Barcoding of<i>Giardia duodenalis</i>isolates and derived lines from an established cryobank by a mutation scanning‐based approach

Nolan, Matthew J.; Jex, Aaron R.; Upcroft, Jacqueline; Upcroft, Peter; Gasser, Robin B.

doi:10.1002/elps.201100283

Cited by 17 publications

(15 citation statements)

References 111 publications

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“…Current evidence indicates that, on a global level, assemblage B is slightly more prevalent than assemblage A in both developed and developing countries (Feng and Xiao, 2011). The only two previous studies, which analysed a small number of Giardia isolates from Queensland, identified both assemblage A and B (Nolan et al 2011;Ebner et al 2015). Analysis of genetic variability within assemblages has shown that isolates of assemblage A can be divided into four sub-assemblages (AI, AII, AIII and AIV) by protein polymorphisms of 23 loci (Monis et al 1996(Monis et al , 2003, with human isolates belonging to AI and AII and animal isolates belonged to AI, AIII and AIV (Monis et al 2003;Cacciò et al 2008;Sprong et al 2009;Ryan and Cacciò, 2013).…”

Section: Discussionmentioning

confidence: 97%

Molecular typing ofGiardia duodenalisin humans in Queensland – first report of Assemblage E

2017

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SUMMARYLittle is known about the genetic diversity of the protozoan parasite, Giardia duodenalis, infecting humans in Queensland, Australia. The present study typed 88 microscopically Giardia-positive isolates using assemblage-specific primers at the triose phosphate isomerase (tpi) gene and sequenced a subset of isolates at the glutamate dehydrogenase (gdh) gene (n = 30) and tpi locus (n = 27). Using the tpi-assemblage specific primers, G. duodenalis assemblage A and assemblage B were detected in 50% (44/88) and 38·6% (34/88) of samples, respectively. Mixed infections with assemblages A and B were identified in 4·5% (4/88) and assemblage E was identified in 6·8% (6/88) of samples. Sequence analysis at the gdh and tpi loci also confirmed the presence of assemblage E in these isolates. Cyst numbers per gram of feces (g−1) were determined using quantitative polymerase chain reaction and of the isolates that were typed as assemblage E, cyst numbers ranged 13·8–68·3 × 106 cysts g−1. This is the first report of assemblage E in humans in Australia, indicating that in certain settings, this assemblage may be zoonotic.

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Section: Discussionmentioning

confidence: 97%

Molecular typing ofGiardia duodenalisin humans in Queensland – first report of Assemblage E

2017

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“…Although the SSCP‐based analyses have been used routinely in our laboratory for the detection and characterization of species and genotypes/assemblages of Cryptosporidium or Giardia , it had not been employed previously for the analysis of ITS‐2 products PCR‐amplified directly from human fecal DNA samples (rather than parasite DNA). The detection of single ITS‐2 bands on agarose gels, discrete profiles by SSCP, and unambiguous sequences resulting from selective sequencing of amplicons has inferred exquisite specificity of the PCR (determined by primer NC1).…”

Section: Discussionmentioning

confidence: 99%

“…In particular, SSCP has found applicability because a standard protocol can be applied to a wide range of genetic markers and organisms. For instance, PCR‐based SSCP analysis of internal transcribed spacer sequences of nuclear ribosomal DNA allows the specific identification of key parasitic nematodes of major importance and nuclear genes, such as 60 kDa glycoprotein ( gp60 ) and triose phosphate isomerase ( tpi ), are commonly employed for the specific detection or characterization of protozoa, such as Cryptosporidium and Giardia . The method has been applied to DNA isolated directly from parasitic protozoans and from biological matrices, including feces.…”

