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de Paula Baptista R, Tucker MS, Valente MJ, Srivastava SK, Chehab N, Li A, Shaik JS, Ramirez JD, Rosenthal BM, Khan A. Comparative genomics of Giardia duodenalis sub-assemblage AI beaver (Be-2) and human (WB-C6) strains show remarkable homozygosity, sequence similarity, and conservation of VSP genes. Sci Rep 2024; 14:13582. [PMID: 38866814 PMCID: PMC11169602 DOI: 10.1038/s41598-024-63783-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 06/03/2024] [Indexed: 06/14/2024] Open
Abstract
Giardia duodenalis, a major cause of waterborne infection, infects a wide range of mammalian hosts and is subdivided into eight genetically well-defined assemblages named A through H. However, fragmented genomes and a lack of comparative analysis within and between the assemblages render unclear the molecular mechanisms controlling host specificity and differential disease outcomes. To address this, we generated a near-complete de novo genome of AI assemblage using the Oxford Nanopore platform by sequencing the Be-2 genome. We generated 148,144 long-reads with quality scores of > 7. The final genome assembly consists of only nine contigs with an N50 of 3,045,186 bp. This assembly agrees closely with the assembly of another strain in the AI assemblage (WB-C6). However, a critical difference is that a region previously placed in the five-prime region of Chr5 belongs to Chr4 of Be-2. We find a high degree of conservation in the ploidy, homozygosity, and the presence of cysteine-rich variant-specific surface proteins (VSPs) within the AI assemblage. Our assembly provides a nearly complete genome of a member of the AI assemblage of G. duodenalis, aiding population genomic studies capable of elucidating Giardia transmission, host range, and pathogenicity.
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Affiliation(s)
- Rodrigo de Paula Baptista
- Houston Methodist Research Institute, Houston, TX, 77030, USA
- Department of Medicine, Weill Cornell Medicine College, New York, NY, 10065, USA
| | - Matthew S Tucker
- Animal Parasitic Diseases Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, MD, 20705, USA
| | - Matthew J Valente
- Animal Parasitic Diseases Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, MD, 20705, USA
| | - Subodh K Srivastava
- Animal Parasitic Diseases Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, MD, 20705, USA
| | - Nadya Chehab
- Animal Parasitic Diseases Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, MD, 20705, USA
| | - Alison Li
- Animal Parasitic Diseases Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, MD, 20705, USA
| | - Jahangheer S Shaik
- Insights and Analytics, Applied Data Science and Learning, Data Science Institute, Takeda, Cambridge, MA, 02142, USA
| | - Juan David Ramirez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
- Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Benjamin M Rosenthal
- Animal Parasitic Diseases Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, MD, 20705, USA
| | - Asis Khan
- Animal Parasitic Diseases Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, MD, 20705, USA.
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Genotypic and Epidemiologic Profiles of Giardia duodenalis in Four Brazilian Biogeographic Regions. Microorganisms 2022; 10:microorganisms10050940. [PMID: 35630389 PMCID: PMC9142931 DOI: 10.3390/microorganisms10050940] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/25/2022] [Accepted: 03/28/2022] [Indexed: 02/01/2023] Open
Abstract
Human infections with gut protozoan parasites are neglected and not targeted by specific control initiatives, leading to a knowledge gap concerning their regional diversity and epidemiology. The present study aims to explore Giardia duodenalis genetic diversity and assess the epidemiologic scenario of subclinical infections in different Brazilian biogeographic regions. Cross-sectional surveys (n = 1334 subjects) were conducted in four municipalities in order to obtain fecal samples and socioenvironmental data. Microscopy of non-diarrheal feces and nucleotide sequencing of a β-giardin gene fragment were performed. From a total of 51 samples that could be sequenced, 27 (52.9%) β-giardin sequences were characterized as assemblage A and 24 (47.1%) as assemblage B. In the Amazon, assemblage B was the most frequently detected, predominantly BIII, and with two novel sub-assemblages. Assemblage A predominated in the extra-Amazon region, with five novel sub-assemblages. Prevalence reached 17.8% (64/360) in the Amazon, 8.8% (48/544) in the Atlantic Forest, 7.4% (22/299) in Cerrado and 2.3% (3/131) in the Semiarid. People living in poverty and extreme poverty presented significantly higher positivity rates. In conclusion, subclinical giardiasis is endemic in Brazilian communities in different biogeographic regions, presenting high genetic diversity and a heterogeneous genotypic distribution.
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Zajaczkowski P, Lee R, Fletcher-Lartey SM, Alexander K, Mahimbo A, Stark D, Ellis JT. The controversies surrounding Giardia intestinalis assemblages A and B. CURRENT RESEARCH IN PARASITOLOGY & VECTOR-BORNE DISEASES 2022; 1:100055. [PMID: 35284870 PMCID: PMC8906113 DOI: 10.1016/j.crpvbd.2021.100055] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 10/09/2021] [Indexed: 11/27/2022]
Abstract
Giardia intestinalis continues to be one of the most encountered parasitic diseases around the world. Although more frequently detected in developing countries, Giardia infections nonetheless pose significant public health problems in developed countries as well. Molecular characterisation of Giardia isolates from humans and animals reveals that there are two genetically different assemblages (known as assemblage A and B) that cause human infections. However, the current molecular assays used to genotype G. intestinalis isolates are quite controversial. This is in part due to a complex phenomenon where assemblages are incorrectly typed and underreported depending on which targeted locus is sequenced. In this review, we outline current knowledge based on molecular epidemiological studies and raise questions as to the reliability of current genotyping assays and a lack of a globally accepted method. Additionally, we discuss the clinical symptoms caused by G. intestinalis infection and how these symptoms vary depending on the assemblage infecting an individual. We also introduce the host-parasite factors that play a role in the subsequent clinical presentation of an infected person, and explore which assemblages are most seen globally.
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Affiliation(s)
- Patricia Zajaczkowski
- Faculty of Science, School of Life Sciences, University of Technology Sydney, Australia
| | - Rogan Lee
- Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR, Westmead Hospital, Westmead, New South Wales, Australia.,Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Westmead Hospital, Westmead, NSW, Australia
| | | | - Kate Alexander
- Public Health Unit, South Western Sydney Local Health District, Liverpool, Australia
| | - Abela Mahimbo
- Faculty of Health, School of Public Health, University of Technology Sydney, Australia
| | - Damien Stark
- Department of Microbiology, St Vincent's Hospital Sydney, Darlinghurst, New South Wales, Australia
| | - John T Ellis
- Faculty of Science, School of Life Sciences, University of Technology Sydney, Australia
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Cai W, Ryan U, Xiao L, Feng Y. Zoonotic giardiasis: an update. Parasitol Res 2021; 120:4199-4218. [PMID: 34623485 DOI: 10.1007/s00436-021-07325-2] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 09/16/2021] [Indexed: 12/15/2022]
Abstract
Giardia duodenalis is a common intestinal parasite in various hosts, with the disease giardiasis being a zoonosis. The use of molecular typing tools has improved our understanding of the distribution and zoonotic potential of G. duodenalis genotypes in different animals. The present review summarizes recent data on the distribution of G. duodenalis genotypes in humans and animals in different areas. The dominance of G. duodenalis assemblages A and B in humans and common occurrence of host-adapted assemblages in most domesticated animals suggests that zoonotic giardiasis is probably less common than believed and could be attributed mainly to contact with or contamination from just a few species of animals such as nonhuman primates, equines, rabbits, guinea pigs, chinchillas, and beavers. Future studies should be directed to advanced genetic characterization of isolates from well-designed epidemiological investigations, especially comparative analyses of isolates from humans and animals living in the same household or community. This will likely lead to better understanding of zoonotic transmission of G. duodenalis in different environmental and socioeconomic settings.
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Affiliation(s)
- Weilong Cai
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Una Ryan
- Vector- and Water-Borne Pathogen Research Group, Harry Butler Institute, Murdoch University, Murdoch, WA, 6150, Australia
| | - Lihua Xiao
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China. .,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
| | - Yaoyu Feng
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China. .,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
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Multilocus Genotyping of Giardia duodenalis in Mostly Asymptomatic Indigenous People from the Tapirapé Tribe, Brazilian Amazon. Pathogens 2021; 10:pathogens10020206. [PMID: 33672794 PMCID: PMC7917967 DOI: 10.3390/pathogens10020206] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/01/2021] [Accepted: 02/08/2021] [Indexed: 02/06/2023] Open
Abstract
Little information is available on the occurrence and genetic variability of the diarrhoea-causing enteric protozoan parasite Giardia duodenalis in indigenous communities in Brazil. This cross-sectional epidemiological survey describes the frequency, genotypes, and risk associations for this pathogen in Tapirapé people (Brazilian Amazon) at four sampling campaigns during 2008–2009. Microscopy was used as a screening test, and molecular (PCR and Sanger sequencing) assays targeting the small subunit ribosomal RNA, the glutamate dehydrogenase, the beta-giardin, and the triosephosphate isomerase genes as confirmatory/genotyping methods. Associations between G. duodenalis and sociodemographic and clinical variables were investigated using Chi-squared test and univariable/multivariable logistic regression models. Overall, 574 individuals belonging to six tribes participated in the study, with G. duodenalis prevalence rates varying from 13.5–21.7%. The infection was positively linked to younger age and tribe. Infected children <15 years old reported more frequent gastrointestinal symptoms compared to adults. Assemblage B accounted for three out of four G. duodenalis infections and showed a high genetic diversity. No association between assemblage and age or occurrence of diarrhoea was demonstrated. These data indicate that the most likely source of infection was anthropic and that different pathways (e.g., drinking water) may be involved in the transmission of the parasite.
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Messa A, Köster PC, Garrine M, Gilchrist C, Bartelt LA, Nhampossa T, Massora S, Kotloff K, Levine MM, Alonso PL, Carmena D, Mandomando I. Molecular diversity of Giardia duodenalis in children under 5 years from the Manhiça district, Southern Mozambique enrolled in a matched case-control study on the aetiology of diarrhoea. PLoS Negl Trop Dis 2021; 15:e0008987. [PMID: 33465074 PMCID: PMC7846004 DOI: 10.1371/journal.pntd.0008987] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 01/29/2021] [Accepted: 11/18/2020] [Indexed: 12/23/2022] Open
Abstract
Giardia duodenalis is an enteric parasite commonly detected in children. Exposure to this organism may lead to asymptomatic or symptomatic infection. Additionally, early-life infections by this protozoan have been associated with impaired growth and cognitive function in poor resource settings. The Global Enteric Multicenter Study (GEMS) in Mozambique demonstrated that G. duodenalis was more frequent among controls than in diarrhoeal cases (≥3 loosing stools in the previous 24 hours). However, no molecular investigation was conducted to ascertain the molecular variability of the parasite. Therefore, we describe here the frequency and genetic diversity of G. duodenalis infections in children younger than five years of age with and without diarrhoea from the Manhiça district in southern Mozambique enrolled in the context of GEMS. Genomic DNA from 757 G. duodenalis-positive stool samples by immunoassay collected between 2007-2012, were reanalysed by multiplex PCR targeting the E1-HP and C1-P21 genes for the differentiation of assemblages A and B. Overall, 47% (353) of the samples were successfully amplified in at least one locus. Assemblage B accounted for 90% (319/353) of all positives, followed by assemblage A (8%, 29/353) and mixed A+B infections (1%, 5/353). No association between the presence of a given assemblage and the occurrence of diarrhoea could be demonstrated. A total of 351 samples were further analysed by a multi-locus sequence genotyping (MLSG) approach at the glutamate dehydrogenase (gdh), ß-giardin (bg) and triose phosphate isomerase (tpi) genes. Overall, 63% (222/351) of samples were genotyped and/or sub-genotyped in at least one of the three markers. Sequence analysis revealed the presence of assemblages A (10%; 23/222) and B (90%; 199/222) with high molecular diversity at the nucleotide level within the latter; no mixed infections were identified under the MLSG scheme. Assemblage A sequences were assigned to sub-assemblages AI (0.5%, 1/222), AII (7%, 15/222) or ambiguous AII/AIII (3%, 7/222). Within assemblage B, sequences were assigned to sub-assemblages BIII (13%, 28/222), BIV (14%, 31/222) and ambiguous BIII/BIV (59%, 132/222). BIII/BIV sequences accumulated the majority of the single nucleotide polymorphisms detected, particularly in the form of double peaks at chromatogram inspection. This study demonstrated that the occurrence of gastrointestinal illness (diarrhoea) was not associated to a given genotype of G. duodenalis in Mozambican children younger than five years of age. The assemblage B of the parasite was responsible for nine out of ten infections detected in this paediatric population. The extremely high genetic diversity observed within assemblage B isolates was compatible with an hyperendemic epidemiological scenario where infections and reinfections were common. The obtained molecular data may be indicative of high coinfection rates by different G. duodenalis assemblages/sub-assemblages and/or genetic recombination events, although the exact contribution of both mechanisms to the genetic diversity of the parasite remains unknown.
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Affiliation(s)
- Augusto Messa
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Pamela C. Köster
- Parasitology Reference and Research Laboratory, National Centre for Microbiology, Health Institute Carlos III, Majadahonda, Madrid, Spain
| | - Marcelino Garrine
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Lisbon, Portugal
| | - Carol Gilchrist
- University of Virginia, Charlottesville, Virginia, United States of America
| | - Luther A. Bartelt
- Division of Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Tacilta Nhampossa
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
- Instituto Nacional de Saúde (INS), Ministério da Saúde, Maputo, Mozambique
| | - Sérgio Massora
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Karen Kotloff
- Center for Vaccine Development (CVD), University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Myron M. Levine
- Center for Vaccine Development (CVD), University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Pedro L. Alonso
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
- ISGlobal, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - David Carmena
- Parasitology Reference and Research Laboratory, National Centre for Microbiology, Health Institute Carlos III, Majadahonda, Madrid, Spain
| | - Inácio Mandomando
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
- Instituto Nacional de Saúde (INS), Ministério da Saúde, Maputo, Mozambique
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Saghaug CS, Klotz C, Kallio JP, Aebischer T, Langeland N, Hanevik K. Genetic Diversity of the Flavohemoprotein Gene of Giardia lamblia: Evidence for High Allelic Heterozygosity and Copy Number Variation. Infect Drug Resist 2020; 13:4531-4545. [PMID: 33376360 PMCID: PMC7755369 DOI: 10.2147/idr.s274543] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 10/29/2020] [Indexed: 12/12/2022] Open
Abstract
Purpose The flavohemoprotein (gFlHb) in Giardia plays an important role in managing nitrosative and oxidative stress, and potentially also in virulence and nitroimidazole drug tolerance. The aim of this study was to analyze the genetic diversity of gFlHb in Giardia assemblages A and B clinical isolates. Methods gFlHb genes from 20 cultured clinical Giardia isolates were subjected to PCR amplification and cloning, followed by Sanger sequencing. Sequences of all cloned PCR fragments from each isolate were analyzed for single nucleotide variants (SNVs) and compared to genomic Illumina sequence data. Identical clone sequences were sorted into alleles, and diversity was further analyzed. The number of gFlHb gene copies was assessed by mining PacBio de novo assembled genomes in eight isolates. Homology models for assessment of SNV's potential impact on protein function were created using Phyre2. Results A variable copy number of the gFlHb gene, between two and six copies, depending on isolate, was found. A total of 37 distinct sequences, representing different alleles of the gFlHb gene, were identified in AII isolates, and 41 were identified in B isolates. In some isolates, up to 12 different alleles were found. The total allelic diversity was high for both assemblages (>0.9) and was coupled with a nucleotide diversity of <0.01. The genetic variation (SNVs per CDS length) was 4.8% in sub-assemblage AII and 5.4% in assemblage B. The number of non-synonymous (ns) SNVs was high in gFIHb of both assemblages, 1.6% in A and 3.0% in B, respectively. Some of the identified nsSNV are predicted to alter protein structure and possibly function. Conclusion In this study, we present evidence that gFlHb, a putative protective enzyme against oxidative and nitrosative stress in Giardia, is a variable copy number gene with high allelic diversity. The genetic variability of gFlHb may contribute metabolic adaptability against metronidazole toxicity.
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Affiliation(s)
- Christina S Saghaug
- Department of Clinical Science, University of Bergen, Bergen, Norway.,Norwegian National Advisory Unit on Tropical Infectious Diseases, Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Christian Klotz
- Department of Infectious Diseases, Unit 16 Mycotic and Parasitic Agents and Mycobacteria, Robert Koch-Institute, Berlin, Germany
| | - Juha P Kallio
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Toni Aebischer
- Department of Infectious Diseases, Unit 16 Mycotic and Parasitic Agents and Mycobacteria, Robert Koch-Institute, Berlin, Germany
| | - Nina Langeland
- Department of Clinical Science, University of Bergen, Bergen, Norway.,Norwegian National Advisory Unit on Tropical Infectious Diseases, Department of Medicine, Haukeland University Hospital, Bergen, Norway.,Department of Medicine, Haraldsplass Deaconess Hospital, Bergen, Norway
| | - Kurt Hanevik
- Department of Clinical Science, University of Bergen, Bergen, Norway
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Capewell P, Krumrie S, Katzer F, Alexander CL, Weir W. Molecular Epidemiology of Giardia Infections in the Genomic Era. Trends Parasitol 2020; 37:142-153. [PMID: 33067130 DOI: 10.1016/j.pt.2020.09.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 09/22/2020] [Accepted: 09/22/2020] [Indexed: 12/19/2022]
Abstract
Giardia duodenalis is a major gastrointestinal parasite of humans and animals across the globe. It is also of interest from an evolutionary perspective as it possesses many features that are unique among the eukaryotes, including its distinctive binucleate cell structure. While genomic analysis of a small number of isolates has provided valuable insights, efforts to understand the epidemiology of the disease and the population biology of the parasite have been limited by the molecular tools currently available. We review these tools and assess the impact of affordable and rapid genome sequencing systems increasingly being deployed in diagnostic settings. While these technologies have direct implications for public and veterinary health, they will also improve our understanding of the unique biology of this fascinating parasite.
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Affiliation(s)
- Paul Capewell
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G61 1QH, UK
| | - Sarah Krumrie
- School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G61 1QH, UK
| | - Frank Katzer
- Moredun Research Institute, Pentlands Science Park, Edinburgh, EH26 0PZ, UK
| | - Claire L Alexander
- Scottish Parasitology Diagnostic and Reference Laboratories, Glasgow, G31 2ER, UK
| | - William Weir
- School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G61 1QH, UK.
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Development of a Multilocus Sequence Typing Scheme for Giardia intestinalis. Genes (Basel) 2020; 11:genes11070764. [PMID: 32650382 PMCID: PMC7397270 DOI: 10.3390/genes11070764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 06/27/2020] [Accepted: 06/28/2020] [Indexed: 11/16/2022] Open
Abstract
Giardia intestinalis is an intestinal protozoan most commonly found in humans. It has been grouped into 8 assemblages (A-H). Markers such as the glutamate dehydrogenase gene, triose phosphate isomerase and beta-giardin (β-giardin) have been widely used for genotyping. In addition, different genetic targets have been proposed as a valuable alternative to assess diversity and genetics of this microorganism. Thus, our objective was to evaluate new markers for the study of the diversity and intra-taxa genetic structure of G. intestinalis in silico and in DNA obtained from stool samples. We analysed nine constitutive genes in 80 complete genome sequences and in a group of 24 stool samples from Colombia. Allelic diversity was evaluated by locus and for the concatenated sequence of nine loci that could discriminate up to 53 alleles. Phylogenetic reconstructions allowed us to identify AI, AII and B assemblages. We found evidence of intra- and inter-assemblage recombination events. Population structure analysis showed genetic differentiation among the assemblages analysed.
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Mizuno T, Matey EJ, Bi X, Songok EM, Ichimura H, Tokoro M. Extremely diversified haplotypes observed among assemblage B population of Giardia intestinalis in Kenya. Parasitol Int 2019; 75:102038. [PMID: 31837398 DOI: 10.1016/j.parint.2019.102038] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 12/09/2019] [Accepted: 12/10/2019] [Indexed: 12/15/2022]
Abstract
In molecular epidemiological studies of Giardia intestinalis, an pathogenic intestinal flagellate, due to the presence of allelic sequence heterogeneity (ASH) on the tetraploid genome, the image of haplotype diversity in the field remains uncertain. Here we employed the nine assemblage B positive stool samples, which had previously reported from Kenyan children, for the clonal sequence analysis of multiple gene loci (glutamate dehydrogenase (GDH), triosephosphate isomerase (TPI), and beta-giardin (BG)). The diversified unique assemblage B haplotypes as GDH (n = 67), TPI (n = 84), and BG (n = 62), and the assemblage A haplotypes as GDH (n = 7), TPI (n = 14), and BG (n = 15), which were hidden in the previous direct-sequence results, were detected. Among the assemblage B haplotypes, Bayesian phylogeny revealed multiple statistically significant clusters (9, 7, and 7 clusters for GDH, TPI, and BG, respectively). A part of the clusters (2 for GDH and 1 for BG), which included >4 haplotypes from an individual sample, indicated the presence of co-transmission with multiple strains sharing a recent ancestor. Locus-dependent discrepancies, such as different compositions of derived samples in clusters and different genotyping results for the assemblages, were also observed and considered to be the traces of both intra- and inter-assemblage genetic recombination respectively. Our clonal sequence analysis for giardial population, which applied firstly in Kenya, could reveal the higher rates of ASH far beyond the levels reported in other areas and address the complex population structure. The clonal analysis is indispensable for the molecular field study of G. intestinalis.
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Affiliation(s)
- Tetsushi Mizuno
- Department of Parasitology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | | | - Xiuqiong Bi
- Department of Viral Infection and International Health, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | | | - Hiroshi Ichimura
- Department of Viral Infection and International Health, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Masaharu Tokoro
- Department of Parasitology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan.
