Clone-based haplotyping of Giardia intestinalis assemblage B human isolates

Genetic diversity in the metronidazole metabolism genes nitroreductases and pyruvate ferredoxin oxidoreductases in susceptible and refractory clinical samples of Giardia lamblia

The effectiveness of metronidazole against the tetraploid intestinal parasite Giardia lamblia is dependent on its activation/inactivation within the cytoplasm. There are several activating enzymes, including pyruvate ferredoxin reductase (PFOR) and nitroreductase (NR) 1 which metabolize metronidazole into toxic forms, while NR2 on the other hand inactivates it. Metronidazole treatment failures have been increasing rapidly over the last decade, indicating genetic resistance mechanisms. Analyzing genetic variation in the PFOR and NR genes in susceptible and refractory Giardia isolates may help identify potential markers of resistance. Full length PFOR1, PFOR2, NR1 and NR2 genes from clinical culturable isolates and non-cultured clinical Giardia assemblage B samples were cloned, sequenced and single nucleotide variants (SNVs) were analyzed to assess genetic diversity and alleles. A similar ratio of amino acid changing SNVs per gene length was found for the NRs; 4.2% for NR1 and 6.4% for NR2, while the PFOR1 and PFOR2 genes had less variability with a ratio of 1.1% and 1.6%, respectively. One of the samples from a refractory case had a nonsense mutation which caused a truncated NR1 gene in one out of six alleles. Further, we found three NR2 alleles with frameshift mutations, possibly causing a truncated protein in two susceptible isolates. One of these isolates was homozygous for the affected NR2 allele. Three nsSNVs with potential for affecting protein function were found in the ferredoxin domain of the PFOR2 gene. The considerable variation and discovery of mutations possibly causing dysfunctional NR proteins in clinical Giardia assemblage B isolates, reveal a potential for genetic link to metronidazole susceptibility and resistance.

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).

Prevalence and multi-locus genotyping of Giardia duodenalis in rabbits from Shaanxi province in northwestern China

Giardia duodenalis is an important parasite with veterinary and public health significance worldwide. The presence and zoonotic assemblages of G. duodenalis have previously been reported in rabbits. In this study, to understand the infection status of G. duodenalis in rabbits from Shaanxi province, a total of 537 fecal samples were collected from two breeds of rabbits in four age groups (<30 days, 31–90 days, 91–200 days and >200 days) from four geographical origins (Fengxiang, Yangling, Tongchuan, and Shanyang). The presence of G. duodenalis in these samples was assessed using molecular assays based on beta-giardin (bg). The glutamate dehydrogenase (gdh) and triosephosphate isomerase (tpi) loci were then amplified in the bg-positive samples for multi-locus genotype (MLG) analysis. The total prevalence of G. duodenalis in these rabbits was 3.54% (19/537). Giardia duodenalis infection was found in both breeds of rabbits, and in all farms and age groups, but with no statistically significant differences related to these factors (p > 0.05). Two assemblages, including B and E, were identified, with the former the predominant assemblage detected in both breeds, and in all age groups and farms. Sequence analysis revealed 2 (named as rbg1-2), 1 (named as rtpi1), and 2 (named as rgdh1-2) haplotypes at the gene loci of bg, tpi, and gdh, respectively, forming a multilocus genotype (MLG) of assemblage B (rbg1, rtpi1, and rgdh1). These findings reveal the significant zoonotic potential and genetic diversity of G. duodenalis in rabbits in Shaanxi Province, PR China.

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.

FELINE GIARDIASIS IN TURKEY: PREVALENCE AND GENETIC AND HAPLOTYPE DIVERSITY OF GIARDIA DUODENALIS BASED ON THE β-GIARDIN GENE SEQUENCE IN SYMPTOMATIC CATS

Giardia duodenalis is a common zoonotic protozoan parasite with a broad host distribution. The main objectives of the present study were to determine the prevalence of giardiasis and to reveal the genetic and haplotype diversity of G. duodenalis in symptomatic cats in Turkey. Fecal samples were collected from cats (n = 102) with diarrhea that were admitted to different pet clinics in the Central Anatolia region of Turkey. All samples were analyzed by microscopic examination (ME), rapid immunochromatographic test (ICT), and PCR targeting the β-giardin (bg) loci of the parasite. Phylogenetic, haplotype, and network analyses of G. duodenalis based on the bg gene were carried out. Overall, G. duodenalis was detected in 70/102 (68.6%) of the cats with diarrhea by ME (38/102, 37.3%), ICT (51/102, 50%), and PCR (30/102, 29.4%). According to sequence analyses of the bg gene region, all isolates were identified as G. duodenalis assemblage B. Haplotype analyses revealed 2 known and 8 novel haplotypes for G. duodenalis assemblage B. This study provides first prevalence and genetic and haplotype diversity data on G. duodenalis assemblage B from cats in Turkey.