Section: Introductionmentioning

confidence: 99%

Genetic characterization of selected parasites from people with histories of gastrointestinal disorders using a mutation scanning‐coupled approach

et al. 2013

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A SSCP analysis and targeted sequencing approach was used for the genetic characterization of some major pathogens from a cohort of 227 people with histories of gastrointestinal disorders. Genomic DNAs from fecal samples were subjected to PCR-amplification of regions in the glycoprotein (gp60) or triose phosphate isomerase (tpi) gene, or the second internal transcribed spacer of nuclear ribosomal DNA (ITS-2). Cryptosporidium, Giardia, and strongylid nematodes were detected in 94, 132 and 12 samples. Cryptosporidium hominis subgenotypes IbA10G2, IdA15G1, IgA17, IgA18, and IfA13G1 were identified in 74.6, 16.9, 5.6, 1.4, and 1.4% of 71 samples, respectively. For Cryptosporidium parvum, subgenotypes IIaA17G2R1 (47.6%) and IIaA18G3R1 (23.8%) were identified in 23 samples. Giardia duodenalis assemblage B (78%) was more common than assemblage A (22%). In addition, DNA of the nematodes Ancylostoma ceylanicum (n = 2), Ancylostoma duodenale (4), Necator americanus (5), and Haemonchus contortus (1) was specifically detected. This is the first report of A. ceylanicum in two persons in Australia and, we provide molecular evidence of H. contortus in a child. This SSCP-based approach should provide a useful diagnostic and analytical tool for a wide range of pathogens.

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“…Although a considerable amount of genetic information is available for G. duodenalis , more baseline data is required at the proteomic level for a systems biology approach to be pursued. In this study, we analyzed eight assemblage A strains of diverse origins previously characterized in the literature according to karotype , assemblage , virulence , geographic variation , and drug resistance . Of these eight strains, three are from animals (one each of wild, companion, and livestock animal) and five were isolated from human infections, including one A2 strain as well as the subassemblage A1 genome strain (full strain classification information can be found in Supporting Information Table 1).…”

Section: Summary Of Peptide and Protein Identification Data Of G Duomentioning

confidence: 99%

Quantitative proteomic analysis of Giardia duodenalis assemblage A: A baseline for host, assemblage, and isolate variation

Emery

Lacey²,

Haynes

2015

Proteomics

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Giardia duodenalis is a gastrointestinal protozoan parasite of vertebrates and is a species complex comprised of eight assemblages, with the zoonotic assemblage A one of two subtypes infective for humans. With increasing genomic and transcriptomic data publicly available through the centralized giardiaDB.org, we have quantitatively analyzed the proteomes of eight G. duodenalis assemblage A strains (seven A1 and one A2) to provide a proteomic baseline to complement the available data. A nonredundant total of 1197 subassemblage A1 proteins and 719 subassemblage A2 proteins were identified with an average of 770 proteins in each strain. The eight strains were also searched against both assemblage A genome sequences (subassemblage A1 and A2 genomes) and demonstrated subassemblage specific differences in protein identifications, especially for variable gene families. Substantial differences were observed in the numbers and abundance in the variable surface protein family, and two different variable surface protein expression profiles that were independent of host origin, subassemblage, or geographic origin. We hypothesize that this variation in surface antigen switching events may be related to karotype and chromosomal variation, which would indicate an assemblage-independent mechanism of diversity generation in G. duodenalis. All MS data have been deposited in the ProteomeXchange with identifier PXD001272 (http://proteomecentral.proteomexchange.org/dataset/PXD001272).

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Barcoding ofGiardia duodenalisisolates and derived lines from an established cryobank by a mutation scanning‐based approach

Cited by 17 publications

References 111 publications

Molecular typing ofGiardia duodenalisin humans in Queensland – first report of Assemblage E

Molecular typing ofGiardia duodenalisin humans in Queensland – first report of Assemblage E

Genetic characterization of selected parasites from people with histories of gastrointestinal disorders using a mutation scanning‐coupled approach

Quantitative proteomic analysis of Giardia duodenalis assemblage A: A baseline for host, assemblage, and isolate variation

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