Coproscopy and molecular screening for detection of intestinal protozoa

Design and evaluation of loop-mediated isothermal amplification for rapid detection of Enterocytozoon bieneusi

Enterocytozoon bieneusi is one of the most prevalent microsporidia species, responsible for more than 90% of human and animal microsporidiosis. Microsporidia species, particularly E. bieneusi, are frequently reported from waterborne and foodborne outbreaks. Therefore, early detection is crucial in clinics and outbreak investigations. This study aimed to design a loop-mediated isothermal amplification (LAMP) for rapid detection of E. bieneusi. Total DNA was extracted from 30 E. bieneusi -positive samples, which had been confirmed with nested PCR. LAMP primers were designed based on the identical fragment of small subunit ribosomal RNA (SSU rRNA) gene. LAMP reactions were performed at 63 °C for 60 min. The sensitivity and specificity of the assay were analyzed and the results of amplification were compared to real-time PCR. Our results showed that the LAMP assay successfully amplified 25/30 (83.3%) samples. The specificity results indicated no false positive with other microorganisms. Furthermore, the LAMP method exhibited a sensitivity (limit of detection, LoD) as low as 34 ag/μL of total DNA. Compared to the LAMP assay, real-time PCR was able to detect all 30 nested PCR-positive samples. Our findings showed that the LAMP assay was able to detect 83.3% of E. bieneusi-positive samples. Although the current assay was not able to detect all nested PCR-positive samples, the lack of need for specific instruments, rapid processes, and high specificity makes LAMP assay a suitable tool for screening.

Prevalence and genetic diversity of Blastocystis sp. among autochthonous and immigrant patients in Italy

The prevalence of Blastocystis sp., its genetic diversity and the distribution of circulating subtypes (STs) were molecularly investigated in a cohort of autochthonous and immigrant patients with gastrointestinal symptoms hospitalized over the period February 2022-June 2023 at the Policlinico Ospedaliero-Universitario "Riuniti", Foggia, in Southern Italy. The population variables, including patient geographical origin, gender and age classes were reported. Out of the 927 investigated patients, 36 (3.9%) were positive for Blastocystis sp. A statistically significant association with African origin and age classes >18 years old was found. ST1 (allele 4), ST2 (alleles 9, 13), ST3 (alleles 34, 36) and ST4 (allele 92) were the subtypes detected with a different distribution between autochthonous and immigrant patients. Co-infections with enteric protozoa such as Giardia duodenalis and Dientamoeba fragilis, pathogenic bacteria as Clostridioides difficile, Campylobacter jejuni and Aeromonas sp. and viral infections such as Norovirus were found in 33% of cases. This is the first study of Blastocystis sp., its circulating subtypes and allele variability among patients with different geographical origin in an area of Southern Italy, in the Central Mediterranean, characterized by high immigrant pressure. These results provide baseline data to better investigate a potential interaction between Blastocystis sp. and other risk factors in patients with gastrointestinal symptoms.

Prevalence and Associated Factors of Blastocystis sp. Infection in Patients with Gastrointestinal Symptoms in Spain: A Case-Control Study

Blastocystis sp. is known to be the most prevalent parasite in fecal samples of humans worldwide. In the present report, a case–control study (1:9.89 (≈10)) was performed, by analyzing data from 3682 patients who attended a public hospital in the northern area of Spain showing gastrointestinal symptoms. Diagnosis was performed in human fecal samples by means of optical microscopy. The prevalence of Blastocystis sp. in patients with gastrointestinal symptoms was 9.18% (338/3682). Most of the Blastocystis sp.-infected patients tested negative for protozoa and helminths, and were underweight and foreign-born (26.4%), mainly from Africa and Central/South America. Gastrointestinal symptoms, such as abdominal pain, anorexia, halitosis, plus relative eosinophilia, as well as co-infections with pathogenic bacteria were associated with Blastocystis sp. infection. Both type 2 diabetes and treatment with immunosuppressive medicines at the time of Blastocystis sp. detection were associated with a higher proportion of infected patients. This is the first case–control study of Blastocystis sp. in humans in northern Spain and may contribute to surveillance and intervention strategies by public health authorities.

