A novel high-resolution multilocus sequence typing of Giardia intestinalis Assemblage A isolates reveals zoonotic transmission, clonal outbreaks and recombination

Zoonotic assemblages A and B of Giardia duodenalis in Chiroptera from Brazilian Amazon biome

Bats are important reservoirs and spreaders of pathogens. Giardia duodenalis is a globally important protozoan that infects humans and other mammals with considerable public health burden, particularly on the child development. Based on genetic variation and host specificity, G. duodenalis is categorized into eight genotypes/assemblages A-H. Assemblages A and B are widespread globally and are associated with human and animal disease. There is evidence of Giardia in the bat feces from diverse geographic regions, but the G. duodenalis assemblages are unknown, which is a key point for the One Health view. Here, we successfully amplified the BG/GDH/DIS3/HCMP2/HCMP3 targets of G. duodenalis from five bat species captured in the Brazilian Amazon biome revealing the presence of zoonotic G. duodenalis assemblages A and B in the feces of these flying mammals. Our study reveals that bats may play a role in transmission of zoonotic G. duodenalis, at least in this biome.

Autochthonous and imported giardiasis cases: An analysis of two decades of national surveillance data, Germany, 2002 to 2021

BackgroundGiardia duodenalis is a major cause of gastroenteritis globally, and is the most common food- and waterborne parasitic infection in Europe.AimTo describe the epidemiology of reported acute giardiasis cases in Germany and compare demographic and clinical characteristics between imported and autochthonous cases.MethodsWe conducted a descriptive analysis of giardiasis cases that fulfilled the national case definition and were reported between January 2002 and December 2021. We defined an imported case as having at least one place of exposure abroad in the 3-25 days before symptom onset. We analysed case numbers and incidence by age, sex, month reported and geographic region, both overall and stratified by autochthonous and imported cases.ResultsFrom 2002 to 2021, 72,318 giardiasis cases were reported in Germany, corresponding to a mean annual incidence of 4.4 per 100,000 population. Annual incidence gradually decreased since 2013, declining sharply during the COVID-19 pandemic in 2020-21. Of 69,345 cases reported between 2002 and 2019, 35% were imported. Incidence of autochthonous cases (overall yearly mean: 3.1/100,000) was highest in males and young children (< 5 years); imported cases were predominantly adults aged 20-39 years. We identified seasonal patterns for imported and autochthonous cases.ConclusionsGiardiasis in Germany is typically assumed to be imported. Our data, however, underline the importance of autochthonous giardiasis. Travel advice might reduce imported infections, but prevention strategies for autochthonous infections are less clear. Dietary, behavioural and environmental risk factors need to be further investigated to enhance infection prevention measures for autochthonous giardiasis.

Rabbits as reservoirs: An updated perspective of the zoonotic risk from Cryptosporidium and Giardia

Rabbits are highly abundant in many countries and can serve as reservoirs of diseases for a diversity of pathogens including the enteric protozoan parasites, Cryptosporidium and Giardia. Both parasites shed environmentally robust environmental stages (oo/cysts) and have been responsible for numerous waterborne outbreaks of diseases. Cryptosporidium hominis and C. parvum are responsible for most infections in humans, while Giardia duodenalis assemblages A and B, cause most human cases of giardiasis. Cryptosporidium cuniculus, the dominant species infecting rabbits, is the only spceies other than C. hominis and C. parvum to have caused a waterborne outbreak of gastritis, which occurred in the United Kingdom in 2008. This review examines the prevalence of Cryptosporidium and Giardia species in rabbits to better understand the public health risks of contamination of water sources with Cryptosporidium and Giardia oo/cysts from rabbits. Despite the abundance of C. cuniculus in rabbits, reports in humans are relatively rare, with the exception of the United Kingdom and New Zealand, and reports of C. cuniculus in humans from the United Kingdom have declined substantially since the 2008 outbreak. Subtyping of C. cuniculus has supported the potential for zoonotic transmission. Relatively few studies have been conducted on Giardia, but assemblage B dominates. However, improved typing methods are required to better understand the transmission dynamics of Giardia assemblages in rabbits. Similarly, it is not well understood if pet rabbits or contaminated water are the main source of C. cuniculus infections in humans. Well-planned studies using high-resolution typing tools are required to understand the transmission dynamics better and quantify the public health risk of Cryptosporidium and Giardia from rabbits.

Assemblages and Subassemblages of Giardia duodenalis in Rural Western, Kenya: Association with Sources, Signs, and Symptoms

Background

Giardia duodenalis causes sporadic or epidemic infections in humans. The parasite comprises assemblages A-H with A and B subdivided further into AI-IV and BI-IV subassemblages. Attempts aimed at linking these genotypes with sources and gastrointestinal manifestations of the infection are largely unexplored in rural communities.

Methods

In this cross-sectional study, G. duodenalis infection was genotyped and associated with sources, and gastrointestinal signs and symptoms of the disease among residents of Busia County, a rural setting in western Kenya. Demographic and clinical information were captured using standardized forms. Stool specimens were obtained from the patients and used for genotyping at glutamate dehydrogenase and triose-phosphate isomerase loci using the polymerase chain reaction and restriction fragment length polymorphism.

