Genotypes of Giardia intestinalis clinical isolates of gastrointestinal symptomatic and asymptomatic Saudi children

Molecular epidemiology and multilocus genotyping of Giardia duodenalis in individuals attending major public hospitals in Shiraz, southwestern Iran: A public health concern

Giardia duodenalis is one of the most common causes of waterborne disease worldwide, and is often associated with outbreaks of diarrhea in areas with poor sanitation and hygiene. This study aimed to assess the prevalence and genetic diversity of G. duodenalis assemblages in individuals attending major public hospitals in Shiraz, southwestern Iran. From August 2022 to May 2023, a total of 614 stool samples from individuals were collected and initially examined for G. duodenalis cysts using parasitological techniques, sucrose flotation, and microscopy. Microscopy-positive samples were validated by SSU-PCR amplification of the parasite DNA. A multilocus genotyping (MLG) scheme, which focused on the triose phosphate isomerase (tpi) and the glutamate dehydrogenase (gdh) genes, was employed for genotyping purposes. G. duodenalis cysts were found in 7.5% (46/614) and 8.5% (52/614) of samples through microscopy and SSU-PCR, respectively. Successful amplification and sequencing results were obtained for 77.3% (17/22) and 45.5% (10/22) of the infected samples at the tpi and gdh loci, respectively. MLG data for the two loci were available for only five samples. Out of the 22 samples genotyped at any loci, 54.5% (12/22) were identified as assemblage A, while 45.5% (10/22) were identified as assemblage B. AII was the most predominant sub-assemblage identified [54.5% (12/22)], followed by BIII [27% (6/22)], discordant BIII/BIV [13.6% (3/22)], and BIV [4.5% (1/22)]. In the present study, no assemblages suited for non-human animal hosts (e.g., C-F) were detected. This suggests that the transmission of human giardiasis in Shiraz is primarily anthroponotic. Further molecular-based analyses are necessary to confirm and expand upon these findings. These analyses will also help determine the presence and public health importance of the parasite in environmental samples, such as drinking water.

Assemblage characterization of Giardia duodenalis in South Khorasan province, eastern Iran, using HRM real-time PCR method

BACKGROUND

Giardia duodenalis is a common parasitic protozoan causing gastrointestinal illness in humans worldwide. The genetic diversity of G. duodenalis is reflected through the identification of different assemblages. In this study, we aimed to determine the assemblages of G. duodenalis in eastern Iran using nested-PCR and high-resolution melting (HRM) real-time PCR methods.

METHODS

A total of 58 positive G. duodenalis, which were isolated from 1800 subjects, referred to medical center laboratories in South Khorasan province, eastern Iran, from April 2020 to March 2022, were included in this study. DNA was extracted and HRM real-time PCR was performed for assemblage characterization.

RESULTS

HRM real-time PCR successfully characterized all samples. Accordingly, out of 58 positive samples, 53 (91.36%) and 5 (8.62%) were identified as assemblage A and B, respectively.

CONCLUSIONS

Our findings showed that HRM real-time PCR was able to characterize the assemblages of G. duodenalis. In addition, our results suggest high prevalence of assemblage A in eastern region of Iran.

Genotyping and epidemiological distribution of diarrhea-causing isolates of Giardia duodenalis in southeastern part of West Bengal, India

The prevalence and genetic diversity of the protozoan pathogen Giardia duodenalis have been extensively studied worldwide. There is currently a lack of data regarding the genetic variability of the organism in eastern India. Understanding the circulating genotypes and associated risk factors is crucial for effective planning and implementing control measures. Therefore, the objective of the study was to conduct an epidemiological study to determine the prevalence and identify the various genotypes present. This survey adds to our knowledge on the occurrence and distribution of Giardia genotypes in the studied region. The overall prevalence was found to be 6.8%. This parasitic infection was significantly associated with two age groups, i.e., >0-5 years and >5-12 years. Using a multilocus genotyping method, we genotyped 52 human Giardia isolates that were obtained from diarrheal patients. Two distinct assemblages were found in the population-30.8% belonged to assemblage A; 63.5% belonged to assemblage B, prevalent in the population; and 5.7% belonged to a combined assemblage A+B. Sub-assemblage AII was found in 17.3% of the cases, followed by sub-assemblage AI (13.5%). High levels of genetic diversity were found within the population of assemblage B undergoing balancing selection. Overall, the high prevalence of the parasite observed, particularly among children, raises a major concern and necessitates implementation of robust control measures. Furthermore, we report the presence of numerous unique genotypes, circulating in this limited geographical boundary, which can be useful dataset for future studies.

Prevalence and molecular characterization of Giardia intestinalis isolated from children and calves in Babylon province, Iraq

Background and Aim

Giardia intestinalis is one of the most prevalent intestinal parasites in humans and animals, and children in close contact with livestock are particularly at risk of infection. This study aimed to detect assemblages of G. intestinalis and determine the origin of zoonotic transmission of Giardia in children and calves in different parts of Babylon province, Iraq.

Materials and Methods

One hundred stool samples from children (68 boys and 32 girls) and 100 fecal samples from calves (46 males and 54 females) of different ages were randomly collected. Molecular techniques were used to estimate the prevalence of G. intestinalis in children and calves. A nested polymerase chain reaction (PCR) was performed by targeting the triose phosphate isomerase gene in the samples to detect G. intestinalis assemblages.

Results

The overall rates of infection with G. intestinalis in children and calves were 21% and 34%, respectively, using the conventional microscopic method. The results illustrated that 61.90% (13/21) and 38.09% (8/21) of positive samples from children were allocated to assemblages A and B, respectively (p > 0.05). In calves, assemblages A and B were detecte in 82.35% (28/34) and 17.64% (6/34) of positive samples from calves, respectively (p ≤ 0.001). Ten PCR products were sequenced and submitted to the GenBank database. Phylogenetic analysis detected five human sequences each belonging to G. intestinalis assemblages A (OM850335-OM850339) and B (OM850340-OM850344). Similarly, five calf sequences each belonged to G. intestinalis assemblages A (ON75756-ON757660) and B (ON757661-ON757665).

Conclusion

The detection of large numbers of G. intestinalis assemblage A in both humans and cattle indicated that cattle could be a main source of zoonotic G. intestinalis infection in children in Babylon province, Iraq.

Diagnosis of protozoa diarrhoea in Campylobacter patients increases markedly with molecular techniques

Cryptosporidium and Giardia are major causes of diarrhoea globally, and two of the most notified infectious diseases in New Zealand. Diagnosis requires laboratory confirmation carried out mostly via antigen or microscopy-based techniques. However, these methods are increasingly being superseded by molecular techniques. Here we investigate the level of protozoa detection by molecular methods in campylobacteriosis cases missed through antigen-based assays and investigate different molecular testing protocols. We report findings from two observational studies; the first among 111 people during a Campylobacter outbreak and the second during normal surveillance activities among 158 people presenting with diarrhoea and a positive Campylobacter test, but negative Cryptosporidium and Giardia antigen-based test results. The molecular methods used for comparison were in-house end-point PCR tests targeting the gp60 gene for Cryptosporidium and gdh gene for Giardia. DNA extraction was performed with and without bead-beating and comparisons with commercial real-time quantitative (qPCR) were made using clinical Cryptosporidium positive sample dilutions down to 10-5. The Cryptosporidium prevalence was 9% (95% CI: 3-15; 10/111) and Giardia prevalence 21% (95% CI: 12-29; 23/111) in the 111 Campylobacter outbreak patients. The Cryptosporidium prevalence was 40% (95% CI: 32-48; 62/158) and Giardia prevalence 1.3% (95% CI: 0.2-4.5; 2/158) in the 158 routine surveillance samples. Sequencing identified Cryptosporidium hominis, C. parvum, and Giardia intestinalis assemblages A and B. We found no statistical difference in positive test results between samples using end-point PCR with or without bead-beating prior to DNA extraction, or between the in-house end-point PCR and qPCR. The qPCR Ct value was 36 (95% CI: 35-37) for 1 oocyst, suggesting a high limit of detection. In conclusion in surveillance and outbreak situations we found diagnostic serology testing underdiagnoses Cryptosporidium and Giardia coinfections in Campylobacter patients, suggesting the impact of protozoa infections may be underestimated through underdiagnosis using antigen-based assays.

