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Záhonová K, Low RS, Warren CJ, Cantoni D, Herman EK, Yiangou L, Ribeiro CA, Phanprasert Y, Brown IR, Rueckert S, Baker NL, Tachezy J, Betts EL, Gentekaki E, van der Giezen M, Clark CG, Jackson AP, Dacks JB, Tsaousis AD. Evolutionary analysis of cellular reduction and anaerobicity in the hyper-prevalent gut microbe Blastocystis. Curr Biol 2023:S0960-9822(23)00620-6. [PMID: 37267944 DOI: 10.1016/j.cub.2023.05.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 03/22/2023] [Accepted: 05/11/2023] [Indexed: 06/04/2023]
Abstract
Blastocystis is the most prevalent microbial eukaryote in the human and animal gut, yet its role as commensal or parasite is still under debate. Blastocystis has clearly undergone evolutionary adaptation to the gut environment and possesses minimal cellular compartmentalization, reduced anaerobic mitochondria, no flagella, and no reported peroxisomes. To address this poorly understood evolutionary transition, we have taken a multi-disciplinary approach to characterize Proteromonas lacertae, the closest canonical stramenopile relative of Blastocystis. Genomic data reveal an abundance of unique genes in P. lacertae but also reductive evolution of the genomic complement in Blastocystis. Comparative genomic analysis sheds light on flagellar evolution, including 37 new candidate components implicated with mastigonemes, the stramenopile morphological hallmark. The P. lacertae membrane-trafficking system (MTS) complement is only slightly more canonical than that of Blastocystis, but notably, we identified that both organisms encode the complete enigmatic endocytic TSET complex, a first for the entire stramenopile lineage. Investigation also details the modulation of mitochondrial composition and metabolism in both P. lacertae and Blastocystis. Unexpectedly, we identify in P. lacertae the most reduced peroxisome-derived organelle reported to date, which leads us to speculate on a mechanism of constraint guiding the dynamics of peroxisome-mitochondrion reductive evolution on the path to anaerobiosis. Overall, these analyses provide a launching point to investigate organellar evolution and reveal in detail the evolutionary path that Blastocystis has taken from a canonical flagellated protist to the hyper-divergent and hyper-prevalent animal and human gut microbe.
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Affiliation(s)
- Kristína Záhonová
- Division of Infectious Diseases, Department of Medicine, University of Alberta, 1-124 Clinical Sciences Building, 11350-83 Avenue, Edmonton T6G 2G3, Canada; Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská 1160/31, České Budějovice (Budweis) 370 05, Czech Republic; Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, Vestec 252 50, Czech Republic; Life Science Research Centre, Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, Ostrava 710 00, Czech Republic
| | - Ross S Low
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK; The Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Christopher J Warren
- Laboratory of Molecular & Evolutionary Parasitology, RAPID Group, School of Biosciences, University of Kent, Giles Lane, Stacey Building, Canterbury, Kent CT2 7NJ, UK
| | - Diego Cantoni
- Laboratory of Molecular & Evolutionary Parasitology, RAPID Group, School of Biosciences, University of Kent, Giles Lane, Stacey Building, Canterbury, Kent CT2 7NJ, UK
| | - Emily K Herman
- Division of Infectious Diseases, Department of Medicine, University of Alberta, 1-124 Clinical Sciences Building, 11350-83 Avenue, Edmonton T6G 2G3, Canada; Department of Agricultural, Food, and Nutritional Science, Faculty of Agricultural, Life, and Environmental Sciences, University of Alberta, 2-31 General Services Building, Edmonton, AB T6G 2H1, Canada
| | - Lyto Yiangou
- Laboratory of Molecular & Evolutionary Parasitology, RAPID Group, School of Biosciences, University of Kent, Giles Lane, Stacey Building, Canterbury, Kent CT2 7NJ, UK
| | - Cláudia A Ribeiro
- Laboratory of Molecular & Evolutionary Parasitology, RAPID Group, School of Biosciences, University of Kent, Giles Lane, Stacey Building, Canterbury, Kent CT2 7NJ, UK
| | - Yasinee Phanprasert
- Division of Infectious Diseases, Department of Medicine, University of Alberta, 1-124 Clinical Sciences Building, 11350-83 Avenue, Edmonton T6G 2G3, Canada; School of Science, Mae Fah Luang Universit, 333 Moo 1, T. Tasud, Muang District, Chiang Rai 57100, Thailand
| | - Ian R Brown
- Laboratory of Molecular & Evolutionary Parasitology, RAPID Group, School of Biosciences, University of Kent, Giles Lane, Stacey Building, Canterbury, Kent CT2 7NJ, UK
| | - Sonja Rueckert
- School of Applied Sciences, Sighthill Campus, Room 3.B.36, Edinburgh EH11 4BN, Scotland; Faculty of Biology, AG Eukaryotische Mikrobiologie, Universitätsstrasse 5, S05 R04 H83, Essen 45141, Germany
| | - Nicola L Baker
- Laboratory of Molecular & Evolutionary Parasitology, RAPID Group, School of Biosciences, University of Kent, Giles Lane, Stacey Building, Canterbury, Kent CT2 7NJ, UK
| | - Jan Tachezy
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, Vestec 252 50, Czech Republic
| | - Emma L Betts
- Laboratory of Molecular & Evolutionary Parasitology, RAPID Group, School of Biosciences, University of Kent, Giles Lane, Stacey Building, Canterbury, Kent CT2 7NJ, UK; School of Applied Sciences, Sighthill Campus, Room 3.B.36, Edinburgh EH11 4BN, Scotland
| | - Eleni Gentekaki
- School of Science, Mae Fah Luang Universit, 333 Moo 1, T. Tasud, Muang District, Chiang Rai 57100, Thailand; Gut Microbiome Research Group, Mae Fah Luang University, 333 Moo 1, T. Tasud, Muang District, Chiang Rai 57100, Thailand
| | - Mark van der Giezen
- Department of Chemistry, Bioscience and Environmental Engineering, University of Stavanger Richard Johnsens Gate 4, 4021 Stavanger, Norway; Biosciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - C Graham Clark
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Andrew P Jackson
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Joel B Dacks
- Division of Infectious Diseases, Department of Medicine, University of Alberta, 1-124 Clinical Sciences Building, 11350-83 Avenue, Edmonton T6G 2G3, Canada; Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská 1160/31, České Budějovice (Budweis) 370 05, Czech Republic; Centre for Life's Origin and Evolution, Division of Biosciences, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK.
| | - Anastasios D Tsaousis
- Laboratory of Molecular & Evolutionary Parasitology, RAPID Group, School of Biosciences, University of Kent, Giles Lane, Stacey Building, Canterbury, Kent CT2 7NJ, UK.
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Stensvold CR, Ascuña-Durand K, Chihi A, Belkessa S, Kurt Ö, El-Badry A, van der Giezen M, Clark CG. Further insight into the genetic diversity of Entamoeba coli and Entamoeba hartmanni. J Eukaryot Microbiol 2023; 70:e12949. [PMID: 36168968 DOI: 10.1111/jeu.12949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/16/2022] [Accepted: 09/16/2022] [Indexed: 11/30/2022]
Abstract
Despite the species' wide distribution, studies of the genetic diversity within Entamoeba coli and Entamoeba hartmanni remain limited. In the present study, we provide further insight into the genetic diversity of both species based on analysis of partial nuclear small subunit ribosomal DNA sequences generated from human fecal DNAs from samples collected in Africa, South America, and Europe. Reinforcing the previous recognition that E. coli is a species complex, our data confirm the existence of the two subtypes, ST1 and ST2, previously identified plus, potentially, a new subtype, ST3. While ST1 appears to be genetically quite homogenous, ST2 shows a substantial degree of intrasubtype diversity. ST2 was more common in samples collected outside Europe, whereas ST1 showed no geographical restriction. The potentially novel subtype is represented to date exclusively by sequences from South American and African samples. In contrast to previous reports, our new data also indicate substantial variation in E. hartmanni that could also support the establishment of subtypes within this species. Here, however, no links were identified between subtype and geographical origin.
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Affiliation(s)
| | - Kasandra Ascuña-Durand
- Laboratorio de Microbiología Molecular, Facultad de Medicina, Universidad Nacional de San Agustín, Arequipa, Peru
| | - Amal Chihi
- Laboratoire de Recherche 'Parasitologie Médicale, Biotechnologies et Biomolécules', LR 16-IPT-06, Institut Pasteur de Tunis, Université Tunis El-Manar, Tunis, Tunisia
| | - Salem Belkessa
- Department of Biology, Faculty of Nature and Life Sciences, Ziane Achour University of Djelfa, Djelfa, Algeria
| | - Özgür Kurt
- Department of Medical Microbiology, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Ayman El-Badry
- Department of Microbiology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Mark van der Giezen
- Department of Chemistry, Bioscience and Environmental Engineering, University of Stavanger, Stavanger, Norway
| | - C Graham Clark
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
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Hocke EF, Jamy M, Burki F, Clark CG, Stensvold CR. Unravelling the Phylogeny of a Common Intestinal Protist: Intrageneric Diversity of Endolimax. Protist 2022; 173:125908. [PMID: 36152390 DOI: 10.1016/j.protis.2022.125908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 06/17/2022] [Accepted: 09/01/2022] [Indexed: 12/30/2022]
Abstract
Endolimax nana is a common endobiont of the human intestine, but members of the genus have also been reported in non-human hosts and in non-intestinal organs. Limited information is available regarding the genetic diversity of Endolimax, which is necessary to delineate species, host specificity and potential differences in clinical impact on the host. Here, we used cloning of PCR products followed by Sanger sequencing and next-generation PacBio Sequencing to obtain Endolimax-related nuclear ribosomal gene sequences and undertook a phylogenetic analysis to gain additional insight into the taxonomy of Endolimax and related organisms. The new sequences confirmed that E. nana forms a discrete clade within the Archamoebae and is related to Endolimax piscium and Iodamoeba. However, we identified substantial sequence divergence within E. nana and evidence for two distinct clades, which we propose to name E. nana ribosomal lineage 1 and E. nana ribosomal lineage 2. Both of the sequencing approaches applied in the study helped us to improve our understanding of genetic diversity across Endolimax, and it is likely that wider application of next-generation sequencing technologies will facilitate the generation of Endolimax-related DNA sequence data and help complete our understanding of its phylogenetic position and intrageneric diversity.
