOI: 10.1186/s13071-020-3929-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/03/2020] [Indexed: 02/05/2023] Open
Abstract
Background Trichinella nematodes are globally distributed food-borne pathogens, in which Trichinella spiralis is the most common species in China. Microsatellites are a powerful tool in population genetics and phylogeographic analysis. However, only a few microsatellite markers were reported in T. spiralis. Thus, there is a need to develop and validate genome-wide microsatellite markers for T. spiralis. Methods Microsatellites were selected from shotgun genomic sequences using MIcroSAtellite identification tool (MISA). The identified markers were validated in 12 isolates of T. spiralis in China. Results A total of 93,140 microsatellites were identified by MISA from 9267 contigs in T. spiralis genome sequences, in which 16 polymorphic loci were selected for validation by PCR with single larvae from 12 isolates of T. spiralis in China. There were 7–19 alleles per locus (average 11.25 alleles per locus). The observed heterozygosity (HO) and expected heterozygosity (HE) ranged from 0.325 to 0.750 and 0.737 to 0.918, respectively. The polymorphism information content (PIC) ranged from 0.719 to 0.978 (average 0.826). Among the 16 loci, markers for 10 loci could be amplified from all 12 international standard strains of Trichinella spp. Conclusions Sixteen highly polymorphic markers were selected and validated for T. spiralis. Primary phylogenetic analysis showed that these markers might serve as a useful tool for genetic studies of Trichinella parasites.![]()
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Affiliation(s)
- Ting-Ting Li
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, 130062, Jilin, People's Republic of China
| | - Bin Tang
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, 130062, Jilin, People's Republic of China
| | - Xue Bai
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, 130062, Jilin, People's Republic of China
| | - Xue-Lin Wang
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, 130062, Jilin, People's Republic of China
| | - Xue-Nong Luo
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, CAAS, Lanzhou, 730046, Gansu, People's Republic of China
| | - Hong-Bin Yan
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, CAAS, Lanzhou, 730046, Gansu, People's Republic of China
| | - Hong-Fei Zhu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
| | - Hong Jia
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
| | - Xiao-Lei Liu
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, 130062, Jilin, People's Republic of China.
| | - Ming-Yuan Liu
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, 130062, Jilin, People's Republic of China. .,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, People's Republic of China.
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Zhang X, Han LL, Hong X, Jiang P, Niu YF, Wang ZQ, Cui J. Genotyping and Phylogenetic Position of Trichinella spiralis Isolates from Different Geographical Locations in China. Front Genet 2019; 10:1093. [PMID: 31737057 PMCID: PMC6834790 DOI: 10.3389/fgene.2019.01093] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 10/10/2019] [Indexed: 11/29/2022] Open
Abstract
In China, the nematode Trichinella spiralis is the main aetiological agent of human trichinellosis. We performed multi-locus microsatellite typing of T. spiralis isolates to improve the current knowledge of the evolution and population diversity. First, seven polymorphic microsatellite loci were used to infer the genetic diversity of T. spiralis collected in 10 endemic regions. Then, a Bayesian model-based STRUCTURE analysis, a clustering based on the neighbor-joining method, and a principal coordinate analysis (PCA) were performed to identify the genetic structure. Finally, the phylogenetic position of Chinese isolates was explored based on six mitochondrial and nuclear genetic markers (cox1, cytb, 5S ISR, ESV, ITS1, and 18S rDNA) using the maximum likelihood and Bayesian methods. In addition, the divergence time was estimated with multiple genes using an uncorrelated log-normal relaxed molecular-clock model. A total of 16 alleles were detected in 2,310 individuals (1,650 muscle larvae and 660 adult worms) using seven loci. The STRUCTURE analysis indicated that the T. spiralis isolates could be organized and derived from the admixture of two ancestral clusters, which was also substantiated through the clustering analysis based on the allelic data. PCA separated most samples from Tiandong, Guangxi (GX-td), and Linzhi, Tibet (Tibet-lz), from the remaining isolates. However, both maximum likelihood and Bayesian inference supported the close relationship between Xiangfan, Hubei (HB-xf), and GX-td. The molecular dating analysis suggested that the Chinese isolates started to diverge during the Late Pleistocene (0.69 Mya). Generally, T. spiralis was observed to harbor low genetic variation, and further investigation with deeper sampling is needed to elucidate the population structure.