Multilocus sequence typing of Giardia duodenalis genotypes circulating in humans in a major metropolitan area

Giardia duodenalis is an intestinal protozoan parasite of humans and animal hosts and comprises eight microscopically indistinguishable molecularly-diverse lineages designated as assemblages A-H. Assemblages A and B are the primary sources of infections in humans and a wide range of mammals. Here, we identified assemblages, and inter-/intra-assemblage genetic diversity of human G. duodenalis isolates based on the multilocus sequence typing of the triosephosphate isomerase (tpi), β -giardin (bg), and glutamate dehydrogenase (gdh) loci. Multilocus sequence analysis of 62 microscopically-positive G. duodenalis fecal samples identified 26 (41.9%), 27 (43.5%), and nine (14.5%) isolates belonging to assemblages A, B, and discordant assemblages, respectively. The tpi locus assemblage-specific primers identified dual infections with A and B assemblages (45.2%). The sequence analysis of multiple alignments and phylogenetic analysis showed low genetic polymorphism in assemblage A isolates, classified as sub-assemblage AII at three loci, subtype A2 at tpi and gdh loci, and subtype A2 or A3 at bg locus. High genetic variations were found in assemblage B isolates with 14, 15, and 23 nucleotide patterns at tpi, bg, and gdh loci, respectively. Further concatenated sequence analysis revealed four multilocus genotypes (MLG) in 24 assemblages A isolates, two previously-identified (AII-1 and AII-5), with one novel multilocus genotype. However, the high genetic variations observed in assemblage B isolates among and within the three genetic loci prevented the definitive designation of specific MLGs for these isolates. Multilocus sequence typing may provide new insight into the genetic diversity of G. duodenalis isolates in Tehran, suggesting that humans are likely a potential source of G. duodenalis infection. Further host-specific experimental transmission studies are warranted to elucidate the modes of transmission within multiple host populations.

Genotypic and Epidemiologic Profiles of Giardia duodenalis in Four Brazilian Biogeographic Regions

Human infections with gut protozoan parasites are neglected and not targeted by specific control initiatives, leading to a knowledge gap concerning their regional diversity and epidemiology. The present study aims to explore Giardia duodenalis genetic diversity and assess the epidemiologic scenario of subclinical infections in different Brazilian biogeographic regions. Cross-sectional surveys (n = 1334 subjects) were conducted in four municipalities in order to obtain fecal samples and socioenvironmental data. Microscopy of non-diarrheal feces and nucleotide sequencing of a β-giardin gene fragment were performed. From a total of 51 samples that could be sequenced, 27 (52.9%) β-giardin sequences were characterized as assemblage A and 24 (47.1%) as assemblage B. In the Amazon, assemblage B was the most frequently detected, predominantly BIII, and with two novel sub-assemblages. Assemblage A predominated in the extra-Amazon region, with five novel sub-assemblages. Prevalence reached 17.8% (64/360) in the Amazon, 8.8% (48/544) in the Atlantic Forest, 7.4% (22/299) in Cerrado and 2.3% (3/131) in the Semiarid. People living in poverty and extreme poverty presented significantly higher positivity rates. In conclusion, subclinical giardiasis is endemic in Brazilian communities in different biogeographic regions, presenting high genetic diversity and a heterogeneous genotypic distribution.

The controversies surrounding Giardia intestinalis assemblages A and B

Giardia intestinalis continues to be one of the most encountered parasitic diseases around the world. Although more frequently detected in developing countries, Giardia infections nonetheless pose significant public health problems in developed countries as well. Molecular characterisation of Giardia isolates from humans and animals reveals that there are two genetically different assemblages (known as assemblage A and B) that cause human infections. However, the current molecular assays used to genotype G. intestinalis isolates are quite controversial. This is in part due to a complex phenomenon where assemblages are incorrectly typed and underreported depending on which targeted locus is sequenced. In this review, we outline current knowledge based on molecular epidemiological studies and raise questions as to the reliability of current genotyping assays and a lack of a globally accepted method. Additionally, we discuss the clinical symptoms caused by G. intestinalis infection and how these symptoms vary depending on the assemblage infecting an individual. We also introduce the host-parasite factors that play a role in the subsequent clinical presentation of an infected person, and explore which assemblages are most seen globally.

A review of the molecular epidemiology of Cryptosporidium spp. and Giardia duodenalis in the Middle East and North Africa (MENA) region

Cryptosporidium spp. and Giardia duodenalis are important protozoan parasites which are associated with diarrheal diseases in humans and animals worldwide. Relatively little is known about the molecular epidemiology of Cryptosporidium spp. and Giardia duodenalis in the Middle East Countries and North Africa (MENA region). Therefore, this review aimed to inspect published genotyping and subtyping studies on Cryptosporidium spp. and Giardia duodenalis in the MENA region. These studies indicate that both anthroponotic and zoonotic transmission of Cryptosporidium occurs with the predominance of zoonotic transmission in most countries. Seven Cryptosporidium species were identified in humans (C. parvum, C. hominis, Cryptosporidium meleagridis, C. felis, Cryptosporidium muris, C. canis and C. bovis), with C. parvum by far being the most prevalent species (reported in 95.4% of the retrieved studies). Among C. parvum gp60 subtype families, IIa and IId predominated, suggesting potential zoonotic transmission. However, in four MENA countries (Lebanon, Israel, Egypt and Tunisia), C. hominis was the predominant species with five subtype families reported including Ia, Ib, Id, If and Ie, all of which are usually anthroponotically transmitted between humans. In animals, the majority of studies were conducted mainly on livestock and poultry, 15 species were identified (C. parvum, C. hominis, C. muris, Cryptosporidium cuniculus, C. andersoni, C. bovis, C. meleagridis, C. baileyi, C. erinacei, C. ryanae, C. felis, C. suis, Cryptosporidium galli, C. xiaoi and C. ubiquitum) with C. parvum (IIa and IId subtypes) the dominant species in livestock and C. meleagridis and C. baileyi the dominant species in poultry. With G. duodenalis, five assemblages (A, B, C, E and F) were identified in humans and six (A, B, C, E, D and F) in animals in MENA countries with assemblages A and B commonly reported in humans, and assemblages A and E dominant in livestock. This review also identified a major knowledge gap in the lack of Cryptosporidium spp. and Giardia duodenalis typing studies in water and food sources in the MENA region. Of the few studies conducted on water sources (including drinking and tap water), ten Cryptosporidium species and four genotypes were identified, highlighting the potential role of water as the major route of Cryptosporidium spp. transmission in the region. In addition, three G. duodenalis assemblages (A, B and E) were detected in different water sources with AI, AII and BIV being the main sub-assemblages reported. More research is required in order to better understand the molecular diversity and transmission dynamics of Cryptsporidum spp. and Giardia duodenalis in humans, animals, water and food sources in MENA region.

Development of HRM real-time PCR for assemblage characterization of Giardia lamblia

A total of 90 stool samples were collected from dogs, referred to a dog shelter and a veterinary clinic. In addition, 395 stool samples obtained from pet dog owners and shelter keepers, as well as individuals referred to a medical laboratory as controls, were collected in Shahryar district, Tehran, Iran. Stool samples were parasitologically examined and the positive G. lamblia isolates were tested with Nested-PCR/sequencing for the tpi, gdh, and bg genes, and HRM real-time PCR. Microscopical examination revealed 20 (22.2%) and 34 (8.6%) Giardia-positive samples from dogs and humans, respectively. Regarding HRM real-time PCR, the prevalence of assemblages A and B in humans was 55.8% and 14.7%, respectively. In addition, 14.7% of samples were mix assemblages. HRM real-time PCR detected most of microscopically-positive samples in comparison to PCR/sequencing in both humans and dogs. The high prevalence of assemblages A and B in dogs signified the importance of a same source for infection between dogs and humans.