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Saghaug CS, Klotz C, Kallio JP, Brattbakk HR, Stokowy T, Aebischer T, Kursula I, Langeland N, Hanevik K. Genetic variation in metronidazole metabolism and oxidative stress pathways in clinical Giardia lamblia assemblage A and B isolates. Infect Drug Resist 2019; 12:1221-1235. [PMID: 31190910 PMCID: PMC6519707 DOI: 10.2147/idr.s177997] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 01/16/2019] [Indexed: 12/12/2022] Open
Abstract
Purpose: Treatment-refractory Giardia cases have increased rapidly within the last decade. No markers of resistance nor a standardized susceptibility test have been established yet, but several enzymes and their pathways have been associated with metronidazole (MTZ) resistant Giardia. Very limited data are available regarding genetic variation in these pathways. We aimed to investigate genetic variation in metabolic pathway genes proposed to be involved in MTZ resistance in recently acquired, cultured clinical isolates. Methods: Whole genome sequencing of 12 assemblage A2 and 8 assemblage B isolates was done, to decipher genomic variation in Giardia. Twenty-nine genes were identified in a literature search and investigated for their single nucleotide variants (SNVs) in the coding/non-coding regions of the genes, either as amino acid changing (non-synonymous SNVs) or non-changing SNVs (synonymous). Results: In Giardia assemblage B, several genes involved in MTZ activation or oxidative stress management were found to have higher numbers of non-synonymous SNVs (thioredoxin peroxidase, nitroreductase 1, ferredoxin 2, NADH oxidase, nitroreductase 2, alcohol dehydrogenase, ferredoxin 4 and ferredoxin 1) than the average variation. For Giardia assemblage A2, the highest genetic variability was found in the ferredoxin 2, ferredoxin 6 and in nicotinamide adenine dinucleotide phosphate (NADPH) oxidoreductase putative genes. SNVs found in the ferredoxins and nitroreductases were analyzed further by alignment and homology modeling. SNVs close to the iron-sulfur cluster binding sites in nitroreductase-1 and 2 and ferredoxin 2 and 4 could potentially affect protein function. Flavohemoprotein seems to be a variable-copy gene, due to higher, but variable coverage compared to other genes investigated. Conclusion: In clinical Giardia isolates, genetic variability is common in important genes in the MTZ metabolizing pathway and in the management of oxidative and nitrosative stress and includes high numbers of non-synonymous SNVs. Some of the identified amino acid changes could potentially affect the respective proteins important in the MTZ metabolism.
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Affiliation(s)
- Christina S Saghaug
- Department of Clinical Science, University of Bergen, Bergen, Hordaland, Norway.,Norwegian National Advisory Unit on Tropical Infectious Diseases, Department of Medicine, Haukeland University Hospital, Bergen, Hordaland, Norway
| | - Christian Klotz
- Department of Infectious Diseases, Unit 16 Mycotic and Parasitic Agents and Mycobacteria, Robert Koch-Institute, Berlin, Germany
| | - Juha P Kallio
- Department of Biomedicine, University of Bergen, Bergen, Hordaland, Norway
| | - Hans-Richard Brattbakk
- Department of Clinical Science, University of Bergen, Bergen, Hordaland, Norway.,Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Hordaland, Norway
| | - Tomasz Stokowy
- Department of Clinical Science, University of Bergen, Bergen, Hordaland, Norway.,Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Hordaland, Norway
| | - Toni Aebischer
- Department of Infectious Diseases, Unit 16 Mycotic and Parasitic Agents and Mycobacteria, Robert Koch-Institute, Berlin, Germany
| | - Inari Kursula
- Department of Biomedicine, University of Bergen, Bergen, Hordaland, Norway.,Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Nina Langeland
- Department of Clinical Science, University of Bergen, Bergen, Hordaland, Norway.,Norwegian National Advisory Unit on Tropical Infectious Diseases, Department of Medicine, Haukeland University Hospital, Bergen, Hordaland, Norway.,Department of Medicine, Haraldsplass Deaconess Hospital, Bergen, Hordaland, Norway
| | - Kurt Hanevik
- Department of Clinical Science, University of Bergen, Bergen, Hordaland, Norway.,Norwegian National Advisory Unit on Tropical Infectious Diseases, Department of Medicine, Haukeland University Hospital, Bergen, Hordaland, Norway
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12
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Genetic variability and transcontinental sharing of Giardia duodenalis infrapopulations determined by glutamate dehydrogenase gene. Acta Trop 2018; 177:146-156. [PMID: 29030042 DOI: 10.1016/j.actatropica.2017.10.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 09/18/2017] [Accepted: 10/02/2017] [Indexed: 12/07/2022]
Abstract
Microevolutionary data of Giardia duodenalis sub-assemblages is a prerequisite for determining the invasion zoonotic patterns of the parasite. To infer transmission patterns that could not be differentiated by the phenotypic features, a population genetic investigation is crucial for the elucidation of the genetic structure of G. duodenalis among the continents. Forty G. duodenalis positive fecal samples were collected from different foci of Northwest Iran. The specimens were subjected to Trichrome staining and sucrose gradient flotation. DNA samples were extracted, amplified, and sequenced by targeting glutamate dehydrogenase (gdh) gene. The global gdh sequences of sub-assemblages AII and BIV retrieved from NCBI GenBank were analyzed to estimate diversity indices, neutrality indices, and gene migration tests. Sequencing analyses indicated various levels of genetic variability of sub-assemblages AII and BIV among the five continents. Sub-assemblage BIV had greater genetic variability (haplotype diversity: 0.975; nucleotide diversity: 0.04246) than sub-assemblage AII. The statistical Fst value demonstrated that the genetic structure of sub-assemblages AII and BIV are moderately differentiated between European-American populations (Fst: 0.05352-0.15182), whereas a significant differentiation was not seen among other geographical population pairs. We conclude that a high gene flow of G. duodenalis sub-assemblages AII and BIV is unequivocally sharing among the continents. The current findings strengthen our knowledge to assess the evolutionary patterns of G. duodenalis in endemic foci of the world and it will become the basis of public health policy to control human giardiasis.
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Spotin A, Moslemzadeh HR, Mahami-Oskouei M, Ahmadpour E, Niyyati M, Hejazi SH, Memari F, Noori J. Phylogeography, genetic variability and structure of Acanthamoeba metapopulations in Iran inferred by 18S ribosomal RNA sequences: A systematic review and meta-analysis. ASIAN PAC J TROP MED 2017; 10:855-863. [PMID: 29080613 DOI: 10.1016/j.apjtm.2017.08.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 07/30/2017] [Accepted: 08/10/2017] [Indexed: 11/26/2022] Open
Abstract
OBJECTIVE To verify phylogeography and genetic structure of Acanthamoeba populations among the Iranian clinical isolates and natural/artificial environments distributed in various regions of the country. METHODS We searched electronic databases including Medline, PubMed, Science Direct, Scopus and Google Scholar from 2005 to 2016. To explore the genetic variability of Acanthamoeba sp, 205 sequences were retrieved from keratitis patients, immunosuppressed cases and environmental sources as of various geographies of Iran. RESULTS T4 genotype was the predominant strain in Iran, and the rare genotypes belonged to T2, T3, T5 (Acanthamoeba lenticulata), T6, T9, T11, T13 and T15 (Acanthamoeba jacobsi). A total of 47 unique haplotypes of T4 were identified. A parsimonious network of the sequence haplotypes demonstrated star-like feature containing haplogroups IR6 (34.1%) and IR7 (31.2%) as the most common haplotypes. In accordance with the analysis of molecular variance, the high value of haplotype diversity (0.612-0.848) of Acanthamoeba T4 represented genetic variability within populations. Neutrality indices of the 18S ribosomal RNA demonstrated negative values in all populations which represented a considerable divergence from neutrality. The majority of genetic diversity belonged to the infected contact lens and dust samples in immunodeficiency and ophthalmology wards, which indicated potential routes for exposure to a pathogenic Acanthamoeba sp. in at-risk individuals. A pairwise fixation index (FST) was from low to high values (0.02433-0.41892). The statistically FST points out that T4 is genetically differentiated between north-west, north-south and central-south metapopulations, but not differentiated between west-central, west-south, central-south, and north-central isolates. CONCLUSIONS An occurrence of IR6 and IR7 displays that possibly a gene flow of Acanthamoeba T4 occurred after the founder effect or bottleneck experience through ecological changes or host mobility. This is the first systematic review and meta-analysis providing new approaches into gene migration and transmission patterns of Acanthamoeba sp, and targeting at the high-risk individuals/sources among the various regions of Iran.
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Affiliation(s)
- Adel Spotin
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | | | - Mahmoud Mahami-Oskouei
- Department of Parasitology and Mycology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ehsan Ahmadpour
- Department of Parasitology and Mycology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Maryam Niyyati
- Department of Medical Parasitology and Mycology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Seyed Hossein Hejazi
- Department of Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Fatemeh Memari
- Department of Medical Parasitology and Mycology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Jafar Noori
- Department of Parasitology and Mycology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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Gabín-García LB, Bartolomé C, Abal-Fabeiro JL, Méndez S, Llovo J, Maside X. Strong genetic structure revealed by multilocus patterns of variation in Giardia duodenalis isolates of patients from Galicia (NW-Iberian Peninsula). INFECTION GENETICS AND EVOLUTION 2016; 48:131-141. [PMID: 27993728 DOI: 10.1016/j.meegid.2016.12.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 11/28/2016] [Accepted: 12/13/2016] [Indexed: 10/20/2022]
Abstract
We report a survey of genetic variation at three coding loci in Giardia duodenalis of assemblages A and B obtained from stool samples of patients from Santiago de Compostela (Galicia, NW-Iberian Peninsula). The mean pooled synonymous diversity for assemblage A was nearly five times lower than for assemblage B (0.77%±0.30% and 4.14%±1.65%, respectively). Synonymous variation in both assemblages was in mutation-drift equilibrium and an excess of low-frequency nonsynonymous variants suggested the action of purifying selection at the three loci. Differences between isolates contributed to 40% and 60% of total genetic variance in assemblages A and B, respectively, which revealed a significant genetic structure. These results, together with the lack of evidence for recombination, support that (i) Giardia assemblages A and B are in demographic equilibrium and behave as two genetically isolated populations, (ii) infections are initiated by a reduced number of individuals, which may be genetically diverse and even belong to different assemblages, and (iii) parasites reproduce clonally within the host. However, the observation of invariant loci in some isolates means that mechanisms for the homogenization of the genetic content of the two diploid nuclei in each individual must exist.
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Affiliation(s)
- Luis B Gabín-García
- Grupo de Medicina Xenómica, Centro de Investigación en Medicina Molecular e Enfermidades Crónicas da Universidade de Santiago de Compostela (CIMUS), Avda. Barcelona s/n, 15782 Santiago, Galicia, Spain; Xenómica Comparada de Parasitos Humanos, Instituto de Investigacións Sanitarias de Santiago (IDIS), Travesia da Choupana s/n, 15706 Santiago, Galicia, Spain.
