Population genetic analysis of <i>Giardia duodenalis</i>: genetic diversity and haplotype sharing between clinical and environmental sources

Durigan, Maurício; Ciampi‐Guillardi, Maisa; Rodrigues, Ricardo Conde Alves; Greinert-Goulart, Juliane Araújo; Siqueira-Castro, Isabel Cristina Vidal; Leal, Diego Averaldo Guiguet; Yamashiro, Sandra; Bonatti, Taís Rondello; Zucchi, Maria Imaculada; Franco, Regina Maura Bueno; Souza, Anete Pereira de

doi:10.1002/mbo3.424

Cited by 11 publications

(13 citation statements)

References 40 publications

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“…At the same time, it is noted that the research method used in the current study has its own biases (primarily related to trophozoite propagation as noted above). For example, the lack of assemblages C, D, and E detected in animal samples and the relatively low proportion of assemblage A2 in the study collection ( 51 ) may be based on the phenotypic ability of the isolates to adapt to in vitro growth.…”

Section: Discussionmentioning

confidence: 99%

Beaver Fever: Whole-Genome Characterization of Waterborne Outbreak and Sporadic Isolates To Study the Zoonotic Transmission of Giardiasis

Tsui

Miller

Uyaguari

et al. 2018

mSphere

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Giardia duodenalis causes large numbers of gastrointestinal illness in humans. Its transmission through the contaminated surface water/wildlife intersect is significant, and the water-dwelling rodents beavers have been implicated as one important reservoir. To trace human infections to their source, we used genome techniques to characterize genetic relationships among 89 Giardia isolates from surface water, humans, and animals. Our study showed the presence of two previously described genetic assemblages, A and B, with mixed infections detected from isolates collected during outbreaks. Study findings also showed that while assemblage A could be divided into A1 and A2, A1 showed little genetic variation among animal and human hosts in isolates collected from across the globe. Assemblage B, the most common type found in the study surface water samples, was shown to be highly variable. Our study demonstrates that the beaver is a possible source of human infections from contaminated surface water, while acknowledging that theirs is only one role in the complex cycle of zoonotic spread. Mixes of parasite groups have been detected in waterborne outbreaks. More information on Giardia diversity and its evolution using genomics will further the understanding of the epidemiology of spread of this disease-causing protozoan.

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Section: Discussionmentioning

confidence: 99%

Beaver Fever: Whole-Genome Characterization of Waterborne Outbreak and Sporadic Isolates To Study the Zoonotic Transmission of Giardiasis

Tsui

Miller

Uyaguari

et al. 2018

mSphere

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“…As the DNA samples used in this study were the same ones from our previous studies [34,35] we could compare some of the SSR results with the conventional Giardia molecular markers (gdh, tpi and bg) regarding the molecular genotyping of the samples. SSR profiles of the polymorphic markers GduA10, GduA16, GduA20, GduA24 showed that samples HC31, HC48 and HC22, considered clonal according to the conventional (MLG BRA01) markers [34] were different based on the MLG profiles obtained by microsatellites we characterized.…”

Section: Resultsmentioning

confidence: 99%

“…DNA samples from specimens from different genotypes such as AI, AII, BIII, BIV, C, D, and E used in this study were evaluated in previous studies to confirm their corresponding genetic assemblages and the absence of mixed assemblages [34,35]. Only samples undoubtedly assigned to a specific genetic assemblage and with no evidence of mixed assemblages according to conventional markers such the tpi , gdh and bg genes, were used in this study.…”

Section: Methodsmentioning

confidence: 99%

“…To screen for genetic variation at inter- and intra-assemblage levels, thus validate the application of the microsatellite markers developed in this study as tools population genetics-based epidemiological studies, the genotyping profiles obtained in this study were compared with the conventional Giardia molecular markers (gdh, tpi and bg) as the DNA samples used in this study were previously analyzed [34,35]. Additionally, we analyzed one dataset composed only by isolates from genetic assemblages AI and AII and another composed by samples from genetic assemblage BIV.…”

Section: Methodsmentioning

confidence: 99%

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Molecular genotyping, diversity studies and high-resolution molecular markers unveiled by microsatellites in Giardia duodenalis

et al. 2018

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BackgroundGiardia duodenalis (synonyms G. lamblia and G. intestinalis) is an enteric protozoan parasite of a wide range of mammalian hosts, including humans and various domestic and wild animals. There is considerable genetic variability in G. duodenalis and isolates of this parasite have been divided into eight genetic assemblages. Microsatellites markers can be used to discriminate isolates with a high level of sensitivity. This study was conducted to identify and characterize genomic microsatellites (simple sequence repeats—SSRs), sequences of one- to six-nucleotide motifs repeated in tandem, present in the available genomes of G. duodenalis and to develop new markers that can serve as a tool for detection and for characterizing the genetic diversity of this parasite.Methodology/ Principal findingsFor each genetic assemblage, polymorphism levels for the microsatellite markers were evaluated. After performing the analysis using the MISA and SciRoKo software, 1,853 simple sequence repeats (SSRs) were identified. In all the genomes, trinucleotide repeats were the most common class followed by tetranucleotide. Many of the SSR loci are assemblage-specific, and 36 SSR loci shared among all the genomes were identified. Together with hypothetical proteins, variant-specific surface proteins represented nearly half of the annotated SSR loci. The results regarding the most common repeat among the SSRs led us to infer that positive selection occurred to avoid frameshift mutations. Additionally, based on inter- and intra-genetic assemblages polymorphism analyses, we unveiled previously undetected genetic variation, indicating that the microsatellite markers we developed are useful molecular tools for epidemiological inferences based on population genetics patterns and processes.ConclusionsThere is increasing demand for the development of new molecular markers and for the characterization of pathogens at a higher resolution level. In this study, we present 60 G. duodenalis microsatellites markers that exhibited high polymerase chain reaction (PCR) amplification efficiency among the different genetic assemblages. Twenty of these markers presented nucleotide sequence polymorphisms and may be used as a genotyping tool. The monomorphic markers can be used for the detection of the parasite at the species and genetic assemblage level. These polymorphic markers revealed a genetic diversity that was previously undetectable, thus they can be considered valuable molecular tools for high resolution markers in future studies investigating Giardia and may also be used for epidemiological inferences based on populations genetics patterns and processes.

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“…Such markers should possess sufficient discriminatory power to establish groupings related to epidemiological factors. Thus, investigation of new markers should focus on detection and typing, and allow additional inference on reproduction, evolution, zoonotic potential and population structure [ 30 , 31 , 32 ]. Some studies show that multilocus sequences are useful for identifying species, genera and populations, characterising isolates with conserved genes with low variation, and thus establishing allelic profiles in study populations [ 33 ].…”

Section: Introductionmentioning

confidence: 99%

Development of a Multilocus Sequence Typing Scheme for Giardia intestinalis

Higuera

Muñoz

López

et al. 2020

Genes

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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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Population genetic analysis of Giardia duodenalis: genetic diversity and haplotype sharing between clinical and environmental sources

Cited by 11 publications

References 40 publications

Beaver Fever: Whole-Genome Characterization of Waterborne Outbreak and Sporadic Isolates To Study the Zoonotic Transmission of Giardiasis

Beaver Fever: Whole-Genome Characterization of Waterborne Outbreak and Sporadic Isolates To Study the Zoonotic Transmission of Giardiasis

Molecular genotyping, diversity studies and high-resolution molecular markers unveiled by microsatellites in Giardia duodenalis

Development of a Multilocus Sequence Typing Scheme for Giardia intestinalis

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