Epidemiology of Giardia duodenalis assemblages in Brazil: there is still a long way to go

Giardia duodenalis infection is distributed worldwide and can achieve prevalence around 60%, especially in developing countries. This protozoan is divided into eight assemblages, in which A and B have high zoonotic potential, whereas C to H are host-specific. This scenario is changing as molecular studies progress, highlighting that knowledge on host-specificity still has a long way to go. Understanding the players involved in transmission routes enables rational designs of control strategies. Considering the high prevalence of giardiasis, this review aims to gather together the data on available studies on the distribution of G. duodenalis assemblages in Brazil until September 2020.

Genotyping of Giardia duodenalis in children in upper Egypt using assemblage- specific PCR technique

Giardia duodenalis is a common gastrointestinal protozoan parasite, causing diarrheal illness in humans worldwide. Yet, the distribution of G. duodenalis genotypes among human patients and their clinical relevance remains controversial. This study aimed to detect G. duodenalis in children in Upper Egypt and identify causative genotypes and elucidate a possible correlation between genotype and clinical presentation. One hundred sixty-five children, regardless of symptoms, were tested for giardiasis. Giardia positive stool samples (40/165) were subjected to PCR amplification targeting the tpi gene with positive PCR results in only 35 cases (87.5%). Assemblage-specific amplification of genotypes (A, B, and the zoonotic E strains) revealed predominantly G. duodenalis Assemblage A (45.7%). Assemblage B and mixed A and B infections were detected in 31.4% and 22.8% of children, respectively. Assemblage E was not detected. G. duodenalis assemblage A was dominant in children who complained of diarrhea and abdominal cramps. In contrast, asymptomatic children with positive stool samples display a higher frequency of assemblage B and mixed infections. The study highlights the predominance of Giardia Assemblage A in our study locality. This study is the first for this endemic area to use the copro-PCR technique for diagnosis and genotyping of giardiasis. Study results show the value of simple species-specific primers for genotyping in communities with little access to laboratory resources. Further genetic studies are needed to clarify the association between parasite genetic diversity and patient symptomatology.

Molecular Characterization of Giardia intestinalis Detected in Humans and Water Samples in Egypt

BACKGROUND

Giardia intestinalis is a common cause of gastrointestinal illness especially in children of developing countries. Giardia assemblages A and B are the major human infective genotypes.

OBJECTIVE

The present study aimed to investigate the role of water supply in the epidemiology of giardiasis via genotyping G. intestinalis detected in diarrheic children and in water samples in Egyptian rural areas.

METHODS

Stool samples of 100 diarrheic children, 40 drinking water samples and 10 raw water samples of canals were examined microscopically for Giardia. DNA was extracted from microscopically positive faecal samples and from all of the collected water samples. Amplification of Giardia tpi gene was performed by a nested PCR using assemblage A- and assemblage B-specific primers. Giardia gdh gene was amplified by a heminested PCR. Giardia genotypes were determined by restriction fragment polymorphism (RFLP) analysis of the amplified products. Sequencing of the amplified products was performed in two faecal and two water samples RESULTS: Giardia intestinalis was detected in 24 children, in none of the drinking water samples and in all canal water samples. Giardia sub-assemblage AII was identified in all stool and raw water samples. The RFLP pattern was confirmed in sequenced samples.

CONCLUSION

The presence of the same Giardia sub-assemblage in diarrheic children and in raw water samples shows by molecular evidence the potential for waterborne dissemination of Giardia in Egypt. Further studies are needed to monitor cyst levels and infectivity of the genotype detected in water for risk assessment and management.

Molecular and epidemiological characterization of Giardia Intestinalis assemblages detected in Djelfa, Algeria

Giardia intestinalis is a flagellated protozoan that lives and proliferates in the small intestine of the host causing giardiasis. The route of transmission is the fecal-oral route, either directly or indirectly. Limited genetic information on G. intestinalis is known in Algeria. This study aimed to estimate the prevalence of G. intestinalis assemblages in the city of Djelfa. A total of 355 fecal samples were collected from symptomatic and asymptomatic school children aged ranged between 6 and 11 years old. Genotyping was done to the Giardia positive samples (n = 30) targeting the beta-giardin gene by applying PCR/RFLP assay. Our data showed that most of the cases were asymptomatic (56.7%). Co-infection with other intestinal parasites was found in 16.6% of cases. We obtained 28/30 positive PCR products while two samples only showed false-negative results, and only 20 samples have shown strong PCR products suitable for RFLP analysis. Assemblage A (70%) was more prevalent than assemblage B (30%) and was more expressed by signs than assemblage B. Moreover, only assemblage A was associated with close contacts with domestic animals and birds. In conclusion, this study gave the first molecular data on G. intestinalis isolates in the city of Djelfa. Further expanded studies using more genes and covering other cities in Algeria are mostly needed.

Prevalence and genetic characterization of Giardia lamblia in relation to diarrhea in Limpopo and Gauteng provinces, South Africa

Background

Very few studies have determined the prevalence and assemblage distribution of Giardia lamblia in South Africa. The present study aimed to ascertain the prevalence of G. lamblia infection and the spread of the various assemblages in two communities in South Africa - Giyani, Limpopo province (rural community) and Pretoria Guateng province (urban community).

Methods

Prevalence was determined by immunological and molecular methods analyzing a total of 516 stool samples collected from patients visiting different health centres in Giyani and Pretoria. For immunological assays, samples were screened by ELISA to detect G. lamblia antigen. Furthermore, a semi nested PCR amplifying the triose phosphate isomerase (tpi) gene was used to differentiate between the two most common human assemblages (A and B).

Findings

Of the 516 participants, 40 (7.75%) were identified as positive by ELISA. A statistically significant correlation was observed between the stool texture and Giardia infection (ᵡ² = 10.533; p = .005). G. lamblia was significantly associated with watery stool types in females p = .008. Furthermore, a significant association was also noticed between the origin of samples (ᵡ² = 9.725; p = .002). No significant correlation between age and gender was noted. Regarding the age groups, most people who were infected were between 3 and 20 years. A statistically significant association was seen (p = .001) with the distribution of the pathogen with the stool type. The prevalence of Giardia infection was higher in watery stool samples (71.4%) in Giyani region (rural) whereas in Pretoria, high prevalence was found in loose stool samples (6.2%). Generally, the distribution was statistically significant in the stool type collected for the study (p = .005). Genotyping revealed more G. lamblia assemblage B (17.8%) than assemblage A (1.7%). Furthermore, 21.0% of the samples exhibited single infection while 4.2% had mixed infections. Assemblage B was more common in Giyani than in urban Pretoria.

Conclusions

The study confirms Giardia as an important cause of diarrhea in the concerned communities with people in rural areas more at risk compared to those in urban areas with higher prevalence among younger patients. Therefore, health education campaigns should target young age groups.

Improvement in cyst recovery and molecular detection of Giardia duodenalis from stool samples

Molecular detection of Giardia duodenalis by polymerase chain reaction (PCR) is difficult in faecal samples due to inhibitors that contaminate DNA preparations, or due to low cyst concentrations. In order to eliminate inhibitors, improve cyst recovery and molecular detection of G. duodenalis, different types of water, distillates (MDs), deionized (MDz), injection (MI) or Milli-Q^® (MM) were used instead of formaldehyde (F) in the laboratory routine method (Ritchie). Cysts were isolated from faecal samples with low cyst concentrations (< 1 cyst/field), medium (1-2 cysts/field) or high (> 2 cysts/field). Cyst recovery was improved using all water types (MDs, MDz, MI, MM) compared to formaldehyde. At all cyst concentrations, the use of MM consistently showed the greatest recovery of G. duodenalis cysts . DNA samples from recovered cysts were tested for the glutamate dehydrogenase (GDH) and β-giardin (βg) genes. The use of Milli-Q^® water allowed to detect both genes in all cyst concentrations, including low. The method processed with the other types of water amplified these genes at high and medium cyst concentrations. GDH and βg genes were not detected when the sample was processed with formaldehyde. These experimental results were confirmed in clinical samples. The results suggest that Milli-Q^® water provides the highest cyst recovery from stool samples and, correspondingly, the highest sensitivity for detecting G. duodenalis by microscopy or PCR for GDH and βg genes, even at low concentration of cysts.