Results

Assemblage B (63.6%) was the most prevalent G. duodenalis infection, while A (20.5%) and mixed A/B (15.9%) were also detected. Among the subassemblages, AI (5.7%), AII (8.0%), AIII (3.4), BIII (30.7%), and BIV (17.0%) were diagnosed including the mixed AII/BIII (15.9%), BIII/BIV (15.9%), AI/AIII (2.3%), and AI/AII (1.1%) infections. Binary logistic regression indicated associations for assemblage A with stomach upset, history of nitroimidazole treatment, and residing in a homestead with cattle and B with age < 18 years, history of eating outdoors, vomiting, steatorrhea, and residing in a homestead with cattle, goats, and poultry (p < 0.05 for all). Among the subassemblages, associations were found for AI with residing in a homestead having cattle and history of nitroimidazole treatment, BIII with residing in a homestead having cattle and poultry, and BIV with steatorrhea (p < 0.05 for all). Altogether, this study illustrates that G. duodenalis assemblage B and subassemblage BIII are the most predominant and are linked to age < 18 years, gastrointestinal manifestations, and living in a homestead with domestic ruminants and poultry.

Conclusion

Targeted mass prophylactic treatment of domestic animals and utilization of gastrointestinal presentations, age < 18 years, and a history of nitroimidazole use are useful in the diagnosis and prevention of giardiasis among residents of rural communities.

Zoonotic Cryptosporidium and Giardia in marsupials-an update

Marsupials, inhabiting diverse ecosystems, including urban and peri-urban regions in Australasia and the Americas, intersect with human activities, leading to zoonotic spill-over and anthroponotic spill-back of pathogens, including Cryptosporidium and Giardia. This review assesses the current knowledge on the diversity of Cryptosporidium and Giardia species in marsupials, focusing on the potential zoonotic risks. Cryptosporidium fayeri and C. macropodum are the dominant species in marsupials, while in possums, the host-specific possum genotype dominates. Of these three species/genotypes, only C. fayeri has been identified in two humans and the zoonotic risk is considered low. Generally, oocyst shedding in marsupials is low, further supporting a low transmission risk. However, there is some evidence of spill-back of C. hominis into kangaroo populations, which requires continued monitoring. Although C. hominis does not appear to be established in small marsupials like possums, comprehensive screening and analysis are essential for a better understanding of the prevalence and potential establishment of zoonotic Cryptosporidium species in small marsupials. Both host-specific and zoonotic Giardia species have been identified in marsupials. The dominance of zoonotic G. duodenalis assemblages A and B in marsupials may result from spill-back from livestock and humans and it is not yet understood if these are transient or established infections. Future studies using multilocus typing tools and whole-genome sequencing are required for a better understanding of the zoonotic risk from Giardia infections in marsupials. Moreover, much more extensive screening of a wider range of marsupial species, particularly in peri-urban areas, is required to provide a clearer understanding of the zoonotic risk of Cryptosporidium and Giardia in marsupials.

Zoonotic Giardia duodenalis assemblage A in northern sloth from Brazilian Amazon

BACKGROUND

The parasite Giardia duodenalis infects a wide range of vertebrate hosts, including domestic and wild animals as well as humans. Giardia is genotyped into eight assemblages (A-H). Zoonotic assemblages A and B have already been identified in humans and wild and domestic animals (non-human primates and cats) from Brazilian Amazon and in the world. Due to its zoonotic/zooanthroponotic nature, surveillance initiatives and the definition of Giardia assemblages are important in order to characterise the epidemiological scenario and to implement further control measures.

OBJECTIVES

Determine assemblages of G. duodenalis in sloths from the Brazilian Amazon Region.

METHODS

Faecal parasitological examination of sloths from Amazonas State. Polymerase chain reaction (PCR) targeting the beta giardin (BG), and genes from multilocus sequence typing (MLST) scheme, amplicon sequencing and phylogenetic analysis.

FINDINGS

Here, we identified, by microscopy, Giardia in two northern sloths (Bradypus tridactylus). These two samples were submitted to molecular assays and it was revealed that both were infected by G. duodenalis assemblage A. Phylogenetic analysis showed that they belong to assemblage A within sequences from humans and wild and domestic animals.

CONCLUSION

Therefore, besides showing, by the first time, the current presence of this parasite in sloths, our findings reveals that this wild animal species would be part of the zoonotic/zooanthroponotic scenario of this parasite in the Brazilian Amazon.

Parasites and zoonotic bacteria in the feces of cats and dogs from animal shelters in Carinthia, Austria

Due to their close associations with humans, dogs and cats can be important reservoirs for zoonotic pathogens. In the current study 200 fecal samples of dogs (n = 70 samples) and cats (n = 130 samples) from animal shelters in Carinthia, southern Austria, were examined for the presence of parasites (fecal flotation and larval migration assay) and selected bacteria. Overall, 17.1% of the canine and 38.5% of the feline samples were positive for parasites (p < 0.001), most commonly Giardia duodenalis (dogs and cats), including potentially zoonotic genotypes revealed by multilocus genotyping, and Toxocara cati (cats). Cryptosporidium (C. felis), Cystoisospora spp. (dogs and cats), hookworms (dog), Trichuris (dog) Capillaria hepatica (cats), taeniids (cat), and Aelurostrongylus abstrusus (cat) were also found. Zoonotic bacteria were detected in 10.5% of the samples, Salmonella enterica (dogs), Campylobacter jejuni (dogs and cats) and Yersinia enterocolitica (cat) and were significantly associated with parasite infections in cats but not in dogs. Samples that were positive for several pathogens were common; especially G. duodenalis and T. cati were frequently found in association with each other, other parasites or bacteria. The spectrum of detected pathogens is comparable to that of other dog and cat populations in central Europe. However, since animals from shelters are frequently rehomed, diagnostic measures, appropriate hygiene and therapy as well as training of shelter staff are recommended to prevent zoonotic transmission of enteropathogens to staff or new owners. The presence of heteroxenic parasites, i.e. Aelurostrongylus abstrusus and Taenia taeniaeformis, and spurious excretion of Ca. hepatica in cats, indicates that these animals preyed on intermediate hosts, and that biosafety measures in pet shelters need to be evaluated for their efficacy in the prevention of pathogen transmission.

Genetic diversity and molecular diagnosis of Giardia

Giardia is a genus of flagellated protozoan parasites that infect the small intestine of humans and animals, causing the diarrheal illness known as giardiasis. Giardia exhibits significant genetic diversity among its isolates, which can have important implications for disease transmission and clinical presentation. This diversity is influenced by the coevolution of Giardia with its host, resulting in the development of unique genetic assemblages with distinct phenotypic characteristics. Although panmixia has not been observed, some assemblages appear to have a broader host range and exhibit higher transmission rates. Molecular diagnostic methods enable researchers to examine the genetic diversity of Giardia populations, enhancing our understanding of the genetic diversity, population structure, and transmission patterns of this pathogen and providing insights into clinical presentations of giardiasis.

Proposed taxonomic revision of Giardia duodenalis

Giardia duodenalis, Giardia enterica, Giardia intestinalis and Giardia lamblia are the synonyms for a species complex of 8-11 phylogenetically distinct species of Giardia infecting a broad range of animals including humans. Retrospective alignment of 8409 gene sequences from 3 loci confirmed host associations of Assemblages and sub-Assemblages within this species complex and molecular species delimitation testing confirmed that the Assemblages and sub-Assemblages AI and AII should be recognised as distinct species. It is recommended to synonymise the Assemblages with historic species descriptions based on host associations and consider descriptions for new species where no corresponding description exists. Synonyms, Giardia duodenalis, Giardia intestinalis and Giardia enterica, to be removed from synonymy: synonymise "Giardia duodenalis-Assemblage AI" syn. n. to Giardia duodenalis (Davaine, 1875), Kofoid and Christansen, 1915, synonymise "Giardia duodenalis-Assemblage AII" syn. n. to Giardia intestinalis (Lambl, 1859; Blanchard, 1885), Alexeieff, 1914 and synonymise "Giardia duodenalis-Assemblage B" syn. n. to Giardia enterica (Grassi, 1881a), Kofoid, 1920. Host specific Assemblages synonymised: synonymise canid-associated "Giardia duodenalis-Assemblage C" syn. n. to Giardia canisHegner, 1922; synonymise artiodactyl-associated "Giardia duodenalis-Assemblage E" syn. n. to Giardia bovisFantham, 1921; synonymise feline-associated "Giardia duodenalis-Assemblage F" syn. n. to Giardia catiDeschiens, 1925; and synonymise rodent-associated "Giardia duodenalis-Assemblage G" syn. n. to Giardia simoniLavier, 1924. New description for parasite type infecting specific host: canid-associated "Giardia duodenalis-Assemblage D" named Giardia lupus, sp. n. (LSID: urn:lsid:zoobank.org:act:1651A8CB-CBA8-40D9-AB59-D4AB11AC18A3). New proposed names and descriptions for consideration for parasite types infecting specific hosts: cervid-associated "Giardia duodenalis-sub-Assemblage AIII" for consideration "cervus" and Pinnipedia-associated "Giardia duodenalis-Assemblage H" for consideration "pinnipedis".

High Diversity of Giardia duodenalis Assemblages and Sub-Assemblages in Asymptomatic School Children in Ibadan, Nigeria

Giardia duodenalis is a significant contributor to the burden of diarrheal disease in sub-Saharan Africa. This study assesses the occurrence and molecular diversity of G. duodenalis and other intestinal parasites in apparently healthy children (n = 311) in Ibadan, Nigeria. Microscopy was used as a screening method and PCR and Sanger sequencing as confirmatory and genotyping methods, respectively. Haplotype analyses were performed to examine associations between genetic variants and epidemiological variables. At microscopy examination, G. duodenalis was the most prevalent parasite found (29.3%, 91/311; 95% CI: 24.3–34.7), followed by Entamoeba spp. (18.7%, 58/311; 14.5–23.4), Ascaris lumbricoides (1.3%, 4/311; 0.4–3.3), and Taenia sp. (0.3%, 1/311; 0.01–1.8). qPCR confirmed the presence of G. duodenalis in 76.9% (70/91) of the microscopy-positive samples. Of them, 65.9% (60/91) were successfully genotyped. Assemblage B (68.3%, 41/60) was more prevalent than assemblage A (28.3%, 17/60). Mixed A + B infections were identified in two samples (3.3%, 2/60). These facts, together with the absence of animal-adapted assemblages, suggest that human transmission of giardiasis was primarily anthroponotic. Efforts to control G. duodenalis (and other fecal-orally transmitted pathogens) should focus on providing safe drinking water and improving sanitation and personal hygiene practices.

