Population expansion and gene flow in Giardia duodenalis as revealed by triosephosphate isomerase gene

Choy, Seow Huey; Mahdy, Mohammed A. K.; Al-Mekhlafi, Hesham M.; Low, Van Lun; Surin, Johari

doi:10.1186/s13071-015-1084-y

Cited by 28 publications

(15 citation statements)

References 41 publications

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“…These results are similar to that observed in protozoa such as G. duodenalis [65] and some of the coding genes for the variant surface antigens in Plasmodium vivax [67]. This expansion might be due to a possible selection that has occurred in the Blastocystis genetic pool, which varied depending on the mutational rate or the recombination rate [68].…”

Section: Discussionsupporting

confidence: 83%

“…Some haplotypes were found to be associated specifically in the sampled geographic regions, principally in the Amazonas, but some shared haplotypes were observed by region and by ST ( Figure 5d and Supplementary material Figure S1). This could be explained by different reasons, such as inadequate sampling (low numbers of samples collected), limited divergence, hybridization, cryptic speciation, and incomplete lineage sorting [63,64,65]. Interestingly, when the ST analysis was conducted, groups of haplotypes that were associated with ST1 and ST2 were observed, while the haplotypes associated with ST3 were seen at a greater distribution in the sampled regions (Supplementary material Figure S1).…”

Section: Discussionmentioning

confidence: 99%

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Succinate dehydrogenase gene as a marker for studying Blastocystis genetic diversity

Higuera

Muñoz

López

et al. 2020

Heliyon

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Blastocystis has been reported as the most common eukaryotic microorganism residing in the intestines of both humans and animals, with a prevalence of up to 100% in some populations. Since this is a cryptic species, sequence polymorphism are the single strategy to analyses its genetic diversity, being traditionally used the analysis of ssu rRNA gene sequence to determine alleles and subtypes (STs) for this species. This multicopy gene has shown high diversity among different STs, making necessary to explore other genes to assess intraspecific diversity. This study evaluated the use of a novel genetic marker, succinate dehydrogenase (SDHA), for the typing and evaluation of the genetic diversity and genetic population structure of Blastocystis. In total, 375 human fecal samples were collected and subjected to PCR, subtyped using the ssu rRNA marker, and then the SDHA gene was amplified via PCR for 117 samples. We found some incongruences between tree topologies for both molecular markers. However, the clustering by ST previously established for Blastocystis was congruent in the concatenated sequence. SDHA showed lower reticulation (The origination of a lineage through the partial merging of two ancestor lineages) signals and better intra ST clustering ability. Clusters with geographical associations were observed intra ST. The genetic diversity was lower in the marker evaluated compared to that of the ssu rRNA gene (nucleotide diversity ¼ 0.03344 and 0.16986, respectively) and the sequences analyzed showed population expansion with genetic differentiation principally among STs. The ssu rRNA gene was useful to explore interspecific diversity but together with the SDHA gene the resolution power to evaluate intra ST diversity was higher. These results showed the potential of the SDHA marker for studying the intra ST genetic diversity of Blastocystis related with geographical location and the inter ST diversity using the concatenated sequences.

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Section: Discussionsupporting

confidence: 83%

Section: Discussionmentioning

confidence: 99%

Succinate dehydrogenase gene as a marker for studying Blastocystis genetic diversity

Higuera

Muñoz

López

et al. 2020

Heliyon

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“…Within assemblage B there is a consistently greater degree of genetic diversity than assemblage A [51, 52]. Additionally, there is ongoing population expansion of Giardia haplotype diversity across all continents [53]. Even within a single isolate, Giardia displays a high degree of allelic sequence heterozygosity [54].…”

Section: Giardia By Any Other Name…mentioning

confidence: 99%

Giardia: a pathogen or commensal for children in high-prevalence settings?

