Detection of Giardia intestinalis in water samples collected from natural water reservoirs and wells in northern and north-eastern Poland using LAMP, real-time PCR and nested PCR

Metagenomic Analysis of Surface Waters and Wastewater in the Colombian Andean Highlands: Implications for Health and Disease

Urban water bodies serve as critical reservoirs of microbial diversity, with major implications for public health and environmental quality. This study aimed to characterize the microbial diversity of surface waters and wastewater from the Pasto River in the Colombian Andean Highlands, offering insights that may support water quality monitoring efforts. Sampling was conducted at three river sites and one wastewater location. Standard physicochemical and microbiological analyses were performed, including real-time PCR to detect protozoan pathogens Giardia spp. and Cryptosporidium spp. Metagenomic sequencing provided an in-depth taxonomic and functional profile of microbial communities through two complementary approaches: (i) read-based analysis to identify abundant families and species, both pathogenic and beneficial, and (ii) detection of health-related molecular markers, including antimicrobial resistance markers and virulence factors. Physicochemical analyses showed distinct profiles between wastewater and surface water, with wastewater exhibiting elevated levels of suspended solids (113.6 mg/L), biochemical oxygen demand (BOD, 311.2 mg/L), and chemical oxygen demand (COD, 426.7 mg/L). Real-time PCR detected Giardia spp. DNA in 75% (76/102) of the samples and Cryptosporidium spp. DNA in 94% (96/102) of samples. The metagenomic read-based profiling identified Aeromonas media as a prevalent pathogen and Polaromonas naphthalenivorans as a potential biodegradative agent. The metagenomic assembly produced 270 high-quality genomes, revealing 16 bacterial species (e. g., Acinetobacter johnsonii and Megamonas funiformis) that provided insights into fecal contaminants and native aquatic microbes. Functional profiling further revealed a high prevalence of antimicrobial resistance markers, particularly for tetracyclines, aminoglycosides, and macrolides, with the highest abundance found in wastewater samples. Additionally, virulence factors were notably present in Zoogloea ramigera. The findings underscore the value of metagenomic profiling as a comprehensive tool for water quality monitoring, facilitating the detection of pathogens, beneficial species, and molecular markers indicative of potential health risks. This approach supports continuous monitoring efforts, offering actionable data for water management strategies to safeguard public health and maintain ecological integrity.

Direct or DNA Extraction-Free Amplification and Quantification of Foodborne Pathogens

The use of direct nucleic acid amplification of pathogens from food matrices has the potential to reduce time to results over DNA extraction-based approaches as well as traditional culture-based approaches. Here we describe protocols for assay design and experiments for direct amplification of foodborne pathogens in food sample matrices using loop-mediated isothermal amplification (LAMP) and polymerase chain reaction (PCR). The examples provided include the detection of Escherichia coli in milk samples and Salmonella in pork meat samples. This protocol includes relevant reagents and methods including obtaining target sequences, assay design, sample processing, and amplification. These methods, though used for specific example matrices, could be applied to many other foodborne pathogens and sample types.

Prevalence and molecular characterization of Giardia duodenalis in companion dogs, domestic livestock and wildlife in the Jordan Basin, Israel

Giardiasis is a small intestinal disease caused by the zoonotic parasite, Giardia duodenalis. This study presents the molecular findings of G. duodenalis infection in companion dogs, domestic livestock and wildlife in the Northern Jordan Basin, Israel. Identification of G. duodenalis was accomplished by nested PCR (nPCR) targeting the 18S rRNA gene. Samples were collected from water (five samples from four sources of which one was recycled water), as well as feces from wolves (Canis lupus) (n = 34), jackals (Canis aureus) (n = 24), wild boars (Sus scrofa) (n = 40), cattle (Bos taurus) (n = 40), dogs (Canis lupus familiaris) (n = 37) and nutria (Mayocastor coypus) (n = 100). All positive samples were sequenced and a phylogenetic tree was drawn using the Bayesian Inference (BI) algorithm. Differences in G. duodenalis prevalence between the different hosts were analyzed by Pearson's chi-square (p < 0.05). Of the total 275 fecal samples, 36 were positive for G. duodenalis (13%). Frequency rates among different animal species was highest in wolves (32.3%), whilst rates in wild boars (22.5%), dogs (16.2%), cattle (12.5%) and jackals (4.2%), were observed to be significantly lower (p < 0.001). Three out of 5 recycled water (RW) samples were G. duodenalis positive. Three clusters with high posterior probabilities (PP) were found in the BI: Cluster 1: samples from wolves, wild boars, water and cattle together with database sequences of assemblages A, B and F, Cluster 2: samples from dogs, nutria and a jackal with sequences from assemblage D and Cluster 3: samples from cattle, wild boars, wolves and dogs with sequences from assemblage C and D. We suggest that wolves serve as reservoirs of G. duodenalis in this region. The finding of Giardia in RW suggests that this vehicle may further contaminate crops intended for human consumption as this water source is used for agricultural irrigation.