Subspecific Nomenclature of Giardia duodenalis in the Light of a Compared Population Genomics of Pathogens

Genetic and genomic data have long recognized that the species Giardia duodenalis is subdivided into at least eight genetic clusters that have been named "assemblages" by specialists in the field. Some of these assemblages have been given the status of species, with Linnean binames. In the framework of the predominant clonal evolution model (PCE), we have shown that, from an evolutionary point of view, G. duodenalis assemblages are equatable to "near-clades", that is to say: clades whose discreteness is somewhat clouded by occasional genetic exchange, but remain discrete and stable in space and time. The implications of this evolutionary status for the species described within G. duodenalis are discussed in light of the most recent genetic and genomic studies. The pattern of this species' subspecific genetic variability and genetic clustering appears to be very similar to the ones of various parasitic, fungal and bacteria species. This underlines the relevance of a compared population genomics of pathogenic species allowed by the broad framework of the PCE model.

Extensive testing of a multi-locus sequence typing scheme for Giardia duodenalis assemblage A confirms its good discriminatory power

BACKGROUND

The flagellated parasite Giardia duodenalis is a major and global cause of diarrhoeal disease. Eight genetically very distinct groups, known as assemblages A to H, have been recognized in the G. duodenalis species complex, two of which (assemblages A and B) infect humans and other mammalian hosts. Informative typing schemes are essential to understand transmission pathways, characterize outbreaks and trace zoonotic transmission. In this study, we evaluated a published multi-locus sequence typing (MLST) scheme for G. duodenalis assemblage A, which is based on six polymorphic markers.

METHODS

We genotyped 60 human-derived and 11 animal-derived G. duodenalis isolates collected in Europe and on other continents based on the published protocol. After retrieving previously published genotyping data and excluding isolates whose sequences showed allelic sequence heterozygosity, we analysed a dataset comprising 146 isolates.

RESULTS

We identified novel variants at five of the six markers and identified 78 distinct MLST types in the overall dataset. Phylogenetic interpretation of typing data confirmed that sub-assemblage AII only comprises human-derived isolates, whereas sub-assemblage AI comprises all animal-derived isolates and a few human-derived isolates, suggesting limited zoonotic transmission. Within sub-assemblage AII, isolates from two outbreaks, which occurred in Sweden and Italy, respectively, had unique and distinct MLST types. Population genetic analysis showed a lack of clustering by geographical origin of the isolates.

CONCLUSION

The MLST scheme evaluated provides sufficient discriminatory power for epidemiological studies of G. duodenalis assemblage A.

Genomic comparisons confirm Giardia duodenalis sub-assemblage AII as a unique species

Giardia duodenalis is a parasitic flagellated protozoan which infects a wide range of mammalian hosts, including humans, and is subdivided into at least eight genetic assemblages commonly thought to represent cryptic species. Molecular studies have shown that G. duodenalis assemblage A, which parasitizes humans and animals, contains several phylogenetically distinct groupings known as sub-assemblages. Molecular studies employing poor phylogenetic-resolution markers routinely recover these sub-assemblages, implying that they represent evolutionarily distinct clades and possibly cryptic species, a hypothesis which is supported by epidemiologic trends. Here, we further tested this hypothesis by using available data from 41 whole genomes to characterize sub-assemblages and coalescent techniques for statistical estimation of species boundaries coupled to functional gene content analysis, thereby assessing the stability and distinctiveness of clades. Our analysis revealed two new sub-assemblage clades as well as novel signatures of gene content geared toward differential host adaptation and population structuring via vertical inheritance rather than recombination or panmixia. We formally propose sub-assemblage AII as a new species, Giardia hominis, while preserving the name Giardia duodenalis for sub-assemblage AI. Additionally, our bioinformatic methods broadly address the challenges of identifying cryptic microbial species to advance our understanding of emerging disease epidemiology, which should be broadly applicable to other lower eukaryotic taxa of interest. Giardia hominis n. sp. Zoobank LSID: urn:lsid: zoobank.org:pub:4298F3E1-E3EF-4977-B9DD-5CC59378C80E.

Cryptosporidium and Giardia infections in humans in Tigray, Northern Ethiopia: an unexpectedly low occurrence of anthropozoonotic transmission

Enteric protozoans Cryptosporidium spp. and Giardia duodenalis are among the leading causes of diarrhoea in children. These parasites have particular impact in low- and middle-income countries. In these countries, people often live in close contact with their animals, highlighting the potential role of zoonotic routes of transmission in disease spread. The occurrence and species/genotypes of Cryptosporidium and Giardia duodenalis infecting humans in Tigray, Ethiopia were investigated, along with the risk associated with infection. Stool samples from 249 asymptomatic people (4-80 years of age) in four rural districts in Tigray and 58 from symptomatic young children (1-33 months) attending health centres in Mekelle, Tigray's main city, were analysed for Cryptosporidium oocysts and Giardia cysts. Participants in the rural areas completed questionnaires regarding potential risk factors, with emphasis on livestock contact and sources of water. The occurrence of Cryptosporidium infection was 6% and 5% in people in the rural districts and young children from Mekelle, respectively; equivalent figures for Giardia infection were 29% and 14%. Molecular characterization of Cryptosporidium isolates revealed C. ubiquitum, subtype XIIa in a sample from rural districts, and C. hominis subtype IdA17 (1 sample) and IbA9G3 (2 samples) in infants from Mekelle with diarrhoea. For Giardia, Assemblage B predominated (22/25; 88%), but we also identified three samples with Assemblage A (AII). Our major finding was that, despite the close contact between people and livestock in our rural study sites, transmission of Cryptosporidium and Giardia between humans and their animals seems to be surprisingly uncommon. Our results are discussed in relation to other relevant studies, and also draws attention to the possibility that introduction of zoonotic species and/or subtypes, such as C. parvum, could have serious consequences for both human and animal health. As our study was conducted in Tigray, further investigation in different settings in Ethiopia could provide relevant information on transmission and zoonotic potential, and the potential for spread of zoonotic transmission. In addition, given the importance of these two parasites in causing diarrhoea in children, this information is vital for developing effective appropriate interventions against transmission that can be applied not only in Tigray or Ethiopia, but throughout Africa and beyond.