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Affiliation(s)
| | | | | | | | | | - Zhong Quan Wang
- Department of Parasitology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Jing Cui
- Department of Parasitology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
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Bilska-Zając E, Franssen F, Różycki M, Swart A, Karamon J, Sroka J, Zdybel J, Ziętek-Barszcz A, Cencek T. Intraspecific genetic variation in Trichinella spiralis and Trichinella britovi populations circulating in different geographical regions of Poland. INTERNATIONAL JOURNAL FOR PARASITOLOGY-PARASITES AND WILDLIFE 2019; 10:101-112. [PMID: 31440446 PMCID: PMC6698805 DOI: 10.1016/j.ijppaw.2019.07.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 07/26/2019] [Accepted: 07/27/2019] [Indexed: 11/25/2022]
Abstract
Trichinella spiralis and Trichinella britovi are species of nematodes which are responsible for the majority of Trichinella infections in the world and the most prevalent in Poland. The most abundant species – T. spiralis, is considered to be more genetically homogeneous in Europe than T. britovi. The aim of the present study was to determine the genetic variability in T. spiralis and T. britovi populations based on nuclear 5S rDNA intergenic spacer region (5S rDNA) and cytochrome c oxidase 1 (COX1) gene sequences. For the study, 55 isolates of T. spiralis and 50 isolates of T. britovi isolated from wild boars, pigs, brown rat and a red fox were analyzed. Based on the analysis of both genes, the genetic variability within populations of T. spiralis and T. britovi differed. In T. spiralis, two single nucleotide polymorphisms (SNPs) were observed in the 612 bp 5S rDNA gene fragment, and one SNP was detected in the 700 bp COX1 gene fragment. In T. britovi, 17 single nucleotide variations (SNVs) were detected in the 5S rDNA gene fragment (among them 16 SNPs), while COX1 sequence analysis revealed the occurrence of 20 SNVs between the sequences tested (among them 19 SNPs). For the majority of T. spiralis isolates the investigated larvae presented uniform haplotypes. In contrast, most of the isolates of T. britovi consisted of larvae of different haplotypes. Geographical analysis showed that each region exhibited different haplotype composition and richness. Warmińsko-Mazurskie and Zachodniopomorskie regions were the richest in haplotypes (15 and 16 haplotypes, respectively). We used heatmaps showing a characteristic pattern for each region graphically. This may allow to differentiate regions based on the occurrence of particular haplotypes. Furthermore, a PCA analysis on the SNP level yielded biplots that show that certain haplotypes/genotypes are associated with (clusters of) regions. The genetic variability within the Polish T. britovi population is high. 5S rDNA and COX1 variability in T. spiralis is low compared to T. britovi. T. britovi variability may correlate to geographical origin. Heatmap and PCA analysis could be helpful analytical tool for epidemiological investigations.
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Affiliation(s)
- Ewa Bilska-Zając
- Department of Parasitology and Invasive Diseases, National Veterinary Research Institute in Pulawy, Al. Partyzantow 57, 24-100, Pulawy, Poland
| | - Frits Franssen
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Mirosław Różycki
- Department of Parasitology and Invasive Diseases, National Veterinary Research Institute in Pulawy, Al. Partyzantow 57, 24-100, Pulawy, Poland
| | - Arno Swart
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Jacek Karamon
- Department of Parasitology and Invasive Diseases, National Veterinary Research Institute in Pulawy, Al. Partyzantow 57, 24-100, Pulawy, Poland
| | - Jacek Sroka
- Department of Parasitology and Invasive Diseases, National Veterinary Research Institute in Pulawy, Al. Partyzantow 57, 24-100, Pulawy, Poland
| | - Jolanta Zdybel
- Department of Parasitology and Invasive Diseases, National Veterinary Research Institute in Pulawy, Al. Partyzantow 57, 24-100, Pulawy, Poland
| | - Anna Ziętek-Barszcz
- Department of Epidemiology and Risk Assessment, National Veterinary Research InstitutePulawy, Al. Partyzantow 57, 24-100, Pulawy, Poland
| | - Tomasz Cencek
- Department of Parasitology and Invasive Diseases, National Veterinary Research Institute in Pulawy, Al. Partyzantow 57, 24-100, Pulawy, Poland
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Junqueira ACM, Azeredo-Espin AML, Paulo DF, Marinho MAT, Tomsho LP, Drautz-Moses DI, Purbojati RW, Ratan A, Schuster SC. Large-scale mitogenomics enables insights into Schizophora (Diptera) radiation and population diversity. Sci Rep 2016; 6:21762. [PMID: 26912394 PMCID: PMC4766414 DOI: 10.1038/srep21762] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 01/28/2016] [Indexed: 11/21/2022] Open