Concordance of Giardia duodenalis assemblages determined by different PCR methodologies in three observational studies in Cuba

Giardia duodenalis is one of the most important intestinal parasites globally, especially in children, and in Cuba is the leading cause of chronic paediatric diarrhoea in this population. G. duodenalis is composed of eight genetic groups (or assemblages), two of which (A and B) are apparently zoonotic, occurring in both humans and other animals. However, consensus on the most appropriate genotyping scheme for optimal characterization of G. duodenalis isolates is lacking. In this article we present the results of three descriptive observational studies conducted in Havana, Cuba between 2010 and 2013, with the aim of comparing the results from molecular (PCR) approaches targeting different genes in order to assign with confidence 224 isolates of G. duodenalis to the correct assemblages. In each sub-study, following DNA isolation by the phenol/chloroform/isoamyl alcohol extraction method, PCR targeting the triose phosphate isomerase (tpi) gene was used for molecular characterization, as well as one additional PCR-method targeting another gene or pair of genes. DNA amplification was obtained in 87%, 83%, and 80% in the three sub-studies. Although excellent agreement (kappa index = 1) was recorded between results from some pairs of genes, for other combinations only moderate or substantial agreement was achieved. These results highlight the importance of interpretation of genotyping data, especially when single genetic markers are used. From the results of our studies, PCR targeting a combination of the tpi gene and the intergenic spacer region of rDNA may be a useful approach for the molecular characterization of G. duodenalis isolates.

Giardia lamblia assemblages A and B isolated from symptomatic and asymptomatic persons in Hamadan, west of Iran

Giardia is a very abundant organism bringing about diarrhoea in human beings. The focus of this analysis was the detection of Giardia lamblia assemblages in human stool specimens in Hamadan, west of Iran, as well as the association between obtained assemblages and clinical symptoms. Faecal samples of 4066 individuals admitted to the medical and health care facilities in Hamadan were inspected microscopically for the existence of Giardia cysts/trophozoites, and the clinical symptoms of the patients were recorded. The DNA of positive samples was isolated from and the nucleotide sequences of both glutamate dehydrogenase (gdh) (n = 15) and triose phosphate isomerase (tpi) (n = 8) genes were analyzed. In direct microscopy, a total of sixty-four samples (1.6%), were considered as positive for G. lamblia cysts or trophozoites. The sequence analysis showed that 18 out of 23 sequenced isolates (78.2%) were assemblage A and 5 (21.7%) were assemblage B. Clinical symptoms were observed in 44.4% and 40% of patients with assemblages A and B, respectively. Overall, the predominant assemblage A detected in the tested samples along with bioinformatics analysis suggest a potential zoonotic transmission in the region of the study. Although advanced analyses are necessary to understand the foundation and path of the infection, it seems that more sanitary regulations regarding contact with livestock and pet animals are essential.

Molecular Genotyping of Giardia duodenalis in Humans in the Andimeshk County, Southwestern Iran

INTRODUCTION

Giardia duodenalis, one of the most common intestinal protozoa, infects a wide range of vertebrates, including humans and animals.

MATERIALS AND METHODS

In this study, 84 Giardia duodenalis positive stool samples were collected from 3580 patients attending the Imam Ali Hospital and two public health centers in Andimeshk County, southwestern Iran. Stool samples were examined initially by microscopy, and then G. duodenalis was confirmed by SSU rRNA gene and genotypes were determined by amplification of the gdh and β-giardin genes.

RESULTS

The SSU rRNA, gdh, and β-giardin genes were successfully amplified in 89.3%, 58.3%, and 51.2% samples, respectively. Of the positive samples for gdh and β-giardin, 40 isolates were successfully sequenced. Twenty-three isolates belonged to assemblage A, sub-assemblage AII, and 17 belonged to assemblage B. Of the 24 successfully amplified asymptomatic cases, 12 belonged to assemblage A and 12 belonged to assemblage B.

CONCLUSION

The current study found that 64.3% of the patients were asymptomatic. From an epidemiological point of view, the high percentage of asymptomatic patients is important because of their role in the transmission of Giardia. The predominant assemblage was assemblage A, sub-assemblage AII. In general, therefore, it seems that most infections are probably transmitted by anthroponotic pathways in the region.

Molecular characterization of Giardia lamblia in children less than 5 years of age with diarrhoea attending the Bengo General Hospital, Angola

Background

Giardia lamblia is a pathogenic intestinal protozoan with high prevalence in developing countries, especially among children. Molecular characterization has revealed the existence of eight assemblages, with A and B being more commonly described in human infections. Despite its importance, to our knowledge this is the first published molecular analysis of G. lamblia assemblages in Angola.

Methods

The present study aimed to identify the assemblages of G. lamblia in children with acute diarrhoea presenting at the Bengo General Hospital, Angola. A stool sample was collected and microscopy and immunochromatographic tests were used. DNA was extracted and assemblage determination was performed through amplification of the gene fragment ssu-rRNA (175 bp) and β-giardin (511 bp) through polymerase chain reaction and DNA sequencing.

Results

Of the 16 stool samples screened, 12 were successfully sequenced. Eleven isolates were assigned to assemblage B and one to assemblage A. Subassemblage determination was not possible for assemblage B, while the single isolate assigned to assemblage A was identified as belonging to subassemblage A3.

Conclusion

This study provides information about G. lamblia assemblages in Bengo Province, Angola and may contribute as a first step in understanding the molecular epidemiology of this protozoan in the country.

GenBank accession numbers for the ssur-RNA gene: MF479750, MF479751, MF479752, MF479753, MF479754, MF479755, MF479756, MF479757, MF479758, MF479759, MF479760, MF479761.

GenBank accession numbers for the β-giardin gene: MF565378, MF565379, MF565380, MF565381.

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

Background

Giardia 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.

Methods

From 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.

Results

The 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.

Conclusions

This 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 material

The online version of this article (10.1186/s40249-018-0397-4) contains supplementary material, which is available to authorized users.

Host specificity in the Giardia duodenalis species complex

Giardia duodenalis is a unicellular flagellated parasite that infects the gastrointestinal tract of a wide range of mammalian species, including humans. Investigations of protein and DNA polymorphisms revealed that G. duodenalis should be considered as a species complex, whose members, despite being morphologically indistinguishable, can be classified into eight groups, or Assemblages, separated by large genetic distances. Assemblages display various degree of host specificity, with Assemblages A and B occurring in humans and many other hosts, Assemblage C and D in canids, Assemblage E in hoofed animals, Assemblage F in cats, Assemblage G in rodents, and Assemblage H in pinnipeds. The factors determining host specificity are only partially understood, and clearly involve both the host and the parasite. Here, we review the results of in vitro and in vivo experiments, and clinical observations to highlight relevant biological and genetic differences between Assemblages, with a focus on human infection.

Molecular epidemiologic tools for waterborne pathogens Cryptosporidium spp. and Giardia duodenalis

Molecular diagnostic tools have played an important role in improving our understanding of the transmission of Cryptosporidium spp. and Giardia duodenalis, which are two of the most important waterborne parasites in industrialized nations. Genotyping tools are frequently used in the identification of host-adapted Cryptosporidium species and G. duodenalis assemblages, allowing the assessment of infection sources in humans and public health potential of parasites found in animals and the environment. In contrast, subtyping tools are more often used in case linkages, advanced tracking of infections sources, and assessment of disease burdens attributable to anthroponotic and zoonotic transmission. More recently, multilocus typing tools have been developed for population genetic characterizations of transmission dynamics and delineation of mechanisms for the emergence of virulent subtypes. With the recent development in next generation sequencing techniques, whole genome sequencing and comparative genomic analysis are increasingly used in characterizing Cryptosporidium spp. and G. duodenalis. The use of these tools in epidemiologic studies has identified significant differences in the transmission of Cryptosporidium spp. in humans between developing countries and industrialized nations, especially the role of zoonotic transmission in human infection. Geographic differences are also present in the distribution of G. duodenalis assemblages A and B in humans. In contrast, there is little evidence for widespread zoonotic transmission of giardiasis in both developing and industrialized countries. Differences in virulence have been identified among Cryptosporidium species and subtypes, and possibly between G. duodenalis assemblages A and B, and genetic recombination has been identified as one mechanism for the emergence of virulent C. hominis subtypes. These recent advances are providing insight into the epidemiology of waterborne protozoan parasites in both developing and developed countries.