Efficient CRISPR/Cas9-mediated gene disruption in the tetraploid protist Giardia intestinalis

CRISPR/Cas9-mediated genome editing has become an extremely powerful technique used to modify gene expression in many organisms, including parasitic protists. Giardia intestinalis, a protist parasite that infects approximately 280 million people around the world each year, has been eluding the use of CRISPR/Cas9 to generate knockout cell lines due to its tetraploid genome. In this work, we show the ability of the in vitro assembled CRISPR/Cas9 components to successfully edit the genome of G. intestinalis. The cell line that stably expresses Cas9 in both nuclei of G. intestinalis showed effective recombination of the cassette containing the transcription units for the gRNA and the resistance marker. This highly efficient process led to the removal of all gene copies at once for three independent experimental genes, mem, cwp1 and mlf1. The method was also applicable to incomplete disruption of the essential gene, as evidenced by significantly reduced expression of tom40. Finally, testing the efficiency of Cas9-induced recombination revealed that homologous arms as short as 150 bp can be sufficient to establish a complete knockout cell line in G. intestinalis.

Zoonotic giardiasis: an update

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.

Giardia duodenalis: Biology and Pathogenesis

Giardia duodenalis captured the attention of Leeuwenhoek in 1681 while he was examining his own diarrheal stool, but, ironically, it did not really gain attention as a human pathogen until the 1960s, when outbreaks were reported. Key technological advances, including in vitro cultivation, genomic and proteomic databases, and advances in microscopic and molecular approaches, have led to an understanding that this is a eukaryotic organism with a reduced genome rather than a truly premitochondriate eukaryote. This has included the discovery of mitosomes (vestiges of mitochondria), a transport system with many of the features of the Golgi apparatus, and even evidence for a sexual or parasexual cycle. Cell biology approaches have led to a better understanding of how Giardia survives with two nuclei and how it goes through its life cycle as a noninvasive organism in the hostile environment of the lumen of the host intestine. Studies of its immunology and pathogenesis have moved past the general understanding of the importance of the antibody response in controlling infection to determining the key role of the Th17 response. This work has led to understanding of the requirement for a balanced host immune response that avoids the extremes of an excessive response with collateral damage or one that is unable to clear the organism. This understanding is especially important in view of the remarkable ranges of early manifestations, which range from asymptomatic to persistent diarrhea and weight loss, and longer-term sequelae that include growth stunting in children who had no obvious symptoms and a high frequency of postinfectious irritable bowel syndrome (IBS).

First report of novel assemblages and mixed infections of Giardia duodenalis in human isolates from New Zealand

Giardia duodenalis (syn. G. intestinalis and G. lamblia) is a protozoan parasite that cause disease (giardiasis) in humans and other animals. The pathogen is classified into eight assemblages, further divided into sub-assemblages, based on genetic divergence and host specificities. There are two zoonotic subtypes known as assemblages A and B, whilst assemblages from C to H are mainly found in domesticated animals, rodents and marine mammals. Here, we report for the first time the presence of assemblage E and sub-assemblage AIII in human isolates from the South Island in New Zealand. We identified a > 99% nucleotide similarity of assemblage E and sub-assemblage AIII with sequences of the gdh gene available in GenBank from individual human samples collected in Dunedin and Christchurch, respectively. We also performed a deep sequencing approach to assess intra-host assemblage variation. The sample from Dunedin showed evidence of mixed assemblage E and zoonotic sub-assemblage BIV. The report of two novel assemblages and mixed infections provides insights into the genetic diversity, epidemiology and transmission dynamics of Giardia duodenalis in New Zealand.

The sexual side of parasitic protists

Much of the vast evolutionary landscape occupied by Eukaryotes is dominated by protists. Though parasitism has arisen in many lineages, there are three main groups of parasitic protists of relevance to human and livestock health: the Apicomplexa, including the malaria parasite Plasmodium and coccidian pathogens of livestock such as Eimeria; the excavate flagellates, encompassing a diverse range of protist pathogens including trypanosomes, Leishmania, Giardia and Trichomonas; and the Amoebozoa, including pathogenic amoebae such as Entamoeba. These three groups represent separate, deep branches of the eukaryote tree, underlining their divergent evolutionary histories. Here, I explore what is known about sex in these three main groups of parasitic protists.

