Molecular Biology Can Change the Classic Laboratory Approach for Intestinal Protozoan Infections

Microscopy detection and molecular characterisation of Giardia duodenalis infection in outpatients seeking medical care in Egypt

Introduction

Giardiosis remains one of the most prevalent enteric parasitic infections globally. Earlier molecular-based studies conducted in Egypt have primarily focused on paediatric clinical populations and most were based on single genotyping markers. As a result, there is limited information on the frequency and genetic diversity of G. duodenalis infections in individuals of all age groups.

Methods

Individual stool samples (n = 460) from outpatients seeking medical care were collected during January-December 2021 in Kafr El-Sheikh governorate, northern Egypt. Initial screening for the presence of G. duodenalis was conducted by coprological examination. Microscopy-positive samples were further confirmed by real-time PCR. A multilocus sequence typing approach targeted amplification of the glutamate dehydrogenase (gdh), beta-giardin (bg), and triose phosphate isomerase (tpi) genes was used for genotyping purposes. A standardised epidemiological questionnaire was used to gather basic sociodemographic and clinical features of the recruited patients.

Results

Giardia duodenalis cysts were observed in 5.4% (25/460, 95% CI: 3.6-7.9) of the stool samples examined by conventional microscopy. The infection was more frequent in children under the age of 10 years and in individuals presenting with diarrhoea but without reaching statistical significance. Stool samples collected during the winter period were more likely to harbour G. duodenalis. All 25 microscopy-positive samples were confirmed by real-time PCR, but genotyping data was only available for 56.0% (14/25) of the isolates. Sequence analyses revealed the presence of assemblages A (78.6%, 11/14) and B (21.4%, 3/14). All assemblage A isolates were identified as sub-assemblage AII, whereas the three assemblage B sequences belonged to the sub-assemblage BIII. Patients with giardiosis presenting with diarrhoea were more frequently infected by the assemblage A of the parasite.

Conclusion

This is one of the largest epidemiological studies evaluating G. duodenalis infection in individuals of all age groups in Egypt. Our molecular data suggest that G. duodenalis infections in the surveyed population are primarily of anthropic origin. However, because assemblages A and B are zoonotic, some of the infections identified can have an animal origin. Additional investigations targeting animal (domestic and free-living) and environmental (water) samples are warranted to better understand the epidemiology of giardiosis in Egypt.

Screening of Schistosomiasis, Strongyloidiasis and Sexually Transmitted Infections in Nigerian Female Sex Workers Living in Rome

BACKGROUND

Female Sex Workers (FSWs) are at high risk for acquisition and transmission of sexually transmission infections (STIs). Although several studies investigated the diffusion of STIs in this population, none of them investigated the occurrence of helminth infections in FSW coming from endemic regions. This study aims to assess the prevalence of STIs and helminth infections in a cohort of FSWs.

METHOD

authors conducted a prevalent, observational, and descriptive study on 97 Nigerian FSWs aged 17 to 52 years from January to December 2020.

RESULTS

a total of 97 FSWs were recruited. Of these, only 82 had completed screening for hepatitis B, C, syphilis, and HIV, while all 97 were screened for schistosomiasis and strongyloidiasis. The prevalence of STIs among FSWs in Rome was lower than in other European countries. The overall prevalence of HIV and HBsAg were 1.2%, (1/82) and 2.4% (2/82), respectively, while no case of hepatitis C and syphilis was found. Regarding parasitological screening, the overall prevalence of schistosoma species was 4.1% (4/97) while 5.15% (5/97) were positive for strongyloidiasis.

CONCLUSIONS

our study shows a low prevalence of STIs in Nigerian FSWs except for Hepatitis B and a higher prevalence of schistosomiasis and strongyloidiasis. The permanent monitoring of STI and parasitic infections in sex workers coming from Africa is strongly warranted, especially for hepatitis B, schistosomiasis and strongyloidiasis, to allow a timely diagnosis and treatment, and to plan preventive strategies.

Frequency, spatial distribution, and genetic diversity of Blastocystis among referred individuals to a clinical laboratory: First report of subtype 9 in Brazil