Genetic Diversity of the Flavohemoprotein Gene of Giardia lamblia: Evidence for High Allelic Heterozygosity and Copy Number Variation

Purpose

The flavohemoprotein (gFlHb) in Giardia plays an important role in managing nitrosative and oxidative stress, and potentially also in virulence and nitroimidazole drug tolerance. The aim of this study was to analyze the genetic diversity of gFlHb in Giardia assemblages A and B clinical isolates.

Methods

gFlHb genes from 20 cultured clinical Giardia isolates were subjected to PCR amplification and cloning, followed by Sanger sequencing. Sequences of all cloned PCR fragments from each isolate were analyzed for single nucleotide variants (SNVs) and compared to genomic Illumina sequence data. Identical clone sequences were sorted into alleles, and diversity was further analyzed. The number of gFlHb gene copies was assessed by mining PacBio de novo assembled genomes in eight isolates. Homology models for assessment of SNV's potential impact on protein function were created using Phyre2.

Results

A variable copy number of the gFlHb gene, between two and six copies, depending on isolate, was found. A total of 37 distinct sequences, representing different alleles of the gFlHb gene, were identified in AII isolates, and 41 were identified in B isolates. In some isolates, up to 12 different alleles were found. The total allelic diversity was high for both assemblages (>0.9) and was coupled with a nucleotide diversity of <0.01. The genetic variation (SNVs per CDS length) was 4.8% in sub-assemblage AII and 5.4% in assemblage B. The number of non-synonymous (ns) SNVs was high in gFIHb of both assemblages, 1.6% in A and 3.0% in B, respectively. Some of the identified nsSNV are predicted to alter protein structure and possibly function.

Conclusion

In this study, we present evidence that gFlHb, a putative protective enzyme against oxidative and nitrosative stress in Giardia, is a variable copy number gene with high allelic diversity. The genetic variability of gFlHb may contribute metabolic adaptability against metronidazole toxicity.

Companion animals as a potential source of Giardia intestinalis infection in humans in the Czech Republic - A pilot study

Giardia intestinalis is a common enteric single-celled parasite infecting both humans and animals. Its eight morphologically identical but genetically distinct groups called assemblages differ from each other in host range. While assemblages A and B infect a wide range of hosts, including humans, the other assemblages (C to H) limit their host preferences to particular animal groups only. In companion animals as Giardia hosts, genotyping data have previously shown various results depending on pet species, location, environmental or breeding conditions, and the study design. To strengthen available epidemiological data from developed countries and to evaluate the role of pets in Giardia zoonotic transmission, we investigated Giardia-positive stool samples of three pet species (54 dogs, 18 cats, and 18 chinchillas) by a sequence-based analysis of three Giardia genes (β-giardin, glutamate dehydrogenase and triose phosphate isomerase). In dog samples, we confirmed assemblage C (21/54), assemblage D (32/54), and one case of a mixed infection C + D (1/54). In cats, we found assemblage F (16/18) and assemblage A, specifically sub-assemblage AI (2/18). All Giardia samples from chinchillas were characterised as assemblage B, specifically sub-assemblage BIV (18/18). These results indicate that in the Czech Republic, pet dogs may not represent a source of Giardia infection for humans because of the presence of only canid-specific genotypes C and D. In contrast, other pets, namely, chinchillas and, to a lesser extent, cats, may pose a potential risk of Giardia transmission to owners or breeders because they can host zoonotic Giardia genotypes.

Extremely diversified haplotypes observed among assemblage B population of Giardia intestinalis in Kenya

In molecular epidemiological studies of Giardia intestinalis, an pathogenic intestinal flagellate, due to the presence of allelic sequence heterogeneity (ASH) on the tetraploid genome, the image of haplotype diversity in the field remains uncertain. Here we employed the nine assemblage B positive stool samples, which had previously reported from Kenyan children, for the clonal sequence analysis of multiple gene loci (glutamate dehydrogenase (GDH), triosephosphate isomerase (TPI), and beta-giardin (BG)). The diversified unique assemblage B haplotypes as GDH (n = 67), TPI (n = 84), and BG (n = 62), and the assemblage A haplotypes as GDH (n = 7), TPI (n = 14), and BG (n = 15), which were hidden in the previous direct-sequence results, were detected. Among the assemblage B haplotypes, Bayesian phylogeny revealed multiple statistically significant clusters (9, 7, and 7 clusters for GDH, TPI, and BG, respectively). A part of the clusters (2 for GDH and 1 for BG), which included >4 haplotypes from an individual sample, indicated the presence of co-transmission with multiple strains sharing a recent ancestor. Locus-dependent discrepancies, such as different compositions of derived samples in clusters and different genotyping results for the assemblages, were also observed and considered to be the traces of both intra- and inter-assemblage genetic recombination respectively. Our clonal sequence analysis for giardial population, which applied firstly in Kenya, could reveal the higher rates of ASH far beyond the levels reported in other areas and address the complex population structure. The clonal analysis is indispensable for the molecular field study of G. intestinalis.