Detection and pathological role of intestinal protozoa in children

INTRODUCTION

Intestinal parasites are considered a growing public health problem, being protozoa the main cause of intestinal disease. The objective of our study is to compare the detection of intestinal protozoa by microscopy versus real-time PCR, as well as to determine the most prevalent protozoa in our environment in the paediatric population.

METHOD

An observational longitudinal study was carried out, both by microscopy and real time-PCR in stool samples from children (0-15 years) received from April 2019 to March 2021.Children were classified in two groups according if they had or not had clinical parasitosis. Microscopic examination was performed in all samples using the Ritchie concentration technique with the commercial Mini PARASEP system (Movaco-Grifols®). The presence of Cryptosporidium sp. was evaluated with the modified Ziehl-Neelsen acid-fast stain. The real-time PCR was performed to all samples using the Allplex ™ gastrointestinal parasite panel 4 (Seegene®).

RESULTS

During the study period, 500 samples were received, being positive 31 (6.2%) by microscopy and 256 (51.2%) by PCR. By microscopy, Blastocystis hominis was the most frequently observed (4.8%), followed by Giardia lamblia (1.6%), Dientamoeba fragilis (0.2%) and Cryptosporidium species (0.2%). Regarding the identification by PCR, D. fragilis (35.2%) was mainly identified, followed by B. hominis (28.1%), G. lamblia (7%) and Cryptosporidium sp. (0.8%) without finding clear differences in aetiology according to age. In the case of B. hominis and D. fragilis, there were not differences in the detection of these protozoa between the control group and children with clinical parasitosis (p = 0.11).

CONCLUSIONS

Real-time PCR increases the detection of intestinal protozoa, being underdiagnosed by microscopy, especially D. fragilis, in which PCR is considered the most appropriate method for its detection.

The Coexistence of Blastocystis spp. in Humans, Animals and Environmental Sources from 2010-2021 in Asia

Blastocystis spp. are controversial unicellular protists that inhabit the gastrointestinal tract of humans and a wide range of animals worldwide. This review provides an overview of the prevalence and distribution of Blastocystis spp. and their subtypes throughout Asia. Research articles reporting on the presence of Blastocystis spp. in locations within Asia, between 1 January 2010, and 10 May 2021, were obtained from Scopus, PubMed, and Google Scholar. In 427 articles, the prevalence of Blastocystis spp. in 31 countries within the last decade was revealed. Isolates were found in humans, various mammals, birds, reptiles, insects, water sources, vegetables, and ambient air. Prevalence of Blastocystis spp. varied widely across host categories. Subtypes identified throughout Asia were STs 1-14, and ST18-22 (novel subtypes). ST1, ST2, ST3, ST4 were the most frequently isolated in humans; ST5 in pigs; ST10 and ST14 in goats, sheep, and cattle; and ST6 and ST7 in chickens. ST1 and ST3 were most common in water samples. ST1, ST2, ST3, ST4, ST5 and ST6 were shared by humans, animals, and water sources. There is a growing interest in the study of Blastocystis spp. and their subtypes in Asia. Due to the isolation of Blastocystis spp. from biotic and abiotic sources in Asia, the application of the One Health (OH) approach to the study of Blastocystis spp. is proposed for improved perception of this organism.

Comparison of Microscopy and PCR for Detection of Giardia Lamblia and Entamoeba Histolytica in Human Stool Specimens in a Resource Limited Setting in Western Kenya

Background

Accurate diagnosis of Giardia lamblia and Entamoeba histolytica is important since these intestinal parasites account for a significant proportion of morbidity and mortality globally. Microscopy is the key diagnostic test used for diagnosis of the two parasites. Other tests including rapid diagnostic tests and polymerase chain reaction have been developed to improve the detection of these parasites. Most of these newer tests are not affordable in resource limited settings, hence the over reliance on microscopy. The objective of this study was to determine the reliability of microscopy in a resource limited setting in Western Kenya, a region endemic for the two intestinal parasites.

Methods

Polymerase chain reaction, the gold standard test, was performed on stool samples suspected for G. lamblia and E. histolytica. Microscopy was then performed on the same samples and the two tests compared.

Results

Microscopy was found to be 64.4% sensitive, 86.6% specific for the detection of G. lamblia. Additionally, this test was 64.2% sensitive and 83.6% specific for the diagnosis of E. histolytica. Cohen's kappa values of 0.51 and 0.47 were determined for microscopy for G. lamblia and E. histolytica respectively. McNemar's test revealed a significant difference between the two tests, P<0.001.

