Cryptosporidium species and subtypes in river water and riverbed sediment using next-generation sequencing

Identification of a novel GP60 subtype family of Cryptosporidium wrairi from capybaras (Hydrochoerus hydrochaeris) inhabiting urban areas in the state of Mato Grosso do Sul, Brazil

Capybaras (Hydrochoerus hydrochaeris) are hosts for several parasites of public health importance, including Cryptosporidium spp. Therefore, this study aimed to perform the molecular characterization of Cryptosporidium spp. in fecal samples from capybaras inhabiting urban areas. We analyzed 401 fecal samples from capybaras in two municipalities of the state of Mato Grosso do Sul, Brazil. