1
|
Wyrobisz-Papiewska A, Kowal J, Łopieńska-Biernat E, Nosal P, Polak I, Paukszto Ł, Rehbein S. Morphometric and Molecular Analyses of Ostertagia leptospicularis Assadov, 1953 from Ruminants: Species Diversity or Host Influence? Animals (Basel) 2021; 11:ani11010182. [PMID: 33466738 PMCID: PMC7829921 DOI: 10.3390/ani11010182] [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: 12/02/2020] [Accepted: 01/11/2021] [Indexed: 11/24/2022] Open
Abstract
Simple Summary Pathogenic nematode Ostertagia leptospicularis, as the sole member of the subfamily Ostertagiinae, occurs in both cervid and bovid host species. The broad host specificity of this parasite draws special attention and requires a more in-depth investigation. This study was carried out to find out whether the differences in the nematode morphology were only due to the host influence, or whether genetic differences should be taken into account. To resolve this issue, the classification of O. leptospicularis was raised and discussed based on its host specificity, as well as morphological and genetic characteristics. A combined morphological–molecular approach was used to compare specimens resembling O. leptospicularis collected from naturally infected hosts of various ruminant species (roe deer, red deer, fallow deer, and cattle). Both morphological and molecular analyses highlighted the distinctiveness of O. leptospicularis collected from cattle in Germany, and therefore should now be considered to be a different strain that those collected form cervids in central Europe. Abstract Ostertagia leptospicularis Assadov, 1953 was formally described in roe deer Capreolus capreolus and has been reported in a wide range of ruminants, including other Cervidae, as well as Bovidae. Nematode specimens derived from various host species exhibit morphological similarity; however, some differences can be observed. It is unclear if this is due to the differential reaction of one nematode species in different host species (i.e., host-induced changes) or because of distinct nematode species in these hosts (i.e., species complex). This paper focuses on specimens resembling O. leptospicularis f. leptospicularis and its closely related species (Ostertagia ostertagi f. ostertagi) collected from various hosts. Morphometric and molecular techniques were applied to assess host-induced changes in nematode morphology and to clarify its systematic classification. There was an overall effect of host species on measurements of nematodes resembling O. leptospicularis (both males and females), but the distinctiveness of the specimens from cattle Bos taurus were highlighted. The results obtained may suggest that the specimens of O. leptospicularis from cattle in Germany and cervids in central Europe belong to different strains. Furthermore, nematodes from the cervid strain appear to circulate within particular host species, which can be seen in the stated morphological variations.
Collapse
Affiliation(s)
- Anna Wyrobisz-Papiewska
- Department of Zoology and Animal Welfare, Faculty of Animal Sciences, University of Agriculture in Krakow, Mickiewicza av. 24/28, 30-059 Krakow, Poland; (J.K.); (P.N.)
- Correspondence:
| | - Jerzy Kowal
- Department of Zoology and Animal Welfare, Faculty of Animal Sciences, University of Agriculture in Krakow, Mickiewicza av. 24/28, 30-059 Krakow, Poland; (J.K.); (P.N.)
| | - Elżbieta Łopieńska-Biernat
- Department of Biochemistry, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-917 Olsztyn, Poland; (E.Ł.-B.); (I.P.)
| | - Paweł Nosal
- Department of Zoology and Animal Welfare, Faculty of Animal Sciences, University of Agriculture in Krakow, Mickiewicza av. 24/28, 30-059 Krakow, Poland; (J.K.); (P.N.)
| | - Iwona Polak
- Department of Biochemistry, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-917 Olsztyn, Poland; (E.Ł.-B.); (I.P.)
| | - Łukasz Paukszto
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-719 Olsztyn, Poland;
| | - Steffen Rehbein
- Boehringer Ingelheim Vetmedica GmbH, Kathrinenhof Research Center, Walchenseestr. 8-12, 83101 Rohrdorf, Germany;
| |
Collapse
|
2
|
Ghatee MA, Malek Hosseini SAA, Marashifard M, Karamian M, Taylor WR, Jamshidi A, Mobedi I, Azarmehr H. Phylogenetic analysis of Trichostrongylus vitrinus isolates from southwest Iran. Parasit Vectors 2020; 13:553. [PMID: 33160415 PMCID: PMC7648934 DOI: 10.1186/s13071-020-04438-y] [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: 04/27/2020] [Accepted: 10/30/2020] [Indexed: 11/11/2022] Open
Abstract
Background Trichostrongylus is one of the most important zoonotic trichostrongylid nematodes, infecting mostly livestock. Data on its genetic characteristics are lacking in Iran. Methods We determined the phylogenetic relationships of Trichostrongylus species in three counties of Kohgiloyeh and Boyerahmad (K-B) province, southwest Iran. Small intestine and abomasum of 70 sheep and goats were investigated. Results A total of 35 isolates of Trichostrongylus worms were detected and all were genetically identified as Trichostrongylus vitrinus. Analysis of 321 bp of the internal transcribed spacer 2 (ITS2) of ribosomal DNA revealed 16 genotypes. All genotypes were single nucleotide polymorphisms, including some hypervariable points. All sequences were trimmed to 170 bp, compared with sequences on GenBank including short sequences from other endemic foci of Iran and other countries and all isolates were used to generate a maximum likelihood phylogenetic tree, which consisted of two clades A and B. Clade A included isolates from Iran, Russia, New Zealand, Australia and the UK; clade B only contained South African isolates. Most clade A isolates (north, southwest and west Iran, Russia, New Zealand, Australia and UK) were in a similar phylogenetic position. One subclade was detected in clade A (isolates from Southwest Iran, New Zealand and UK). Conclusions We hypothesize that drug resistant T. vitrinus may account for its exclusive detection in our samples. The high similarity of genotypes from Iran, New Zealand and UK may be due to their close political relationships during the colonial era. More research is needed to understand better the phylogeny of T. vitrinus and its relationship with drug resistance and human transmission. ![]()
Collapse
Affiliation(s)
- Mohammad Amin Ghatee
- Cellular and Molecular Research Center, Yasuj University of Medical Sciences, Yasuj, Iran. .,Department of Parasitology, School of Medicine, Yasuj University of Medical Sciences, Yasuj, Iran.
| | | | - Masoud Marashifard
- Student Research Committee, Yasuj University of Medical Sciences, Yasuj, Iran
| | - Mehdi Karamian
- Department of Parasitology and Mycology, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Walter Robert Taylor
- Mahidol Oxford Tropical Medicine Research Unit, Bangkok, Thailand.,Oxford Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - Ali Jamshidi
- Cellular and Molecular Research Center, Yasuj University of Medical Sciences, Yasuj, Iran
| | - Iraj Mobedi
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Hasan Azarmehr
- Student Research Committee, Yasuj University of Medical Sciences, Yasuj, Iran
| |
Collapse
|
3
|
Delaunay A, Dallot S, Filloux D, Dupuy V, Roumagnac P, Jacquot E. SNaPshot and CE-SSCP: Two Simple and Cost-Effective Methods to Reveal Genetic Variability Within a Virus Species. Methods Mol Biol 2016; 1302:187-206. [PMID: 25981256 DOI: 10.1007/978-1-4939-2620-6_15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The multiplex SNaPshot and the capillary electrophoresis-single-strand conformation polymorphism (CE-SSCP) procedures are here used for rapid and high-throughput description of the molecular variability of viral populations. Both approaches are based on (1) standard amplification of genomic sequence(s), (2) labeled primers or labeled single-stranded DNA, and (3) migration of fluorescent-labeled molecules in capillary electrophoresis system. The SNaPshot technology was used to describe the diversity of 20 targeted single nucleotide polymorphisms (SNPs) selected from alignment of viral genomic sequences retrieved from public database. The CE-SSCP procedure was applied to identify the polymorphisms of two small (<500 bases in length) genomic regions of viral genomes. The different steps of SNaPshot and CE-SSCP setup procedures are presented using Potato virus Y (PVY, Potyvirus) and Plum pox virus (PPV, Potyvirus) RNA viruses as molecular targets, respectively.
Collapse
Affiliation(s)
- Agnès Delaunay
- INRA-Cirad-Montpellier SupAgro, UMR 385 BGPI, Cirad TA A-54K, Montpellier cedex, 34398, France
| | | | | | | | | | | |
Collapse
|
4
|
Roeber F, Jex AR, Gasser RB. Advances in the diagnosis of key gastrointestinal nematode infections of livestock, with an emphasis on small ruminants. Biotechnol Adv 2013; 31:1135-52. [PMID: 23376340 PMCID: PMC7126997 DOI: 10.1016/j.biotechadv.2013.01.008] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 01/21/2013] [Accepted: 01/22/2013] [Indexed: 12/19/2022]
Abstract
Parasitic nematodes (roundworms) of livestock have major economic impact globally. In spite of the diseases caused by these nematodes and some advances in the design of new therapeutic agents (anthelmintics) and attempts to develop vaccines against some of them, there has been limited progress in the establishment of practical diagnostic techniques. The specific and sensitive diagnosis of gastrointestinal nematode infections of livestock underpins effective disease control, which is highly relevant now that anthelmintic resistance (AR) is a major problem. Traditional diagnostic techniques have major constraints, in terms of sensitivity and specificity. The purpose of this article is to provide a brief background on gastrointestinal nematodes (Strongylida) of livestock and their control; to summarize conventional methods used for the diagnosis and discuss their constraints; to review key molecular-diagnostic methods and recent progress in the development of advanced amplification-based and sequencing technologies, and their implications for epidemiological investigations and the control of parasitic diseases.
Collapse
Affiliation(s)
| | | | - Robin B. Gasser
- Faculty of Veterinary Science, The University of Melbourne, Victoria 3010, Australia
| |
Collapse
|
5
|
Ferrari FAG, Goddard J, Caprio M, Paddock CD, Mixson-Hayden T, Varela-Stokes AS. Population analyses of Amblyomma maculatum ticks and Rickettsia parkeri using single-strand conformation polymorphism. Ticks Tick Borne Dis 2013; 4:439-44. [PMID: 23856472 DOI: 10.1016/j.ttbdis.2013.04.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Revised: 04/24/2013] [Accepted: 04/24/2013] [Indexed: 10/26/2022]
Abstract
Gulf Coast ticks, Amblyomma maculatum, and the zoonotic agents they transmit, Rickettsia parkeri, are expanding into areas in the United States where they were not previously reported, and are emerging threats for public and veterinary health. The dynamics of this tick-pathogen system and implications for disease transmission are still unclear. To assess genetic variation of tick and rickettsial populations, we collected adult A. maculatum from 10 sites in Mississippi, 4 in the northern, one in the central, and 5 in the southern part of the state. PCR amplicons from tick mitochondrial 16S rRNA and rickettsial ompA genes as well as 5 intergenic spacer regions were evaluated for genetic variation using single-strand conformation polymorphism analysis. Frequencies of the 4 tick 16S haplotypes were not significantly different among regions of Mississippi, but within sites there were differences in distribution that can be explained by high migration rates. Phylogenetically, one lineage of tick haplotypes was a species-poor sister group to remaining haplotypes in the species-rich sister group. No genetic variation was identified in any of the 6 selected gene targets of R. parkeri examined in the infected ticks, suggesting high levels of intermixing.
Collapse
Affiliation(s)
- Flavia A G Ferrari
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA
| | | | | | | | | | | |
Collapse
|
6
|
A perfect time to harness advanced molecular technologies to explore the fundamental biology of Toxocara species. Vet Parasitol 2013; 193:353-64. [DOI: 10.1016/j.vetpar.2012.12.031] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
7
|
Roeber F, Jex AR, Gasser RB. Next-generation molecular-diagnostic tools for gastrointestinal nematodes of livestock, with an emphasis on small ruminants: a turning point? ADVANCES IN PARASITOLOGY 2013; 83:267-333. [PMID: 23876874 PMCID: PMC7150098 DOI: 10.1016/b978-0-12-407705-8.00004-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Parasitic nematodes of livestock have major economic impact worldwide. Despite the diseases caused by these nematodes, some advances towards the development of new therapeutic agents and attempts to develop effective vaccines against some of them, there has been limited progress in the development of practical diagnostic methods. The specific and sensitive diagnosis of parasitic nematode infections of livestock underpins effective disease control, which is now particularly important given the problems associated with anthelmintic resistance in parasite populations. Traditional diagnostic methods have major limitations, in terms of sensitivity and specificity. This chapter provides an account of the significance of parasitic nematodes (order Strongylida), reviews conventional diagnostic techniques that are presently used routinely and describes advances in polymerase chain reaction (PCR)-based methods for the specific diagnosis of nematode infections. A particular emphasis is placed on the recent development of a robotic PCR-based platform for high-throughput diagnosis, and its significance and implications for epidemiological investigations and for use in control programmes.
Collapse
Affiliation(s)
| | | | - Robin B. Gasser
- Faculty of Veterinary Science, The University of Melbourne, Parkville, Victoria, Australia
| |
Collapse
|
8
|
A fluorescence-based polymerase chain reaction-linked single-strand conformation polymorphism (F-PCR-SSCP) assay for the identification of Fasciola spp. Parasitol Res 2010; 108:1513-7. [PMID: 21170657 DOI: 10.1007/s00436-010-2209-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Accepted: 11/30/2010] [Indexed: 12/22/2022]
Abstract
The present study aimed to establish a fluorescence-based polymerase chain reaction-linked single-strand conformation polymorphism (F-PCR-SSCP) assay for the identification of Fasciola spp. Based on the sequences of the second internal transcribed spacer (ITS-2) of the nuclear ribosomal DNA, we designed a set of genus-specific primers for the amplification of Fasciola ITS-2, with an estimated size of 140 bp. These primers were labelled by fluorescence dyes, and the PCR products were analyzed by capillary electrophoresis under non-denaturing conditions (F-PCR-SSCP). Capillary electrophoresis analysis of the fluorescence-labelled DNA fragments displayed three different peak profiles that allowed the accurate identification of Fasciola species: one single peak specific for either Fasciola hepatica or Fasciola gigantica and a doublet peak corresponding to the "intermediate" Fasciola. Validation of our novel method was performed using Fasciola specimens from different host animals from China, Spain, Nigeria, and Egypt. This F-PCR-SSCP assay provides a rapid, simple, and robust tool for the identification and differentiation between Fasciola spp.
Collapse
|
9
|
Power ML, Holley M, Ryan UM, Worden P, Gillings MR. Identification and differentiation of Cryptosporidium species by capillary electrophoresis single-strand conformation polymorphism. FEMS Microbiol Lett 2010; 314:34-41. [DOI: 10.1111/j.1574-6968.2010.02134.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
|
10
|
Sim KA, Hoar B, Kutz SJ, Chilton NB. Amplification of the Second Internal Transcribed Spacer Ribosomal DNA of Individual Trichostrongylid Nematode Larvae by Nested Polymerase Chain Reaction. J Vet Diagn Invest 2010; 22:433-7. [DOI: 10.1177/104063871002200316] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Kathrin A. Sim
- Department of Biology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Bryanne Hoar
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Susan J. Kutz
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Neil B. Chilton
- Department of Biology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| |
Collapse
|
11
|
Fazenda IP, Beveridge I, Chilton NB, Jex AR, Pangasa A, Campbell BE, Huby-Chilton F, Carvalho LM, Gasser RB. Analysis of genetic variation in Globocephaloides populations from macropodid marsupials using a mutation scanning-based approach. Electrophoresis 2009; 30:2758-64. [PMID: 19650048 DOI: 10.1002/elps.200900306] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Three species of Globocephaloides, parasitic nematodes occurring in macropodid marsupials in different areas of Australia, were characterized by the sequences of the first and second internal transcribed spacers (ITS-1 and ITS-2) of nuclear ribosomal DNA. Samples were subjected to PCR-coupled SSCP analysis and targeted sequencing, in order to assess genetic variation within and among individuals from different host species. Both SSCP and sequence data supported the current classification of morphospecies. Contrary to a previous hypothesis that cryptic species exist within the Globocephaloides trifidospicularis "complex", no or minor (0.2%) variation was detected among individuals from different hosts or geographical origins. Within G. macropodis populations, there was a consistent difference in both the ITS-1 (5.2%) and ITS-2 (7.1%) sequences between individuals derived from Macropus agilis and those from Macropus dorsalis. Although the results suggested that G. macropodis from each host species represented sibling species, future morphological study of individuals representing each G. macropodis genotype is warranted to provide further support for this hypothesis. (Nucleotide sequence data have been deposited in the GenBank database under accession nos. GQ131400-GQ131409.).
Collapse
Affiliation(s)
- Inês P Fazenda
- Department of Veterinary Science, The University of Melbourne, Victoria, Australia
| | | | | | | | | | | | | | | | | |
Collapse
|
12
|
Is single-strand conformation polymorphism analysis of the full 5' untranslated region an adequate approach to study hepatitis C virus quasispecies distribution? J Virol 2009; 83:9018-21. [PMID: 19553315 DOI: 10.1128/jvi.00971-09] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Single-strand conformation polymorphism (SSCP) analysis is used by many laboratories to study the quasispecies distribution of the hepatitis C virus (HCV). Here we question the validity of this experimental approach, as conclusions are drawn from the analysis of the migration patterns of two ssDNA molecules and not from RNA. Using previously characterized mutants of the HCV 5' untranslated regions, we show that contrary to what has been predicted, SSCP migration patterns of DNA amplicons with differences in their nucleotide sequences generated from the full 5' UTR of HCV are not necessarily unique.
Collapse
|
13
|
Delaunay A, Rolland M, Jacquot E. Analysis of population structures of viral isolates using single-strand conformation polymorphism method. Methods Mol Biol 2009; 508:235-247. [PMID: 19301759 DOI: 10.1007/978-1-59745-062-1_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The analysis of viral populations requires the use of techniques that describe characteristics of individuals. The single-strand conformation polymorphism (SSCP) makes possible the identification of genetic differences between viral sequences and constitutes an alternative to the expensive and time-consuming cloning and sequencing strategies. Applied to small genomic regions (from 100 to 500 bases in length), SSCP patterns could describe, under appropriate experimental conditions, single nucleotide variations in the studied sequence. The different steps of a complete SSCP procedure, from sampling to pattern analysis (including nucleic acid extraction, RT-PCR amplification, double-stranded DNA quantification, polyacrylamide gel preparation, electrophoresis conditions, and staining procedures), are described using a region (500 bases) of the barley yellow dwarfvirus-PAV (BYDV-PAV, Luteovirus) genome as molecular target.
Collapse
|
14
|
Toward practical, DNA-based diagnostic methods for parasitic nematodes of livestock — Bionomic and biotechnological implications. Biotechnol Adv 2008; 26:325-34. [DOI: 10.1016/j.biotechadv.2008.03.003] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2008] [Revised: 03/06/2008] [Accepted: 03/14/2008] [Indexed: 11/22/2022]
|
15
|
Muzulin PM, Kamenetzky L, Gutierrez AM, Guarnera EA, Rosenzvit MC. Echinococcus granulosus antigen B gene family: Further studies of strain polymorphism at the genomic and transcriptional levels. Exp Parasitol 2008; 118:156-64. [PMID: 17825293 DOI: 10.1016/j.exppara.2007.07.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2007] [Revised: 07/03/2007] [Accepted: 07/16/2007] [Indexed: 11/18/2022]
Abstract
Echinococcus granulosus AgB gene family is constituted by five gene loci. In a previous study, we analyzed the strain variation of EgAgB2/B4 sequences. Here, we have analyzed, by SSCP and sequencing, 250 genomic clones of EgAgB1/B3/B5 gene cluster from five E. granulosus strains. Several new EgAgB genomic variants were found. EgAgB1 and EgAgB3 genomic sequences grouped E. granulosus strains by phylogenetic tools in two clusters: one formed by G1/G2 and the other by G5, G6/G7 strains, in accordance with other molecular markers. EgAgB5 genomic and cDNA sequences were only found in G1/G2 cluster. Reverse transcription-PCR analysis using subunit specific primers revealed that all the EgAgB genes were transcribed in G1 and G7 strains with the exception of EgAgB5 transcripts that were not detected in G7 strain. Interestingly, AgB2 transcripts that were probably processed by an aberrant splicing mechanism leading to a non-functional B2 protein were found in G7 strain.
Collapse
Affiliation(s)
- Patricia Marcela Muzulin
- Departamento de Parasitología, Instituto Nacional de Enfermedades Infecciosas ANLIS Dr. Carlos G. Malbrán, Av. Vélez Sarsfield 563, Buenos Aires (1281), Argentina
| | | | | | | | | |
Collapse
|
16
|
Gasser RB, Hu M, Chilton NB, Campbell BE, Jex AJ, Otranto D, Cafarchia C, Beveridge I, Zhu X. Single-strand conformation polymorphism (SSCP) for the analysis of genetic variation. Nat Protoc 2007; 1:3121-8. [PMID: 17406575 DOI: 10.1038/nprot.2006.485] [Citation(s) in RCA: 197] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The accurate analysis of genetic variation has major implications in many areas of biomedical research, including the identification of infectious agents (such as parasites), the diagnosis of infections, and the detection of unknown or known disease-causing mutations. Mutation scanning methods, including PCR-coupled single-strand conformation polymorphism (SSCP), have significant advantages over many other nucleic acid techniques for the accurate analysis of allelic and mutational sequence variation. The present protocol describes the SSCP method of analysis, including all steps from the small-scale isolation of genomic DNA and PCR amplification of target sequences, through to the gel-based separation of amplicons and scanning for mutations by SSCP (either by the analysis of radiolabeled amplicons in mutation detection enhancement (MDE) gels or by non-isotopic SSCP using precast GMA gels). The subsequent sequence analysis of polymorphic bands isolated from gels is also detailed. The SSCP protocol can readily detect point mutations for amplicon sizes of up to 450-500 bp, and usually takes 1-2 days to carry out. This user-friendly, low-cost, potentially high-throughput platform has demonstrated the utility to study a wide range of pathogens and diseases, and has the potential to be applied to any gene of any organism.
Collapse
Affiliation(s)
- Robin B Gasser
- Department of Veterinary Science, The University of Melbourne, 250 Princes Highway, Werribee, Victoria 3030, Australia.
| | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Verweij JJ, Campbell BE, Gasser RB. Differentiation of Entamoeba histolytica from Entamoeba dispar by PCR-coupled nonisotopic SSCP analysis. Electrophoresis 2006; 27:4419-22. [PMID: 17058306 DOI: 10.1002/elps.200600211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Entamoeba histolytica is a pathogenic protozoan parasite, which causes amoebic colitis, dysentery and liver abscesses in humans. Since the cyst and small trophozoite stages of this parasite are indistinguishable by light microscopy from Entamoeba dispar (which is nonpathogenic), specific diagnosis is compromised. To overcome this limitation, a PCR-coupled SSCP approach, utilising a sequence difference of 4.6% in a short region ( approximately 173-174 bp) of the small subunit of nuclear ribosomal DNA, was evaluated for the differentiation of the two species of Entamoeba. Including a range of well-defined control DNA samples (n = 67) to evaluate the specificity of the PCR, 45 DNA samples representing E. histolytica and E. dispar from human faecal samples were tested by SSCP, and unequivocal delineation between the species was achieved. This SSCP approach should provide a practical tool for the specific diagnosis of E. histolytica in humans and for investigating its epidemiology.
Collapse
Affiliation(s)
- Jaco J Verweij
- Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands
| | | | | |
Collapse
|
18
|
Troell K, Engström A, Morrison DA, Mattsson JG, Höglund J. Global patterns reveal strong population structure in Haemonchus contortus, a nematode parasite of domesticated ruminants. Int J Parasitol 2006; 36:1305-16. [PMID: 16950266 DOI: 10.1016/j.ijpara.2006.06.015] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2006] [Revised: 05/09/2006] [Accepted: 06/27/2006] [Indexed: 10/24/2022]
Abstract
We have examined the global population genetic structure of Haemonchus contortus. The genetic variability was studied using both amplified fragment length polymorphism (AFLP) and nad4 sequences of the mitochondrial genome. To examine the performance and information content of the two different marker systems, comparative assessment of population genetic diversity was undertaken in 19 isolates of H. contortus, a parasitic nematode of small ruminants. A total of 150 individual adult worms representing 14 countries from all inhabited continents were analysed. Altogether 1,429 informative AFLP markers were generated using four different primer combinations. Also, the genetic variation was high, which agrees with results from previous AFLP studies of nematode parasites of livestock. The genetic structure was high, indicating limited gene flow between the different isolates and populations from each continent mostly formed monophyletic groups in the phylogenetic analysis. However, for isolates representing Australia, Greece and one laboratory strain that originated from South Africa (WRS), there was no clear genetic relationship between the isolates and the distance between their geographical origins. Basically the same pattern was observed for the mitochondrial marker, although the phylogenetic analysis was less resolved than for AFLP. In contrast with previous findings on the population genetic structure of H. contortus, the calculation of population structure gave high values (Nst=0.59). The strong structure was present also for the four Swedish isolates (Nst=0.16) representing a small geographical area.
Collapse
Affiliation(s)
- Karin Troell
- Department of Parasitology (SWEPAR), National Veterinary Institute and Swedish University of Agricultural Sciences, 751 89 Uppsala, Sweden
| | | | | | | | | |
Collapse
|
19
|
Abstract
Modern molecular technologies are having a substantial impact in many fundamental and applied areas of parasitology. In particular, polymerase chain reaction (PCR)-coupled approaches have found broad applicability because their sensitivity permits the enzymatic amplification of gene fragments from minute quantities of nucleic acids from tiny amounts of parasite material. Also, high-resolution electrophoretic and genomic methods are finding increased utility. This paper briefly discusses some developments and applications of DNA methods to parasites and highlights their usefulness or potential for those of veterinary importance. Selected examples of applications with implications in fundamental (systematics, population genetics, epidemiology and ecology) and applied (diagnosis, prevention and control) areas are presented. The focus is mainly on tools for the accurate identification of parasitic nematodes and protozoa of socio-economic importance, the diagnosis of infections and the detection of genetic variability using PCR-coupled mutation scanning technology.
Collapse
Affiliation(s)
- Robin B Gasser
- Department of Veterinary Science, The University of Melbourne, Werribee, Victoria 3030, Australia.
| |
Collapse
|
20
|
Hu M, Gasser RB. Mitochondrial genomes of parasitic nematodes – progress and perspectives. Trends Parasitol 2006; 22:78-84. [PMID: 16377245 DOI: 10.1016/j.pt.2005.12.003] [Citation(s) in RCA: 114] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2005] [Revised: 10/13/2005] [Accepted: 12/08/2005] [Indexed: 10/25/2022]
Abstract
Mitochondria are subcellular organelles in which oxidative phosphorylation and other important biochemical functions take place within the cell. Within these organelles is a mitochondrial (mt) genome, which is distinct from, but cooperates with, the nuclear genome of the cell. Studying mt genomes has implications for various fundamental areas, including mt biochemistry, physiology and molecular biology. Importantly, the mt genome is a rich source of markers for population genetic and systematic studies. To date, more than 696 mt genomes have been sequenced for a range of metazoan organisms. However, few of these are from parasitic nematodes, despite their socioeconomic importance and the need for fundamental investigations into areas such as nematode genetics, systematics and ecology. In this article, we review knowledge and recent progress in mt genomics of parasitic nematodes, summarize applications of mt gene markers to the study of population genetics, systematics, epidemiology and evolution of key nematodes, and highlight some prospects and opportunities for future research.
Collapse
Affiliation(s)
- Min Hu
- Department of Veterinary Science, University of Melbourne, Werribee, Victoria 3030, Australia
| | | |
Collapse
|
21
|
Chilton NB. The use of nuclear ribosomal DNA markers for the identification of bursate nematodes (order Strongylida) and for the diagnosis of infections. Anim Health Res Rev 2005; 5:173-87. [PMID: 15984323 DOI: 10.1079/ahr200497] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Many bursate nematodes are of major importance to animal health. Animals are often parasitized by multiple species that differ in their prevalence, relative abundance and/or pathogenicity. Implementation of effective management strategies for these parasites requires reliable methods for their detection in hosts, identification to the species level and measurement of intensity of infection. One major problem is the difficulty of accurately identifying and distinguishing many species of bursate nematode because of the remarkable morphological similarity of their eggs and larvae. The inability to identify, with confidence, individual nematodes (irrespective of their life-cycle stage) to the species level by morphological methods has often led to a search for species-specific genetic markers. Studies over the past 15 years have shown that sequences of the internal transcribed spacers of ribosomal DNA provide useful genetic markers, providing the basis for the development of PCR-based diagnostic tools. Such molecular methods represent powerful tools for studying the systematics, epidemiology and ecology of bursate nematodes and, importantly, for the specific diagnosis of infections in animals and humans, thus contributing to improved control and prevention strategies for these parasites.
Collapse
Affiliation(s)
- Neil B Chilton
- Department of Biology, University of Saskatchewan, 112 Science Place, Saskatoon, Saskatchewan S7N 5E2, Canada.
| |
Collapse
|
22
|
Gasser RB, Hu M, El-Osta YA, Zarlenga DS, Pozio E. Genetic analysis of Trichinella populations by ‘cold’ single-strand conformation polymorphism analysis. Vet Parasitol 2005; 132:23-6. [PMID: 16076533 DOI: 10.1016/j.vetpar.2005.05.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A non-isotopic single-strand conformation polymorphism ('cold' SSCP) technique has been assessed for the analysis of sequence variability in the expansion segment 5 (ES5) of domain IV and the D3 domain of nuclear ribosomal DNA within and/or among isolates and individual muscle (first-stage) larvae representing all currently recognized species/genotypes of Trichinella. Data are consistent with the ability of cold SSCP to identify intra-specific as well as inter-specific variability among Trichinella genotypes. The cold SSCP approach should be applicable to a range of other genetic markers for comparative studies of Trichinella populations globally.
Collapse
Affiliation(s)
- Robin B Gasser
- Department of Veterinary Science, The University of Melbourne, 250 Princes Highway, Werribee, Victoria 3030, Australia.
| | | | | | | | | |
Collapse
|
23
|
Morrison DA, Höglund J. Testing the hypothesis of recent population expansions in nematode parasites of human-associated hosts. Heredity (Edinb) 2005; 94:426-34. [PMID: 15674388 DOI: 10.1038/sj.hdy.6800623] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
It has been predicted that parasites of human-associated organisms (eg humans, domestic pets, farm animals, agricultural and silvicultural plants) are more likely to show rapid recent population expansions than are parasites of other hosts. Here, we directly test the generality of this demographic prediction for species of parasitic nematodes that currently have mitochondrial sequence data available in the literature or the public-access genetic databases. Of the 23 host/parasite combinations analysed, there are seven human-associated parasite species with expanding populations and three without, and there are three non-human-associated parasite species with expanding populations and 10 without. This statistically significant pattern confirms the prediction. However, it is likely that the situation is more complicated than the simple hypothesis test suggests, and those species that do not fit the predicted general pattern provide interesting insights into other evolutionary processes that influence the historical population genetics of host-parasite relationships. These processes include the effects of postglacial migrations, evolutionary relationships and possibly life-history characteristics. Furthermore, the analysis highlights the limitations of this form of bioinformatic data-mining, in comparison to controlled experimental hypothesis tests.