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Affiliation(s)
- Emma Filtenborg Hocke
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Mahwash Jamy
- Department of Organismal Biology, Systematic Biology, Uppsala University, Uppsala, Sweden
| | - Fabien Burki
- Department of Organismal Biology, Systematic Biology, Uppsala University, Uppsala, Sweden; Science for Life Laboratory, Uppsala, Sweden
| | - C Graham Clark
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom.
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Affiliation(s)
| | | | - C Graham Clark
- London School of Hygiene and Tropical Medicine, London, UK
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Stensvold CR, Clark CG. Pre-empting Pandora's Box: Blastocystis Subtypes Revisited. Trends Parasitol 2020; 36:229-232. [PMID: 32001133 DOI: 10.1016/j.pt.2019.12.009] [Citation(s) in RCA: 135] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 12/20/2019] [Accepted: 12/25/2019] [Indexed: 11/30/2022]
Abstract
Blastocystis is a genetically diverse intestinal protist colonizing both human and non-human hosts. By 2013, 17 subtypes had been acknowledged. Since then, nine more subtypes have been proposed. We argue that several recently proposed subtypes are invalid. We also revisit recommendations regarding the requirements for annotating sequences as new subtypes.
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Affiliation(s)
| | - C Graham Clark
- London School of Hygiene and Tropical Medicine, London, UK
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Stensvold CR, Lebbad M, Hansen A, Beser J, Belkessa S, O'Brien Andersen L, Clark CG. Differentiation of Blastocystis and parasitic archamoebids encountered in untreated wastewater samples by amplicon-based next-generation sequencing. Parasite Epidemiol Control 2019; 9:e00131. [PMID: 31909230 PMCID: PMC6940715 DOI: 10.1016/j.parepi.2019.e00131] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 11/06/2019] [Accepted: 12/16/2019] [Indexed: 01/08/2023] Open
Abstract
Background Application of next-generation sequencing (NGS) to genomic DNA extracted from sewage offers a unique and cost-effective opportunity to study the genetic diversity of intestinal parasites. In this study, we used amplicon-based NGS to reveal and differentiate several common luminal intestinal parasitic protists, specifically Entamoeba, Endolimax, Iodamoeba, and Blastocystis, in sewage samples from Swedish treatment plants. Materials and methods Influent sewage samples were subject to gradient centrifugation, DNA extraction and PCR-based amplification using three primer pairs designed for amplification of eukaryotic nuclear 18S ribosomal DNA. PCR products were sequenced using ILLUMINA® technology, and resulting sequences were annotated to species and subtype level using the in-house BION software, sequence clustering, and phylogenetic analysis. Results A total of 26 samples from eight treatment plants in central/southern Sweden were analysed. Blastocystis sp. and Entamoeba moshkovskii were detected in all samples, and most samples (n = 20) were positive for Entamoeba coli. Moreover, we detected Entamoeba histolytica, Entamoeba dispar, Entamoeba hartmanni, Endolimax nana, and Iodamoeba bütschlii in 1, 11, 4, 10, and 7 samples, respectively. The level of genetic divergence observed within E. nana and E. moshkovskii was 20.2% and 7.7%, respectively, across the ~400-bp region studied, and two clades of E. moshkovskii were found. As expected, Blastocystis sp. subtypes 1–4 were present in almost all samples; however, ST8 was present in 10 samples and was the only subtype not commonly found in humans that was present in multiple samples. Conclusions Entamoeba and Blastocystis were identified as universal members of the “sewage microbiome”. Blastocystis sp. ST8, which has been rarely reported in humans, was a very common finding, indicating that a hitherto unidentified but common host of ST8 contributed to the sewage influent. The study also provided substantial new insight into the intra-generic diversity of Entamoeba and Endolimax.
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Affiliation(s)
- Christen Rune Stensvold
- Laboratory of Parasitology, Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark
| | - Marianne Lebbad
- Department of Microbiology, Public Health Agency of Sweden, SE-171 82 Solna, Sweden
| | - Anette Hansen
- Department of Microbiology, Public Health Agency of Sweden, SE-171 82 Solna, Sweden
| | - Jessica Beser
- Department of Microbiology, Public Health Agency of Sweden, SE-171 82 Solna, Sweden
| | - Salem Belkessa
- Laboratory of Parasitology, Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark.,Department of Biochemistry and Microbiology, Faculty of Biological and Agronomic Sciences, Mouloud Mammeri University of Tizi Ouzou, 15000 Tizi Ouzou, Algeria.,Department of Natural and Life Sciences, Faculty of Exact Sciences and Natural and Life Sciences, Mohamed Khider University of Biskra, 07000 Biskra, Algeria
| | - Lee O'Brien Andersen
- Laboratory of Parasitology, Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark
| | - C Graham Clark
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
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Robertson LJ, Clark CG, Debenham JJ, Dubey J, Kváč M, Li J, Ponce-Gordo F, Ryan U, Schares G, Su C, Tsaousis AD. Are molecular tools clarifying or confusing our understanding of the public health threat from zoonotic enteric protozoa in wildlife? Int J Parasitol Parasites Wildl 2019; 9:323-341. [PMID: 31338293 PMCID: PMC6626983 DOI: 10.1016/j.ijppaw.2019.01.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 01/30/2019] [Accepted: 01/31/2019] [Indexed: 12/13/2022]
Abstract
Emerging infectious diseases are frequently zoonotic, often originating in wildlife, but enteric protozoa are considered relatively minor contributors. Opinions regarding whether pathogenic enteric protozoa may be transmitted between wildlife and humans have been shaped by our investigation tools, and have led to oscillations regarding whether particular species are zoonotic or have host-adapted life cycles. When the only approach for identifying enteric protozoa was morphology, it was assumed that many enteric protozoa colonized multiple hosts and were probably zoonotic. When molecular tools revealed genetic differences in morphologically identical species colonizing humans and other animals, host specificity seemed more likely. Parasites from animals found to be genetically identical - at the few genes investigated - to morphologically indistinguishable parasites from human hosts, were described as having zoonotic potential. More discriminatory molecular tools have now sub-divided some protozoa again. Meanwhile, some infection events indicate that, circumstances permitting, some "host-specific" protozoa, can actually infect various hosts. These repeated changes in our understanding are linked intrinsically to the investigative tools available. Here we review how molecular tools have assisted, or sometimes confused, our understanding of the public health threat from nine enteric protozoa and example wildlife hosts (Balantoides coli - wild boar; Blastocystis sp. - wild rodents; Cryptosporidium spp. - wild fish; Encephalitozoon spp. - wild birds; Entamoeba spp. - non-human primates; Enterocytozoon bieneusi - wild cervids; Giardia duodenalis - red foxes; Sarcocystis nesbitti - snakes; Toxoplasma gondii - bobcats). Molecular tools have provided evidence that some enteric protozoa in wildlife may infect humans, but due to limited discriminatory power, often only the zoonotic potential of the parasite is indicated. Molecular analyses, which should be as discriminatory as possible, are one, but not the only, component of the toolbox for investigating potential public health impacts from pathogenic enteric protozoa in wildlife.
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Affiliation(s)
- Lucy J. Robertson
- Parasitology Laboratory, Department of Food Safety and Infection Biology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, PO Box 369 Sentrum, 0102, Oslo, Norway
| | - C. Graham Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, United Kingdom
| | - John J. Debenham
- Department of Companion Animal Clinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, PO Box 369 Sentrum, 0102, Oslo, Norway
| | - J.P. Dubey
- United States Department of Agriculture, Agricultural Research Service, Beltsville Agricultural Research Center, Animal Parasitic Diseases Laboratory, Building 1001, Beltsville, MD, 20705-2350, USA
| | - Martin Kváč
- Institute of Parasitology, Biology Centre of the Academy of Sciences of the Czech Republic, Branišovská 31, 370 05, České Budějovice, Czech Republic
- Faculty of Agriculture, University of South Bohemia in České Budějovice, Studentská 1668, 370 05, Czech Republic
| | - Junqiang Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China
| | - Francisco Ponce-Gordo
- Department of Microbiology and Parasitology, Faculty of Pharmacy, Complutense University, Plaza Ramón y Cajal s/n, 28040, Madrid, Spain
| | - Una Ryan
- Centre for Sustainable Aquatic Ecosystems, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, 6150, Australia
| | - Gereon Schares
- Institute of Epidemiology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493, Greifswald, Insel Riems, Germany
| | - Chunlei Su
- Department of Microbiology, University of Tennessee, Knoxville, TN, 37996-1937, USA
| | - Anastasios D. Tsaousis
- Laboratory of Molecular & Evolutionary Parasitology, RAPID Group, School of Biosciences, University of Kent, Canterbury, UK
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8
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Wilson IW, Weedall GD, Lorenzi H, Howcroft T, Hon CC, Deloger M, Guillén N, Paterson S, Clark CG, Hall N. Genetic Diversity and Gene Family Expansions in Members of the Genus Entamoeba. Genome Biol Evol 2019; 11:688-705. [PMID: 30668670 PMCID: PMC6414313 DOI: 10.1093/gbe/evz009] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2019] [Indexed: 12/18/2022] Open
Abstract
Amoebiasis is the third-most common cause of mortality worldwide from a parasitic disease. Although the primary etiological agent of amoebiasis is the obligate human parasite Entamoeba histolytica, other members of the genus Entamoeba can infect humans and may be pathogenic. Here, we present the first annotated reference genome for Entamoeba moshkovskii, a species that has been associated with human infections, and compare the genomes of E. moshkovskii, E. histolytica, the human commensal Entamoeba dispar, and the nonhuman pathogen Entamoeba invadens. Gene clustering and phylogenetic analyses show differences in expansion and contraction of families of proteins associated with host or bacterial interactions. They intimate the importance to parasitic Entamoeba species of surface-bound proteins involved in adhesion to extracellular membranes, such as the Gal/GalNAc lectin and members of the BspA and Ariel1 families. Furthermore, E. dispar is the only one of the four species to lack a functional copy of the key virulence factor cysteine protease CP-A5, whereas the gene's presence in E. moshkovskii is consistent with the species' potentially pathogenic nature. Entamoeba moshkovskii was found to be more diverse than E. histolytica across all sequence classes. The former is ∼200 times more diverse than latter, with the four E. moshkovskii strains tested having a most recent common ancestor nearly 500 times more ancient than the tested E. histolytica strains. A four-haplotype test indicates that these E. moshkovskii strains are not the same species and should be regarded as a species complex.