Associations of Giardia lamblia assemblages with HIV infections and symptomatology: HIV virus and assemblage B were they born to each other?

Giardia lamblia is an intestinal parasite that has an extensive genetic variation among isolates. This species is divided into eight different assemblages (A-H), but only assemblages A and B have been associated with human infections. Studies on the associations of G. lamblia assemblages and symptoms have been done but were inconclusive. The aim of this study was to correlate G. lamblia assemblages with symptoms in patients with and without HIV/AIDS and its association with the CD4T cell count. The cross-sectional survey was conducted among patients attending the Evandro Chagas National Institute of Infectious Diseases (INI/FIOCRUZ) in Rio de Janeiro from January 2011 to February 2015. Thirty-eight of 65 microscopically positive stool samples for G. lamblia were from HIV positive patients and 27 were from HIV negative patients. Of the HIV infected patients, 19 (55.9%) were genotyped as assemblage B of which 9 (47.4%) had a CD4Tcell count below 200cells/mm³. In addition, we found a greater number of samples belonging to assemblage B in symptomatic cases (11 of 19; 57.9%). Our data suggest that assemblage B is very likely to be found in HIV infected patients and probably the lower CD4T count gives advantages for assemblage B replication. Furthermore, assemblage B seems to be associated with symptomatology, particularly abdominal pain, asthenia, diarrhea, fever, headache and myalgia. This study provides information on G. lamblia assemblages and symptoms in patients with and without HIV/AIDS virus and their association with CD4Tcell counts.

Molecular analysis of Giardia duodenalis isolates from symptomatic and asymptomatic children from La Habana, Cuba

Giardiasis is considered the most common intestinal parasitic disease in humans worldwide. In Cuba, this infection has particularly a strong clinical impact on the child population. Giardia duodenalis is a highly diverse protozoan, which comprises a complex of eight morphologically identical genetic assemblages, further divided into sub-assemblages. The present study used triose phosphate isomerase (tpi) and small-subunit ribosomal RNA (SSU rRNA) genes as genetic markers for the identification of G. duodenalis assemblages and sub-assemblages in correlation with clinical and epidemiological data in children attended at the Paediatric Hospital “William Soler” and at Pedro Kouri Institute, between 2015 and 2016. A prevalence of 8% of G. duodenalis infection was recorded in stool samples after concentration techniques from 68 children out of 847 analysed. A 100% detection of Giardia DNA was achieved by a SSU-rRNA PCR, whereas DNA from 63 of 68 (92.6%) was successfully amplified by tpi-PCR. By this assemblage-specific tpi-PCR 32 (50.8%) assemblage B, 17 (27.0%) assemblage A and 14 (22.2%) mixed infection (A + B) were identified. Assemblage B was significantly (P < 0.02) more frequently found in children with diarrhoea. Sequence analysis of the tpi gene of Giardia isolates from symptomatic children showed that assemblage A belonged to the sub-assemblage AII, and 4 sub assemblages BIV and 1 sub assemblage BIII were also recorded. Only 2 discordant genotyping results were observed by phylogenetic comparison of SSU-rRNA and tpi sequences. Further studies with novel molecular tools for a better discrimination at the sub-assemblage level are needed to identify the dynamics of spread of giardiasis and to verify possible correlations between Giardia genetic diversity and clinical manifestation.

Nested PCR targeting intergenic spacer (IGS) in genotyping of Giardia duodenalis isolated from symptomatic and asymptomatic infected Egyptian school children

Distinct sequences of Giardia duodenalis assemblages raised the hypothesis that certain assemblages may contribute to its clinical outcome. However, sequences analysis is time consuming, expensive, and needs many manual operations. Nested PCR targeting intergenic spacer (IGS) region was applied successfully to genotype G. duodenalis. This study aimed to identify the prevalence of G. duodenalis assemblages among giardiasis school children and its relation to the presence of symptoms using nested IGS/PCR. Of 65 microscopically confirmed Giardia-positive samples, 65 samples were genotyped proving high sensitivity (92.3%) of IGS/PCR. Negative IGS/PCR samples were also negative for β-giardin gene. Subassemblage AI was the commonest with 66.6% (20/30) among asymptomatic children compared to 53.3% (16/30) of symptomatic, while assemblage B was found in 40% (12/30) of symptomatic compared to 20% (6/30) of asymptomatic. The difference was significant. AII was only found in asymptomatic with 13.4% (4/30), while mixed infections (AI&B) were recorded only in 6.6% (2/30) of symptomatic group. A significant relation was found between younger children susceptibility for AI and B infections as presented in 77.7 (12/16) and 83.3% (10/12) of symptomatic, respectively, and 80 (16/80) and 33.4% (2/4) of asymptomatic, respectively. Significant relations were found between AI with intermittent diarrhea and B with chronic. A significant relation was found between assemblage distributions and heavy infection intensity. In conclusion, higher incidence of assemblage B among symptomatic children compared to asymptomatic could denote its possible pathogenic potential.

Prevalence of Giardia duodenalis assemblages and sub-assemblages in symptomatic patients from Damascus city and its suburbs

Giardia duodenalis is one of the most important human enteric parasites worldwide and is endemic throughout the world with a vast range of mammalian hosts. However, there is limited information on the prevalent genetic variability of G. duodenalis in Syria. This study aimed to evaluate the predominance of G. duodenalis assemblages/sub-assemblages causing humans infection in the city of Damascus and its suburbs. 40 symptomatic giardiasis patients were recruited in this study. Fecal samples were genotyped using PCR/RFLP assay targeting the β-giardin and glutamate dehydrogenase (gdh) genes. HaeIII, BspL1 and RsaI restriction enzymes were used to differentiate between G. duodenalis assemblages/sub-assemblages. Our data showed that 65% of isolates were of assemblage A; 45% belonged to sub-assemblage AII and 20% to sub-assemblage AI. Assemblage B was detected in 27.5% of isolates; 12.5% fit in sub-assemblage BIV, 5% fit in sub-assemblage BIII and 10.5% fit in Discordant genotype BIII/BIV. Mixed genotypes (AII+BIII and AI+BIV) were identified in 3 isolates (7.5%). Significant correlation was found between Giardia AII sub-assemblage and weight loss symptom (P-value=0.05) as well as between contact with domestic animals (cats, P-value=0.027). Moreover, a significant correlation was found between sub-assemblage AI and livestock breeding (P-value=0.000). In conclusion genotyping of human Giardia duodenalis isolates suggests anthroponotic transmission for the route of infection in Damascus and its suburbs. Further studies are needed to screen a wide geographic areas in Syria and to estimate the prevalence of G. duodenalis infection in our population.

Frequency, diagnostic performance of coproantigen detection and genotyping of the Giardia among patients referred to a multi-level teaching hospital in northern India

Giardiasis, a common gastrointestinal parasitic infection in tropics, is diagnosed on stool microscopy (gold standard); however, its sensitivity is low due to intermittent fecal shedding. Coproantigen detection (ELISA) is useful but requires further evaluation. We aimed to study: (a) detection of Giardia by stool microscopy and/or coproantigen, (b) diagnostic performance of fecal antigen detection and microscopy, and c) genotypic characterization of G. lamblia using PCR specific for triose phosphate isomerase (tpi) gene. Stool samples from 2992 patients were examined by microscopy from March 2013 to March 2015 in a multi level teaching hospital in northern India. Giardia coproantigen detection was performed by ELISA in a subset of patients. Genetic characterization of G. lamblia was performed by PCR targeting tpi gene in a subset of microscopy positive stool samples. Of 2992 patients, 132 (4.4%) had Giardia by microscopy (cyst/trophozoite) and/or ELISA. ELISA was performed in 264 patients; of them, 127 were positive by microscopy. Sensitivity, specificity, positive and negative predictive values of ELISA were 91, 91, 94, and 91%, respectively, using microscopy as a gold standard. PCR was performed in 116 randomly selected samples having Giardia using tpi gene. Assemblages A and B were found among 44 (38%) and 72 (62%) patients, respectively. Assemblage B was more often associated with malnutrition and loss of appetite than A (48/72 [67%] vs. 21/44 [48%], P = 0.044 and 17/72 [24%] vs. 14/44 [32%], P = 0.019). We conclude that 4.4% of studied population had giardiasis. Fecal antigen is a useful method for diagnosis and assemblage B is the most common genotype.