Conclusion

This study found microscopy to be a reliable diagnostic test in this resource limited setting.

Prevalence and genetic characteristics of Blastocystis hominis and Cystoisospora belli in HIV/AIDS patients in Guangxi Zhuang Autonomous Region, China

Blastocystis hominis and Cystoisospora belli are considered to be common opportunistic intestinal protozoa in HIV/AIDS patients. In order to investigate the prevalence and genetic characteristics of B. hominis and C. belli in HIV/AIDS patients, a total of 285 faecal samples were individually collected from HIV/AIDS patients in Guangxi, China. B. hominis and C. belli were investigated by amplifying the barcode region of the SSU rRNA gene and the internal transcribed spacer 1 (ITS-1) region of the rRNA gene, respectively. Chi-square test or Fisher’s exact test were conducted to assess the risk factors related to B. hominis and C. belli infection. The prevalence of B. hominis and C. belli was 6.0% (17/285) and 1.1% (3/285) respectively. Four genotypes of B. hominis were detected, with ST3 (n = 8) and ST1 (n = 6) being predominant, followed by ST6 (n = 2) and ST7 (n = 1). Females had a statistically higher prevalence of B. hominis (11.6%) than males (4.2%). The statistical analysis also showed that the prevalence of B. hominis was significantly associated with age group and educational level. Our study provides convincing evidence for the genetic diversity of B. hominis, which indicates its potential zoonotic transmission and is the first report on the molecular characteristics of C. belli in HIV/AIDS patients in China.

Epidemiology and clinical features of intestinal protozoan infections detected by Real-time PCR in non-native children within an Italian tertiary care children's hospital: A cross-sectional study

BACKGROUND

Enteric parasite infections are underestimated due to the limited sensitivity and specificity of microscopy, which remains the diagnostic gold standard in routine clinical practice. This could be a major problem in high-income countries, where the burden of parasitic diseases is low. In recent years, Multiplex Real-Time polymerase chain reaction (RT-PCR) based methods have been implemented. Therefore, the aim of this study was to evaluate the prevalence of four enteric protozoan species detected by RT-PCR in non-native children in Italy, and to describe their clinical characteristics.

METHODS

Adopted and immigrant children, evaluated for migration health assessment between 2017 and 2020 in a tertiary care children's hospital in Italy, were enrolled. Molecular analysis for Giardia lamblia, Dientamoeba fragilis, Blastocystis hominis, and Entamoeba histolytica, was conducted by in-house RT-PCR.

RESULTS

Overall, 209 children were enrolled and 70% of them resulted positive by RT-PCR for at least one enteric parasite. B. hominis (47.8%) was the most commonly identified protozoa, followed by D. fragilis (44.5%). Co-infections with multiple pathogens were detected in 35.4% of the samples. Almost 80% of parasite-positive children were asymptomatic and the most common symptom was flatulence (60.7% of symptomatic children). Eosinophils were significantly increased in RT-PCR positive children compared to the negative ones and children with D. fragilis presented the highest eosinophils count.

CONCLUSIONS

The In-house Multiplex RT-PCR assay provides a valid molecular detection system for selected enteric parasites. This novel and accurate diagnostic method can help in increasing the detection rate of parasite infection, especially in high-risk population.

Rodent-Related Zoonotic Pathogens at the Human-Animal-Environment Interface in Qatar: A Systematic Review and Meta-Analysis