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Affiliation(s)
- Ian W Wilson
- Institute of Integrative Biology, University of Liverpool, United Kingdom
| | - Gareth D Weedall
- Institute of Integrative Biology, University of Liverpool, United Kingdom.,School of Natural Sciences and Psychology, Liverpool John Moores University, United Kingdom
| | | | - Timothy Howcroft
- Institute of Integrative Biology, University of Liverpool, United Kingdom
| | - Chung-Chau Hon
- Unité Biologie Cellulaire du Parasitisme, Institut Pasteur, Paris, France
| | - Marc Deloger
- Unité Biologie Cellulaire du Parasitisme, Institut Pasteur, Paris, France
| | - Nancy Guillén
- Unité Biologie Cellulaire du Parasitisme, Institut Pasteur, Paris, France
| | - Steve Paterson
- Institute of Integrative Biology, University of Liverpool, United Kingdom
| | - C Graham Clark
- London School of Hygiene & Tropical Medicine, Faculty of Infectious and Tropical Diseases, London, United Kingdom
| | - Neil Hall
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom.,School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ United Kingdom
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Abstract
The answers to a questionnaire concerning attitudes of members of the British Society of Gastroenterology to the management of acute upper gastrointestinal bleeding are analysed. In the majority of cases patients were admitted to general wards under the care of physicians. Use of intensive therapy units and venous pressure monitoring varied widely. Emergency endoscopy appeared readily available and was usually the first diagnostic procedure. Double contrast radiology and emergency angiography were available in relatively few centres. Specific nonoperative treatments (angiographic and endoscopic) were scarcely employed. Most respondents agreed that elderly patients fared badly, but there was little agreement concerning other factors which influence re-bleeding or outcome. There was a wide divergence of opinion concerning the need for surgical intervention in certain hypothetical clinical situations. Despite the difficulties involved, we believe that controlled trials are necessary to improve the management of bleeding patients.
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Affiliation(s)
- G E Thomas
- Gastrointestinal Unit, Middlesex Hospital, London W1N 8AA
| | - P B Cotton
- Gastrointestinal Unit, Middlesex Hospital, London W1N 8AA
| | - C G Clark
- Departments of Surgery and Gastroenterology University College Hospital, London WC1E 6AU
| | - P B Boulos
- Departments of Surgery and Gastroenterology University College Hospital, London WC1E 6AU
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Elsheikha HM, Regan CS, Clark CG. Novel Entamoeba Findings in Nonhuman Primates. Trends Parasitol 2018; 34:283-294. [PMID: 29396202 DOI: 10.1016/j.pt.2017.12.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 12/18/2017] [Accepted: 12/19/2017] [Indexed: 12/19/2022]
Abstract
In addition to well-known human-infecting species, Entamoeba species not found in humans have been identified recently in nonhuman primates (NHPs). Importantly, it has become clear that the organism identified as Entamoeba histolytica in NHPs is usually a distinct species, Entamoeba nuttalli. Many DNA-based stool surveys use species-specific detection methods and so may miss the full range of Entamoeba species present. In addition, authors may be using the same species name to describe distinct organisms. These various shortcomings may not be obvious to readers. In this review, we clarify the relationships between Entamoeba species' names based on morphological and molecular data, and highlight gaps in recently published data on Entamoeba species in wild NHPs resulting from the use of variable methodology.
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Affiliation(s)
- Hany M Elsheikha
- Faculty of Medicine and Health Sciences, School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Carl S Regan
- Faculty of Medicine and Health Sciences, School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK; Current address: Vets4pets Dover Whitfield, White Cliffs Retail Park, Whitfield, Dover, CT16 3PS, UK
| | - C Graham Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.
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Gentekaki E, Curtis BA, Stairs CW, Klimeš V, Eliáš M, Salas-Leiva DE, Herman EK, Eme L, Arias MC, Henrissat B, Hilliou F, Klute MJ, Suga H, Malik SB, Pightling AW, Kolisko M, Rachubinski RA, Schlacht A, Soanes DM, Tsaousis AD, Archibald JM, Ball SG, Dacks JB, Clark CG, van der Giezen M, Roger AJ. Extreme genome diversity in the hyper-prevalent parasitic eukaryote Blastocystis. PLoS Biol 2017; 15:e2003769. [PMID: 28892507 PMCID: PMC5608401 DOI: 10.1371/journal.pbio.2003769] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 09/21/2017] [Accepted: 08/25/2017] [Indexed: 12/11/2022] Open
Abstract
Blastocystis is the most prevalent eukaryotic microbe colonizing the human gut, infecting approximately 1 billion individuals worldwide. Although Blastocystis has been linked to intestinal disorders, its pathogenicity remains controversial because most carriers are asymptomatic. Here, the genome sequence of Blastocystis subtype (ST) 1 is presented and compared to previously published sequences for ST4 and ST7. Despite a conserved core of genes, there is unexpected diversity between these STs in terms of their genome sizes, guanine-cytosine (GC) content, intron numbers, and gene content. ST1 has 6,544 protein-coding genes, which is several hundred more than reported for ST4 and ST7. The percentage of proteins unique to each ST ranges from 6.2% to 20.5%, greatly exceeding the differences observed within parasite genera. Orthologous proteins also display extreme divergence in amino acid sequence identity between STs (i.e., 59%-61% median identity), on par with observations of the most distantly related species pairs of parasite genera. The STs also display substantial variation in gene family distributions and sizes, especially for protein kinase and protease gene families, which could reflect differences in virulence. It remains to be seen to what extent these inter-ST differences persist at the intra-ST level. A full 26% of genes in ST1 have stop codons that are created on the mRNA level by a novel polyadenylation mechanism found only in Blastocystis. Reconstructions of pathways and organellar systems revealed that ST1 has a relatively complete membrane-trafficking system and a near-complete meiotic toolkit, possibly indicating a sexual cycle. Unlike some intestinal protistan parasites, Blastocystis ST1 has near-complete de novo pyrimidine, purine, and thiamine biosynthesis pathways and is unique amongst studied stramenopiles in being able to metabolize α-glucans rather than β-glucans. It lacks all genes encoding heme-containing cytochrome P450 proteins. Predictions of the mitochondrion-related organelle (MRO) proteome reveal an expanded repertoire of functions, including lipid, cofactor, and vitamin biosynthesis, as well as proteins that may be involved in regulating mitochondrial morphology and MRO/endoplasmic reticulum (ER) interactions. In sharp contrast, genes for peroxisome-associated functions are absent, suggesting Blastocystis STs lack this organelle. Overall, this study provides an important window into the biology of Blastocystis, showcasing significant differences between STs that can guide future experimental investigations into differences in their virulence and clarifying the roles of these organisms in gut health and disease.
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Affiliation(s)
- Eleni Gentekaki
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Bruce A. Curtis
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Courtney W. Stairs
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Vladimír Klimeš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Marek Eliáš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Dayana E. Salas-Leiva
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Emily K. Herman
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
| | - Laura Eme
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Maria C. Arias
- Université des Sciences et Technologies de Lille, Unité de Glycobiologie Structurale et Fonctionnelle, UMR8576 CNRS-USTL, Cité Scientifique, Villeneuve d’Ascq Cedex, France
| | - Bernard Henrissat
- CNRS UMR 7257, Aix-Marseille University, Marseille, France
- INRA, USC 1408 AFMB, Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Mary J. Klute
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
| | - Hiroshi Suga
- Faculty of Life and Environmental Sciences, Prefectural University of Hiroshima, Nanatsuka 562, Shobara, Hiroshima, Japan
| | - Shehre-Banoo Malik
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Arthur W. Pightling
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Martin Kolisko
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | | | - Alexander Schlacht
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
| | - Darren M. Soanes
- College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Anastasios D. Tsaousis
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - John M. Archibald
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
- Canadian Institute for Advanced Research, CIFAR Program in Integrated Microbial Biodiversity, Toronto, Canada
| | - Steven G. Ball
- Université des Sciences et Technologies de Lille, Unité de Glycobiologie Structurale et Fonctionnelle, UMR8576 CNRS-USTL, Cité Scientifique, Villeneuve d’Ascq Cedex, France
| | - Joel B. Dacks
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
| | - C. Graham Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | - Andrew J. Roger
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
- Canadian Institute for Advanced Research, CIFAR Program in Integrated Microbial Biodiversity, Toronto, Canada
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Jacob AS, Andersen LO, Bitar PP, Richards VP, Shah S, Stanhope MJ, Stensvold CR, Clark CG. Blastocystis Mitochondrial Genomes Appear to Show Multiple Independent Gains and Losses of Start and Stop Codons. Genome Biol Evol 2016; 8:3340-3350. [PMID: 27811175 PMCID: PMC5203790 DOI: 10.1093/gbe/evw255] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Complete mitochondrion-related organelle (MRO) genomes of several subtypes (STs) of the unicellular stramenopile Blastocystis are presented. Complete conservation of gene content and synteny in gene order is observed across all MRO genomes, comprising 27 protein coding genes, 2 ribosomal RNA genes, and 16 transfer RNA (tRNA) genes. Despite the synteny, differences in the degree of overlap between genes were observed between subtypes and also between isolates within the same subtype. Other notable features include unusual base-pairing mismatches in the predicted secondary structures of some tRNAs. Intriguingly, the rps4 gene in some MRO genomes is missing a start codon and, based on phylogenetic relationships among STs, this loss has happened twice independently. One unidentified open reading frame (orf160) is present in all MRO genomes. However, with the exception of ST4 where the feature has been lost secondarily, orf160 contains variously one or two in-frame stop codons. The overall evidence suggests that both the orf160 and rps4 genes are functional in all STs, but how they are expressed remains unclear.