Giardia lamblia infections in children in Ghana

INTRODUCTION

Though giardiasis is an important public health problem in Ghana, several aspects of its epidemiology, particularly the molecular epidemiology has not been investigated adequately. This could be a major hindrance to effective surveillance and control of giardiasis in the country. The study was carried out to determine the prevalence, risk factors and genotypes of Giardia lamblia infecting children at a paediatric hospital in Ghana.

METHODS

A total of 485 patients including 365 diarrhoea and 120 non-diarrhoea children were enrolled into the study. Stool samples were collected and analysed for parasite presence using microscopy, ELISA and PCR. Positive samples were subsequently characterized into assemblages by PCR-RFLP, and further confirmed with sequencing of the glutamate dehydrogenase (gdh) gene. Epidemiological data on demographic, clinical and behavioral features of the study subjects were also collected.

RESULTS

Prevalence of G. lamblia infections in diarrhoea and non-diarrhoea children were 5.8% and 5% respectively (P>0.5). Sequence data confirmed Giardia lamblia assemblage B as the predominant genotype in both diarrhoea and non-diarrhoea cases. There was no significant association of G. lamblia infection with any of the epidemiological variables investigated.

CONCLUSION

Our findings suggest that assemblage B could be the predominant genotype causing giardiasis in children. Increased public health education focusing on good sanitary practices, particularly among mothers and children, could decrease the risk of G. lamblia infection.

First genetic characterisation of Giardia in human isolates from Jordan

Little is known about the epidemiology of Giardia in Jordan and to date, no genotyping studies have been conducted on Giardia isolates from Jordanians. In the present study, a total of 49 microscopy-positive faecal samples from Jordanian patients suffering from giardiasis were analysed at two loci: the triose phosphate isomerase (tpi) gene and the glutamate dehydrogenase (gdh) gene. At the tpi locus, a total of 28 samples amplified and assemblage A was identified in 46.4 % (13/28) samples, while assemblage B was identified in 50 % (14/28) samples and a mixed assemblage A and B was identified in one sample (3.6 %) (Table 1). At the gdh locus 48 isolates amplified and of these assemblages A was identified in 43.7 % (21/48) of isolates and assemblage B in 56.3 % (27/48) of isolates. No mixed infections were detected at the gdh locus. Subtyping at the gdh locus identified sub-assemblage AII in 43.7 % (21/48) of isolates and sub-assemblages BIII and BIV in 25 % (12/48) and 31.2 % (15/48) of isolates, respectively, with more genetic diversity in AII isolates than BIII or BIV isolates. Novel sub-types within each sub-assemblage were identified suggesting unique endemicity and anthroponotic transmission of Giardia in Jordanian patients suffering from giardiasis. Further studies are required to better understand the epidemiology and transmission of Giardia in Jordan.

PCR-RFLP method to detect zoonotic and host-specific Giardia duodenalis assemblages in dog fecal samples

Giardia duodenalis is a zoonotic protozoan that parasitizes the upper small intestine of human and many mammals including dogs. To develop a restriction fragment length polymorphism (RFLP) method for typing zoonotic (A, B) and host-specific (C, D) assemblages of G. duodenalis from dog, β-giardin gene was amplified with design primer pairs B3 and B4. The PCR products were digested with restriction enzyme Afa I and Msp I; then, PCR-RFLP method was compared with HRM genotyping and sequencing method for G. duodenalis from dog. The results showed that each of assemblages A-D had unique restriction pattern, which was consistent with the predictive results. Among 21 samples tested by PCR-RFLP, 1 human-derived and 8 dog-derived G. duodenalis were identified as assemblage A; 5 dog-derived G. duodenalis as assemblage C; 7 dog-derived G. duodenalis as assemblage D, which were coincided with the HRM genotyping and sequencing results. It is concluded that the PCR-RFLP is quick, easy, and accurate method for the sequence typing of G. duodenalis zoonotic and specific assemblages from dogs.

Predominance of Giardia lamblia assemblage A among iron deficiency anaemic pre-school Egyptian children

Intestinal parasites and nutritional deficiency can coexist and influence each other. This study aimed to clarify the association between Giardia genotypes and presence of iron deficiency anaemia (IDA) among pre-school Egyptian children. Two groups (IDA and non-anaemic) of giardiasis children (44/group) were selected according to their recovery response after treatment of giardiasis. Each group included 24 and 20 gastrointestinal symptomatic and asymptomatic, respectively. Giardia human genotypes were performed by intergenic spacer (IGS) gene based polymerase chain reaction (PCR) with high-resolution melting curve (HRM). PCR/HRM proved that Tms of assemblage A and B ranged from 79.31 ± 0.29 to 84.77 ± 0.31. In IDA patients, assemblages A and B were found among 40/44 (90.9 %) and 4/44 (9.1 %), respectively, while in non-anaemic patients, assemblages A and B were found in 10/44 (22.7 %) and 32/44 (72.7 %), respectively, beside two (4.6 %) cases had mixed infection. The difference was statistically significant. No significant relation was found between symptomatic or asymptomatic assemblages and IDA as assemblage A was found in 21/24 (87.5 %) and 19/20 (95 %) of symptomatic and asymptomatic, respectively, while 3/24 (12.5 %) and 1/20 (5 %) of assemblage B were symptomatic was asymptomatic, respectively. A significant relation was found between assemblage A subtypes distribution among IDA patients as AI and AII were detected on 23 (52.3 %) and 16 (36.4 %) of patients, respectively, while one case (2.3 %) had mixed infection. In conclusion, assemblage A is predominant among IDA giardiasis children suggesting its role in enhancing the occurrence of IDA while B has a protective role.

Determination of Giardia duodenalis assemblages and multi-locus genotypes in patients with sporadic giardiasis from England

Background

The protozoan Giardia duodenalis is a common but highly diverse human parasite that comprises a complex of seven morphologically identical genetic assemblages, further divided into sub-assemblages. There is very little information available on the diversity of Giardia sub-assemblages and multi-locus genotypes infecting people in the United Kingdom. In this study we studied the molecular epidemiology of Giardia in symptomatic patients from North West England.

Methods

Whole faecal DNA was extracted from the faecal samples of 406 Giardia cases and the parasites assemblage, sub-assemblage and multi-locus genotype were determined using PCR amplification, DNA sequencing and phylogenetic analysis of the beta-giardin, glutamate dehydrogenase, triose-phosphate isomerase and small-subunit ribosomal RNA genes. Information about age, gender and self-reported clinical outcomes was also collected from the patients to check for differences associated with the infecting Giardia assemblage.

Results

Our results showed a difference in the age prevalence of the two assemblages, with assemblage A being more common in older cases. Cases infected with assemblage B more often reported vomiting and a longer illness than cases infected with assemblage A. The majority of infections (64 %) were caused by assemblage B followed by assemblage A (33 %), while mixed-assemblage infections were rare (3 %). Assemblage A isolates mostly belonged to the sub-assemblage AII and showed completed identity with previously described isolates. The level of genetic sub-structuring was significantly higher in assemblage B isolates, since a higher proportion of novel assemblage B sequences was detected compared to assemblage A. A high number of assemblage B sequences showed heterogeneous nucleotide positions that prevented the unambiguous assignment to a specific sub-assemblage. Both previously described and novel multi-locus genotypes were described in both assemblages, and up to 17 different assemblage B multi-locus genotypes were found.

Conclusions

We have produced the first data on the parasite multi-locus genotypes in the UK and have demonstrated that the molecular diversity of Giardia is similar to other developed countries. Furthermore, we showed that the parasite assemblages infecting humans may be associated with patients of different ages and with different clinical outcomes.