Detection of enteric parasites and molecular characterization of Giardia duodenalis and Blastocystis sp. in patients admitted to hospital in Ankara, Turkey

This epidemiological study assesses the occurrence of enteric parasites in 4303 patients attended at two public hospitals in Ankara (Turkey) during 2018-2019. Microscopy was used as a screening test. Giardia duodenalis was also identified using a commercial ELISA for the detection of parasite-specific coproantigens. Giardia-positive samples by microscopy/ELISA were confirmed by real-time PCR and characterized using a multilocus genotyping scheme. Blastocystis sp. was genotyped in a sample subset. Blastocystis sp. (11.1%, 95% CI 11.4‒14.8%) and G. duodenalis (1.56%, 95% CI 1.22‒1.96) were the most prevalent pathogens found. Cryptosporidium spp., Entamoeba histolytica and intestinal helminths were only sporadically (<0.5%) found. For G. duodenalis, sequence (n = 30) analyses revealed the presence of sub-assemblages AII (23.3%), discordant AII/AIII (23.3%) and mixed AII + AIII (6.7%) within assemblage A, and BIII (10.0%), BIV (3.3%) and discordant BIII/BIV (23.3%) within assemblage B. Two additional sequences (6.7%) were assigned to the latter assemblage but sub-assemblage information was unknown. No associations between G. duodenalis assemblages/sub-assemblages and sociodemographic and clinical variables could be demonstrated. For Blastocystis sp., sequence (n = 6) analyses identified subtypes ST1, ST2 and ST3 at equal proportions. This is the first molecular characterization of G. duodenalis based on MLG conducted in Turkey to date.

Suitability of current typing procedures to identify epidemiologically linked human Giardia duodenalis isolates

Background

Giardia duodenalis is a leading cause of gastroenteritis worldwide. Humans are mainly infected by two different subtypes, i.e., assemblage A and B. Genotyping is hampered by allelic sequence heterozygosity (ASH) mainly in assemblage B, and by occurrence of mixed infections. Here we assessed the suitability of current genotyping protocols of G. duodenalis for epidemiological applications such as molecular tracing of transmission chains.

Methodology/Principal findings

Two G. duodenalis isolate collections, from an outpatient tropical medicine clinic and from several primary care laboratories, were characterized by assemblage-specific qPCR (TIF, CATH gene loci) and a common multi locus sequence typing (MLST; TPI, BG, GDH gene loci). Assemblage A isolates were further typed at additional loci (HCMP22547, CID1, RHP26, HCMP6372, DIS3, NEK15411).

Of 175/202 (86.6%) patients the G. duodenalis assemblage could be identified: Assemblages A 25/175 (14.3%), B 115/175 (65.7%) and A+B mixed 35/175 (20.0%). By incorporating allelic sequence heterozygosity in the analysis, the three marker MLST correctly identified 6/9 (66,7%) and 4/5 (80.0%) consecutive samples from chronic assemblage B infections in the two collections, respectively, and identified a cluster of five independent patients carrying assemblage B parasites of identical MLST type. Extended MLST for assemblage A altogether identified 5/6 (83,3%) consecutive samples from chronic assemblage A infections and 15 novel genotypes. Based on the observed A+B mixed infections it is estimated that only 75% and 50% of assemblage A or B only cases represent single strain infections, respectively. We demonstrate that typing results are consistent with this prediction.

Conclusions/Significance

Typing of assemblage A and B isolates with resolution for epidemiological applications is possible but requires separate genotyping protocols. The high frequency of multiple infections and their impact on typing results are findings with immediate consequences for result interpretation in this field.

Giardia duodenalis is a leading cause of gastroenteritis worldwide. Humans are mainly infected by the two different genetic subtypes, assemblage A and B. Molecular typing tools for epidemiological applications such as tracking transmission, attribution to a source and outbreak investigations have been developed and are highly desirable. However, to what degree the tetraploid genome with allelic sequence heterogeneity (ASH), and the frequent occurrence of mixed, assemblage A and B infections hamper performance is unclear. Here, we assessed the suitability of current genotyping protocols for deciphering the molecular epidemiology of G. duodenalis. Against a common reporting bias, we incorporated ASH in the analysis and we show that typing with resolution for epidemiological applications is possible for both, assemblage A and B isolates, but requires separate protocols. We also demonstrate how the high frequency of multiple infections overall impacts on typing results, which has immediate consequences for result interpretation in this field.

Multilocus Genotyping of Giardia duodenalis in Mostly Asymptomatic Indigenous People from the Tapirapé Tribe, Brazilian Amazon

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.

Occurrence and Multi-Locus Analysis of Giardia duodenalis in Coypus (Myocastor coypus) in China

Giardia duodenalis is a major gastrointestinal parasite found globally in both humans and animals. This work examined the occurrence of G. duodenalis in coypus (Myocastor coypus) in China. Multi-locus analysis was conducted to evaluate the level of genetic variation and the potential zoonotic role of the isolates. In total, 308 fecal samples were collected from seven farms in China and subjected to PCR screening to reveal G. duodenalis. Notably, G. duodenalis was detected in 38 (12.3%) specimens from assemblages A (n = 2) and B (n = 36). Positive samples were further characterized by PCR and nucleotide sequencing of the triose phosphate isomerase (tpi), beta giardin (bg), and glutamate dehydrogenase (gdh) genes. Multi-locus genotyping yielded 10 novel multi-locus genotypes (MLGs) (one MLG and nine MLGs for assemblages A and B, respectively). Based on the generated phylogenetic tree, AI-novel 1 clustered more closely with MLG AI-2. Furthermore, within the assemblage B phylogenetic analysis, the novel assemblage B MLGs were identified as BIV and clustered in the MLG BIV branch. This is the first report of G. duodenalis in coypus in China. The presence of zoonotic genotypes and subtypes of G. duodenalis in coypus suggests that these animals can transmit human giardiasis.