The enteric protist Blastocystis has a worldwide distribution, however its prevalence in the human population is still underestimated, especially in developing countries where proper diagnosis is not performed in the routine of clinical laboratories. In this study, we aimed to assess the frequency, genetic diversity, and spatial distribution of Blastocystis isolates detected in fecal samples referred to a clinical laboratory for routine examination in inner São Paulo State, Brazil. A total of 348 leftover stool samples available for disposal from female and male individuals with age ranging from 3 months to 88 years were analyzed by both microscopic examination and PCR/sequencing of the SSU rRNA gene. The overall frequency of Blastocystis sp. was 31% (108/348), including 20.1% (70/348) and 31% (108/348) by microscopic examination and PCR/sequencing, respectively. Significant association was found only between Blastocystis infection and age, since the highest rate of positive samples was detected among 5-9 years old individuals (p < 0.0001). In addition, spatial distribution revealed a wide distribution of the positive samples, however they were densely concentrated in more populated areas. Seven subtypes were identified, namely ST1 (40.7%), ST2 (9.2%), ST3 (45.3%), ST4 (0.9%), ST6 (1.8%), ST7 (0.9%) and ST9 (0.9%). The intra-subtype analysis revealed a total of 25 different alleles previously reported. Here, the findings lead us to highlight the following aspects: (1) the identification of a ST9 isolate is a relevant finding since it is considered a very rare subtype in human infections as well as this is the first report in Brazil; (2) the high frequency of Blastocystis in fecal samples submitted for examination in a clinical laboratory points to the need to consider its search in routine parasitological examinations, (3) the spatial distribution of Blastocystis infection was not homogeneous but concentrated in more populated areas where the access for population to diagnostic services in healthcare is likely to be easier and, (4) the genetic variability of Blastocystis isolates suggests exposure of inhabitants living in inner municipalities to different sources of contamination involving anthroponotic and zoonotic transmission pathways.

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.

Occurrence of Blastocystis-subtypes in patients from Italy revealed association of ST3 with a healthy gut microbiota

An epidemiological survey on Blastocystis was carried out enrolling a total of 2524 subjects referred to the Umberto I Academic Hospital in Rome, for the routine parasitological exams, during 2017–2018. The studied population included a sample of immunocompromised individuals (N = 130) followed at the same hospital.

DNA sequencing of the small subunit rRNA gene (SSU rDNA) locus was performed on samples positive to the coproparasitological analysis to molecular characterize the Blastocystis-subtypes.

Microscopical analysis detected Blastocystis in 192/2524 (7.6%) of the enrolled subjects. It was the organism most frequently identified in the analysed faecal samples diagnosed in single infection (5.6%) or in co-infection with other enteric protozoa (2%). Furthermore, it was found mainly in immunocompromised patients (22.3%) compared to immunocompetent ones (6.8%).

As expected, ST3 was the most occurring subtype identified in 40% of the subjects, followed by ST1 (29%), ST2 (16%), ST4 (12%), and ST7 (3%).

Next-generation sequencing (NGS) of the 16S rDNA was performed on a sub-sample of Blastocystis-ST3-carriers, homogenous by age and gender, as well as on Blastocystis-free subjects, to profile and compare their gut bacterial composition. A higher bacterial diversity was found in ST3-Blastocystis-carriers, which exhibited a high abundance of Prevotella, Methanobrevibacter and Ruminococcus while, a high percentage of Bacteroides was found in Blastocystis-free subjects.

This study evidenced the presence of Blastocystis in 7.6% of faecal samples in Italy and a high circulation of the protist among immunocompromised patients (22.3%). Molecular characterization of positive samples evidenced the occurrence of five different subtypes, including zoonotic ST such as the ST7, highlighting the risk of transmission from animals. Study of the gut microbiota composition confirms previous evidences according to which, the colonisation by Blastocystis would be linked with an eubiotic gut characterized by potentially beneficial species such as Prevotella and Ruminococcus, rather than with a dysbiotic state, with a high abundance of Enterobacteriaceae, and corroborated the role of the protist as “an old friend” of the human gut.

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Microscopical analysis detected Blastocystis in 7.6% subjects in Italy.

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Molecular methods allowed the identification of 5 STs (ST1, ST2, ST3, ST4, ST7).

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ST3 resulted the most frequent subtype.

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NGS of the 16S rDNA gene was performed in Blastocystis-ST3-carriers.

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Blastocystis-ST3 resulted correlated to an eubiotic gut characterized by potentially beneficial species.

Tropheryma whipplei intestinal colonization in Italian and migrant population: a retrospective observational study

AIM

To obtain the first molecular epidemiological survey of Tropheryma whipplei intestinal colonization in Italy. Materials & methods: Retrospective, observational study to assess the prevalence of T. whipplei, the causative agent of Whipple's disease, in stool samples (real-time PCR) of patients attending the Center for Tropical Diseases (Italy) and risk factors associated.

RESULTS

Overall prevalence was 6.9% (85/1240). The younger age group showed a significantly higher rate than older age group (12.7 vs 5.9%, p = 0.002). The prevalence was 4.9% for Italians and 9.3% for migrants (p = 0.003). Among the latter, children less than 10 years had higher prevalence than older ones (17.3 vs 7.3%, p = 0.003). The young age, male gender and Giardia duodenalis and Entamoeba histolytica coinfection were risk factors.

CONCLUSION

Our study confirms an increased risk of acquiring T. whipplei infection during childhood, under poor sanitary conditions.