Meta-analysis of the prevalence of Giardia duodenalis in sheep and goats in China

Giardia duodenum (G. duodenalis) can cause giardiasis and infect a variety of hosts. So far, there have been no detailed data regarding the positive rate of G. duodenalis in sheep and goats in China. Here, a systematic literature review was carried out to investigate the epidemiology of G. duodenalis in sheep and goats in China. To perform the meta-analysis, the databases CNKI, VIP, WanFang, PubMed, Web of science and ScienceDirect were employed for screening studies related to the prevalence of G. duodenalis in sheep and goats in China. The total prevalence of G. duodenalis in sheep and goats was estimated to be 7.00% (95% CI: 4.00-10.00). In the age subgroup, the prevalence of G. duodenalis in sheep and goats of >12 months (11.29%; 95% CI: 8.08-14.97) was higher than that in sheep and goats of ≤12 months (7.57%; 95% CI: 3.95-12.24). An analysis based on seasons showed that the prevalence of G. duodenalis in sheep and goats was higher in summer (11.90%; 95% CI: 0.50-35.05) than that in other seasons. The prevalence of G. duodenalis in sheep and goats after 2016 was 8.57% (95% CI: 5.34-11.79), which was higher than others. The highest prevalence of G. duodenalis in sheep and goats was 13.06% (95% CI: 6.26-19.86) recorded in Southwestern China. The prevalence of Giardia infection in sheep (7.28%; 95% CI: 2.30-14.73) was higher than that in goats (5.43%; 95% CI: 2.73-8.98). The NOAA's National Center for Environmental Information (https://gis.ncdc.noaa.gov/maps/ncei/cdo/monthly) was used to extract relevant geoclimatic data (latitude, longitude, elevation, temperature, precipitation, humidity, and climate). By analyzing the data of each subgroup, it was shown that region, genetype, and climate were potential risk factors for giardiasis prevalence in sheep and goats. Based on the analysis of common factors and geographical factors, it is recommended to strengthen effective management measures (e.g. ventilation and disinfection in warm and humid areas) and formulate relevant policies according to local conditions. Breeders should strengthen the detection of G. duodenalis in sheep and goats, customize corresponding control measures according to the diet and living habits of sheep and goats, and strengthen the protection of sheep and lamb calves, so as to reduce the incidence rate and reduce the economic loss of China's animal husbandry.

Molecular Identification of Protozoan Sarcocystis in Different Types of Water Bodies in Lithuania

Representatives of the genus Sarcocystis are unicellular parasites having a two-host life cycle and infecting mammals, birds, and reptiles. Until now, Sarcocystis spp. have been mainly investigated in definitive and intermediate hosts. Only a few studies have been conducted on the detection of Sarcocystis parasites in water samples. The aim of this research was to examine whether the prevalence of Sarcocystis spp. parasitizing farm animals varies in different types of water bodies. Water samples (n = 150) were collected from the entire territory of Lithuania, dividing water bodies into five groups (lakes, rivers, ponds/canals, swamps, and the inshore zone of the territorial Baltic Sea area). One-liter samples were filtered and subsequently analyzed using nested PCR. At least one of the analyzed Sarcocystis spp. (S. arieticanis, S. bertrami, S. bovifelis, S. capracanis, S. cruzi, S. hirsuta, S. miescheriana, and S. tenella) was determined in all examined samples from water bodies. No significant difference in Sarcocystis spp. prevalence between different types of water sources was detected. Our research proved that selecting appropriate primers is important for the accurate identification of parasites in samples collected from water bodies.