Electronic supplementary material

The online version of this article (doi:10.1186/s13071-015-1059-z) contains supplementary material, which is available to authorized users.

Rapid detection and identification of four major Schistosoma species by high-resolution melt (HRM) analysis

Schistosomiasis, caused by blood flukes belonging to several species of the genus Schistosoma, is a serious and widespread parasitic disease. Accurate and rapid differentiation of these etiological agents of animal and human schistosomiasis to species level can be difficult. We report a real-time PCR assay coupled with a high-resolution melt (HRM) assay targeting a portion of the nuclear 18S rDNA to detect, identify, and distinguish between four major blood fluke species (Schistosoma japonicum, Schistosoma mansoni, Schistosoma haematobium, and Schistosoma mekongi). Using this system, the Schistosoma spp. was accurately identified and could also be distinguished from all other trematode species with which they were compared. As little as 10(-5) ng genomic DNA from a Schistosoma sp. could be detected. This process is inexpensive, easy, and can be completed within 3 h. Examination of 21 representative Schistosoma samples from 15 geographical localities in seven endemic countries validated the value of the HRM detection assay and proved its reliability. The melting curves were characterized by peaks of 83.65 °C for S. japonicum and S. mekongi, 85.65 °C for S. mansoni, and 85.85 °C for S. haematobium. The present study developed a real-time PCR coupled with HRM analysis assay for detection and differential identification of S. mansoni, S. haematobium, S. japonicum, and S. mekongi. This method is rapid, sensitive, and inexpensive. It has important implications for epidemiological studies of Schistosoma.

Development of a rapid HRM genotyping method for detection of dog-derived Giardia lamblia

Giardia lamblia is a zoonotic flagellate protozoan in the intestine of human and many mammals including dogs. To assess a threat of dog-derived G. lamblia to humans, the common dog-derived G. lamblia assemblages A, C, and D were genotyped by high-resolution melting (HRM) technology. According to β-giardin gene sequence, the qPCR-HRM primers BG5 and BG7 were designed. A series of experiments on the stability, sensitivity, and accuracy of the HRM method were also tested. Results showed that the primers BG5 and BG7 could distinguish among three assemblages A, C, and D, which Tm value differences were about 1 °C to each other. The melting curves of intra-assay reproducibility were almost coincided, and those of inter-assay reproducibility were much the same shape. The lowest detection concentration was about 5 × 10(-6)-ng/μL sample. The genotyping results from 21 G. lamblia samples by the HRM method were in complete accordance with sequencing results. It is concluded that the HRM genotyping method is rapid, stable, specific, highly sensitive, and suitable for clinical detection and molecular epidemiological survey of dog-derived G. lamblia.

Giardia duodenalis assemblages in Egyptian children with diarrhea

Giardia duodenalis is considered the most common cause of parasitic diarrhea worldwide. Genetic studies revealed that at least eight assemblages (A-H) exist. Of these assemblages, A and B are found primarily in human beings and occasionally in animals. The association between clinical symptoms and G. duodenalis assemblages is controversial. The aim of the present study was to determine the assemblages of G. duodenalis prevalent among Egyptian children with diarrhea. Therefore, 96 positive stool samples for Giardia by light microscopy were subjected to multilocus genotyping targeting the triose phosphate isomerase (tpi), β-giardin (bg), and glutamate dehydrogenase (gdh) genes. Amplified polymerase chain reaction (PCR) products were then purified, sequenced, and aligned with reference strains to determine the assemblages of the Giardia isolates. Out of the 96 microscopically positive stool samples for Giardia, 77 (80 %) were successfully amplified and sequenced at least at one locus. Of these, 21 (27.3 %) were shown to be assemblage A, 54 (70.1 %) assemblage B, while discordant sequence typing results were observed in 2 (2.6 %) samples. AII was the predominant subassemblage of assemblage A, while it was generally difficult to further classify assemblage B. It was concluded that infection with assemblage B was more common than that with assemblage A. No associations between epidemiological information and assemblage were detected, except with age. Although infections with assemblage B were more frequently associated with abdominal pain and acute diarrhea than with assemblage A, the difference was not statistically significant.

Genotyping and phylogenetic analysis of Giardia duodenalis isolates from Turkish children

Background

Giardiasis is caused by the intestinal protozoan parasite Giardia duodenalis (synonyms: G. lamblia, G. intestinalis), which is one of the most frequent parasites that infect Turkish children. However, molecular characterization of G. duodenalis in Turkey is relatively scarce. The present work aimed at genotyping G. duodenalis isolates from Turkey using molecular techniques.

Material/Methods

In the present study, 145 fecal samples from children were collected to search for the presence of Giardia by microscopy and PCR screening. PCR generated a 384 bp fragment for β-giardin. The PCR products were sequenced and the sequences were subjected to phylogenetic analysis by using PHYLIP.

Results

Based on the phylogenetic analysis of the sequences, assemblage A, B, and mixed subtypes were determined. Of 22 isolates, 11 were identified as assemblage A (50%), 7 were assemblage B (31.8%), and 4 were assemblage AB (18.2%). Association between G. duodenalis assemblages and the epidemiological data was analyzed. No correlation was found between symptoms and infection with specific assemblages (P>0.05), but we found statistically significant association between age and the assemblage AB (P=0.001).

Conclusions

The association between G. duodenalis and the epidemiologic data were analyzed. Since assemblage A is the more prevalent subgroup compared with assemblage B, this subgroup might be responsible for common Giardia infections in Turkey. This is the first study that included a detailed phylogenetic analysis of Giardia strains from Turkey.

Genetic diversity of Giardia duodenalis: multilocus genotyping reveals zoonotic potential between clinical and environmental sources in a metropolitan region of Brazil

BACKGROUND

Giardia duodenalis is a flagellate protozoan that parasitizes humans and several other mammals. Protozoan contamination has been regularly documented at important environmental sites, although most of these studies were performed at the species level. There is a lack of studies that correlate environmental contamination and clinical infections in the same region. The aim of this study is to evaluate the genetic diversity of a set of clinical and environmental samples and to use the obtained data to characterize the genetic profile of the distribution of G. duodenalis and the potential for zoonotic transmission in a metropolitan region of Brazil.

METHODOLOGY/PRINCIPAL FINDINGS

The genetic assemblages and subtypes of G. duodenalis isolates obtained from hospitals, a veterinary clinic, a day-care center and important environmental sites were determined via multilocus sequence-based genotyping using three unlinked gene loci. Cysts of Giardia were detected at all of the environmental sites. Mixed assemblages were detected in 25% of the total samples, and an elevated number of haplotypes was identified. The main haplotypes were shared among the groups, and new subtypes were identified at all loci. Ten multilocus genotypes were identified: 7 for assemblage A and 3 for assemblage B.

CONCLUSIONS/SIGNIFICANCE

There is persistent G. duodenalis contamination at important environmental sites in the city. The identified mixed assemblages likely represent mixed infections, suggesting high endemicity of Giardia in these hosts. Most Giardia isolates obtained in this study displayed zoonotic potential. The high degree of genetic diversity in the isolates obtained from both clinical and environmental samples suggests that multiple sources of infection are likely responsible for the detected contamination events. The finding that many multilocus genotypes (MLGs) and haplotypes are shared by different groups suggests that these sources of infection may be related and indicates that there is a notable risk of human infection caused by Giardia in this region.

Detection and molecular characterisation of Giardia lamblia genotypes in Sharjah, United Arab Emirates

BACKGROUND

No data are available on Giardia lamblia genotypes in the United Arab Emirates (UAE). This study aimed to identify G. lamblia from DNA extracted from human stool samples to gain information on its prevalence and to perform molecular analysis on isolates collected from expatriates from different localities residing in Sharjah, UAE.

METHODS

In total, 111 healthy expatriates residing in Sharjah were screened for G. lamblia using nested PCR amplification of the small subunit ribosomal RNA (ssu-rRNA) gene. Positive samples were genotyped using a nested PCR amplifying the triosephosphate isomerase (tpi) gene to differentiate between the two human assemblages (A and B). A subset of the PCR products (n=23) were sequenced and their phylogenetic relationships were determined.