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Affiliation(s)
- Alison S Jacob
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom.,Present address: Faculty of Natural Sciences, Imperial College, London, United Kingdom
| | - Lee O'Brien Andersen
- Department of Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark
| | - Paulina Pavinski Bitar
- Department of Population Medicine and Diagnostic Sciences, Cornell College of Veterinary Medicine, Cornell University, Ithaca, NY
| | - Vincent P Richards
- Department of Population Medicine and Diagnostic Sciences, Cornell College of Veterinary Medicine, Cornell University, Ithaca, NY.,Present address: Department of Biological Sciences, College of Agriculture, Forestry and Life Sciences, Clemson University, Clemson, SC
| | - Sarah Shah
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Michael J Stanhope
- Department of Population Medicine and Diagnostic Sciences, Cornell College of Veterinary Medicine, Cornell University, Ithaca, NY
| | - C Rune Stensvold
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom.,Department of Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark
| | - C Graham Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
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13
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Abstract
Blastocystis is an intestinal parasite that is very easily isolated in culture from fresh stool samples. In fact, the parasite grows so readily in culture that short-term in vitro culture is sometimes used as a diagnostic tool in the absence of DNA-based methods. While axenizing Blastocystis cultures remains a significant challenge, the parasite can be propagated for several months in the presence of metabolically active bacteria (xenic culture). Hence, culture can be used for maintaining live Blastocystis strain libraries. This enables the production of a stable resource of reference material, which for instance can be used for DNA-based assays and research. Blastocystis isolates can also be cryopreserved with a view to reestablishing them in culture. Here, we provide protocols for xenic in vitro culture and cryopreservation of Blastocystis. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- C Graham Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - C Rune Stensvold
- Department of Microbiology and Infection, Statens Serum Institut, Copenhagen, Denmark
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14
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Abstract
Several typing methods have been used in studies aiming to unravel the molecular epidemiology of Blastocystis, which is one of the most common intestinal parasites in human and many non-human hosts. Such studies have the potential to add to knowledge on Blastocystis transmission, host specificity, phylogeography, and clinical and public health significance, but rely on robust, standardized methods by which data can be generated and compared directly between studies. One of the most used methods is "barcoding,", which involves single-round PCR amplification and sequencing of partial small subunit ribosomal RNA genes of the parasites. Recently, a publicly available online facility was developed for quick and standardized identification of subtypes (ribosomal lineages) and subtype alleles (variation within subtypes) based on sequence data obtained by barcoding PCR. Moreover, a modified barcoding approach is now available using nested PCR, which enables detection of mixed subtype infections. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- C Rune Stensvold
- Department of Microbiology and Infection, Statens Serum Institut, Copenhagen, Denmark
| | - C Graham Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, U.K
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15
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Affiliation(s)
| | | | - C G Clark
- University College Hospital, London WC1
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16
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Stensvold CR, Clark CG. Current status of Blastocystis: A personal view. Parasitol Int 2016; 65:763-771. [PMID: 27247124 DOI: 10.1016/j.parint.2016.05.015] [Citation(s) in RCA: 213] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 05/10/2016] [Accepted: 05/27/2016] [Indexed: 12/15/2022]
Abstract
Despite Blastocystis being one of the most widespread and prevalent intestinal eukaryotes, its role in health and disease remains elusive. DNA-based detection methods have led to a recognition that the organism is much more common than previously thought, at least in some geographic regions and some groups of individuals. Molecular methods have also enabled us to start categorizing the vast genetic heterogeneity that exists among Blastocystis isolates, wherein the key to potential differences in the clinical outcome of Blastocystis carriage may lie. In this review we summarize some of the recent developments and advances in Blastocystis research, including updates on diagnostic methods, molecular epidemiology, genetic diversity, host specificity, clinical significance, taxonomy, and genomics. As we are now in the microbiome era, we also review some of the steps taken towards understanding the place of Blastocystis in the intestinal microbiota.
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Affiliation(s)
| | - C Graham Clark
- London School of Hygiene and Tropical Medicine, London, UK
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17
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Stensvold CR, Lebbad M, Victory EL, Verweij JJ, Tannich E, Alfellani M, Legarraga P, Clark CG. Corrigendum to “Increased Sampling Reveals Novel Lineages of Entamoeba: Consequences of Genetic Diversity and Host Specificity for Taxonomy and Molecular Detection” [Protist 162 (2011) 525-541]. Protist 2016. [DOI: 10.1016/j.protis.2015.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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18
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Abu-Madi M, Aly M, Behnke JM, Clark CG, Balkhy H. The distribution of Blastocystis subtypes in isolates from Qatar. Parasit Vectors 2015; 8:465. [PMID: 26384209 PMCID: PMC4573284 DOI: 10.1186/s13071-015-1071-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2015] [Accepted: 09/03/2015] [Indexed: 11/12/2022] Open
Abstract
Background Blastocystis is a common single-celled intestinal parasite of humans and other animals comprising at least 17 genetically distinct small subunit ribosomal RNA lineages (subtypes (STs)), nine of which have been found in humans. The geographic distribution of Blastocystis subtypes is variable, but the subtypes present in Qatar are at present unknown. Methods Stool samples were collected from randomly selected, apparently healthy subjects arriving in Qatar for the first time. Blastocystis subtypes were determined by sequencing of the small subunit rRNA gene (SSU rDNA) PCR products. Phylogenetic analyses were done using Maximum Composite Likelihood method. Results 71.1 % of samples were positive for Blastocystis infection based on PCR-detection methodology compared to only 6.9 % by microscopy. Prevalence of Blastocystis did not differ between the sexes nor between age classes. However, there was a regional difference in prevalence with subjects arriving from Africa showing the highest (87.6 %), those from Western Asia intermediate (68.6 %) and from Eastern Asia the lowest prevalence (67.6 %). Genetic analysis detected only three STs. ST3 was the most common (69.3 %) and ST2 was the rarest (3.5 %), while ST1 had a prevalence of 27.2 %. ST2 showed a regional variation, being absent from the 64 Western Asian Blastocystis-positive subjects. Both ST1 and ST3 showed significant differences in prevalence between the sexes. Conclusions This is the first report exploring the distribution of Blastocystis subtypes in our region. We recommend that stool screening via microscopy for the presence of Blastocystis should be abandoned since it is extremely insensitive. In future, the prevalence of Blastocystis infections should be based on PCR methodology and we predict that in the years ahead diagnostic PCR will become the tool of choice. More work is needed to identify the full range of Blastocystis subtypes that circulate in our region.
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Affiliation(s)
- Marawan Abu-Madi
- Department of Health Sciences, College of Arts and Science, Biomedical Research Center, Qatar University, P.O. Box 2713, Doha, Qatar.
| | - Mahmoud Aly
- King Abdullah International Medical Research Center, National Guard Health Affairs, Mail Code: 2216, P.O. Box 22490, Riyadh, 11426, KSA. .,King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia.
| | - Jerzy M Behnke
- School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom, NG7 2RD.
| | - C Graham Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, WC1E 7HT, London, United Kingdom.
| | - Hanan Balkhy
- King Abdullah International Medical Research Center, National Guard Health Affairs, Mail Code: 2216, P.O. Box 22490, Riyadh, 11426, KSA. .,King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia.
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Jacob AS, Busby EJ, Levy AD, Komm N, Clark CG. Expanding the Entamoeba Universe: New Hosts Yield Novel Ribosomal Lineages. J Eukaryot Microbiol 2015; 63:69-78. [PMID: 26130044 DOI: 10.1111/jeu.12249] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 06/24/2015] [Accepted: 06/24/2015] [Indexed: 11/30/2022]
Abstract
Removing the requirement for cell culture has led to a substantial increase in the number of lineages of Entamoeba recognized as distinct. Surveying the range of potential host species for this parasite genus has barely been started and it is clear that additional sampling of the same host in different locations often identifies additional diversity. In this study, using small subunit ribosomal RNA gene sequencing, we identify four new lineages of Entamoeba, including the first report of Entamoeba from an elephant, and extend the host range of some previously described lineages. In addition, examination of microbiome data from a number of host animals suggests that substantial Entamoeba diversity remains to be uncovered.
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Affiliation(s)
- Alison S Jacob
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, United Kingdom
| | - Eloise J Busby
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, United Kingdom
| | - Abigail D Levy
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, United Kingdom
| | - Natasha Komm
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, United Kingdom
| | - C Graham Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, United Kingdom
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20
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Serrano A, Graham Clark C, Martín A. Announcement. J Eukaryot Microbiol 2014. [DOI: 10.1111/jeu.12107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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21
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Clark CG, Röser D, Stensvold CR. Transmission of Dientamoeba fragilis: pinworm or cysts? Trends Parasitol 2014; 30:136-40. [PMID: 24492020 DOI: 10.1016/j.pt.2014.01.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 01/09/2014] [Accepted: 01/09/2014] [Indexed: 10/25/2022]
Abstract
Recently, conflicting evidence has been published on the mode of transmission of the trichomonad Dientamoeba fragilis. Detection of D. fragilis DNA inside Enterobius vermicularis eggs agrees with the prediction of Dobell in 1940 that the eggs of a nematode act as a vector for transmission. However, the identification of a cyst stage of D. fragilis in the stool of rodents infected with a human isolate has also been reported, and this implies a life cycle similar to those of most other intestinal protistan parasites. Herein we discuss the recent data, identify gaps in the experimental evidence, and propose a method for determining which view of the life cycle of this organism is correct.
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Affiliation(s)
- C Graham Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Dennis Röser
- Department of Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark
| | - C Rune Stensvold
- Department of Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark.