Abstract
True flies are insects of the order Diptera and encompass one of the most diverse groups of animals on Earth. Within dipterans, Schizophora represents a recent radiation of insects that was used as a model to develop a pipeline for generating complete mitogenomes using various sequencing platforms and strategies. 91 mitogenomes from 32 different species were sequenced and assembled with high fidelity, using amplicon, whole genome shotgun or single molecule sequencing approaches. Based on the novel mitogenomes, we estimate the origin of Schizophora within the Cretaceous-Paleogene (K-Pg) boundary, about 68.3 Ma. Detailed analyses of the blowfly family (Calliphoridae) place its origin at 22 Ma, concomitant with the radiation of grazing mammals. The emergence of ectoparasitism within calliphorids was dated 6.95 Ma for the screwworm fly and 2.3 Ma for the Australian sheep blowfly. Varying population histories were observed for the blowfly Chrysomya megacephala and the housefly Musca domestica samples in our dataset. Whereas blowflies (n = 50) appear to have undergone selective sweeps and/or severe bottlenecks in the New World, houseflies (n = 14) display variation among populations from different zoogeographical zones and low levels of gene flow. The reported high-throughput mitogenomics approach for insects enables new insights into schizophoran diversity and population history of flies.
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Affiliation(s)
- Ana Carolina M. Junqueira
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551
| | - Ana Maria L. Azeredo-Espin
- Centro de Biologia Molecular e Engenharia Genética and Departamento de Genética, Evolução e Bioagentes, Universidade Estadual de Campinas, Campinas, SP, 13083-875, Brazil
| | - Daniel F. Paulo
- Centro de Biologia Molecular e Engenharia Genética and Departamento de Genética, Evolução e Bioagentes, Universidade Estadual de Campinas, Campinas, SP, 13083-875, Brazil
| | - Marco Antonio T. Marinho
- Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Departamento de Biologia, Universidade de São Paulo, Ribeirão Preto, SP, 14040-901, Brazil
| | - Lynn P. Tomsho
- Center for Comparative Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Daniela I. Drautz-Moses
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551
| | - Rikky W. Purbojati
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551
| | - Aakrosh Ratan
- Department of Public Health Sciences and Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Stephan C. Schuster
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551
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Franssen F, Bilska-Zając E, Deksne G, Sprong H, Pozio E, Rosenthal B, Rozycki M, van der Giessen J. Genetic evidence of interspecies introgression of mitochondrial genomes between Trichinella spiralis and Trichinella britovi under natural conditions. INFECTION GENETICS AND EVOLUTION 2015; 36:323-332. [PMID: 26458526 DOI: 10.1016/j.meegid.2015.10.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2015] [Revised: 09/25/2015] [Accepted: 10/05/2015] [Indexed: 11/17/2022]
Abstract
Trichinellosis is a zoonotic disease caused by Trichinella muscle larvae (ML) through ingestion of raw or undercooked meat. To date, 12 taxa are recognized in this genus, of which four are circulating in Europe (Trichinella spiralis, Trichinella nativa, Trichinella britovi and Trichinella pseudospiralis). T. spiralis and T. britovi circulate in European wildlife and occur simultaneously in the same host species. The possibility of hybrid formation between T. britovi and T. spiralis has hardly been addressed and so far, results of experimental hybridisation attempts between T. britovi and T. spiralis are inconclusive. The aim of the present study was to analyse molecular polymorphisms of single T. spiralis and T. britovi ML from natural infections based on nuclear 5S rDNA intergenic spacer region (5S rDNA-ISR) and mitochondrial cytochrome c oxidase 1 (CO1) gene sequences. Six haplotypes of the 5S rDNA intergenic spacer region (5S rDNA-ISR) and 14 of the cytochrome c oxidase 1 (CO1) gene were demonstrated in 89 individual T. britovi ML from Latvia and Poland. In contrast, only two haplotypes were observed at both 5S rDNA-ISR and CO1 of 57 individual T. spiralis ML from Polish wild boar and red foxes. Moreover, this study demonstrates hybridisation in eight individual ML between T. britovi and T. spiralis under natural conditions in four Polish wild boar and two red foxes, revealed by combining 5S rDNA-ISR and CO1 sequence information of individual Trichinella ML. To our knowledge, this is the first report of interspecies hybridisation between T. spiralis and T. britovi under field conditions.