Rodents are one of the most diversified terrestrial mammals, and they perform several beneficial activities in nature. These animals are also important as carriers of many pathogens with public health importance. The current systematic review was conducted to formulate a true depiction of rodent-related zoonoses in Qatar. Following systematic searches on PubMed, Scopus, Science Direct, and Web of Science and a screening process, a total of 94 published articles were selected and studied. The studied articles reported 23 rodent-related zoonotic pathogens that include nine bacterial, eleven parasitic, and three viral pathogens, from which the frequently reported pathogens were Mycobacterium tuberculosis (32 reports), Escherichia coli (23), and Salmonella spp. (16). The possible pathway of entry of the rodent-borne pathogens can be the land port, seaports, and airport of Qatar through carrier humans and animals, contaminated food, and agricultural products. The pathogens can be conserved internally by rodents, pets, and livestock; by agricultural production systems; and by food marketing chains. The overall estimated pooled prevalence of the pathogens among the human population was 4.27% (95%CI: 4.03–4.51%; p < 0.001) with significant heterogeneity (I² = 99.50%). The top three highest prevalent pathogens were M.tuberculosis (30.90%; 22.75–39.04%; p < 0.001; I² = 99.70%) followed by Toxoplasma gondii (21.93%; 6.23–37.61%; p < 0.001; I² = 99.30%) and hepatitis E virus (18.29%; 11.72–24.86%; p < 0.001; I² = 96.70%). However, there is a knowledge gap about the listed pathogens regarding the occurrence, transmission pathways, and rodent role in transmission dynamics at the human–animal–environment interface in Qatar. Further studies are required to explore the role of rodents in spreading zoonotic pathogens through the One Health framework, consisting of zoologists, ecologists, microbiologists, entomologists, veterinarians, and public health experts in this country.

Genetic Diversity and Prevalence of Giardia duodenalis in Qatar

Background

Giardia duodenalis is a common human intestinal parasite worldwide, and the causative agent of diarrhea, with the severity of disease ranging from asymptomatic to intense and debilitating infection. G. duodenalis is known to consist of eight genetically distinct assemblages, named from A to H. No data available on the genotypes and genetic diversity of G. duodenalis circulating in Qatar.

Methods

We genotyped 54 human Giardia isolates, collected from asymptomatic immigrants in Qatar, using a multilocus genotyping (MLGs) tool. We also investigated relationships between the subjects’ genotypes and their demographic data.

Results

Genomic DNA from 54 isolates were tested by PCR and sequence analysis at three loci: glutamate dehydrogenase (gdh), β-giardin (bg) and triose phosphate (tpi)). Assemblage A was identified in nine (16.67%), assemblage B in thirty (55.55%), and a mixture of assemblages A+B in fifteen (27.78%) isolates. All assemblage A isolates, genotyped in different loci, were assigned to sub-assemblage AII, and six of them had MLGs AII-1 while one new MLG was identified in two isolates. Sequences of assemblage B isolates have high level of genetic diversity and high presence of heterogeneous peaks, especially within the gdh gene. No significant associations between genotypes and the immigrants’ demographic data were found due to the extensive number of new variants.

Conclusions

MLGs was used herein to genotype 54 immigrant Giardia isolates. The high level of genetic variability found in our isolates hampered MLGs determination, more investigations are now required to consolidate our findings, and to enable a comprehensive understanding of the diversity within G. duodenalis assemblage B isolates.

Socio-demographic influences on the prevalence of intestinal parasitic infections among workers in Qatar

Background

The rapid growth of Qatar in the last two decades has been associated with an enormous expansion of building programs in its cities and in the provision of new service industries. This in turn has attracted a large influx of immigrant workers seeking employment in jobs associated with food handling, domestic service, and the building industry. Many of these immigrants come from countries in the tropics and subtropics where intestinal parasitic infections are common. In this study, we explored the environmental and socio-demographic characteristics of immigrant workers in Doha Qatar, which might explain the persistence of the parasites that they harbor.

Methodology

This cross-sectional survey was conducted among 2486 newly arrived immigrant workers and those who visited Qatar previously during the period 2012–2014. Through questionnaires and census data, we characterized the socio-demographic conditions at an individual, family, and neighborhood levels.

Results

Overall, the prevalence of combined protozoan infection was 11.7% and that of helminth was 7.0%. Combined protozoan infections were significantly associated with immigrant workers arriving in Doha for the first time. In univariate log-linear statistical models fitted in phase 1 of the analysis, significant associations were observed between the prevalence of combined protozoan infections and personal and familial factors that included religion, the level of education of subjects, both parents’ educational levels and their jobs, and the number of siblings. Furthermore, environmental effects on the prevalence of protozoan infections including the country of origin, the floor of the house, toilet type, household content index, provision of household water, farming background showed strong associations with protozoan infections. However, in phase 2, multifactorial binary logistic generalized linear models focusing only on the significant effects identified in phase 1, showed that only five factors retained significance (age class, floor of the house, household contents index, father’s education, and the number of siblings). The only factors that had a significant effect on the prevalence of helminth infections were the subjects’ age class and the mother’s educational level.