Models in parasite and pathogen evolution: Genomic analysis reveals predominant clonality and progressive evolution at all evolutionary scales in parasitic protozoa, yeasts and bacteria

The predominant clonal evolution (PCE) model of pathogenic microorganisms postulates that the impact of genetic recombination in those pathogens' natural populations is not enough to erase a persistent phylogenetic signal at all evolutionary scales from microevolution till geological times in the whole ecogeographical range of the species considered. We have tested this model with a set of representative parasitic protozoa, yeasts and bacteria in the light of the most recent genomic data. All surveyed species, including those that were considered as highly recombining, exhibit similar PCE patterns above and under the species level, from macro- to micro-evolutionary scales (Russian doll pattern), suggesting gradual evolution. To our knowledge, it is the first time that such a strong common evolutionary feature among very diverse pathogens has been evidenced. The implications of this model for basic biology and applied research are exposed. These implications include our knowledge on the pathogens' reproductive mode, their population structure, the possibility to type strain and to follow up epidemics (molecular epidemiology) and to revisit pathogens' taxonomy through a flexible use of the phylogenetic species concept (Cracraft, 1983).

Recirculation of Giardia lamblia Assemblage A After Metronidazole Treatment in an Area With Assemblages A, B, and E Sympatric Circulation

Giardia lamblia is an intestinal protozoan subdivided into eight assemblages, labeled alphabetically from A to H. Assemblages A, B, and E infect humans and can have a sympatric circulation. We investigated the assemblage recirculation in children living within a high prevalence area of Giardia infection. One hundred and ninety-four children were evaluated and 85 tested positive for Giardia by PCR. These infected individuals were recruited, treated with metronidazole and then reexamined for infections at 20 and 40 days after treatment that included PCR and the genotyping was performed by sequencing beta-giardin and glutamate dehydrogenase gene targets. Giardia assemblages A (n = 43), B (n = 21), E (n = 17), and A/E (n = 4) were identified in infected children. Assemblage A was found in all reoccurrences of infection, including four that had been infected by assemblages B and E. Since both persistence and reinfection could account for the results, the level of nucleotide homology was determined before and after treatment. Most suggested that reinfections were by the same strain, but four presented a distinct genotypic profile. The results suggest that the differences in the genotypic profiles were due to reinfections, which appear to occur with frequency in high Giardia burden areas and soon after the end of therapy. It is not yet possible to define whether the recurrent cases were related to parasite resistance. However, the evidence of rapid reinfections and ready availability of treatment raises the potential for creating resistant strains. This highlights the need to address how Giardia burden is maintained within high prevalence areas.

Molecular Epidemiology of Giardia Infections in the Genomic Era

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.

Update on Giardia: Highlights from the seventh International Giardia and Cryptosporidium Conference

Although Giardia duodenalis is recognized as one of the leading causes of parasitic human diarrhea in the world, knowledge of the mechanisms of infection is limited, as the pathophysiological consequences of infection remain incompletely elucidated. Similarly, the reason for and consequences of the very specific genome-organization in this parasite with 2 active nuclei is only partially known. Consistent with its tradition, the 7th International Giardia and Cryptosporidium Conference (IGCC 2019) was held from June 23 to 26, 2019, at the Faculty of Medicine and Pharmacy of the University of Rouen-Normandie, France, to discuss current research perspectives in the field. This renowned event brought together an international delegation of researchers to present and debate recent advances and identify the main research themes and knowledge gaps. The program for this interdisciplinary conference included all aspects of host-parasite relationships, from basic research to applications in human and veterinary medicine, as well as the environmental issues raised by water-borne parasites and their epidemiological consequences. With regard to Giardia and giardiasis, the main areas of research for which new findings and the most impressive communications were presented and discussed included: parasite ecology and epidemiology of giardiasis, Giardia-host interactions, and cell biology of Giardia, genomes and genomic evolution. The high-quality presentations discussed at the Conference noted breakthroughs and identified new opportunities that will inspire researchers and funding agencies to stimulate future research in a “one health” approach to improve basic knowledge and clinical and public health management of zoonotic giardiasis.

Development of a Multilocus Sequence Typing Scheme for Giardia intestinalis

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.

Whole-genome sequencing of dog-specific assemblages C and D of Giardia duodenalis from single and pooled cysts indicates host-associated genes

Giardia duodenalis (syn. Giardia intestinalis or Giardia lamblia) infSAects over 280 million people each year and numerous animals. G. duodenalis can be subdivided into eight assemblages with different host specificity. Unculturable assemblages have so far resisted genome sequencing efforts. In this study, we isolated single and pooled cysts of assemblages C and D from dog faeces by FACS, and sequenced them using multiple displacement amplification and Illumina paired-end sequencing. The genomes of assemblages C and D were compared with genomes of assemblages A and B from humans and assemblage E from ruminants and pigs. The genomes obtained from the pooled cysts and from the single cysts were considered complete (>99 % marker genes observed) and the allelic sequence heterozygosity (ASH) values of assemblages C and D were 0.89 and 0.74 %, respectively. These ASH values were slightly higher than for assemblage B (>0.43 %) and much higher than for assemblages A and E, which ranged from 0.002 to 0.037 %. The flavohaemoglobin and 4Fe-4S binding domain family encoding genes involved in O₂ and NO detoxification were only present in assemblages A, B and E. Cathepsin B orthologs were found in all genomes. Six clades of cathepsin B orthologs contained one gene of each genome, while in three clades not all assemblages were represented. We conclude that whole-genome sequencing from a single Giardia cyst results in complete draft genomes, making the genomes of unculturable Giardia assemblages accessible. Observed differences between the genomes of assemblages C and D on one hand and the assemblages A, B and E on the other hand are possibly associated with host specificity.