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Affiliation(s)
- Frits Franssen
- National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands.
| | - Ewa Bilska-Zając
- National Veterinary Research Institute in Pulawy (PIWet), Poland.
| | - Gunita Deksne
- Institute of Food Safety, Animal Health and Environment (BIOR), Riga, Latvia.
| | - Hein Sprong
- National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands.
| | | | - Benjamin Rosenthal
- Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, USA.
| | - Mirek Rozycki
- National Veterinary Research Institute in Pulawy (PIWet), Poland.
| | - Joke van der Giessen
- National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands.
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Mitochondrial genomes of Trichinella species and genotypes – a basis for diagnosis, and systematic and epidemiological explorations. Int J Parasitol 2015; 44:1073-80. [PMID: 25245252 DOI: 10.1016/j.ijpara.2014.08.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 08/08/2014] [Accepted: 08/11/2014] [Indexed: 11/22/2022]
Abstract
In the present study we sequenced or re-sequenced, assembled and annotated 15 mitochondrial genomes representing the 12 currently recognised taxa of Trichinella using a deep sequencing-coupled approach. We then defined and compared the gene order in individual mitochondrial genomes (14 to 17.7 kb), evaluated genetic differences among species/genotypes and re-assessed the relationships among these taxa using the mitochondrial nucleic acid or amino acid sequence data sets. In addition, a rich source of mitochondrial genetic markers was defined that could be used in future systematic, epidemiological and population genetic studies of Trichinella. The sequencing-bioinformatic approach employed herein should be applicable to a wide range of eukaryotic parasites.
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Su YB, Kong SC, Wang LX, Chen L, Fang R. Complete mitochondrial genome of Philometra carassii (Nematoda: Philometridae). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:1397-8. [PMID: 25103437 DOI: 10.3109/19401736.2014.947598] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genome of Philometra carassii is 14,378 bp in size, containing 12 protein-coding genes (PCGs), 22 transfer RNA genes, 2 rRNA genes (12S and 16S), as well as one non-coding region (NCR, the control region), but lacks an atp8 gene. The genome organization, nucleotide composition and codon usage do not differ significantly from other nematodes. The complete mitogenome sequence information of P. carassii can provides useful data for further studies on phylogenetics, stock evaluation and conservation genetics.