| | - Carolina Bartolomé
- Grupo de Medicina Xenómica, Centro de Investigación en Medicina Molecular e Enfermidades Crónicas da Universidade de Santiago de Compostela (CIMUS), Avda. Barcelona s/n, 15782 Santiago, Galicia, Spain; Xenómica Comparada de Parasitos Humanos, Instituto de Investigacións Sanitarias de Santiago (IDIS), Travesia da Choupana s/n, 15706 Santiago, Galicia, Spain
| | - José L Abal-Fabeiro
- Grupo de Medicina Xenómica, Centro de Investigación en Medicina Molecular e Enfermidades Crónicas da Universidade de Santiago de Compostela (CIMUS), Avda. Barcelona s/n, 15782 Santiago, Galicia, Spain; Xenómica Comparada de Parasitos Humanos, Instituto de Investigacións Sanitarias de Santiago (IDIS), Travesia da Choupana s/n, 15706 Santiago, Galicia, Spain
| | - Santiago Méndez
- Xenómica Comparada de Parasitos Humanos, Instituto de Investigacións Sanitarias de Santiago (IDIS), Travesia da Choupana s/n, 15706 Santiago, Galicia, Spain; Servizo de Microbioloxía e Parasitoloxía, Complexo Hospitalario Universitario de Santiago, Travesia da Choupana s/n, 15706 Santiago, Galicia, Spain
| | - José Llovo
- Xenómica Comparada de Parasitos Humanos, Instituto de Investigacións Sanitarias de Santiago (IDIS), Travesia da Choupana s/n, 15706 Santiago, Galicia, Spain; Servizo de Microbioloxía e Parasitoloxía, Complexo Hospitalario Universitario de Santiago, Travesia da Choupana s/n, 15706 Santiago, Galicia, Spain
| | - Xulio Maside
- Grupo de Medicina Xenómica, Centro de Investigación en Medicina Molecular e Enfermidades Crónicas da Universidade de Santiago de Compostela (CIMUS), Avda. Barcelona s/n, 15782 Santiago, Galicia, Spain; Xenómica Comparada de Parasitos Humanos, Instituto de Investigacións Sanitarias de Santiago (IDIS), Travesia da Choupana s/n, 15706 Santiago, Galicia, Spain
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Multilocus genotyping of Giardia duodenalis isolates from calves in Oromia Special Zone, Central Ethiopia. INFECTION GENETICS AND EVOLUTION 2016; 43:281-8. [PMID: 27268147 DOI: 10.1016/j.meegid.2016.06.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Revised: 05/28/2016] [Accepted: 06/02/2016] [Indexed: 11/23/2022]
Abstract
Giardia duodenalis is a widespread protozoan parasite that infects human and other mammals. Assessing the zoonotic transmission of the infection requires molecular characterization as there is considerable genetic variation within the species. This study was conducted to identify assemblages of Giardia duodenalis in dairy calves; and to assess the potential role of cattle isolates in zoonotic transmission in central Ethiopia. A total of 449 fecal samples were collected and screened using microscopy and PCR targeting the small-subunit (ssu) rRNA, triose phosphate isomerase (tpi), β-giardin (bg) and glutamate dehydrogenase (gdh) genes. The overall prevalence of Giardia duodenalis in dairy calves was found to be 9.6% (43/449). The prevalence of infection based on sex, age and breed difference was statistically not significant (p>0.05). Genotyping results revealed the presence of assemblage E and assemblage A (AI). The genotypic frequency reported was 95.3% (41/43) for assemblage E and 4.7% (2/43) for assemblage A. There was one mixed infection with assemblages AI and E. Sequence analyses showed the existence of 10 genotypes within assemblage E. One genotype that showed novel nucleotide substitution was identified at the ssu rRNA locus. The other 9 genotypes, 3 at each locus, were identified at the tpi, the bg and the gdh loci with two of the gdh genotypes were novel. Findings of the current study indicate the occurrence of the livestock-specific assemblage E and the potentially zoonotic assemblage A, with the former being more prevalent. Although the zoonotic assemblage was less prevalent, there is a possibility of zoonotic human infection as AI is reported from both animals and humans.
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16
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Thompson R, Ash A. Molecular epidemiology of Giardia and Cryptosporidium infections. INFECTION GENETICS AND EVOLUTION 2016; 40:315-323. [DOI: 10.1016/j.meegid.2015.09.028] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Revised: 09/23/2015] [Accepted: 09/24/2015] [Indexed: 11/28/2022]
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El Basha NR, Zaki MM, Hassanin OM, Rehan MK, Omran D. GiardiaAssemblagesAandBin Diarrheic Patients: A Comparative Study in Egyptian Children and Adults. J Parasitol 2016; 102:69-74. [DOI: 10.1645/14-676] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
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18
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de Lucio A, Martínez-Ruiz R, Merino FJ, Bailo B, Aguilera M, Fuentes I, Carmena D. Molecular Genotyping of Giardia duodenalis Isolates from Symptomatic Individuals Attending Two Major Public Hospitals in Madrid, Spain. PLoS One 2015; 10:e0143981. [PMID: 26641082 PMCID: PMC4671680 DOI: 10.1371/journal.pone.0143981] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 11/11/2015] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The flagellate protozoan Giardia duodenalis is an enteric parasite causing human giardiasis, a major gastrointestinal disease of global distribution affecting both developing and industrialised countries. In Spain, sporadic cases of giardiasis have been regularly identified, particularly in pediatric and immigrant populations. However, there is limited information on the genetic variability of circulating G. duodenalis isolates in the country. METHODS In this longitudinal molecular epidemiological study we report the diversity and frequency of the G. duodenalis assemblages and sub-assemblages identified in 199 stool samples collected from 184 individual with symptoms compatible with giardiasis presenting to two major public hospitals in Madrid for the period December 2013-January 2015. G. duodenalis cysts were initially detected by conventional microscopy and/or immunochomatography on stool samples. Confirmation of the infection was performed by direct immunofluorescence and real-time PCR methods. G. duodenalis assemblages and sub-assemblages were determined by multi-locus genotyping of the glutamate dehydrogenase (GDH) and β-giardin (BG) genes of the parasite. Sociodemographic and clinical features of patients infected with G. duodenalis were also analysed. PRINCIPAL FINDINGS Of 188 confirmed positive samples from 178 giardiasis cases a total of 124 G. duodenalis isolates were successfully typed at the GDH and/or the BG loci, revealing the presence of sub-assemblages BIV (62.1%), AII (15.3%), BIII (4.0%), AI (0.8%), and AIII (0.8%). Additionally, 6.5% of the isolates were only characterised at the assemblage level, being all of them assigned to assemblage B. Discordant genotype results AII/AIII or BIII/BIV were also observed in 10.5% of DNA isolates. A large number of multi-locus genotypes were identified in G. duodenalis assemblage B, but not assemblage A, isolates at both the GDH and BG loci, confirming the high degree of genetic variability observed in other molecular surveys. BIV was the most prevalent genetic variant of G. duodenalis found in individuals with symptomatic giardiasis in the population under study. CONCLUSIONS Human giardiasis is an ongoing public health problem in Spain affecting primarily young children under four years of age but also individuals of all age groups. Our typing and sub-typing results demonstrate that assemblage B is the most prevalent G. duodenalis assemblage circulating in patients with clinical giardiasis in Central Spain. Our analyses also revealed a large genetic variability in assemblage B (but not assemblage A) isolates of the parasite, corroborating the information obtained in similar studies in other geographical regions. We believe that molecular data presented here provide epidemiological evidence at the population level in support of the existence of genetic exchange within assemblages of G. duodenalis.
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Affiliation(s)
- Aida de Lucio
- Parasitology Service, National Centre for Microbiology, Carlos III Health Institute, Majadahonda, Madrid, Spain
| | - Rocío Martínez-Ruiz
- Microbiology and Clinical Parasitology Service, University Hospital Puerta de Hierro Majadahonda, Majadahonda, Madrid, Spain
| | - Francisco J. Merino
- Microbiology Service, University Hospital Severo Ochoa, Leganés, Madrid, Spain
| | - Begoña Bailo
- Parasitology Service, National Centre for Microbiology, Carlos III Health Institute, Majadahonda, Madrid, Spain
| | - María Aguilera
- Parasitology Service, National Centre for Microbiology, Carlos III Health Institute, Majadahonda, Madrid, Spain
| | - Isabel Fuentes
- Parasitology Service, National Centre for Microbiology, Carlos III Health Institute, Majadahonda, Madrid, Spain
| | - David Carmena
- Parasitology Service, National Centre for Microbiology, Carlos III Health Institute, Majadahonda, Madrid, Spain
- * E-mail:
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Choy SH, Mahdy MAK, Al-Mekhlafi HM, Low VL, Surin J. Population expansion and gene flow in Giardia duodenalis as revealed by triosephosphate isomerase gene. Parasit Vectors 2015; 8:454. [PMID: 26373536 PMCID: PMC4572684 DOI: 10.1186/s13071-015-1084-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 09/10/2015] [Indexed: 12/21/2022] Open
Abstract
Background Giardia duodenalis is a protozoan parasite that can cause significant diarrhoeal diseases. Knowledge of population genetics is a prerequisite for ascertaining the invasion patterns of this parasite. In order to infer evolutionary patterns that could not be uncovered based on the morphological features, a population genetic study with the incorporation of molecular marker was carried out to access the genetic structure of G. duodenalis isolated from the Malaysian population and the global populations. Methods A total of 154 samples positive for Giardia, collected from different Malaysian communities, were subjected to DNA amplification and sequencing targeting three genetic loci (tpi, gdh, and bg). The tpi sequences together with sequences from the global data obtained from the NCBI GenBank were used for genetic diversity analyses including identification of haplotypes, haplotype diversity, nucleotide diversity, Tajima’s D and Fu and Li’s D, gene flow and genetic differentiation tests. Results Analysis of the Malaysian and global data showed that assemblages A, B, and E (the most prevalent assemblages in humans and animals), have different levels of genetic diversity. Assemblage B had the highest level of both haplotype diversity and nucleotide diversity, followed by assemblage E. The analysis also revealed population expansion and high gene flow in all assemblages. No clear genetic structure was observed across five continents (i.e., the Americas, Europe, Asia, Australia and Africa). However, median joining network of assemblage B formed a cluster that was exclusively isolated from Asia while other haplotypes were well dispersed across the continents. Conclusions This study provides new insight into the genetic diversity of Giardia assemblages in different geographical regions. The significant result shown by gene flow and genetic differentiation analyses as well as test of neutrality among the populations should have brought a clearer picture to the dynamics and distribution of Giardia infection.
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Affiliation(s)
- Seow Huey Choy
- Department of Parasitology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Mohammed A K Mahdy
- Department of Parasitology, Faculty of Medicine and Health Science, Sana'a University, Sana'a, Yemen. .,Tropical Disease Research Center, University of Science and Technology, Sana'a, Yemen.
| | - Hesham M Al-Mekhlafi
- Department of Parasitology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia. .,Department of Parasitology, Faculty of Medicine and Health Science, Sana'a University, Sana'a, Yemen.
| | - Van Lun Low
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Johari Surin
- Department of Parasitology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia.
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MR (Mre11-Rad50) complex in Giardia duodenalis: In vitro characterization and its response upon DNA damage. Biochimie 2015; 111:45-57. [DOI: 10.1016/j.biochi.2015.01.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Accepted: 01/17/2015] [Indexed: 11/24/2022]
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Karim MR, Wang R, Yu F, Li T, Dong H, Li D, Zhang L, Li J, Jian F, Zhang S, Rume FI, Ning C, Xiao L. Multi-locus analysis of Giardia duodenalis from nonhuman primates kept in zoos in China: geographical segregation and host-adaptation of assemblage B isolates. INFECTION GENETICS AND EVOLUTION 2014; 30:82-88. [PMID: 25530435 DOI: 10.1016/j.meegid.2014.12.013] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Revised: 12/04/2014] [Accepted: 12/09/2014] [Indexed: 10/24/2022]
Abstract
Only a few studies based on single locus characterization have been conducted on the molecular epidemiology of Giardia duodenalis in nonhuman primates (NHPs). The present study was conducted to examine the occurrence and genotype identity of G. duodenalis in NHPs based on multi-locus analysis of the small-subunit ribosomal RNA (SSU rRNA), triose phosphate isomerase (tpi), glutamate dehydrogenase (gdh), and beta-giardin (bg) genes. Fecal specimens were collected from 496 animals of 36 NHP species kept in seven zoos in China and screened for G. duodenalis by tpi-based PCR. G. duodenalis was detected in 92 (18.6%) specimens from 18 NHP species, belonging to assemblage A (n=4) and B (n=88). In positive NHP species, the infection rates ranged from 4.8% to 100%. In tpi sequence analysis, the assemblage A included subtypes A1, A2 and one novel subtype. Multi-locus analysis of the tpi, gdh, and bg genes detected 11 (8 known and 3 new), 6 (3 known and 3 new) and 9 (2 known and 7 new) subtypes in 88, 47 and 35 isolates in assemblage B, respectively. Thirty-two assemblage B isolates with data at all three loci yielded 15 multi-locus genotypes (MLGs), including 2 known and 13 new MLGs. Phylogenetic analysis of concatenated sequences of assemblage B showed that MLGs found here were genetically different from those of humans, NHPs, rabbit and guinea pig in Italy and Sweden. It further indicated that assemblage B isolates in ring-tailed lemurs and squirrel monkeys might be genetically different from those in other NHPs. These data suggest that NHPs are mainly infected with G. duodenalis assemblage B and there might be geographical segregation and host-adaptation in assemblage B in NHPs.