Molecular Epidemiology of Cryptosporidium parvum and Giardia lamblia in Different Water Bodies, Soil, and Vegetables in Pakistan

There is a dearth of knowledge regarding transmission of Cryptosporidium (C) and Giardia (G) species through water and water-related sources in Pakistan. To this end, we conducted a study to evaluate the prevalence of these parasites in different water bodies, soil, and mixed raw vegetables in Pakistan. Researchers collected 200 samples from each reservoir including municipal water, sewage water, canal water, raw vegetables, soil of public parks, and soil of grazing areas. Researchers amplified the 18S ribosomal RNA gene of parasites using newly designed genus-specific primers through polymerase chain reaction testing. The sequencing analysis revealed that the obtained sequences belonged to C parvum and G lamblia. Phylogenetic clustering and sequence analysis of C parvum showed that the C parvum Pak1 (OM540369) and C parvum Pak2 (OM540370) as well as C parvum Pak3 (OM510450) and C parvum Pak6 (OM510445) were closely similar to each other. In the case of G lamblia, all the sequences appeared in the same clade. The epidemiological data showed lower prevalence of C parvum (11.5%) in all reservoirs, compared with G lamblia (20.5%). Among different reservoirs, prevalence of Cryptosporidium and Giardia was observed in sewage water (C = 13%, G = 26.5%), municipal water (C = 10%, G = 35%), canal water (C = 9.5%, G = 18.5%), raw vegetables (C = 5.5%, G = 8%), soil of public parks (C = 13%, G = 14%), and soil of grazing areas (C = 18.5%, G = 21.5%). Among targeted risk factors, poor hygienic conditions significantly affected the prevalence of parasites in sewage water (C = 20%, G = 41.2%), municipal water (C = 14.7%, G = 48.8.5%), raw vegetables (C = 11.3%, G = 15.1%), and soil of public parks (C = 19.5%, G = 21.9%). Similarly, contamination with sewage waste significantly affected (P < .05) the prevalence of these parasites in municipal water (C = 13.6%, G = 41.1%), canal water (C = 13.3%, G = 25%), raw vegetables (C = 12.1%, G = 15.1%), and soil of public parks (C = 23.3%, G = 15%). Results of this study illustrated a high risk of parasitic zoonosis through water bodies, soil, and vegetables.

Detection of Cryptosporidium spp. and Giardia spp. in Environmental Water Samples: A Journey into the Past and New Perspectives

Among the major issues linked with producing safe water for consumption is the presence of the parasitic protozoa Cryptosporidium spp. and Giardia spp. Since they are both responsible for gastrointestinal illnesses that can be waterborne, their monitoring is crucial, especially in water sources feeding treatment plants. Although their discovery was made in the early 1900s and even before, it was only in 1999 that the U.S. Environmental Protection Agency (EPA) published a standardized protocol for the detection of these parasites, modified and named today the U.S. EPA 1623.1 Method. It involves the flow-through filtration of a large volume of the water of interest, the elution of the biological material retained on the filter, the purification of the (oo)cysts, and the detection by immunofluorescence of the target parasites. Since the 1990s, several molecular-biology-based techniques were also developed to detect Cryptosporidium and Giardia cells from environmental or clinical samples. The application of U.S. EPA 1623.1 as well as numerous biomolecular methods are reviewed in this article, and their advantages and disadvantages are discussed guiding the readers, such as graduate students, researchers, drinking water managers, epidemiologists, and public health specialists, through the ever-expanding number of techniques available in the literature for the detection of Cryptosporidium spp. and Giardia spp. in water.

Intestinal Schistosomiasis and Giardiasis Co-Infection in Sub-Saharan Africa: Can a One Health Approach Improve Control of Each Waterborne Parasite Simultaneously?

Both intestinal schistosomiasis and giardiasis are co-endemic throughout many areas of sub-Saharan Africa, significantly impacting the health of millions of children in endemic areas. While giardiasis is not considered a neglected tropical disease (NTD), intestinal schistosomiasis is formally grouped under the NTD umbrella and receives significant advocacy and financial support for large-scale control. Although there are differences in the epidemiology between these two diseases, there are also key similarities that might be exploited within potential integrated control strategies permitting tandem interventions. In this review, we highlight these similarities and discuss opportunities for integrated control of giardiasis in low and middle-income countries where intestinal schistosomiasis is co-endemic. By applying new, advanced methods of disease surveillance, and by improving the provision of water, sanitation and hygiene (WASH) initiatives, (co)infection with intestinal schistosomiasis and/or giardiasis could not only be more effectively controlled but also better understood. In this light, we appraise the suitability of a One Health approach targeting both intestinal schistosomiasis and giardiasis, for if adopted more broadly, transmission of both diseases could be reduced to gain improvements in health and wellbeing.