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Affiliation(s)
- Ying-Bing Su
- a College of Animal Science, Yangtze University , Jingzhou , Hubei , P.R. China
| | - Sheng-Chao Kong
- b Key Laboratory of Freshwater Animal Breeding , Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University , Wuhan , P.R. China .,c Freshwater Aquaculture Collaborative Innovation Center of Hubei Province , Wuhan , P.R. China , and
| | - Li-Xia Wang
- d Hubei Provincial Center for Diseases Control and Prevention , Wuhan , Hubei , P.R. China
| | - Lu Chen
- b Key Laboratory of Freshwater Animal Breeding , Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University , Wuhan , P.R. China .,c Freshwater Aquaculture Collaborative Innovation Center of Hubei Province , Wuhan , P.R. China , and
| | - Rui Fang
- b Key Laboratory of Freshwater Animal Breeding , Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University , Wuhan , P.R. China .,c Freshwater Aquaculture Collaborative Innovation Center of Hubei Province , Wuhan , P.R. China , and
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Jabbar A, Mohandas N, Gasser RB. Characterisation of the mitochondrial genome of Parafilaroides normani (lungworm) of Arctocephalus pusillus doriferus (Australian fur seal). Parasitol Res 2014; 113:3049-55. [DOI: 10.1007/s00436-014-3968-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2014] [Accepted: 05/25/2014] [Indexed: 10/25/2022]
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Jabbar A, Gasser RB. Mutation scanning analysis of genetic variation within and among Echinococcus species: implications and future prospects. Electrophoresis 2014; 34:1852-62. [PMID: 23977679 DOI: 10.1002/elps.201300078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Adult tapeworms of the genus Echinococcus (family Taeniidae) occur in the small intestines of carnivorous definitive hosts and are transmitted to particular intermediate mammalian hosts, in which they develop as fluid-filled larvae (cysts) in internal organs (usually lung and liver), causing the disease echinococcosis. Echinococcus species are of major medical importance and also cause losses to the meat and livestock industries, mainly due to the condemnation of infected offal. Decisions regarding the treatment and control of echinococcosis rely on the accurate identification of species and population variants (strains). Conventional, phenetic methods for specific identification have some significant limitations. Despite advances in the development of molecular tools, there has been limited application of mutation scanning methods to species of Echinococcus. Here, we briefly review key genetic markers used for the identification of Echinococcus species and techniques for the analysis of genetic variation within and among populations, and the diagnosis of echinococcosis. We also discuss the benefits of utilizing mutation scanning approaches to elucidate the population genetics and epidemiology of Echinococcus species. These benefits are likely to become more evident following the complete characterization of the genomes of E. granulosus and E. multilocularis.
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Affiliation(s)
- Abdul Jabbar
- Faculty of Veterinary Science, The University of Melbourne, Parkville, Victoria, Australia
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Jabbar A, Mohandas N, Jex AR, Gasser RB. The mitochondrial genome of Protostrongylus rufescens - implications for population and systematic studies. Parasit Vectors 2013; 6:263. [PMID: 24025317 PMCID: PMC3848625 DOI: 10.1186/1756-3305-6-263] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 08/28/2013] [Indexed: 11/17/2022] Open
Abstract
Background Protostrongylus rufescens is a metastrongyloid nematode of small ruminants, such as sheep and goats, causing protostrongylosis. In spite of its importance, the ecology and epidemiology of this parasite are not entirely understood. In addition, genetic data are scant for P. rufescens and related metastrongyloids. Methods The mt genome was amplified from a single adult worm of P. rufescens (from sheep) by long-PCR, sequenced using 454-technology and annotated using bioinformatic tools. Amino acid sequences inferred from individual genes of the mt genomes were concatenated and subjected to phylogenetic analysis using Bayesian inference. Results The circular mitochondrial genome was 13,619 bp in length and contained two ribosomal RNA, 12 protein-coding and 22 transfer RNA genes, consistent with nematodes of the order Strongylida for which mt genomes have been determined. Phylogenetic analysis of the concatenated amino acid sequence data for the 12 mt proteins showed that P. rufescens was closely related to Aelurostrongylus abstrusus, Angiostrongylus vasorum, Angiostrongylus cantonensis and Angiostrongylus costaricensis. Conclusions The mt genome determined herein provides a source of markers for future investigations of P. rufescens. Molecular tools, employing such mt markers, are likely to find applicability in studies of the population biology of this parasite and the systematics of lungworms.
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Affiliation(s)
- Abdul Jabbar
- Faculty of Veterinary Science, The University of Melbourne, Parkville, Melbourne, Vic 3010, Australia.
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Jabbar A, Jex AR, Mohandas N, Hall RS, Littlewood DTJ, Gasser RB. The mitochondrial genome of Aelurostrongylus abstrusus-diagnostic, epidemiological and systematic implications. Gene 2012; 516:294-300. [PMID: 23142387 DOI: 10.1016/j.gene.2012.10.072] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Revised: 10/27/2012] [Accepted: 10/29/2012] [Indexed: 10/27/2022]
Abstract
Aelurostrongylus abstrusus (Railliet, 1898) is a metastrongylid nematode of major clinical relevance in felids, causing aelurostrongylosis. In spite of its clinical importance in cats, the genetics, epidemiology and biology of this parasite are not entirely understood. mt DNA can provide markers for studies of these areas, but genetic data are scant for A. abstrusus and related lungworms. Here, the mt genome was amplified by long-range polymerase chain reaction (long-PCR) from a single male adult of A. abstrusus, sequenced using 454 technology and annotated using an established bioinformatic pipeline. This circular mt genome is 13,913 bp and contains two ribosomal RNA, 12 protein-coding and 22 transfer RNA genes, consistent with most other chromadorean nematodes. This genome should provide a source of markers for future investigations of the epidemiology and ecology of A. abstrusus. Molecular tools, employing such mt markers, are likely to find utility for explorations into the epidemiology, biology and systematics of this parasite, and the diagnosis of feline aelurostrongylosis.