Collapse
Affiliation(s)
- D A Morrison
- Department of Parasitology (SWEPAR), National Veterinary Institute and Swedish University of Agricultural Sciences, 751 89 Uppsala, Sweden.
| | | |
Collapse
|
24
|
Lun ZR, Chen XG, Zhu XQ, Li XR, Xie MQ. Are Tritrichomonas foetus and Tritrichomonas suis synonyms? Trends Parasitol 2005; 21:122-5. [PMID: 15734659 DOI: 10.1016/j.pt.2004.12.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Tritrichomonas suis, a tritrichomonad of pigs, and the related species Tritrichomonas foetus, a tritrichomonad of cattle, are morphologically identical. The taxonomic relationship between these two tritrichomonads has been questioned ever since they were established as distinct species in 1843 and 1928, respectively. Here, we compare the similarities of morphology, ultrastructure, distribution, host specificity, characteristics of in vitro cultivation, immunology, biochemistry and analysis of molecular data from published sources between these two species. All data indicate that these two tritrichomonad species are identical. Thus, we propose that T. foetus and T. suis are synonyms.
Collapse
Affiliation(s)
- Zhao-Rong Lun
- Center for Parasitic Organisms and Key Laboratory for Tropical Diseases Control of The Ministry of Education, School of Life Sciences, Zhongshan (Sun Yat-Sen) University, Guangzhou 510275, The People's Republic of China.
| | | | | | | | | |
Collapse
|
25
|
Gasser RB, Hu M, Abs El-Osta YG, Zarlenga DS, Pozio E. Nonisotopic single-strand conformation polymorphism analysis of sequence variability in ribosomal DNA expansion segments within the genusTrichinella (Nematoda: Adenophorea). Electrophoresis 2004; 25:3357-64. [PMID: 15490459 DOI: 10.1002/elps.200405985] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
A nonisotopic single-strand conformation polymorphism (SSCP) approach was employed to 'fingerprint' sequence variability in the expansion segment 5 (ES5) of domain IV and the D3 domain of nuclear ribosomal DNA within and/or among isolates and individual muscle (first-stage) larvae representing all currently recognized species/genotypes of Trichinella. In addition, phylogenetic analyses of the D3 sequence data set, employing three different tree-building algorithms, examined the relationships among all of them. These analyses showed strong support that the encapsulated species T. spiralis and T. nelsoni formed a group to the exclusion of the other encapsulated species T. britovi and its related genotypes Trichinella T8 and T9 and T. murrelli, and T. nativa and Trichinella T6, and strong support that T. nativa and Trichinella T6 grouped together. Also, these eight encapsulated members grouped to the exclusion of the nonencapsulated species T. papuae and T. zimbabwensis and the three representatives of T. pseudospiralis investigated. The findings showed that nonencapsulated species constitute a complex group which is distinct from the encapsulated species and supported the current hypothesis that encapsulated Trichinella group external to the nonencapsulated forms, in accordance with independent biological and biochemical data sets.
Collapse
Affiliation(s)
- Robin B Gasser
- Department of Veterinary Science, The University of Melbourne, Werribee, Victoria, Australia.
| | | | | | | | | |
Collapse
|
26
|
Johnson M, Abs El-Osta YG, Hu M, Gasser RB. An electrophoretic tool for the genetic characterisation and delineation of lungworms. Mol Cell Probes 2004; 18:197-203. [PMID: 15135455 DOI: 10.1016/j.mcp.2004.01.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2003] [Accepted: 01/06/2004] [Indexed: 11/28/2022]
Abstract
In the present study, PCR-based single-strand conformation polymorphism (SSCP) analysis of the second internal transcribed spacer (ITS-2) of nuclear ribosomal DNA (rDNA) was applied to the genetic characterisation of Dictyocaulus from red deer from New Zealand and to its differentiation from species of lungworm from cattle and other hosts. Based on SSCP profiles, Dictyocaulus individuals from red deer from different geographical localities in New Zealand could be readily distinguished from those representing other lungworms examined, irrespective of low-level sequence variability in the ITS-2 (0.4-2.6%) detectable among individuals. The ITS-2 of Dictyocaulus from red deer differed in sequence by approximately 7-35% from congeners from other cervid hosts, demonstrating that this parasite is genetically distinct from other species of Dictyocaulus for which ITS-2 sequence data are presently available. The results emphasize the need for a large-scale molecular systematic study of Dictyocaulus specimens from various species of cervid and other ruminant hosts and the usefulness of mutation scanning for taxonomic, epidemiological and population genetic investigations.