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Affiliation(s)
- Md Robiul Karim
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China
| | - Rongjun Wang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China
| | - Fuchang Yu
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China
| | - Tongyi Li
- Zhengzhou Zoo, Zhengzhou 45000, China
| | - Haiju Dong
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China
| | | | - Longxian Zhang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China.
| | - Junqiang Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China
| | - Fuchun Jian
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China
| | - Sumei Zhang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China
| | - Farzana Islam Rume
- Department of Microbiology, Patuakhali Science and Technology University, Patuakhali 8602, Bangladesh
| | - Changshen Ning
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China
| | - Lihua Xiao
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA.
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Villalobos G, Orozco-Mosqueda GE, Lopez-Perez M, Lopez-Escamilla E, Córdoba-Aguilar A, Rangel-Gamboa L, Olivo-Diaz A, Romero-Valdovinos M, Maravilla P, Martinez-Hernandez F. Suitability of internal transcribed spacers (ITS) as markers for the population genetic structure of Blastocystis spp. Parasit Vectors 2014; 7:461. [PMID: 25274498 PMCID: PMC4203911 DOI: 10.1186/s13071-014-0461-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 09/26/2014] [Indexed: 02/04/2023] Open
Abstract
Background The purpose of this study was to assess the genetic variation and differentiation of Blastocystis subtypes (STs) recovered from symptomatic children by analysing partial sequences of the small subunit rDNA gene region (SSUrDNA) and internal transcribed spacers (1 and 2) plus the 5.8S region (ITS, ITS1 + 5.8S + ITS2) and comparing with isolates from other countries. Findings Faecal samples from 47 Blastocystis-infected children with gastrointestinal symptoms and negative for pathogenic enterobacteria were analysed. PCR was performed on DNA from all the samples to identify Blastocystis STs, amplifying a fragment of SSUrDNA and the ITS region. The amplicons were purified and sequenced, and consensus sequences were submitted to GenBank; afterwards, SSUrDNA sequences were analysed for genetic diversity according to geographic area. Regarding the Blastocystis STs found, 51% were ST1, 23% ST2, 19% ST3 and 2% ST7. For ITS, a haplotype network tree and Bayesian inference revealed the presence of two novel variants of ST1, clustering some sequences into ST1A and ST1B. The values of nucleotide diversity (π) and haplotype polymorphism (θ) for ST1, ST2 and ST3 ranged from 0 to 1, whereas the ratio of genetic differentiation (FST)/migration index (Nm) showed the highest differentiation between Libya and Thailand-Philippines for ST2 (0.282/0.63). In contrast, a high flow gene was observed between Czech Republic-Denmark-Holland-Spain and USA-Mexico-Colombia for ST1 (0.003/84). Conclusion Our data on genetic differentiation and gene flow might explain the differences for the prevalence of Blastocystis STs. Moreover, the ITS region could be used as a genetic marker to assess genetic variation in this parasite.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Pablo Maravilla
- Hospital General "Dr, Manuel Gea Gonzalez", Calzada de Tlalpan 4800, Mexico 14080, DF, Mexico.
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Giardia duodenalis and Cryptosporidium occurrence in Australian sea lions (Neophoca cinerea) exposed to varied levels of human interaction. INTERNATIONAL JOURNAL FOR PARASITOLOGY-PARASITES AND WILDLIFE 2014; 3:269-75. [PMID: 25426423 PMCID: PMC4241535 DOI: 10.1016/j.ijppaw.2014.09.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 09/15/2014] [Accepted: 09/16/2014] [Indexed: 11/21/2022]
Abstract
Giardia and Cryptosporidium are amongst the most common protozoan parasites identified as causing enteric disease in pinnipeds. A number of Giardia assemblages and Cryptosporidium species and genotypes are common in humans and terrestrial mammals and have also been identified in marine mammals. To investigate the occurrence of these parasites in an endangered marine mammal, the Australian sea lion (Neophoca cinerea), genomic DNA was extracted from faecal samples collected from wild populations (n = 271) in Southern and Western Australia and three Australian captive populations (n = 19). These were screened using PCR targeting the 18S rRNA of Giardia and Cryptosporidium. Giardia duodenalis was detected in 28 wild sea lions and in seven captive individuals. Successful sequencing of the 18S rRNA gene assigned 27 Giardia isolates to assemblage B and one to assemblage A, both assemblages commonly found in humans. Subsequent screening at the gdh and β-giardin loci resulted in amplification of only one of the 35 18S rRNA positive samples at the β-giardin locus. Sequencing at the β-giardin locus assigned the assemblage B 18S rRNA confirmed isolate to assemblage AI. The geographic distribution of sea lion populations sampled in relation to human settlements indicated that Giardia presence in sea lions was highest in populations less than 25 km from humans. Cryptosporidium was not detected by PCR screening in either wild colonies or captive sea lion populations. These data suggest that the presence of G. duodenalis in the endangered Australian sea lion is likely the result of dispersal from human sources. Multilocus molecular analyses are essential for the determination of G. duodenalis assemblages and subsequent inferences on transmission routes to endangered marine mammal populations.
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Liu A, Yang F, Shen Y, Zhang W, Wang R, Zhao W, Zhang L, Ling H, Cao J. Genetic analysis of the Gdh and Bg genes of animal-derived Giardia duodenalis isolates in Northeastern China and evaluation of zoonotic transmission potential. PLoS One 2014; 9:e95291. [PMID: 24748379 PMCID: PMC3991589 DOI: 10.1371/journal.pone.0095291] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Accepted: 03/25/2014] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Giardia duodenalis is a common intestinal parasite that infects humans and many other mammals, mainly distributing in some areas with poor sanitation. The proportion of the human giardiasis burden attributable to G. duodenalis of animal origin differs in different geographical areas. In Mainland China, genetic data of the gdh and bg genes of G. duodenalis from animals are only limited in dogs and cats. The aim of the study was to provide information on the genetic characterizations of animal-derived G. duodenalis isolates (from rabbits, sheep and cattle) at both loci in Heilongjiang Province, Northeastern China, and to assess the potential for zoonotic transmission. METHODOLOGY/PRINCIPAL FINDINGS 61 G. duodenalis isolates from animal feces (dairy and beef cattle, sheep and rabbits) in Heilongjiang Province were characterized at the gdh and bg loci in the present study. The gdh and bg gene sequences of sheep-derived G. duodenalis assemblage AI, and the gdh sequences of rabbit-derived G. duodenalis assemblage B had 100% similarity with those from humans, respectively. Novel subtypes of G. duodenalis were identified, with one and seven subtypes for assemblages A and E at the gdh locus, and two and three subtypes for assemblages B and E at the bg locus, respectively. Three pairs of the same bg sequences of assemblage E were observed in sheep and cattle. CONCLUSIONS/SIGNIFICANCE This is the first description of genetic characterizations of the gdh and bg genes of G. duodenalis from rabbits, sheep and cattle in Mainland China. Homology analysis of assemblages AI and B implied the possibility of zoonotic transmission. The novel subtypes of assemblages of G. duodenalis may represent the endemic genetic characteristics of G. duodenalis in Heilongjiang Province, China.
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Affiliation(s)
- Aiqin Liu
- Department of Parasitology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Fengkun Yang
- Department of Parasitology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Yujuan Shen
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory of Parasite and Vector Biology, Ministry of Health, WHO Collaborating Centre for Malaria, Schistosomiasis and Filariasis, Shanghai, China
| | - Weizhe Zhang
- Department of Parasitology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Rongjun Wang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University Zhengzhou, Henan, China
| | - Wei Zhao
- Department of Parasitology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Longxian Zhang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University Zhengzhou, Henan, China
| | - Hong Ling
- Department of Parasitology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Jianping Cao
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory of Parasite and Vector Biology, Ministry of Health, WHO Collaborating Centre for Malaria, Schistosomiasis and Filariasis, Shanghai, China
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Singh N, Bhattacharya A, Bhattacharya S. Homologous Recombination Occurs in Entamoeba and Is Enhanced during Growth Stress and Stage Conversion. PLoS One 2013; 8:e74465. [PMID: 24098652 PMCID: PMC3787063 DOI: 10.1371/journal.pone.0074465] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 08/01/2013] [Indexed: 12/28/2022] Open
Abstract
Homologous recombination (HR) has not been demonstrated in the parasitic protists Entamoeba histolytica or Entamoeba invadens, as no convenient method is available to measure it. However, HR must exist to ensure genome integrity, and possible genetic exchange, especially during stage conversion from trophozoite to cyst. Here we show the up regulation of mitotic and meiotic HR genes in Entamoeba during serum starvation, and encystation. To directly demonstrate HR we use a simple PCR-based method involving inverted repeats, which gives a reliable read out, as the recombination junctions can be determined by sequencing the amplicons. Using this read out, we demonstrate enhanced HR under growth stress in E. histolytica, and during encystation in E. invadens. We also demonstrate recombination between chromosomal inverted repeats. This is the first experimental demonstration of HR in Entamoeba and will help future investigations into this process, and to explore the possibility of meiosis in Entamoeba.
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Affiliation(s)
- Nishant Singh
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Alok Bhattacharya
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Sudha Bhattacharya
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India
- * E-mail:
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Broglia A, Weitzel T, Harms G, Cacció SM, Nöckler K. Molecular typing of Giardia duodenalis isolates from German travellers. Parasitol Res 2013; 112:3449-56. [DOI: 10.1007/s00436-013-3524-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 06/25/2013] [Indexed: 01/28/2023]
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Ryan U, Cacciò SM. Zoonotic potential of Giardia. Int J Parasitol 2013; 43:943-56. [PMID: 23856595 DOI: 10.1016/j.ijpara.2013.06.001] [Citation(s) in RCA: 387] [Impact Index Per Article: 35.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 06/12/2013] [Accepted: 06/14/2013] [Indexed: 11/27/2022]
Abstract
Giardia duodenalis (syn. Giardia lamblia and Giardia intestinalis) is a common intestinal parasite of humans and mammals worldwide. Assessing the zoonotic transmission of the infection requires molecular characterization as there is considerable genetic variation within G. duodenalis. To date eight major genetic groups (assemblages) have been identified, two of which (A and B) are found in both humans and animals, whereas the remaining six (C to H) are host-specific and do not infect humans. Sequence-based surveys of single loci have identified a number of genetic variants (genotypes) within assemblages A and B in animal species, some of which may have zoonotic potential. Multi-locus typing data, however, has shown that in most cases, animals do not share identical multi-locus types with humans. Furthermore, interpretation of genotyping data is complicated by the presence of multiple alleles that generate "double peaks" in sequencing files from PCR products, and by the potential exchange of genetic material among isolates, which may account for the non-concordance in the assignment of isolates to specific assemblages. Therefore, a better understanding of the genetics of this parasite is required to allow the design of more sensitive and variable subtyping tools, that in turn may help unravel the complex epidemiology of this infection.