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Affiliation(s)
- Abdul Jabbar
- Faculty of Veterinary Science, The University of Melbourne, Parkville, Victoria 3010, Australia.
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Masny A, Jagiełło A, Płucienniczak G, Golab E. Ribo HRM--detection of inter- and intra-species polymorphisms within ribosomal DNA by high resolution melting analysis supported by application of artificial allelic standards. J Microbiol Methods 2012; 90:336-41. [PMID: 22766326 DOI: 10.1016/j.mimet.2012.06.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Revised: 06/25/2012] [Accepted: 06/25/2012] [Indexed: 10/28/2022]
Abstract
Ribo HRM, a single-tube PCR and high resolution melting (HRM) assay for detection of polymorphisms in the large subunit ribosomal DNA expansion segment V, was developed on a Trichinella model. Four Trichinella species: T. spiralis (isolates ISS3 and ISS160), T. nativa (isolates ISS10 and ISS70), T. britovi (isolates ISS2 and ISS392) and T. pseudospiralis (isolates ISS13 and ISS1348) were genotyped. Cloned allelic variants of the expansion segment V were used as standards to prepare reference HRM curves characteristic for single sequences and mixtures of several cloned sequences imitating allelic composition detected in Trichinella isolates. Using the primer pair Tsr1 and Trich1bi, it was possible to amplify a fragment of the ESV and detect PCR products obtained from the genomic DNA of pools of larvae belonging to the four investigated species: T. pseudospiralis, T. spiralis, T. britovi and T. nativa, in a single tube Real-Time PCR reaction. Differences in the shape of the HRM curves of Trichinella isolates suggested the presence of differences between examined isolates of T. nativa, T. britovi and T. pseudospiralis species. No differences were observed between T. spiralis isolates. The presence of polymorphisms within the amplified ESV sequence fragment of T. nativa T. britovi and T. pseudospiralis was confirmed by sequencing of the cloned PCR products. Novel sequences were discovered and deposited in GenBank (GenBank IDs: JN971020-JN971027, JN120902.1, JN120903.1, JN120904.1, JN120906.1, JN120905.1). Screening the ESV region of Trichinella for polymorphism is possible using the genotyping assay Ribo HRM at the current state of its development. The Ribo HRM assay could be useful in phylogenetic studies of the Trichinella genus.
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Affiliation(s)
- Aleksander Masny
- National Institute of Public Health-National Institute of Hygiene, Warszawa, Poland.
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La Rosa G, Marucci G, Rosenthal BM, Pozio E. Development of a single larva microsatellite analysis to investigate the population structure of Trichinella spiralis. INFECTION GENETICS AND EVOLUTION 2012; 12:369-76. [DOI: 10.1016/j.meegid.2012.01.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Revised: 12/17/2011] [Accepted: 01/11/2012] [Indexed: 11/24/2022]
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Vernet G. Genomics of Infectious Diseases and Private Industry. GENETICS AND EVOLUTION OF INFECTIOUS DISEASE 2011. [PMCID: PMC7149633 DOI: 10.1016/b978-0-12-384890-1.00019-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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A strategy for direct mapping and identification of mutations by whole-genome sequencing. Genetics 2010; 186:427-30. [PMID: 20610404 DOI: 10.1534/genetics.110.119230] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Mutant screens have proven powerful for genetic dissection of a myriad of biological processes, but subsequent identification and isolation of the causative mutations are usually complex and time consuming. We have made the process easier by establishing a novel strategy that employs whole-genome sequencing to simultaneously map and identify mutations without the need for any prior genetic mapping.
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