Conclusions

The prevalence of intestinal protozoan parasites among immigrant workers in Qatar is clearly multifactorial in origin determined by key familial relationships of subjects and also the environment, in which the subjects lived prior to their arrival in Qatar. Moreover, our results suggest that screening protocols for applicants for visas/work permits need to be revised giving more careful attention to the intestinal protozoan infections that potential immigrant workers may harbor.

Cryptosporidium spp., prevalence, molecular characterisation and socio-demographic risk factors among immigrants in Qatar

BACKGROUND

The World Health Organization WHO has estimated that in developed countries, up to 30% of the population may suffer from foodborne diseases each year, and that in developing countries up to 2 million deaths per annum can be attributed to cryptosporidiosis. Reports have already emphasized the role of immigrants in outbreaks of parasitic diseases especially those working in food processing industries.

METHODOLOGY/PRINCIPAL FINDINGS

Herein we assessed Cryptosporidium spp. infections among immigrants in Qatar with a special focus on food handlers and housemaids. The overall prevalence of Cryptosporidium spp. by q-PCR among 839 asymptomatic subjects was 4.5%. Based on the Gp60 gene, the majority of isolates were identified as C. parvum subtype IIdA20G1b. The positive sample for C. hominis was subtyped as IeA12G3T3. Seven mixed infections were also identified (four C. parvum + C. hominis, and three C. parvum + C. meleagridis). The prevalence of Cryptosporidium spp. did not differ significantly between the sexes or age classes but varied significantly between subjects affiliated to different religions with the lowest prevalence among the Muslims. Multifactorial analysis retained also marked significance with education, income, and a house contents index.

CONCLUSIONS/SIGNIFICANCE

Our results contribute to a better understanding of the epidemiology of cryptosporidiosis and the risk factors associated with the likelihood of carrying this infection among immigrant workers from developing countries.

The importance of considering the neglected intestinal protozoan parasite Dientamoeba fragilis

Dientamoebiasis is globally distributed and detected in a large number of subjects with diarrhea, abdominal discomfort, flatulence, fatigue and loss of appetite. The life cycle and transmission of Dientamoeba fragilis are poorly understood. Microscopic examination of permanent stained smears is traditionally employed to diagnose the infection. However, this approach is time-consuming and the success in detecting D. fragilis depends on the microscopist's experience. Hence, only a few laboratories routinely carry out tests for D. fragilis. Consequently, the prevalence of D. fragilis infection is probably underestimated. Although novel, rapid and more sensitive diagnostic tests are becoming available for detecting intestinal parasites, they also possess some limitations. The aim of this study was to emphasize the importance of performing microscopic examination of permanent stained smears from at least one fresh stool specimen after sample arrival at the laboratory, as a mandatory practice for the diagnosis of dientamoebiasis, particulary where it is not possible to perform molecular assays.

Development and evaluation of molecular tools for detecting and differentiating intestinal amoebae in healthy individuals

Amoebae are single-celled parasites frequently colonizing human gut. However, few molecular tools are available for accurate identification. Here, we evaluated a panel of polymerase chain reactions (PCRs) targeting Entamoeba histolytica, Entamoeba dispar, Entamoeba coli, Entamoeba hartmanni, Entamoeba polecki, Endolimax nana and Iodamoeba bütschlii. Thirty-six faecal samples (18 containing at least one amoeba species by microscopy and 18 microscopy negative for amoebae) were tested. Real-time PCRs were used for detection and differentiation of E. histolytica and E. dispar. Conventional PCR with Sanger sequencing were applied for detection and differentiation of E. coli, E. hartmanni, E. polecki, E. nana and I. bütschlii. All microscopy results were confirmed by DNA-based methods. However, more samples were positive for single and mixed amoebic species by DNA-based assays than by microscopy (22 vs 18 and 7 vs 1, respectively). DNA sequencing allowed identification of E. coli subtypes (ST1 and ST2), showed low intra-specific variation within E. hartmanni, identified two phylogenetically distinct groups within E. nana, and identified Iodamoeba at the ribosomal lineage level. Taking into account the high intra-genetic diversity within some of the species at the small subunit (SSU) rRNA gene level, amplification of SSU rRNA genes with subsequent sequencing represents a useful method for detecting, differentiating and subtyping intestinal amoebae.