RESULTS

Of the 111 participants, 67 (60.4%) were identified as positive for the ssu-rRNA gene. When genotyped for the tpi gene, 18.9% (21/111) were of assemblage A, 17.1% (19/111) belonged to assemblage B and 5.4% (6/111) showed patterns compatible with mixed infections. A strong correlation between the presence of diarrhoea and assemblage B was observed (χ(2)=10.553; p=0.001). Moreover, an association was also observed between mixed infections (A+B) and diarrhoea (χ(2)=8.899; p=0.003). No correlation between age, gender and geographic origin of the infected individual was noted. Phylogenetic analysis showed three clusters for the tpi gene. No relationship between the clusters and the origin of samples was noted.

CONCLUSION

This study is the first to determine the infection rate and genotypic composition of Giardia in Sharjah, UAE.

Detection of intestinal protozoa in paediatric patients with gastrointestinal symptoms by multiplex real-time PCR

The performance of a multiplex real-time PCR for the detection of Blastocystis, Dientamoeba fragilis, Giardia lamblia, Cryptosporidium species and Entamoeba species in faecal samples was evaluated in an observational prospective study. Paediatric patients (0-18 years) presenting with gastrointestinal symptoms and suspected of having enteroparasitic disease were included. A questionnaire on gastrointestinal symptoms and the chosen treatment was completed at the start of the study and after 6 weeks. Of 163 paediatric patients (mean age, 7.8 years), 114 (70%) had a PCR-positive faecal sample. D. fragilis was detected most frequently, in 101 patients, followed by Blastocystis in 49. In faecal samples of 47 patients, more than one protozoan was detected, mainly the combination of D. fragilis and Blastocystis. Reported gastrointestinal symptoms were abdominal pain (78%), nausea (30%), and altered bowel habits (28%). Eighty-nine of the PCR-positive patients were treated with antibiotics. A significant reduction in abdominal pain was observed both in treated and in untreated patients. This study demonstrated that multiplex real-time PCR detects a high percentage of intestinal protozoa in paediatric patients with gastrointestinal symptoms. However, interpretation and determination of the clinical relevance of a positive PCR result in this population are still difficult.

Molecular and Clinical Characterization of Giardia duodenalis Infection in Preschool Children from Lisbon, Portugal

Giardia duodenalis is the most prevalent intestinal protozoan infection especially in children. In Portugal scarce data are available relative to this infection in preschoolers. The present study was conducted from April to July 2009 in public preschools in Lisbon enrolling 316 children. Stool examination was performed through microscopy. Molecular analysis was conducted in all positive samples for G. duodenalis in order to determine the assemblage and subassemblage of this parasite. Eight of the preschoolers studied children (2.5%, 8/316) were infected with G. duodenalis. Additionally the brother of one of the infected children was also infected. Genotyping analysis targeting ssu-rRNA and β -giardin loci revealed six infections with assemblage A and 3 with assemblage B. Sub-assemblage determination was possible in four of the samples, with three A2 and one A3. The limited number of cases precluded an association of a determined symptom with an assemblage. The data presented here show the relevance of considering G. duodenalis analysis in children with intestinal complaints even in developed countries.

Identification of Trypanosoma cruzi discrete typing units (DTUs) through the implementation of a high-resolution melting (HRM) genotyping assay

Background

Chagas disease, caused by Trypanosoma cruzi, is a geographically widespread anthropozoonosis that is considered a major public health problem in Latin America. Because this parasite presents high genetic variability, a nomenclature has been adopted to classify the parasite into six discrete typing units (DTUs): TcI, TcII, TcIII, TcIV, TcV, and TcVI, which present different eco-epidemiological, clinical, and geographic associations. Currently, the available genotyping methods present a series of drawbacks that implies the need for developing new methods for characterizing T. cruzi DTU’s. The aim of this work was to genotype reference populations from T. cruzi by means of a High-Resolution Melting (HRM) genotyping assay.

To genotype the DTUs of 38 strains and 14 reference clones of T. cruzi from diverse sources, real-time PCR (qPCR) was coupled to high-resolution melting (HRM) based on the amplification of two molecular markers—the divergent domain of the 24 sα rRNA gene and the intergenic region of the mini-exon gene.

Findings

Amplification of the mini-exon gene allowed the genotyping of three distinct groups: TcI, TcII- TcIV- TcV, and TcIII-TcVI, while amplification of the 24sα gene generated non-overlapping melting temperature ranges for each DTU that were used to identify the groups in the six existing DTUs of Trypanosoma cruzi.

Conclusions

The proposed genotyping assay allowed discrimination of the six genetic groups by obtaining specific melting curves for each DTU. The application of this technique is proposed because of its specificity, sensitivity, high performance, and low cost compared with other previously described characterization methods.

A systematic review and meta-analysis of the association between Giardia lamblia and endemic pediatric diarrhea in developing countries

We performed a systematic literature review and meta-analysis examining the association between diarrhea in young children in nonindustrialized settings and Giardia lamblia infection. Eligible were case/control and longitudinal studies that defined the outcome as acute or persistent (>14 days) diarrhea, adjusted for confounders and lasting for at least 1 year. Data on G. lamblia detection (mainly in stools) from diarrhea patients and controls without diarrhea were abstracted. Random effects model meta-analysis obtained pooled odds ratios (ORs) and 95% confidence intervals (CIs). Twelve nonindustrialized-setting acute pediatric diarrhea studies met the meta-analysis inclusion criteria. Random-effects model meta-analysis of combined results (9774 acute diarrhea cases and 8766 controls) yielded a pooled OR of 0.60 (95% CI, .38-.94; P = .03), indicating that G. lamblia was not associated with acute diarrhea. However, limited data suggest that initial Giardia infections in early infancy may be positively associated with diarrhea. Meta-analysis of 5 persistent diarrhea studies showed a pooled OR of 3.18 (95% CI, 1.50-6.76; P < .001), positively linking Giardia with that syndrome. The well-powered Global Enteric Multicenter Study (GEMS) is prospectively addressing the association between G. lamblia infection and diarrhea in children in developing countries.

Giardia--from genome to proteome

In this review, the current status of genomic and proteomic research on Giardia is examined in terms of evolutionary biology, phylogenetic relationships and taxonomy. The review also describes how characterising genetic variation in Giardia from numerous hosts and endemic areas has provided a better understanding of life cycle patterns, transmission and the epidemiology of Giardia infections in humans, domestic animals and wildlife. Some progress has been made in relating genomic information to the phenotype of Giardia, and as a consequence, new information has been obtained on aspects of developmental biology and the host-parasite relationship. However, deficiencies remain in our understanding of pathogenesis and host specificity, highlighting the limitations of currently available genomic datasets.

The potential of high resolution melting analysis (hrma) to streamline, facilitate and enrich routine diagnostics in medical microbiology

BACKGROUND

Routine medical microbiology diagnostics relies on conventional cultivation followed by phenotypic techniques for identification of pathogenic bacteria and fungi. This is not only due to tradition and economy but also because it provides pure culture needed for antibiotic susceptibility testing. This review focuses on the potential of High Resolution Melting Analysis (HRMA) of double-stranded DNA for future routine medical microbiology.

METHODS AND RESULTS

Search of MEDLINE database for publications showing the advantages of HRMA in routine medical microbiology for identification, strain typing and further characterization of pathogenic bacteria and fungi in particular. The results show increasing numbers of newly-developed and more tailor-made assays in this field. For microbiologists unfamiliar with technical aspects of HRMA, we also provide insight into the technique from the perspective of microbial characterization.

CONCLUSIONS

We can anticipate that the routine availability of HRMA in medical microbiology laboratories will provide a strong stimulus to this field. This is already envisioned by the growing number of medical microbiology applications published recently. The speed, power, convenience and cost effectiveness of this technology virtually predestine that it will advance genetic characterization of microbes and streamline, facilitate and enrich diagnostics in routine medical microbiology without interfering with the proven advantages of conventional cultivation.