Collapse
Affiliation(s)
- Marion Johnson
- Department of Veterinary Science, The University of Melbourne, 250 Princes Highway, Werribee, Victoria 3030, Australia
| | | | | | | |
Collapse
|
27
|
Kleeman SN, Adlard RD, Zhu X, Gasser RB. Mutation scanning analysis of Marteilia sydneyi populations from different geographical locations in eastern Australia. Mol Cell Probes 2004; 18:133-8. [PMID: 15051123 DOI: 10.1016/j.mcp.2003.11.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2003] [Accepted: 11/03/2003] [Indexed: 11/22/2022]
Abstract
Marteilia sydneyi (Paramyxea) is the causative agent of QX disease in oysters. In spite of the economic impact of this disease, its origin and the precise reason(s) for its apparent spread in Australian waters are not yet known. Given such knowledge gaps, investigating the population genetic structure(s) of M. sydneyi populations could provide insights into the epidemiology and ecology of the parasite and could assist in its prevention and control. In this study, single strand conformation polymorphism (SSCP)-based analysis of a region (195 bp) of the first internal transcribed spacer (ITS-1) of ribosomal DNA was employed to investigate genetic variation within and among five populations of M. sydneyi from oysters from five different locations in eastern Australia. The analysis showed the existence of a genetic variant of M. sydneyi common to the Great Sandy Strait, and the Richmond and Georges Rivers, as distinct from variants at the Pimpama and Clarence Rivers. Together with historical and other information relating to the QX disease outbreaks in eastern Australia, the molecular findings support the proposal that the parasite originated in the Great Sandy Strait and/or Richmond River and then extended southward along the coast. From a technical perspective, the study demonstrated the usefulness of SSCP as a tool to study the population genetics and epidemiology of M. sydneyi.
Collapse
Affiliation(s)
- Sarah N Kleeman
- Department of Microbiology and Parasitology, University of Queensland, Brisbane, Qld 4072, Australia
| | | | | | | |
Collapse
|
28
|
Hu M, Chilton NB, Gasser RB. Long PCR-based amplification of the entire mitochondrial genome from single parasitic nematodes. Mol Cell Probes 2003; 16:261-7. [PMID: 12270267 DOI: 10.1006/mcpr.2002.0422] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Mitochondrial genome sequences provide useful markers for investigating population genetic structures because of their maternal inheritance and high evolutionary rates. There is, however, a paucity of information on mitochondrial genomes for many parasitic organisms, including nematodes, which appears to relate mainly to technical limitations and (for modestly funded laboratories) the cost associated with full mitochondrial genome sequencing. In this article, we describe a simple, relatively inexpensive long-PCR approach for the amplification (using two sets of primers) of the entire mitochondrial genome from individual parasitic nematodes for subsequent sequencing, which overcomes these limitations. We employed two species of human hookworm (Ancylostoma duodenale and Necator americanus; order Strongylida) to establish the long-PCR conditions, and then extended its use to a number of other species of parasitic nematode of the class Secernentea (orders Strongylida, Ascaridida and Rhabditida). The long-PCR method for the amplification of the entire mitochondrial genome from single nematodes, coupled with direct sequencing of amplicons, provides a useful tool for the comparative analysis of genome organisation and evolution of a range of nematode groups. It also creates a platform for molecular ecological and population genetic studies.
Collapse
Affiliation(s)
- M Hu
- Department of Veterinary Science, The University of Melbourne, 250 Princes Highway, Werribee, Victoria 3030, Australia
| | | | | |
Collapse
|
29
|
Gasser RB, El-Osta YGA, Chalmers RM. Electrophoretic analysis of genetic variability within Cryptosporidium parvum from imported and autochthonous cases of human cryptosporidiosis in the United Kingdom. Appl Environ Microbiol 2003; 69:2719-30. [PMID: 12732542 PMCID: PMC154546 DOI: 10.1128/aem.69.5.2719-2730.2003] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cryptosporidium parvum oocyst DNA samples (n = 184) from humans with cryptosporidiosis contracted during foreign travel or during outbreaks in the United Kingdom were characterized genetically and categorized by single-strand conformation polymorphism (SSCP)-based analysis of the small-subunit gene (pSSU) (approximately 300 bp) and second internal transcribed spacer (pITS-2) (approximately 230 bp) of nuclear ribosomal DNA. The two recognized genotypes (types 1 and 2) of C. parvum could be readily differentiated by a distinct electrophoretic shift in the pSSU SSCP profile, associated with a nucleotide difference of approximately 1.3 to 1.7%. Of the 102 samples from cases contracted during foreign travel, 88 (86.3%) were identified as C. parvum type 1 and 14 (13.7%) were identified as type 2. For outbreak samples, unequivocal differentiation between type 1 (n = 20; one child nursery outbreak) and type 2 (n = 62; two waterborne outbreaks) was also achieved. Nucleotide variation in pITS-2 (both within and among samples representing each genotype) was substantially greater (10 to 13 different profiles for each genotype, relating to sequence differences of approximately 1 to 42%) than that in pSSU. SSCP analysis of pITS-2 for all samples revealed that some profiles had a broad geographical distribution whereas others were restricted to particular locations, suggesting a link between some subgenotypes and the geographical origin or source. Comparative denaturing polyacrylamide gel electrophoretic analysis revealed the same genotypic identification and a similar subgenotypic classification of samples as SSCP analysis. The findings of this study, particularly the detection of intragenotypic variation by SSCP, should have significant diagnostic implications for investigating transmission patterns and the monitoring of outbreaks.
Collapse
Affiliation(s)
- R B Gasser
- Department of Veterinary Science, The University of Melbourne, 250 Princes Highway, Werribee, Victoria 3030, Australia.
| | | | | |
Collapse
|