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.

Waterborne protozoan pathogens in environmental aquatic biofilms: Implications for water quality assessment strategies

Biofilms containing pathogenic organisms from the water supply are a potential source of protozoan parasite outbreaks and a significant public health concern. The aim of the present study was to demonstrate the simultaneous and multi-spatial occurrence of waterborne protozoan pathogens (WBPP) in substrate-associated biofilms (SAB) and compare it to surface water (SW) and sediments with bottom water (BW) counterparts using manual filtration and elution from low-volume samples. For scenario purposes, simulated environmental biofilm contamination was created from in-situ grown one-month-old SAB (OM-SAB) that were spiked with Cryptosporidium parvum oocysts. Samples were collected from the largest freshwater reservoirs in Luzon, Philippines and a University Lake in Thailand. A total of 69 samples (23 SAB, 23 SW, and 23 BW) were evaluated using traditional staining techniques for Cryptosporidium, and Immunofluorescence staining for the simultaneous detection of Cryptosporidium and Giardia. WBPP were found in 43% SAB, 39% SW, and 39% BW of the samples tested in the present study with SAB results reflecting SW and BW results. Further highlights were demonstrated in the potential of using low-volume samples for the detection of parasites in source water. Scanning electron microscopy of OM-SAB samples revealed a naturally-associated testate amoeba shell, while Cryptosporidium oocysts spiked samples provided a visual profile of what can be expected from naturally contaminated biofilms. This study provides the first evidence for the simultaneous and multi-spatial occurrence of waterborne protozoan pathogens in low-volume aquatic matrices and further warrants SAB testing along with SW and BW matrices for improved water quality assessment strategies (iWQAS).

First detection of Echinococcus multilocularis in environmental water sources in endemic areas using capsule filtration and molecular detection methods

Water is one of the possible transmission routes for water- and foodborne parasites to humans. Echinococcus multilocularis is a parasite, which causes alveolar echinococcosis (AE). Nevertheless, no environmental studies have been performed as yet to confirm the occurrence of E. multilocularis in water supplies. Accordingly, 105 water samples of 50 L volume were collected from surface waters (lakes, rivers, canals) and wells in the Warmia-Masuria Province (Echinococcus endemic area) and Pomerania Province (Echinococcus non-endemic area), Poland. The water was filtered and subsequently analysed with nested PCR and real-time PCR. E. multilocularis DNA was found in two (1.9%) samples, which originated from two lakes localised in the Warmia-Masuria Province. Sequencing of the positive samples confirmed that the PCR products were fragments of the E. multilocularis mitochondrial 12S rRNA gene. This is the first investigation describing E. multilocularis detection in environmental water samples, using molecular diagnostic tools. The results indicate that water could be considered as a potential source of E. multilocularis infections in humans and animals, in endemic areas.

Cryptosporidium and Giardia in Wastewater and Surface Water Environments

and spp. are significant contributors to the global waterborne disease burden. Waterways used as sources of drinking water and for recreational activity can become contaminated through the introduction of fecal materials derived from humans and animals. Multiple studies have reported the occurence or concentrations of these pathogens in the environment. However, this information has not been comprehensively reviewed. Quantitative microbial risk assessment (QMRA) for and can be beneficial, but it often relies on the concentrations in environmental sources reported from the literature. A thorough literature review was conducted to develop an inventory of reported and concentrations in wastewater and surface water available in the literature. This information can be used to develop QMRA inputs. and (oo)cyst concentrations in untreated wastewater were up to 60,000 oocysts L and 100,000 cysts L, respectively. The maximum reported concentrations for and in surface water were 8400 oocysts L and 1000 cysts L, respectively. A summary of the factors for interpretation of concentration information including common quantification methods, survival and persistence, biofilm interactions, genotyping, and treatment removal is provided in this review. This information can help in identifying assumptions implicit in various QMRA parameters, thus providing the context and rationale to guide model formulation and application. Additionally, it can provide valuable information for water quality practitioners striving to meet the recreational water quality or treatment criteria. The goal is for the information provided in the current review to aid in developing source water protection and monitoring strategies that will minimize public health risks.