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Kumari V, Iyer LR, Roy R, Bhargava V, Panda S, Paul J, Verweij JJ, Clark CG, Bhattacharya A, Bhattacharya S. Genomic distribution of SINEs in Entamoeba histolytica strains: implication for genotyping. BMC Genomics 2013; 14:432. [PMID: 23815468 PMCID: PMC3716655 DOI: 10.1186/1471-2164-14-432] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 06/20/2013] [Indexed: 11/01/2022] Open
Abstract
BACKGROUND The major clinical manifestations of Entamoeba histolytica infection include amebic colitis and liver abscess. However the majority of infections remain asymptomatic. Earlier reports have shown that some E. histolytica isolates are more virulent than others, suggesting that virulence may be linked to genotype. Here we have looked at the genomic distribution of the retrotransposable short interspersed nuclear elements EhSINE1 and EhSINE2. Due to their mobile nature, some EhSINE copies may occupy different genomic locations among isolates of E. histolytica possibly affecting adjacent gene expression; this variability in location can be exploited to differentiate strains. RESULTS We have looked for EhSINE1- and EhSINE2-occupied loci in the genome sequence of Entamoeba histolytica HM-1:IMSS and searched for homologous loci in other strains to determine the insertion status of these elements. A total of 393 EhSINE1 and 119 EhSINE2 loci were analyzed in the available sequenced strains (Rahman, DS4-868, HM1:CA, KU48, KU50, KU27 and MS96-3382. Seventeen loci (13 EhSINE1 and 4 EhSINE2) were identified where a EhSINE1/EhSINE2 sequence was missing from the corresponding locus of other strains. Most of these loci were unoccupied in more than one strain. Some of the loci were analyzed experimentally for SINE occupancy using DNA from strain Rahman. These data helped to correctly assemble the nucleotide sequence at three loci in Rahman. SINE occupancy was also checked at these three loci in 7 other axenically cultivated E. histolytica strains and 16 clinical isolates. Each locus gave a single, specific amplicon with the primer sets used, making this a suitable method for strain typing. Based on presence/absence of SINE and amplification with locus-specific primers, the 23 strains could be divided into eleven genotypes. The results obtained by our method correlated with the data from other typing methods. We also report a bioinformatic analysis of EhSINE2 copies. CONCLUSIONS Our results reveal several loci with extensive polymorphism of SINE occupancy among different strains of E. histolytica and prove the principle that the genomic distribution of SINEs is a valid method for typing of E. histolytica strains.
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Affiliation(s)
- Vandana Kumari
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India
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Alfellani MA, Taner-Mulla D, Jacob AS, Imeede CA, Yoshikawa H, Stensvold CR, Clark CG. Genetic diversity of blastocystis in livestock and zoo animals. Protist 2013; 164:497-509. [PMID: 23770574 DOI: 10.1016/j.protis.2013.05.003] [Citation(s) in RCA: 249] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Revised: 04/27/2013] [Accepted: 05/01/2013] [Indexed: 11/30/2022]
Abstract
Blastocystis is a common unicellular anaerobic eukaryote that inhabits the large intestine of many animals worldwide, including humans. The finding of Blastocystis in faeces in mammals and birds has led to proposals of zoonotic potential and that these hosts may be the source of many human infections. Blastocystis is, however, a genetically diverse complex of many distinct organisms (termed subtypes; STs), and sampling to date has been limited, both geographically and in the range of hosts studied. In order to expand our understanding of host specificity of Blastocystis STs, 557 samples were examined from various non-primate animal hosts and from a variety of different countries in Africa, Asia and Europe. STs were identified using 'barcoding' of the small subunit rRNA gene using DNA extracted either from culture or directly from faeces. The host and geographic range of several STs has thereby been greatly expanded and the evidence suggests that livestock is not a major contributor to human infection. Two new STs were detected among the barcode sequences obtained; for these, and for three others where the data were incomplete, the corresponding genes were fully sequenced and phylogenetic analysis was undertaken.
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Affiliation(s)
- Mohammed A Alfellani
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
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Stensvold CR, Clark CG, Röser D. Limited intra-genetic diversity in Dientamoeba fragilis housekeeping genes. Infect Genet Evol 2013; 18:284-6. [PMID: 23681023 DOI: 10.1016/j.meegid.2013.05.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 04/30/2013] [Accepted: 05/03/2013] [Indexed: 11/15/2022]
Abstract
Dientamoeba fragilis is a common intestinal parasite of unsettled clinical significance. Differences in clinical outcome of parasitic infections may reflect parasite genetic diversity, and so tools to study intra-genetic diversity that could potentially reflect differences in clinical phenotypes are warranted. Here, we show that genetic analysis of three D. fragilis housekeeping genes enables clear distinction between the two known genotypes, but that integration of housekeeping genes in multi-locus sequencing tools for D. fragilis may have limited epidemiological and clinical value due to no further added genetic resolution.
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Affiliation(s)
- Christen Rune Stensvold
- Laboratory of Parasitology, Department of Microbiology and Infection Control, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark.
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25
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Alfellani MA, Stensvold CR, Vidal-Lapiedra A, Onuoha ESU, Fagbenro-Beyioku AF, Clark CG. Variable geographic distribution of Blastocystis subtypes and its potential implications. Acta Trop 2013; 126:11-8. [PMID: 23290980 DOI: 10.1016/j.actatropica.2012.12.011] [Citation(s) in RCA: 247] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Revised: 11/29/2012] [Accepted: 12/20/2012] [Indexed: 01/23/2023]
Abstract
Blastocystis is a common intestinal micro-eukaryote found in both humans and non-human hosts and known to be genetically very diverse. It has been divided into numerous subtypes (STs), nine of which have been identified in humans to date. Surveys of ST prevalence have started to emerge over the past few years but to date no data are available for any African country except Egypt and Tanzania. In this study, we determined the prevalence of Blastocystis STs in populations from Libya, Liberia and Nigeria, as well as expanding the dataset available for the UK. A total of 356 Blastocystis STs were identified in this study, 271 from the UK, 38 from Libya, 25 from Liberia and 22 from Nigeria. SSU rRNA gene sequences revealed the presence of eight of the nine STs known from humans but at varying frequencies between countries. ST1 was the most common ST in Libya and Nigeria whereas ST3 showed the highest frequency in the other two countries, as indeed is the case in most populations around the world. ST4 was absent in Libya and ST2 in Nigeria, while no ST5, ST6, ST8 or ST9 infections were detected in any of the three African populations. The picture emerging from this and other surveys suggests that there is significant variation in ST prevalence between populations. Some of the possible reasons for and implications of this diversity are discussed.
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Malheiros AF, Stensvold CR, Clark CG, Braga GB, Shaw JJ. Short report: Molecular characterization of Blastocystis obtained from members of the indigenous Tapirapé ethnic group from the Brazilian Amazon region, Brazil. Am J Trop Med Hyg 2012; 85:1050-3. [PMID: 22144442 DOI: 10.4269/ajtmh.2011.11-0481] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
A total of 382 stool samples were examined during a survey of intestinal parasites in members of the Tapirapé ethnic group, who live in the Brazilian Amazon region of Mato Grosso. Fecal DNAs from Blastocystis-positive samples were extracted, polymerase chain reaction amplified using Blastocystis-specific primers targeting the small subunit rRNA gene, and sequenced. Three subtypes (STs) were identified: ST1 (41%), ST2 (32%), and ST3 (17%). Seven mixed infections were found (11%). The subtype distribution was markedly different from that reported in Europe in that ST4 was not detected and ST3 was not the most common subtype. This study is the first to include molecular characterization of Blastocystis in Brazil and in indigenous communities from Latin America.
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Affiliation(s)
- Antonio F Malheiros
- Department of Biology, Mato Grosso State University, Cáceres, Mato Grosso, Brazil.
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Weedall GD, Clark CG, Koldkjaer P, Kay S, Bruchhaus I, Tannich E, Paterson S, Hall N. Genomic diversity of the human intestinal parasite Entamoeba histolytica. Genome Biol 2012; 13:R38. [PMID: 22630046 PMCID: PMC3446291 DOI: 10.1186/gb-2012-13-5-r38] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Revised: 04/29/2012] [Accepted: 05/25/2012] [Indexed: 11/10/2022] Open
Abstract
Background Results Conclusions
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Stensvold CR, Alfellani M, Clark CG. Levels of genetic diversity vary dramatically between Blastocystis subtypes. Infect Genet Evol 2011; 12:263-73. [PMID: 22116021 DOI: 10.1016/j.meegid.2011.11.002] [Citation(s) in RCA: 138] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Revised: 11/05/2011] [Accepted: 11/07/2011] [Indexed: 11/26/2022]
Abstract
Blastocystis is a common single-celled parasite of humans and other animals comprising at least 13 genetically distinct small subunit ribosomal RNA lineages (subtypes (STs)). In this study we investigated intra-subtype genetic diversity and host specificity of two of the most common subtypes in humans, namely ST3 and ST4, by analysing and comparing over 400 complete and partial nuclear SSU-rDNAs and data from multilocus sequence typing (MLST) of the mitochondrion-like organelle (MLO) genome of 132 samples. Inferences from phylogenetic analyses of nuclear SSU-rDNA and concatenated MLST sequences were compatible. Human ST3 infections were restricted to one of four identified MLO clades except where exposure to non-human primates had occurred. This suggests relatively high host specificity within ST3, that human ST3 infections are caused predominantly by human-to-human transmission, and that human strains falling into other clades are almost certainly the result of zoonotic transmission. ST4 from humans belonged almost exclusively to one of two SSU-rDNA clades, and only five MLST sequence types were found among 50 ST4s belonging to Clade 1 (discriminatory index: 0.41) compared to 58 MLST sequence types among 81 ST3s (discriminatory index: 0.99). The remarkable differences in intra-subtype genetic variability suggest that ST4 has a more recent history of colonising humans than ST3. This is congruent with the apparently restricted geographical distribution of ST4 relative to ST3. The implications of this observation are unclear, however, and the population structure and distribution of ST4 should be subject to further scrutiny in view of the fact ST4 is being increasingly linked with intestinal disease.