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Affiliation(s)
- Una Ryan
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, 6150 Western Australia, Australia.
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Nolan MJ, Jex AR, Upcroft JA, Upcroft P, Gasser RB. Barcoding of Giardia duodenalis isolates and derived lines from an established cryobank by a mutation scanning-based approach. Electrophoresis 2013; 32:2075-90. [PMID: 23479788 DOI: 10.1002/elps.201100283] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We barcoded 25 in vitro isolates (representing 92 samples) of Giardia duodenalis from humans and other animals, which have been assembled by the Upcroft team at the Queensland Institute of Medical Research over a period of almost three decades. We used mutation scanning-coupled sequencing of loci in the triosephosphate isomerase, glutamate dehydrogenase and β-giardin genes, combined with phylogenetic analysis, to genetically characterise them. Specifically, the isolates (n514) of G. duodenalis from humans from Australia (AD113; BRIS/83/HEPU/106; BRIS/87/HEPU/713; BRIS/89/HEPU/1003; BRIS/92/HEPU/1541; BRIS/92/HEPU/1590; BRIS/92/HEPU/2443; BRIS/93/HEPU/1706), Malaysia (KL/92/IMR/1106) and Afghanistan (WB), a cat from Australia (BAC2), a sheep from Canada (OAS1) and a sulphur-crested cockatoo from Australia (BRIS/95/HEPU/2041) represented assemblage A (sub-assemblage AI-1, AI-2 or AII-2); isolates (n510) from humans from Australia (BRIS/91/HEPU/1279; BRIS/92/HEPU/2342; BRIS/92/HEPU/2348; BRIS/93/HEPU/1638; BRIS/93/HEPU/1653; BRIS/93/HEPU/1705; BRIS/93/HEPU/1718; BRIS/93/HEPU/1727), Papua New Guinea (BRIS/92/HEPU/1487) and Canada (H7) represented assemblage B (sub-assemblage BIV) and an isolate from cattle from Australia (BRIS/92/HEPU/1709) had a match to assemblage E. Isolate BRIS/90/HEPU/1229 from a human from Australia was shown to represent a mixed population of assemblages A and B. These barcoded isolates (including stocks and derived lines) now allow direct comparisons of experimental data among laboratories and represent a massive resource for transcriptomic, proteomic, metabolic and functional genomic studies using advanced molecular technologies.
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Affiliation(s)
- Matthew J Nolan
- Department of Veterinary Science, The University of Melbourne, Parkville, Victoria 3052, Australia
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Nolan MJ, Jex AR, Koehler AV, Haydon SR, Stevens MA, Gasser RB. Molecular-based investigation of Cryptosporidium and Giardia from animals in water catchments in southeastern Australia. WATER RESEARCH 2013; 47:1726-1740. [PMID: 23357792 DOI: 10.1016/j.watres.2012.12.027] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Revised: 12/10/2012] [Accepted: 12/14/2012] [Indexed: 06/01/2023]
Abstract
There has been no large-scale systematic molecular epidemiological investigation of the waterborne protozoans, Cryptosporidium or Giardia, in southeastern Australia. Here, we explored, for the first time, the genetic composition of these genera in faecal samples from animals in nine Melbourne Water reservoir areas, collected over a period of two-years. We employed PCR-based single-strand conformation polymorphism (SSCP) and phylogenetic analyses of loci (pSSU and pgp60) in the small subunit (SSU) of ribosomal RNA and 60-kDa glycoprotein (gp60) genes to detect and characterise Cryptosporidium, and another locus (ptpi) in the triose-phosphate isomerase (tpi) gene to identify and characterise Giardia. Cryptosporidium was detected in 2.8% of the 2009 samples examined; the analysis of all amplicons defined 14 distinct sequence types for each of pSSU and pgp60, representing Cryptosporidium hominis (genotype Ib - subgenotype IbA10G2R2), Cryptosporidium parvum (genotype IIa - subgenotypes IIaA15G2R1, IIaA19G2R1, IIaA19G3R1, IIaA19G4R1, IIaA20G3R1, IIaA20G4R1, IIaA20G3R2 and IIaA21G3R1), Cryptosporidium cuniculus (genotype Vb - subgenotypes VbA22R4, VbA23R3, VbA24R3, VbA25R4 and VbA26R4), and Cryptosporidium canis, Cryptosporidium fayeri, Cryptosporidium macropodum and Cryptosporidium ubiquitum as well as six new pSSU sequence types. In addition, Giardia was identified in 3.4% of the samples; all 28 distinct ptpi sequence types defined were linked to assemblage A of Giardia duodenalis. Of all 56 sequence types characterised, eight and one have been recorded previously in Cryptosporidium and Giardia, respectively, from humans. In contrast, nothing is known about the zoonotic potential of 35 new genotypes of Cryptosporidium and Giardia recorded here for the first time. Future work aims to focus on estimating the prevalence of Cryptosporidium and Giardia genotypes in humans and a wide range of animals in Victoria and elsewhere in Australia. (Nucleotide sequences reported in this paper are available in the GenBank database under accession nos. KC282952-KC283005).
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Affiliation(s)
- Matthew J Nolan
- Faculty of Veterinary Science, The University of Melbourne, Parkville, Victoria 3010, Australia.
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Xu F, Jerlstrom-Hultqvist J, Andersson JO. Genome-Wide Analyses of Recombination Suggest That Giardia intestinalis Assemblages Represent Different Species. Mol Biol Evol 2012; 29:2895-8. [DOI: 10.1093/molbev/mss107] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Carpenter ML, Assaf ZJ, Gourguechon S, Cande WZ. Nuclear inheritance and genetic exchange without meiosis in the binucleate parasite Giardia intestinalis. J Cell Sci 2012; 125:2523-32. [PMID: 22366460 DOI: 10.1242/jcs.103879] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The protozoan parasite Giardia intestinalis (also known as Giardia lamblia) is a major waterborne pathogen. During its life cycle, Giardia alternates between the actively growing trophozoite, which has two diploid nuclei with low levels of allelic heterozygosity, and the infectious cyst, which has four nuclei and a tough outer wall. Although the formation of the cyst wall has been studied extensively, we still lack basic knowledge about many fundamental aspects of the cyst, including the sources of the four nuclei and their distribution during the transformation from cyst into trophozoite. In this study, we tracked the identities of the nuclei in the trophozoite and cyst using integrated nuclear markers and immunofluorescence staining. We demonstrate that the cyst is formed from a single trophozoite by a mitotic division without cytokinesis and not by the fusion of two trophozoites. During excystation, the cell completes cytokinesis to form two daughter trophozoites. The non-identical nuclear pairs derived from the parent trophozoite remain associated in the cyst and are distributed to daughter cells during excystation as pairs. Thus, nuclear sorting (such that each daughter cell receives a pair of identical nuclei) does not appear to be a mechanism by which Giardia reduces heterozygosity between its nuclei. Rather, we show that the cyst nuclei exchange chromosomal genetic material, perhaps as a way to reduce heterozygosity in the absence of meiosis and sex, which have not been described in Giardia. These results shed light on fundamental aspects of the Giardia life cycle and have implications for our understanding of the population genetics and cell biology of this binucleate parasite.
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Affiliation(s)
- Meredith L Carpenter
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
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Double peaks reveal rare diplomonad sex. Trends Parasitol 2012; 28:46-52. [DOI: 10.1016/j.pt.2011.11.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Revised: 11/16/2011] [Accepted: 11/17/2011] [Indexed: 01/23/2023]
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Siripattanapipong S, Leelayoova S, Mungthin M, Thompson RCA, Boontanom P, Saksirisampant W, Tan-ariya P. Clonal diversity of the glutamate dehydrogenase gene in Giardia duodenalis from Thai isolates: evidence of genetic exchange or mixed infections? BMC Microbiol 2011; 11:206. [PMID: 21933419 PMCID: PMC3191338 DOI: 10.1186/1471-2180-11-206] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Accepted: 09/20/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The glutamate dehydrogenase gene (gdh) is one of the most popular and useful genetic markers for the genotypic analysis of Giardia duodenalis (syn. G. lamblia, G. intestinalis), the protozoan that widely causes enteric disease in humans. To determine the distribution of genotypes of G. duodenalis in Thai populations and to investigate the extent of sequence variation at this locus, 42 fecal samples were collected from 3 regions of Thailand i.e., Central, Northern, and Eastern regions. All specimens were analyzed using PCR-based genotyping and recombinant subcloning methods. RESULTS The results showed that the prevalence of assemblages A and B among these populations was approximately equal, 20 (47.6%) and 22 (52.4%), respectively. Sequence analysis revealed that the nucleotide diversity of assemblage B was significantly greater than that in assemblage A. Among all assemblage B positive specimens, the allelic sequence divergence within isolates was detected. Nine isolates showed mixed alleles, ranged from three to nine distinct alleles per isolate. Statistical analysis demonstrated the occurrence of genetic recombination within subassemblages BIII and BIV was likely. CONCLUSION This study supports increasing evidence that G. duodenalis has the potential for genetic exchange.
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Affiliation(s)
- Suradej Siripattanapipong
- Department of Microbiology, Faculty of Science, Mahidol University, Rama VI Rd., Bangkok, 10400, Thailand
| | - Saovanee Leelayoova
- Department of Parasitology, Phramongkutklao College of Medicine, Rajawithi Rd., Bangkok, 10400, Thailand
| | - Mathirut Mungthin
- Department of Parasitology, Phramongkutklao College of Medicine, Rajawithi Rd., Bangkok, 10400, Thailand
| | - RC Andrew Thompson
- WHO Collaborating Centre for the Molecular Epidemiology of Parasitic Infections, School of Veterinary and Biomedical Sciences, Murdoch University, South Street, Murdoch, Western Australia, 6150, Australia
| | - Parima Boontanom
- Department of Parasitology, Phramongkutklao College of Medicine, Rajawithi Rd., Bangkok, 10400, Thailand
| | - Wilai Saksirisampant
- Department of Parasitology, Faculty of Medicine, Chulalongkorn University, Rama IV Rd., Bangkok, 10330, Thailand
| | - Peerapan Tan-ariya
- Department of Microbiology, Faculty of Science, Mahidol University, Rama VI Rd., Bangkok, 10400, Thailand
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Limitations of tpi and bg genes sub-genotyping for characterization of human Giardia duodenalis isolates. Parasitol Int 2011; 60:327-30. [DOI: 10.1016/j.parint.2011.05.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Revised: 04/30/2011] [Accepted: 05/17/2011] [Indexed: 11/22/2022]
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Zoonotic potential and molecular epidemiology of Giardia species and giardiasis. Clin Microbiol Rev 2011; 24:110-40. [PMID: 21233509 DOI: 10.1128/cmr.00033-10] [Citation(s) in RCA: 780] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Molecular diagnostic tools have been used recently in assessing the taxonomy, zoonotic potential, and transmission of Giardia species and giardiasis in humans and animals. The results of these studies have firmly established giardiasis as a zoonotic disease, although host adaptation at the genotype and subtype levels has reduced the likelihood of zoonotic transmission. These studies have also identified variations in the distribution of Giardia duodenalis genotypes among geographic areas and between domestic and wild ruminants and differences in clinical manifestations and outbreak potentials of assemblages A and B. Nevertheless, our efforts in characterizing the molecular epidemiology of giardiasis and the roles of various animals in the transmission of human giardiasis are compromised by the lack of case-control and longitudinal cohort studies and the sampling and testing of humans and animals living in the same community, the frequent occurrence of infections with mixed genotypes and subtypes, and the apparent heterozygosity at some genetic loci for some G. duodenalis genotypes. With the increased usage of multilocus genotyping tools, the development of next-generation subtyping tools, the integration of molecular analysis in epidemiological studies, and an improved understanding of the population genetics of G. duodenalis in humans and animals, we should soon have a better appreciation of the molecular epidemiology of giardiasis, the disease burden of zoonotic transmission, the taxonomy status and virulences of various G. duodenalis genotypes, and the ecology of environmental contamination.