Bartelt

Platts-Mills

2016

Current Opinion in Infectious Diseases

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Purpose of review Giardia is a common intestinal parasite worldwide, and infection can be associated with clear and sometimes persistent symptomatology. However, in children in high prevalence settings, it is not associated with or is perhaps even protective against acute diarrhea, and the association with long-term outcomes has been difficult to discern. Recent findings Recent studies have made progress in helping us disentangle this apparent paradox. First, prospective, well-characterized cohort studies have added to the data on the association between Giardia and diarrhea in these settings and have further characterized associations between Giardia infection and nutrition, gut function, and growth. Second, animal models have further characterized the host response to Giardia and helped elucidate mechanisms by which Giardia could impair child development. Finally, new work has shed light on the heterogeneity of human Giardia strains, which may both explain discrepant findings in the literature and help guide higher-resolution analyses of this pathogen in the future. Summary The true clinical impact of endemic pediatric giardiasis remains unclear, but recent prospective studies have confirmed a high prevalence of persistent, subclinical Giardia infections and associated growth shortfalls. Integrating how nutritional, microbial, metabolic, and pathogen-strain variables influence these outcomes could sharpen delineations between pathogenic and potentially beneficial attributes of this enigmatic parasite.

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“…Eight genetically distinct genotypes (assemblage A to H) of G. duodenalis have been identified [ 5 , 6 ]. Two of the assemblages (A and B) have broad host ranges [ 6 , 7 ] and parasitise humans [ 8 , 9 ], marine vertebrates [ 6 ] and certain other mammals [ 10 , 11 ]. The remaining six assemblages (C to H) are host-specific and infect animals [ 6 , 11 ], although assemblages C [ 1 , 12 ] and E [ 13 ] have been reported from human isolates.…”

Section: Introductionmentioning

confidence: 99%

Molecular epidemiology of Giardia duodenalis infection in humans in Southern Ethiopia: a triosephosphate isomerase gene-targeted analysis

et al. 2018

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BackgroundGiardia duodenalis is a species complex consisting of multiple genetically distinct assemblages. The species imposes a major public health crisis on developing countries. However, the molecular diversity, transmission dynamics and risk factors of the species in these countries are indeterminate. This study was conducted to determine the molecular epidemiology of G. duodenalis infection in asymptomatic individuals in Southern Ethiopia.MethodsFrom March to June 2014, fresh stool samples were collected from 590 randomly selected individuals. Socio-demographic data were gathered using a pre-tested structured questionnaire. The genotyping was done using triosephosphate isomerase gene-based nested polymerase chain reaction and DNA sequencing. The genetic identity and relatedness of isolates were determined using the basic local alignment search tool and phylogenetic analysis. Risk factors associated with G. duodenalis infection were analysed using binary and multinomial logistic regression models.ResultsThe results showed that 18.1% (92/509) of the study subjects were infected by G. duodenalis. Among the isolates, 35.9% (33/92) and 21.7% (20/92) were sub-typed into assemblages A and B, respectively, whereas 42.4% (39/92) showed mixed infections of A and B. Most of the assemblage A isolates (94%,31/33) were 100% identical to sequences registered in GenBank, of which the majority belonged to sub-assemblage AII. However, the high genetic variability and frequency of double peaks made sub-genotyping of assemblage B more problematic and only 20% (4/20) of the isolates matched 100% with the sequences. The risk factors of age (P = 0.032) and type of drinking water source (P = 0.003) both showed a significant association with the occurrence G. duodenalis infection.ConclusionsThis study established the endemicity of G. duodenalis in Southern Ethiopia. Infection with assemblage A was more frequent than with assemblage B, and the rate of infection was higher in children and in municipal/tap and open spring water consumers than the other groups. Sub-typing of assemblage B and determining the origin of double peaks were challenging. The present study confirms the need for further inclusive studies to be conducted focusing on sub-types of assemblage B and the origin of heterogeneity.Electronic supplementary materialThe online version of this article (10.1186/s40249-018-0397-4) contains supplementary material, which is available to authorized users.

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Population expansion and gene flow in Giardia duodenalis as revealed by triosephosphate isomerase gene

Cited by 28 publications

References 41 publications

Succinate dehydrogenase gene as a marker for studying Blastocystis genetic diversity

Succinate dehydrogenase gene as a marker for studying Blastocystis genetic diversity

Giardia: a pathogen or commensal for children in high-prevalence settings?

Molecular epidemiology of Giardia duodenalis infection in humans in Southern Ethiopia: a triosephosphate isomerase gene-targeted analysis

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