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Affiliation(s)
- C Rune Stensvold
- Department of Microbiological Diagnostics, Statens Serum Institut, Orestads Boulevard 5, DK-2300 Copenhagen S, Denmark.
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Prokopi M, Chatzitheodorou T, Ackers JP, Clark CG. A preliminary investigation of microsatellite-based genotyping in Trichomonas vaginalis. Trans R Soc Trop Med Hyg 2011; 105:479-81. [PMID: 21700304 DOI: 10.1016/j.trstmh.2011.05.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Revised: 05/10/2011] [Accepted: 05/10/2011] [Indexed: 11/26/2022] Open
Abstract
The genetic epidemiology of Trichomonas vaginalis is poorly understood at present. The recent release of the organism's genome sequence opens the way to investigation of polymorphic markers allowing strain identification. We here report a preliminary analysis of microsatellite loci in T. vaginalis and show that this approach holds promise for future studies of infection transmission and organism diversity.
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Affiliation(s)
- Marianna Prokopi
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, UK
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Clark CG, Gillin FD, Bhattacharya A, Bhattacharya S, Mirelman D. In memoriam: Louis S. "Buddy" Diamond (1920-2009). J Eukaryot Microbiol 2010; 57:449-51. [PMID: 20662997 DOI: 10.1111/j.1550-7408.2010.00493.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- C Graham Clark
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
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Pérez-Brocal V, Shahar-Golan R, Clark CG. A linear molecule with two large inverted repeats: the mitochondrial genome of the stramenopile Proteromonas lacertae. Genome Biol Evol 2010; 2:257-66. [PMID: 20624730 PMCID: PMC2997541 DOI: 10.1093/gbe/evq015] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Mitochondrial evolution has given rise to a complex array of organelles, ranging from classical aerobic mitochondria to mitochondrial remnants known as hydrogenosomes and mitosomes. The latter are found in anaerobic eukaryotes, and these highly derived organelles often retain only scant evidence of their mitochondrial origins. Intermediate evolutionary stages have also been reported as facultatively or even strictly anaerobic mitochondria, and hydrogenosomes that still retain some mitochondrial features. However, the diversity among these organelles with transitional features remains rather unclear and barely studied. Here, we report the sequence, structure, and gene content of the mitochondrial DNA of the anaerobic stramenopile Proteromonas lacertae. It has a linear genome with a unique central region flanked by two identical large inverted repeats containing numerous genes and “telomeres” with short inverted repeats. Comparison with the organelle genome of the strictly anaerobic human parasite Blastocystis reveals that, despite the close similarity of the sequences, features such as the genome structure display striking differences. It remains unclear whether the virtually identical gene repertoires are the result of convergence or descent.
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Affiliation(s)
- Vicente Pérez-Brocal
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
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Stensvold CR, Lebbad M, Clark CG. Genetic characterisation of uninucleated cyst-producing Entamoeba spp. from ruminants. Int J Parasitol 2010; 40:775-8. [DOI: 10.1016/j.ijpara.2010.03.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2010] [Revised: 03/10/2010] [Accepted: 03/11/2010] [Indexed: 10/19/2022]
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Davis PH, Chen M, Zhang X, Clark CG, Townsend RR, Stanley SL. Proteomic comparison of Entamoeba histolytica and Entamoeba dispar and the role of E. histolytica alcohol dehydrogenase 3 in virulence. PLoS Negl Trop Dis 2009; 3:e415. [PMID: 19365541 PMCID: PMC2663792 DOI: 10.1371/journal.pntd.0000415] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2007] [Accepted: 03/17/2009] [Indexed: 11/28/2022] Open
Abstract
The protozoan intestinal parasite Entamoeba histolytica infects millions of people worldwide and is capable of causing amebic dysentery and amebic liver abscess. The closely related species Entamoeba dispar colonizes many more individuals, but this organism does not induce disease. To identify molecular differences between these two organisms that may account for their differential ability to cause disease in humans, we used two-dimensional gel-based (DIGE) proteomic analysis to compare whole cell lysates of E. histolytica and E. dispar. We observed 141 spots expressed at a substantially (>5-fold) higher level in E. histolytica HM-1∶IMSS than E. dispar and 189 spots showing the opposite pattern. Strikingly, 3 of 4 proteins consistently identified as different at a greater than 5-fold level between E. histolytica HM-1∶IMSS and E. dispar were identical to proteins recently identified as differentially expressed between E. histolytica HM-1∶IMSS and the reduced virulence strain E. histolytica Rahman. One of these was E. histolytica alcohol dehydrogenase 3 (EhADH3). We found that E. histolytica possesses a higher level of NADP-dependent alcohol dehydrogenase activity than E. dispar and that some EhADH3 can be localized to the surface of E. histolytica. Episomal overexpression of EhADH3 in E. histolytica trophozoites resulted in only subtle phenotypic differences in E. histolytica virulence in animal models of amebic colitis and amebic liver abscess, making it difficult to directly link EhADH3 levels to virulence differences between E. histolytica and less-pathogenic Entamoeba. Infection with Entamoeba histolytica can result in disabling diarrhea or even death, while the morphologically identical and genetically similar Entamoeba dispar harmlessly colonizes the human intestine. Understanding the molecular differences between these two organisms by comparing their protein repertoire may help us to understand why E. histolytica invades into colonic tissue, while E. dispar remains a benign passenger. Here, we identify four proteins that appear to be differentially expressed between the two species and show that a metabolic enzyme, which would appear to be an unlikely candidate for a role in disease, is expressed at much higher levels in the pathogenic organism.
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Affiliation(s)
- Paul H. Davis
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Minghe Chen
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Xiaochun Zhang
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - C. Graham Clark
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - R. Reid Townsend
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Samuel L. Stanley
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- * E-mail:
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Jackson CJ, Barton RC, Clark CG, Kelly SL. Molecular characterization of a subgroup IE intron with wide distribution in the large subunit rRNA genes of dermatophyte fungi. Med Mycol 2009; 47:609-17. [DOI: 10.1080/13693780802385445] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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Abstract
Amebiasis is defined as infection with Entamoeba histolytica, regardless of associated symptomatology. In resource-rich nations, this parasitic protozoan is seen primarily in travelers to and emigrants from endemic areas. Infections range from asymptomatic colonization to amebic colitis and life-threatening abscesses. Importantly, disease may occur months to years after exposure. Although E histolytica was previously thought to infect 10% of the world's population, 2 morphologically identical but genetically distinct and apparently nonpathogenic Entamoeba species are now recognized as causing most asymptomatic cases. To avoid unnecessary and possibly harmful therapies, clinicians should follow the diagnostic and treatment guidelines of the World Health Organization.
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Affiliation(s)
- Bobbi S Pritt
- Division of Clinical Microbiology, Mayo Clinic, 200 First St SW, Rochester, MN 55905, USA.
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Abstract
In the past few years our understanding of genetic variation within and between species of intestinal parasitic protists has changed significantly. New species names have been assigned and others have been dropped in response to new data. In this review, I summarise these findings and discuss their implications for future studies. In several cases the findings suggest that caution needs to be exercised to prevent premature conclusions being reached.
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Affiliation(s)
- C G Clark
- Infectious and Tropical Disease, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, GB.
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Pérez-Brocal V, Clark CG. Analysis of two genomes from the mitochondrion-like organelle of the intestinal parasite Blastocystis: complete sequences, gene content, and genome organization. Mol Biol Evol 2008; 25:2475-82. [PMID: 18765437 PMCID: PMC2568035 DOI: 10.1093/molbev/msn193] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Acquisition of mitochondria by the ancestor of all living eukaryotes represented a crucial milestone in the evolution of the eukaryotic cell. Nevertheless, a number of anaerobic unicellular eukaryotes have secondarily discarded certain mitochondrial features, leading to modified organelles such as hydrogenosomes and mitosomes via degenerative evolution. These mitochondrion-derived organelles have lost many of the typical characteristics of aerobic mitochondria, including certain metabolic pathways, morphological traits, and, in most cases, the organellar genome. So far, the evolutionary pathway leading from aerobic mitochondria to anaerobic degenerate organelles has remained unclear due to the lack of examples representing intermediate stages. The human parasitic stramenopile Blastocystis is a rare example of an anaerobic eukaryote with organelles that have retained some mitochondrial characteristics, including a genome, whereas they lack others, such as cytochromes. Here we report the sequence and comparative analysis of the organellar genome from two different Blastocystis isolates as well as a comparison to other genomes from stramenopile mitochondria. Analysis of the characteristics displayed by the unique Blastocystis organelle genome gives us an insight into the initial evolutionary steps that may have led from mitochondria to hydrogenosomes and mitosomes.
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Affiliation(s)
- Vicente Pérez-Brocal
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
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Mukherjee C, Clark CG, Lohia A. Entamoeba shows reversible variation in ploidy under different growth conditions and between life cycle phases. PLoS Negl Trop Dis 2008; 2:e281. [PMID: 18714361 PMCID: PMC2500184 DOI: 10.1371/journal.pntd.0000281] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2008] [Accepted: 07/18/2008] [Indexed: 11/18/2022] Open
Abstract
Under axenic growth conditions, trophozoites of Entamoeba histolytica contain heterogenous amounts of DNA due to the presence of both multiple nuclei and different amounts of DNA in individual nuclei. In order to establish if the DNA content and the observed heterogeneity is maintained during different growth conditions, we have compared E. histolytica cells growing in xenic and axenic cultures. Our results show that the nuclear DNA content of E. histolytica trophozoites growing in axenic cultures is at least 10 fold higher than in xenic cultures. Re-association of axenic cultures with their bacterial flora led to a reduction of DNA content to the original xenic values. Thus switching between xenic and axenic growth conditions was accompanied by significant changes in the nuclear DNA content of this parasite. Changes in DNA content during encystation-excystation were studied in the related reptilian parasite E. invadens. During excystation of E. invadens cysts, it was observed that the nuclear DNA content increased approximately 40 fold following emergence of trophozoites in axenic cultures. Based on the observed large changes in nuclear size and DNA content, and the minor differences in relative abundance of representative protein coding sequences, rDNA and tRNA sequences, it appears that gain or loss of whole genome copies may be occurring during changes in the growth conditions. Our studies demonstrate the inherent plasticity and dynamic nature of the Entamoeba genome in at least two species. In contrast to the perception that DNA content of an organism is stable and maintained during different conditions and life cycle stages, new evidence shows that many organisms display changes in their DNA content at different stages of their life cycle. We have earlier identified intra-cellular and inter-cellular differences in DNA content of the protist pathogen Entamoeba histolytica and established that this organism can tolerate large variations in DNA content during axenic culture. In this study we have made an important advancement in the understanding of amoeba biology where we have shown that changes in growth conditions and life cycle stages are accompanied by large differences in DNA content involving gain or loss of whole genome copies. This property may well regulate the outcome of infection and subsequently the disease.