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Genotypic characterisation of Giardia from domestic dogs in the USA. Vet Parasitol 2011; 177:28-32. [DOI: 10.1016/j.vetpar.2010.11.029] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Revised: 11/11/2010] [Accepted: 11/15/2010] [Indexed: 11/23/2022]
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Wielinga C, Ryan U, Andrew Thompson RC, Monis P. Multi-locus analysis of Giardia duodenalis intra-Assemblage B substitution patterns in cloned culture isolates suggests sub-Assemblage B analyses will require multi-locus genotyping with conserved and variable genes. Int J Parasitol 2010; 41:495-503. [PMID: 21176781 DOI: 10.1016/j.ijpara.2010.11.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2010] [Revised: 11/23/2010] [Accepted: 11/30/2010] [Indexed: 10/18/2022]
Abstract
Recent research concerning Giardia duodenalis has focused on resolving possible sub-assemblages within Assemblages A and B to better understand host-specific and zoonotic relationships. In the present study nine cloned, cultured, Assemblage B isolates were used to investigate the intra-Assemblage B substitution patterns of conserved (ssrDNA, ef, h2b, h4) and variable (tpi, gdh, bg) genes to assess their suitability for further application to sub-assemblage analyses. The resolution of each gene was found to be proportional to its substitution rate and for the genetically narrow sample set examined, the variable genes best represented the consensus phylogeny while the conserved genes only established fractions. However it was demonstrated that the spectra of conserved and variable genes were required to ensure accuracy of inferred phylogeny and it was therefore concluded that further research into sub-Assemblage B groups would require a mixture of conserved and variable genes for the multi-locus analyses of this genetically broad assemblage.
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Affiliation(s)
- Caroline Wielinga
- Division of Veterinary and Biomedical Sciences, Murdoch University, South Street, Murdoch, WA 6150, Australia.
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Kowalewski MM, Salzer JS, Deutsch JC, Raño M, Kuhlenschmidt MS, Gillespie TR. Black and gold howler monkeys (Alouatta caraya) as sentinels of ecosystem health: patterns of zoonotic protozoa infection relative to degree of human-primate contact. Am J Primatol 2010; 73:75-83. [DOI: 10.1002/ajp.20803] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Risk of human infection with Giardia duodenalis from cats in Japan and genotyping of the isolates to assess the route of infection in cats. Parasitology 2010; 138:493-500. [PMID: 21040620 DOI: 10.1017/s0031182010001459] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The number of facilities in which customers make contact with cats before eating and drinking, called 'cat cafés', has recently increased in Tokyo, Japan. In a survey to clarify the possibility of zoonotic transmission in Giardia duodenalis, the infection rates of G. duodenalis in 321 stool samples of cats from 16 cat cafés, 31 pet shops, and the Animal Care and Consultation Center of Tokyo were 19·1% (22/115), 1·2% (1/85), and 2·5% (3/121), respectively. In the molecular analysis of 26 G. duodenalis isolates, 6 samples from 2 cat cafés belonged to the zoonotic genotype assemblage A I, and 20 other samples were of assemblage F. Moreover, phylogenetic analysis of glutamate dehydrogenase (GDH) and triosephosphate isomerase (TPI) genes of the 20 assemblage F isolates revealed 2 major lineages. The 6 assemblage A isolates belonged to the same cluster with regard to the GDH gene; however, 2 of the 6 isolates belonged to a different cluster from the other 4 isolates with regard to the TPI gene. Therefore, a risk of transmission from cats to humans is suggested because of the detection of zoonotic Giardia genotypes in cat cafés.
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Ash A, Lymbery A, Lemon J, Vitali S, Thompson RCA. Molecular epidemiology of Giardia duodenalis in an endangered carnivore--the African painted dog. Vet Parasitol 2010; 174:206-12. [PMID: 20851525 DOI: 10.1016/j.vetpar.2010.08.034] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2010] [Revised: 08/12/2010] [Accepted: 08/23/2010] [Indexed: 11/19/2022]
Abstract
The African painted dog (Lycaon pictus) is an endangered carnivore of sub-Saharan Africa. To assist in conservation efforts a parasitological survey was conducted on wild and captive populations. Faecal samples were collected and examined for the presence of parasites using traditional microscopy techniques. The protozoan Giardia duodenalis was identified at a prevalence of approximately 26% in the wild populations and 62% in the captive population. Molecular characterisation of these isolates using three loci, 18S rRNA, β-giardin and the glutamate dehydrogenase gene revealed the zoonotic assemblages A and B existed in high proportions in both populations. The dog assemblages C and D were rarely observed. The identification of the zoonotic genotype suggests this species has the potential to act as a reservoir for human infections. Zoonotic transmission may be possible in captive populations due to the close interaction with humans however, in wild populations anthropozoonotic transmission seems more likely. This study is the first to observe G. duodenalis in the African painted dog and to identify a possible emerging disease in this wild carnivore.
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Affiliation(s)
- A Ash
- WHO Collaborating Centre for the Molecular Epidemiology of Parasitic Infections and State Agricultural Biotechnology Centre, School of Veterinary and Biomedical Sciences, Murdoch University, South Street, Western Australia 6150, Australia
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Lasek-Nesselquist E, Welch DM, Sogin ML. The identification of a new Giardia duodenalis assemblage in marine vertebrates and a preliminary analysis of G. duodenalis population biology in marine systems. Int J Parasitol 2010; 40:1063-74. [PMID: 20361967 DOI: 10.1016/j.ijpara.2010.02.015] [Citation(s) in RCA: 151] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2009] [Revised: 02/24/2010] [Accepted: 02/26/2010] [Indexed: 10/19/2022]
Abstract
Giardia duodenalis is an intestinal parasite of many vertebrates. The presence of G. duodenalis in the marine environment due to anthropogenic and wildlife activity is well documented, including the contributions from untreated sewage and storm water, agricultural run-off and droppings from terrestrial animals. Recently, studies have detected this protistan parasite in the faeces of marine vertebrates such as whales, dolphins, seals and shore birds. To explore the population biology of G. duodenalis in marine life, we determined the prevalence of G. duodenalis in two species of seal (Halichoerus grypus, Phoca vitulina vitulina and Phoca vitulina richardsi) from the east and west coasts of the USA, sequenced two loci from G. duodenalis-positive samples to assess molecular diversity and examined G. duodenalis distribution amongst these seals and other marine vertebrates along the east coast. We found a significant difference in the presence of G. duodenalis between east and west coast seal species. Only the zoonotic lineages of G. duodenalis, Assemblages A and B and a novel lineage, which we designated as Assemblage H, were identified in marine vertebrates. Assemblages A and B are broadly distributed geographically and show a lack of host specificity. Only grey seal (Halichoerus grypus) samples and one gull sample (Larus argentatus) from a northern location of Cape Cod, Massachusetts, USA, showed the presence of Assemblage H haplotypes; only one other study of harbour seals from the Puget Sound region of Washington, USA previously recorded the presence of an Assemblage H haplotype. Assemblage H sequences form a monophyletic clade that appears as divergent from the other seven Assemblages of G. duodenalis as these assemblages are from each other. The discovery of a previously uncharacterised lineage of G. duodenalis suggests that this parasite has more genetic diversity and perhaps a larger host range than previously believed.
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Affiliation(s)
- Erica Lasek-Nesselquist
- Josephine Bay Paul Center for Comparative Evolution and Molecular Biology, MBL, 7 MBL St., Woods Hole, MA 02543, USA.
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Birky CW. Giardia Sex? Yes, but how and how much? Trends Parasitol 2010; 26:70-4. [DOI: 10.1016/j.pt.2009.11.007] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2009] [Revised: 11/11/2009] [Accepted: 11/20/2009] [Indexed: 11/25/2022]
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Genotyping of Giardia duodenalis cysts by new real-time PCR assays for detection of mixed infections in human samples. Appl Environ Microbiol 2010; 76:1895-901. [PMID: 20080999 DOI: 10.1128/aem.02305-09] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Of the seven genetic groups, or assemblages, currently recognized in the Giardia duodenalis species complex, only assemblages A and B are associated with human infection, but they also infect other mammals. Recent investigations have suggested the occurrence of genetic exchanges among isolates of G. duodenalis, and the application of assemblage-specific PCR has shown both assemblages A and B in a significant number of human infections. In this work, three real-time quantitative (qPCR) assays were developed to target the G. duodenalis triose phosphate isomerase, glutamate dehydrogenase, and open reading frame C4 sequences. Primers were designed to allow the specific amplification of the DNA of assemblage A or B and to generate products distinguishable by their melting curves or, after qPCR, by their sequences, sizes, or restriction patterns. The assays showed full specificity and detected DNA from a single trophozoite (4 to 8 target copies). We applied these assays, as well as a TaqMan assay that targets the beta-giardin gene, to genomic DNA extracted from 30 human stools and to Giardia cysts purified by immunomagnetic capture from the same samples. Simultaneous detection of both assemblages was observed in a large number of DNAs extracted from stools, and experiments on the cysts purified from the same samples showed that this was essentially attributable to mixed infections, as only one assemblage was detected when dilutions of cysts were tested. In a few cases, detection of both assemblages was observed even when single cysts were tested. This result, which suggests the presence of recombinants, needs to be confirmed using more accurate methods for cyst separation and enumeration. The assays described in this study can be used to detect Giardia cysts infectious to humans in samples from animals and in water and food.
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Nolan MJ, Jex AR, Pangasa A, Young ND, Campbell AJ, Stevens M, Gasser RB. Analysis of nucleotide variation within the triose-phosphate isomerase gene ofGiardia duodenalisfrom sheep and its zoonotic implications. Electrophoresis 2010; 31:287-98. [DOI: 10.1002/elps.200900480] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Sprong H, Cacciò SM, van der Giessen JWB. Identification of zoonotic genotypes of Giardia duodenalis. PLoS Negl Trop Dis 2009; 3:e558. [PMID: 19956662 PMCID: PMC2777335 DOI: 10.1371/journal.pntd.0000558] [Citation(s) in RCA: 284] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2009] [Accepted: 10/26/2009] [Indexed: 11/24/2022] Open
Abstract
Giardia duodenalis, originally regarded as a commensal organism, is the etiologic agent of giardiasis, a gastrointestinal disease of humans and animals. Giardiasis causes major public and veterinary health concerns worldwide. Transmission is either direct, through the faecal-oral route, or indirect, through ingestion of contaminated water or food. Genetic characterization of G. duodenalis isolates has revealed the existence of seven groups (assemblages A to G) which differ in their host distribution. Assemblages A and B are found in humans and in many other mammals, but the role of animals in the epidemiology of human infection is still unclear, despite the fact that the zoonotic potential of Giardia was recognised by the WHO some 30 years ago. Here, we performed an extensive genetic characterization of 978 human and 1440 animal isolates, which together comprise 3886 sequences from 4 genetic loci. The data were assembled into a molecular epidemiological database developed by a European network of public and veterinary health Institutions. Genotyping was performed at different levels of resolution (single and multiple loci on the same dataset). The zoonotic potential of both assemblages A and B is evident when studied at the level of assemblages, sub-assemblages, and even at each single locus. However, when genotypes are defined using a multi-locus sequence typing scheme, only 2 multi-locus genotypes (MLG) of assemblage A and none of assemblage B appear to have a zoonotic potential. Surprisingly, mixtures of genotypes in individual isolates were repeatedly observed. Possible explanations are the uptake of genetically different Giardia cysts by a host, or subsequent infection of an already infected host, likely without overt symptoms, with a different Giardia species, which may cause disease. Other explanations for mixed genotypes, particularly for assemblage B, are substantial allelic sequence heterogeneity and/or genetic recombination. Although the zoonotic potential of G. duodenalis is evident, evidence on the contribution and frequency is (still) lacking. This newly developed molecular database has the potential to tackle intricate epidemiological questions concerning protozoan diseases. Giardia duodenalis is a parasite causing a gastrointestinal disease in humans, pets, livestock, and wildlife. The role of animals in human disease is unclear, because Giardia from humans and animals is morphologically indistinguishable. An international consortium of both veterinary and public health institutions built a web-based database, where molecular and epidemiological data are combined. After extensive genetic characterization, the zoonotic potential of Giardia became evident, but data on frequency and role in epidemiology is (still) lacking. Surprisingly, mixtures of Giardia genotypes in individual hosts were frequently observed, and have important implications for the etiology of Giardiasis. Possible explanations are the uptake of mixtures of Giardia genotypes by one host, or subsequent infection of an already infected host, likely without overt symptoms, with a different Giardia species, which may cause disease. We demonstrated that collaborative, human and veterinary health integrated databases have the potential to tackle intricate epidemiological questions concerning parasitic diseases, as was demonstrated for G. duodenalis in the present study.