Molecular and descriptive epidemiology of intestinal protozoan parasites of children and their pets in Cauca, Colombia: a cross-sectional study

BACKGROUND

Parasitic infections, particularly those caused by protozoa, represent a considerable public health problem in developing countries. Blastocystis, Giardia duodenalis, Cryptosporidium spp. and the Entamoeba complex (Entamoeba histolytica, Entamoeba dispar and Entamoeba moshkovskii) are the most common etiological causes of intestinal parasitic infections.

METHODS

We carried out a descriptive cross-sectional study in school-age children attending a daycare institution in commune eight of Popayán, Cauca (Southwest Colombia). A total of 266 fecal samples were collected (258 from children and eight from pets). Blastocystis, G. duodenalis, Cryptosporidium spp. and the Entamoeba complex were identified by microscopy, quantitative real-time PCR (qPCR) and conventional PCR. The concordance of qPCR and microscopy was assessed using the Kappa index. Molecular characterization was conducted to identify Blastocystis subtypes (18S), G. duodenalis assemblages (tpi and gdh) and Cryptosporidium species/subtypes (18S and GP60). Potential associations between intestinal parasitism and sociodemographic factors were examined using bivariate analyses.

RESULTS

A total of 258 fecal samples from children were analyzed by microscopy and 255 samples were analyzed by qPCR. The prevalence of Blastocystis was between 25.19% (microscopy) and 39.22% (qPCR), that of G. duodenalis was between 8.14% (microscopy) and 10.59% (qPCR), that of Cryptosporidium spp. was estimated at 9.8% (qPCR), and that of the Entamoeba complex was between 0.39% (conventional PCR) and 0.78% (microscopy). The concordance between microscopy and qPCR was very low. Blastocystis ST1 (alleles 4, 8, and 80), ST2 (alleles 11, 12, and 15), ST3 (alleles 31, 34, 36, 38,57, and 151), and ST4 (alleles 42 and 91), G. duodenalis assemblages AII, BIII, BIV and D, C. parvum subtype IIa and C. hominis subtype IbA9G3R2 were identified. The only identified member of the Entamoeba complex corresponded to E. histolytica. No statistically significant association was identified between parasitic infection and any sociodemographic variable.

CONCLUSION

This study revealed the usefulness of molecular methods to depict the transmission dynamics of parasitic protozoa in southwest Colombia. The presence of some of these protozoa in domestic animals may be involved in their transmission.

A diagnostic study comparing conventional and real-time PCR for Strongyloides stercoralis on urine and on faecal samples

Strongyloides stercoralis is a soil-transmitted helminth with a wide distribution in tropical and subtropical areas. The diagnosis of S. stercoralisinfection can be challenging, due to the low sensitivity of microscopic examination of stool samples and coproculture. In the last decade, different in-house molecular biology techniques for S. stercoralis have been implemented. They demonstrated good accuracy, although sensitivity does not seem sufficiently high yet. Recently, a novel PCR technique has been evaluated for the detection of S. stercoralis DNA in urine. Aim of this work was to compare the sensitivity of the real-time PCR (qPCR) on feces routinely used at the Centre for Tropical Disease (CTD) of Negrar, Verona, Italy, with that of the novel based PCR on urine. As secondary objective, we evaluated a Urine Conditioning Buffer ® (Zymoresearch) with the aim of improving nucleic acid stability in urine during sample storage/transport at ambient temperatures. Patients attending the CTD and resulting positive at routine screening with serology for S. stercoralis were invited, previous written consent, to supply stool and urine samples for molecular biology. A convenience sample of 30 patients was included. The sensitivity of qPCR on feces resulted 63%, and that of based PCR on urine was 17%. In all the samples treated with the Urine Conditioning Buffer ® there was no detectable DNA. In conclusion, the sensitivity of the novel technique resulted low, and needs further implementation before being considered as a valid alternative to the validated method.

Preliminary Comparison of an in-House Real-Time PCR with the Automated BD Max Enteric Parasite Panel for the Detection of Giardia intestinalis

Giardia intestinalis is a parasite that commonly causes diarrheal disease throughout the world. An accurate and rapid diagnosis is essential to reduce the infection. Classical diagnosis of giardiasis is performed by microscopic examination of stool samples, but in recent years many DNA-based methods have been developed. In this preliminary observational study, we compared the results of the commercial BD Max enteric parasite panel (EPP) with an in-house real-time (Rt) PCR for G. intestinalis. The study population was composed of 73 samples. Of these, 27 tested positive with both techniques and 39 tested negative. Seven samples were positive with the in-house Rt PCR and negative with the BD Max EPP. The Cohen's kappa was 0.805 (95% CI 0.670-0.940). In conclusion, these preliminary results suggest that the Rt-PCR could possibly demonstrate higher sensitivity for the diagnosis of G. intestinalis than BD Max EPP, which tended to miss infection of low intensity.