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Affiliation(s)
| | - C. Graham Clark
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Anuradha Lohia
- Department of Biochemistry, Bose Institute, Kolkata, India
- * E-mail:
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Stensvold CR, Alfellani MA, Nørskov-Lauritsen S, Prip K, Victory EL, Maddox C, Nielsen HV, Clark CG. Subtype distribution of Blastocystis isolates from synanthropic and zoo animals and identification of a new subtype. Int J Parasitol 2008; 39:473-9. [PMID: 18755193 DOI: 10.1016/j.ijpara.2008.07.006] [Citation(s) in RCA: 205] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2008] [Revised: 07/22/2008] [Accepted: 07/24/2008] [Indexed: 10/21/2022]
Abstract
Blastocystis isolates from 56 Danish synanthropic and zoo animals, 62 primates primarily from United Kingdom (UK) collections and 16 UK primate handlers were subtyped by PCR, sequencing and phylogenetic analysis. A new subtype (ST) from primates and artiodactyls was identified and designated as Blastocystis sp. ST10. STs isolated from non-human primates (n=70) included ST3 (33%), ST8 (21%), ST2 (16%), ST5 (13%), ST1 (10%), ST4 (4%) and ST10 (3%). A high prevalence of ST8 was seen among primate handlers (25%). This ST is normally very rare in humans, suggesting that acquisition of Blastocystis ST8 infections from primates by their handlers had occurred in these cases. Data from published studies of non-human primates, other mammals and birds were collected and interpreted to generate a comprehensive overview on the ST distribution in such animals. On the basis of information on 438 samples, it was found that Blastocystis from primates belong mainly to ST1, ST2, ST3, ST5 and ST8, ungulates and dogs mainly ST1, ST2, ST3, ST5 and ST10, rodents ST4 and birds mainly ST6 and ST7. The data indicate moderate host specificity, most clearly exemplified by the fact that STs isolated from avian and non-avian hosts rarely overlap.
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Affiliation(s)
- C Rune Stensvold
- Department of Bacteriology, Mycology and Parasitology, Statens Serum Institut, Copenhagen S, Denmark.
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Ali IKM, Clark CG, Petri WA. Molecular epidemiology of amebiasis. Infect Genet Evol 2008; 8:698-707. [PMID: 18571478 DOI: 10.1016/j.meegid.2008.05.004] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2008] [Revised: 04/18/2008] [Accepted: 05/01/2008] [Indexed: 12/13/2022]
Abstract
Entamoeba histolytica, the causative agent of human amebiasis, remains a significant cause of morbidity and mortality in developing countries and is responsible for up to 100,000 deaths worldwide each year. Entamoeba dispar, morphologically indistinguishable from E. histolytica, is more common in humans in many parts of the world. Similarly Entamoeba moshkovskii, which was long considered to be a free-living ameba, is also morphologically identical to E. histolytica and E. dispar, and is highly prevalent in some E. histolytica endemic countries. However, the only species to cause disease in humans is E. histolytica. Most old epidemiological data on E. histolytica are unusable as the techniques employed do not differentiate between the above three Entamoeba species. Molecular tools are now available not only to diagnose these species accurately but also to study intra-species genetic diversity. Recent studies suggest that only a minority of all E. histolytica infections progress to the development of clinical symptoms in the host and there exist population level differences between the E. histolytica strains isolated from the asymptomatic and symptomatic individuals. Nevertheless the underlying factors responsible for variable clinical outcome of infection by E. histolytica remain largely unknown. We anticipate that the recently completed E. histolytica genome sequence and new molecular techniques will rapidly advance our understanding of the epidemiology and pathogenicity of amebiasis.
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Affiliation(s)
- Ibne Karim M Ali
- Division of Infectious Diseases and International Health, University of Virginia Health System, MR4 Building Room 2115, Lane Road, Charlottesville, VA 22908, USA.
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Stechmann A, Hamblin K, Pérez-Brocal V, Gaston D, Richmond GS, van der Giezen M, Clark CG, Roger AJ. Organelles in Blastocystis that blur the distinction between mitochondria and hydrogenosomes. Curr Biol 2008; 18:580-5. [PMID: 18403202 PMCID: PMC2428068 DOI: 10.1016/j.cub.2008.03.037] [Citation(s) in RCA: 122] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2007] [Revised: 03/12/2008] [Accepted: 03/13/2008] [Indexed: 11/25/2022]
Abstract
Blastocystis is a unicellular stramenopile of controversial pathogenicity in humans. Although it is a strict anaerobe, Blastocystis has mitochondrion-like organelles with cristae, a transmembrane potential and DNA. An apparent lack of several typical mitochondrial pathways has led some to suggest that these organelles might be hydrogenosomes, anaerobic organelles related to mitochondria. We generated 12,767 expressed sequence tags (ESTs) from Blastocystis and identified 115 clusters that encode putative mitochondrial and hydrogenosomal proteins. Among these is the canonical hydrogenosomal protein iron-only [FeFe] hydrogenase that we show localizes to the organelles. The organelles also have mitochondrial characteristics, including pathways for amino acid metabolism, iron-sulfur cluster biogenesis, and an incomplete tricarboxylic acid cycle as well as a mitochondrial genome. Although complexes I and II of the electron transport chain (ETC) are present, we found no evidence for complexes III and IV or F1Fo ATPases. The Blastocystis organelles have metabolic properties of aerobic and anaerobic mitochondria and of hydrogenosomes. They are convergently similar to organelles recently described in the unrelated ciliate Nyctotherus ovalis. These findings blur the boundaries between mitochondria, hydrogenosomes, and mitosomes, as currently defined, underscoring the disparate selective forces that shape these organelles in eukaryotes.
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Affiliation(s)
- Alexandra Stechmann
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, B3H 1X5, Canada.
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Ali IKM, Solaymani-Mohammadi S, Akhter J, Roy S, Gorrini C, Calderaro A, Parker SK, Haque R, Petri WA, Clark CG. Tissue invasion by Entamoeba histolytica: evidence of genetic selection and/or DNA reorganization events in organ tropism. PLoS Negl Trop Dis 2008; 2:e219. [PMID: 18398490 PMCID: PMC2274956 DOI: 10.1371/journal.pntd.0000219] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2007] [Accepted: 02/28/2008] [Indexed: 11/19/2022] Open
Abstract
Entamoeba histolytica infection may have various clinical manifestations. Nine out of ten E. histolytica infections remain asymptomatic, while the remainder become invasive and cause disease. The most common form of invasive infection is amebic diarrhea and colitis, whereas the most common extra-intestinal disease is amebic liver abscess. The underlying reasons for the different outcomes are unclear, but a recent study has shown that the parasite genotype is a contributor. To investigate this link further we have examined the genotypes of E. histolytica in stool- and liver abscess-derived samples from the same patients. Analysis of all 18 paired samples (16 from Bangladesh, one from the United States of America, and one from Italy) revealed that the intestinal and liver abscess amebae are genetically distinct. The results suggest either that E. histolytica subpopulations in the same infection show varying organ tropism, or that a DNA reorganization event takes place prior to or during metastasis from intestine to liver. The parasite Entamoeba histolytica can cause serious disease by invading the lining of the large intestine and spreading to other organs of the body. However, most infected individuals never develop symptoms, and it is not clear what determines the different outcomes of infection. Factors that might be having an effect range from the immune response of the infected individual, to concurrent infections with other organisms or genetic differences among the parasites. In the present study we investigated the role of the latter by comparing parasites in the intestine with those that have invaded the liver of the same patient. In all 18 pairs of samples we could detect genetic differences among the parasites. Interpreting the findings is difficult, as we cannot distinguish at present between mutations that have occurred during tissue invasion and genetic diversity that was already present in the population of parasites in the intestine. However, our results strongly support a role for the parasite in determining the outcome of infection with E. histolytica.
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Affiliation(s)
- Ibne Karim M. Ali
- Department of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Division of Infectious Diseases and International Health, University of Virginia Health System, Charlottesville, Virginia, United States of America
| | - Shahram Solaymani-Mohammadi
- Division of Infectious Diseases and International Health, University of Virginia Health System, Charlottesville, Virginia, United States of America
- Division of Intestinal and Genital Protozoal Diseases, Department of Medical Parasitology and Mycology, School of Public Health and Institute of Public Health Research, Tehran University of Medical Sciences, Tehran, Iran
| | - Jasmine Akhter
- International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Shantanu Roy
- Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - Chiara Gorrini
- Department of Pathology and Laboratory Medicine, Section of Microbiology, University of Parma, Parma, Italy
| | - Adriana Calderaro
- Department of Pathology and Laboratory Medicine, Section of Microbiology, University of Parma, Parma, Italy
| | - Sarah K. Parker
- Department of Pediatrics, Division of Infectious Diseases, University of Colorado Health Sciences Center and The Children's Hospital, Aurora, Colorado, United States of America
| | - Rashidul Haque
- International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - William A. Petri
- Division of Infectious Diseases and International Health, University of Virginia Health System, Charlottesville, Virginia, United States of America
- * E-mail: (WAP); (CGC)
| | - C. Graham Clark
- Department of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
- * E-mail: (WAP); (CGC)
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Clark CG, Alsmark UCM, Tazreiter M, Saito-Nakano Y, Ali V, Marion S, Weber C, Mukherjee C, Bruchhaus I, Tannich E, Leippe M, Sicheritz-Ponten T, Foster PG, Samuelson J, Noël CJ, Hirt RP, Embley TM, Gilchrist CA, Mann BJ, Singh U, Ackers JP, Bhattacharya S, Bhattacharya A, Lohia A, Guillén N, Duchêne M, Nozaki T, Hall N. Structure and content of the Entamoeba histolytica genome. Adv Parasitol 2008; 65:51-190. [PMID: 18063096 DOI: 10.1016/s0065-308x(07)65002-7] [Citation(s) in RCA: 133] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The intestinal parasite Entamoeba histolytica is one of the first protists for which a draft genome sequence has been published. Although the genome is still incomplete, it is unlikely that many genes are missing from the list of those already identified. In this chapter we summarise the features of the genome as they are currently understood and provide previously unpublished analyses of many of the genes.