Benchmarking hybrid assemblies of Giardia and prediction of widespread intra-isolate structural variation

Background

Currently available short read genome assemblies of the tetraploid protozoan parasite Giardia intestinalis are highly fragmented, highlighting the need for improved genome assemblies at a reasonable cost. Long nanopore reads are well suited to resolve repetitive genomic regions resulting in better quality assemblies of eukaryotic genomes. Subsequent addition of highly accurate short reads to long-read assemblies further improves assembly quality. Using this hybrid approach, we assembled genomes for three Giardia isolates, two with published assemblies and one novel, to evaluate the improvement in genome quality gained from long reads. We then used the long reads to predict structural variants to examine this previously unexplored source of genetic variation in Giardia.

Methods

With MinION reads for each isolate, we assembled genomes using several assemblers specializing in long reads. Assembly metrics, gene finding, and whole genome alignments to the reference genomes enabled direct comparison to evaluate the performance of the nanopore reads. Further improvements from adding Illumina reads to the long-read assemblies were evaluated using gene finding. Structural variants were predicted from alignments of the long reads to the best hybrid genome for each isolate and enrichment of key genes was analyzed using random genome sampling and calculation of percentiles to find thresholds of significance.

Results

Our hybrid assembly method generated reference quality genomes for each isolate. Consistent with previous findings based on SNPs, examination of heterozygosity using the structural variants found that Giardia BGS was considerably more heterozygous than the other isolates that are from Assemblage A. Further, each isolate was shown to contain structural variant regions enriched for variant-specific surface proteins, a key class of virulence factor in Giardia.

Conclusions

The ability to generate reference quality genomes from a single MinION run and a multiplexed MiSeq run enables future large-scale comparative genomic studies within the genus Giardia. Further, prediction of structural variants from long reads allows for more in-depth analyses of major sources of genetic variation within and between Giardia isolates that could have effects on both pathogenicity and host range.

Epidemiological distribution of genotypes of Giardia duodenalis in humans in Spain

BACKGROUND

Although the distribution of Giardia duodenalis genotypes in humans has been increasingly reported in recent years, data on possible differences in pathogen transmission between age groups and virulence between genotypes are scarce. The purpose of this study is to investigate the genetic diversity of G. duodenalis in humans in Spain and compare the distribution of G. duodenalis assemblages A and B between children and adults and clinical presentations between the two genotypes.

METHODS

In the present study, 125 microscopy-positive fecal samples were collected from humans in Spain over a 7-year period. PCR and sequence analyses of the triosephosphate isomerase, β-giardin and glutamate dehydrogenase genes were used to identify the multilocus genotypes of G. duodenalis.

RESULTS

Sequence analysis of three genetic loci identified both G. duodenalis assemblages A (29) and B (66), with co-infections of the two in two patients. Among the sequences obtained in this study, four multilocus genotypes (MLGs) of the sub-assemblage AII were observed within assemblage A. In contrast, 19 MLGs were detected within assemblage B due to the high sequence diversity at each locus. One MLG, however, was found in 51.9% (27/52) of assemblage B samples. Children were more commonly infected by assemblage B (44/53 or 83%) than adults (22/42 or 52.4%; χ2 = 10.371, df = 1, P = 0.001). Asymptomatic infection was more common in patients with assemblage A (4/29 or 13.8%) than in those with assemblage B (1/66 or 1.5%; χ2 = 6.091, df = 1, P = 0.029), and the frequency of abdominal pain occurrence was higher in assemblage B patients (65/66 or 98.5%) than assemblage A patients (25/29 or 86.2%; χ2 = 6.091, df = 1, P = 0.029).

CONCLUSIONS

These results illustrate the existence of differences in genotype distribution between children and adults and clinical presentations between G. duodenalis genotypes. They are useful in understanding the transmission of G. duodenalis in humans in Spain.

Molecular epidemiology of Giardia and Cryptosporidium infections - What's new?

New information generated since 2016 from the application of molecular tools to infections with Giardia and Cryptosporidium is critically summarised. In the context of molecular epidemiology, nomenclature, taxonomy, in vitro culture, detection, zoonoses, population genetics and pathogenicity, are covered. Whole genome sequencing has had the greatest impact in the last three years. Future advances will provide a much better understanding of the zoonotic potential of both parasites, their diversity and how this is linked to pathogenesis in different hosts.

Giardia: an under-reported foodborne parasite

Foodborne zoonotic pathogens are a serious public health issue and result in significant global economic losses. Despite their importance to public health, epidemiological data on foodborne diseases including giardiasis caused by the enteric parasite, Giardia duodenalis, are lacking. This parasite is estimated to cause ∼28.2 million cases of diarrhoea each year due to contamination of food, but very few foodborne outbreaks have been documented due to the limitations of current detection as well as surveillance methods. The current method for the recovery of Giardia cysts from food matrices using immunomagnetic separation requires further standardisation and cost reduction before it can be widely used. It also should incorporate downstream molecular procedures for genotyping, and traceback and viability analyses. Foodborne giardiasis can be potentially controlled through improvements in national disease surveillance systems and the establishment of Hazard Analysis and Critical Control Point interventions across the food chain. Studies are needed to assess the true prevalence and public health impact of foodborne giardiasis.