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Affiliation(s)
- Hein Sprong
- Laboratory for Zoonoses and Environmental Microbiology, National Institute for Public Health and Environment (RIVM), Bilthoven, The Netherlands
- * E-mail: (HS); (JWBvdG)
| | - Simone M. Cacciò
- Department of Infectious, Parasitic and Immunomediated Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Joke W. B. van der Giessen
- Laboratory for Zoonoses and Environmental Microbiology, National Institute for Public Health and Environment (RIVM), Bilthoven, The Netherlands
- * E-mail: (HS); (JWBvdG)
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Lebbad M, Mattsson JG, Christensson B, Ljungström B, Backhans A, Andersson JO, Svärd SG. From mouse to moose: multilocus genotyping of Giardia isolates from various animal species. Vet Parasitol 2009; 168:231-9. [PMID: 19969422 DOI: 10.1016/j.vetpar.2009.11.003] [Citation(s) in RCA: 170] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2009] [Revised: 10/23/2009] [Accepted: 11/03/2009] [Indexed: 11/19/2022]
Abstract
Giardia intestinalis is a protozoan parasite that consists of seven genetically distinct assemblages (A to G). Assemblage A and B parasites have been detected in a wide range of animals including humans, while the other assemblages (C to G) appear to have a narrower host range. However, the knowledge about zoonotic transmission of G. intestinalis is limited. To address this question, 114 Giardia isolates from various animals in Sweden including pets, livestock, wildlife and captive non-human primates were investigated by a sequence-based analysis of three genes (beta-giardin, glutamate dehydrogenase and triose phosphate isomerase). Assemblage A infections were detected in nine ruminants, five cats and one dog, while three sheep were infected with both assemblages A and E. Multilocus genotypes (MLGs) were defined for assemblage A, and three of these MLGs have previously been detected in Giardia isolates from humans. The newly described sub-assemblage AIII, until now reported mainly in wild hoofed animals, was found in one cat isolate. Assemblage B occurred in three monkeys, one guinea pig and one rabbit. The rabbit isolate exhibited sequences at all three loci previously detected in human isolates. The non-zoonotic assemblages C, D, E, F or G were found in the remaining 83 G. intestinalis isolates, which were successfully amplified and genotyped, generating a wide variety of both novel and known sub-genotypes. Double peaks in chromatograms were seen in assemblage B, C, D and E isolates but were never observed in assemblage A, F and G isolates, which can reflect differences in allelic sequence divergence. No evidence of genetic exchange between assemblages was detected. The study shows that multilocus genotyping of G. intestinalis is a highly discriminatory and useful tool in the determination of zoonotic sub-groups within assemblage A, but less valuable for subtyping assemblages B, C, D and E due to the high frequency of double peaks in the chromatograms. The obtained data also suggest that zoonotic transmission of assemblages A and B might occur to a limited extent in Sweden.
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Affiliation(s)
- Marianne Lebbad
- Department of Parasitology, Mycology and Environmental Microbiology, Swedish Institute for Infectious Disease Control, Solna, Sweden.
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Kosuwin R, Putaporntip C, Pattanawong U, Jongwutiwes S. Clonal diversity in Giardia duodenalis isolates from Thailand: evidences for intragenic recombination and purifying selection at the beta giardin locus. Gene 2009; 449:1-8. [PMID: 19796671 DOI: 10.1016/j.gene.2009.09.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2009] [Revised: 09/04/2009] [Accepted: 09/23/2009] [Indexed: 10/20/2022]
Abstract
The beta giardin locus of Giardia duodenalis encodes a structural component of ventral disc and exhibits sequence variation among isolates rendering it a useful marker for genotypic analysis. To determine the distribution of genotypes of G. duodenalis in Thailand and to explore the extent of sequence variation in this locus, we deployed the PCR-RFLP method and sequence analysis of recombinant subclones from 30 clinical isolates. In total, assemblage B was more prevalent than assemblage A. Sequence analysis revealed that 13 isolates had clonal mixtures, comprising three to five distinct sequences per isolate. Nucleotide diversity of assemblage B was greater than that of assemblage A. A striking transitional bias was noted at the first and the third positions of codons in both assemblages; however, they differed in the patterns of nucleotide diversity at 0-fold and 4-fold-degenerate sites. Most amino acid exchanges were conservative in terms of polarity, charge and volume. Both assemblages have evolved under purifying selection as evidenced by a significantly greater number of mean synonymous substitutions per synonymous site (d(S)) than that of nonsynonymous substitutions per nonsynonymous site (d(N)) as well as significant negative Tajima's D values and its related statistics. The significant negative Tajima's D test at nonsynonymous sites further suggests that elimination of slightly deleterious mutations at these sites by purifying selection is ongoing as predicted in the nearly neutral theory. Furthermore, a minimum number of seven recombination sites was detected by the four gamete test in assemblage B, consistent with previous reports on meiotic recombination in G. duodenalis. Therefore, accurate subassemblage assignment of clinical isolates that has practical consequence for disease control could be complicated by the presence of intra-isolate clonal diversity and interallelic recombination.
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Affiliation(s)
- Rattiporn Kosuwin
- Molecular Biology of Malaria and Opportunistic Parasites Research Unit, Department of Parasitology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
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Abstract
SUMMARYGiardiasis is a common waterborne gastrointestinal illness. In 2007, a community giardiasis outbreak occurred in New Hampshire, USA. We conducted a cohort study to identify risk factors for giardiasis, and stool and environmental samples were analysed. Consuming tap water was significantly associated with illness (risk ratio 4·7, 95% confidence interval 1·5–14·4). Drinking-water samples were coliform-contaminated and a suspectGiardiacyst was identified in a home water filter. One well was coliform-contaminated, and testing indicated that it was potentially under the influence of surface water. The well was located 12·5 m from aGiardia-contaminated brook, although the genotype differed from clinical specimens. Local water regulations require well placement at least 15 m from surface water. This outbreak, which caused illness in 31 persons, represents the largest community drinking-water-associated giardiasis outbreak in the USA in 10 years. Adherence to well placement regulations might have prevented this outbreak.
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Ortega-Pierres G, Smith HV, Cacciò SM, Thompson RA. New tools provide further insights into Giardia and Cryptosporidium biology. Trends Parasitol 2009; 25:410-6. [DOI: 10.1016/j.pt.2009.06.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2009] [Revised: 06/02/2009] [Accepted: 06/12/2009] [Indexed: 12/12/2022]
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Franzén O, Jerlström-Hultqvist J, Castro E, Sherwood E, Ankarklev J, Reiner DS, Palm D, Andersson JO, Andersson B, Svärd SG. Draft genome sequencing of giardia intestinalis assemblage B isolate GS: is human giardiasis caused by two different species? PLoS Pathog 2009; 5:e1000560. [PMID: 19696920 PMCID: PMC2723961 DOI: 10.1371/journal.ppat.1000560] [Citation(s) in RCA: 192] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2009] [Accepted: 07/27/2009] [Indexed: 01/05/2023] Open
Abstract
Giardia intestinalis is a major cause of diarrheal disease worldwide and two major Giardia genotypes, assemblages A and B, infect humans. The genome of assemblage A parasite WB was recently sequenced, and the structurally compact 11.7 Mbp genome contains simplified basic cellular machineries and metabolism. We here performed 454 sequencing to 16× coverage of the assemblage B isolate GS, the only Giardia isolate successfully used to experimentally infect animals and humans. The two genomes show 77% nucleotide and 78% amino-acid identity in protein coding regions. Comparative analysis identified 28 unique GS and 3 unique WB protein coding genes, and the variable surface protein (VSP) repertoires of the two isolates are completely different. The promoters of several enzymes involved in the synthesis of the cyst-wall lack binding sites for encystation-specific transcription factors in GS. Several synteny-breaks were detected and verified. The tetraploid GS genome shows higher levels of overall allelic sequence polymorphism (0.5 versus <0.01% in WB). The genomic differences between WB and GS may explain some of the observed biological and clinical differences between the two isolates, and it suggests that assemblage A and B Giardia can be two different species. Giardia intestinalis is a major contributor to the enormous burden of diarrheal diseases with 250 million symptomatic infections per year, and it is part of the WHO neglected disease initiative. Nonetheless, there is poor insight into how Giardia causes disease; it is not invasive, secretes no known toxin and both the duration and symptoms of giardiasis are highly variable. Currently, there are seven defined variants (assemblages) of G. intestinalis, with only assemblages A and B being known to infect humans. Although assemblage B is the most prevalent worldwide, it is inconclusive whether the various genotypes are associated with different disease outcomes. We have used the 454 sequencing technology to sequence the first assemblage B isolate, and the genome was compared to the earlier sequenced assemblage A isolate. Large genetic differences were detected in genes involved in survival of the parasite during infections. The genomic differences between assemblage A and B can explain some of the observed biological and clinical differences between the two assemblages. Our data suggest that assemblage A and B Giardia can be two different species. The identification of genomic differences between assemblages is indeed very important for further studies of the disease and in the development of new methods for diagnosis and treatment of giardiasis.
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Affiliation(s)
- Oscar Franzén
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | | | - Elsie Castro
- Centre for Microbiological Preparedness, Swedish Institute for Infectious Disease Control, Solna, Sweden
| | - Ellen Sherwood
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Johan Ankarklev
- Department of Cell and Molecular Biology, BMC, Uppsala University, Uppsala, Sweden
| | - David S. Reiner
- The Burnham Institute for Medical Research, La Jolla, California, United States of America
| | - Daniel Palm
- Centre for Microbiological Preparedness, Swedish Institute for Infectious Disease Control, Solna, Sweden
| | - Jan O. Andersson
- Department of Evolution, Genomics and Systematics, EBC, Uppsala University, Uppsala, Sweden
| | - Björn Andersson
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Staffan G. Svärd
- Department of Cell and Molecular Biology, BMC, Uppsala University, Uppsala, Sweden
- * E-mail:
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