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Affiliation(s)
- C G Clark
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
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Tawari B, Ali IKM, Scott C, Quail MA, Berriman M, Hall N, Clark CG. Patterns of evolution in the unique tRNA gene arrays of the genus Entamoeba. Mol Biol Evol 2007; 25:187-98. [PMID: 17974548 PMCID: PMC2652664 DOI: 10.1093/molbev/msm238] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Genome sequencing of the protistan parasite Entamoeba histolytica HM-1:IMSS revealed that almost all the tRNA genes are organized into tandem arrays that make up over 10% of the genome. The 25 distinct array units contain up to 5 tRNA genes each and some also encode the 5S RNA. Between adjacent genes in array units are complex short tandem repeats (STRs) resembling microsatellites. To investigate the origins and evolution of this unique gene organization, we have undertaken a genome survey to determine the array unit organization in 4 other species of Entamoeba—Entamoeba dispar, Entamoeba moshkovskii, Entamoeba terrapinae, and Entamoeba invadens—and have explored the STR structure in other isolates of E. histolytica. The genome surveys revealed that E. dispar has the same array unit organization as E. histolytica, including the presence and numerical variation of STRs between adjacent genes. However, the individual repeat sequences are completely different to those in E. histolytica. All other species of Entamoeba studied also have tandem arrays of clustered tRNA genes, but the gene composition of the array units often differs from that in E. histolytica/E. dispar. None of the other species' arrays exhibit the complex STRs between adjacent genes although simple tandem duplications are occasionally seen. The degree of similarity in organization reflects the phylogenetic relationships among the species studied. Within individual isolates of E. histolytica most copies of the array unit are uniform in sequence with only minor variation in the number and organization of the STRs. Between isolates, however, substantial differences in STR number and organization can exist although the individual repeat sequences tend to be conserved. The origin of this unique gene organization in the genus Entamoeba clearly predates the common ancestor of the species investigated to date and their function remains unclear.
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Affiliation(s)
- Blessing Tawari
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
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46
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Clark CG, Windsor JJ, Tannich E. On the identification of some Entamoeba species – response to Ponce-Gordo and Martínez-Díaz. Int J Syst Evol Microbiol 2007; 57:1176. [PMID: 17551024 DOI: 10.1099/ijs.0.65107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- C Graham Clark
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Jeffrey J Windsor
- National Public Health Service for Wales Aberystwyth, Bronglais Hospital, Aberystwyth, Ceredigion SY23 1ER, Wales, UK
| | - Egbert Tannich
- Department of Molecular Parasitology, Bernhard Nocht Institute for Tropical Medicine, D-20359 Hamburg, Germany
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Stensvold CR, Suresh GK, Tan KSW, Thompson RCA, Traub RJ, Viscogliosi E, Yoshikawa H, Clark CG. Terminology for Blastocystis subtypes--a consensus. Trends Parasitol 2007; 23:93-6. [PMID: 17241816 DOI: 10.1016/j.pt.2007.01.004] [Citation(s) in RCA: 271] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2006] [Revised: 11/15/2006] [Accepted: 01/12/2007] [Indexed: 11/17/2022]
Abstract
Blastocystis is a ubiquitous enteric protistan parasite that has extensive genetic diversity and infects humans and many other animals. Distinct molecular methodologies developed to detect variation and obtain information about transmission patterns and clinical importance have resulted in a confusing array of terminologies for the identification and designation of Blastocystis subtypes. In this article, we propose a standardization of Blastocystis terminology to improve communication and correlate research results. Based primarily on published small-subunit ribosomal RNA gene analyses, we propose that all mammalian and avian isolates should be designated Blastocystis sp. and assigned to one of nine subtypes.
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Affiliation(s)
- C Rune Stensvold
- Laboratory of Parasitology, Department of Bacteriology, Mycology and Parasitology, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark
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Ali IKM, Mondal U, Roy S, Haque R, Petri WA, Clark CG. Evidence for a link between parasite genotype and outcome of infection with Entamoeba histolytica. J Clin Microbiol 2006; 45:285-9. [PMID: 17122021 PMCID: PMC1829016 DOI: 10.1128/jcm.01335-06] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The factors determining whether a person infected with Entamoeba histolytica develops disease remain obscure. To investigate whether the parasite genome contributes to the outcome, we have investigated the distribution of parasite genotypes among E. histolytica-infected individuals in Bangladesh. Samples were obtained from individuals who either were asymptomatic, had diarrhea/dysentery, or had developed a liver abscess. Genotypes were determined by using six tRNA-linked polymorphic markers, and their distributions among the three sample groups were evaluated. A significant population differentiation in the genotype distribution was found for four of the six individual markers as well as for the combined genotypes, suggesting that the parasite genome does contribute in some way to the outcome of infection with E. histolytica. The markers themselves do not indicate the nature of the underlying genetic differences, but they may be linked to loci that do have an impact on the outcome of infection.
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Affiliation(s)
- Ibne Karim M Ali
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, Great Britain
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Clark CG, Kaffashian F, Tawari B, Windsor JJ, Twigg-Flesner A, Davies-Morel MCG, Blessmann J, Ebert F, Peschel B, Van AL, Jackson CJ, Macfarlane L, Tannich E. New insights into the phylogeny of Entamoeba species provided by analysis of four new small-subunit rRNA genes. Int J Syst Evol Microbiol 2006; 56:2235-2239. [PMID: 16957127 DOI: 10.1099/ijs.0.64208-0] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Sequences of small-subunit rRNA genes have been obtained for four new isolates of Entamoeba. Phylogenetic analyses give new insights into the evolution of these organisms. A novel Entamoeba from pigs in Vietnam that produces uninucleate cysts proved to be unrelated to other uninucleated cyst-producing species. Revival of the name Entamoeba suis for this organism is proposed. Instead of being related to Entamoeba polecki, it shares a recent common ancestor with the non-encysting Entamoeba gingivalis in a lineage that is basal to the tetranucleate cyst-producing clade. This suggests that species producing cysts with four nuclei are descended from an ancestor that produced cysts with a single nucleus. An Entamoeba from a horse was isolated in culture. No cysts were observed in the original stool sample but the sequence is placed unequivocally within the clade of tetranucleate cyst-producing species with no other sequences being specifically related. Revival of the name Entamoeba equi for this organism is proposed. The Entamoeba ecuadoriensis sequence was found to be the most closely related to Entamoeba histolytica and Entamoeba dispar, as predicted, despite the organism having been an environmental isolate originally assigned to Entamoeba moshkovskii. Finally, a partial E. polecki gene sequence from a pig proved to be virtually identical to that of Entamoeba struthionis from an ostrich, suggesting that the latter name is a synonym.
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Affiliation(s)
- C Graham Clark
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Farrokh Kaffashian
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Blessing Tawari
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Jeffrey J Windsor
- National Public Health Service for Wales Aberystwyth, Bronglais Hospital, Aberystwyth, Ceredigion SY23 1ER, UK
| | - Anke Twigg-Flesner
- Institute of Rural Sciences, University of Wales, Aberystwyth, Ceredigion SY23 3AL, UK
| | - Mina C G Davies-Morel
- Institute of Rural Sciences, University of Wales, Aberystwyth, Ceredigion SY23 3AL, UK
| | - Joerg Blessmann
- Department of Molecular Parasitology, Bernhard Nocht Institute for Tropical Medicine, D-20359 Hamburg, Germany
| | - Frank Ebert
- Department of Molecular Parasitology, Bernhard Nocht Institute for Tropical Medicine, D-20359 Hamburg, Germany
| | - Babett Peschel
- Department of Molecular Parasitology, Bernhard Nocht Institute for Tropical Medicine, D-20359 Hamburg, Germany
| | - An Le Van
- Medical College, University of Hué, Hué, Vietnam
| | - Colin J Jackson
- Institute of Rural Sciences, University of Wales, Aberystwyth, Ceredigion SY23 3AL, UK
| | - Lorna Macfarlane
- National Public Health Service for Wales Aberystwyth, Bronglais Hospital, Aberystwyth, Ceredigion SY23 1ER, UK
| | - Egbert Tannich
- Department of Molecular Parasitology, Bernhard Nocht Institute for Tropical Medicine, D-20359 Hamburg, Germany
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Abstract
The internal transcribed spacer (ITS) region of the ribosomal RNA operon is frequently used for detecting sequence variation among closely related species as it is usually homogeneous within strains but evolves more rapidly than ribosomal RNA coding regions. We have studied this region in both genotypes of the human intestinal parasite Dientamoeba fragilis. In contrast to most organisms, we have identified extensive variation between copies of the sequence within the same strain. The ITS occurs in 2 major forms in each genotype but additional heterogeneity is also present within each form. The significance of this finding is unclear, but the only precedent for such variation is in the Apicomplexa, which have multiple dispersed ribosomal RNA operons in contrast to the tandem arrays found in most other eukaryotes.
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Affiliation(s)
- Jeffrey J Windsor
- National Public Health Service for Wales Aberystwyth, Bronglais Hospital, Aberystwyth, Ceredigion, SY23 1ER, Wales, United Kingdom
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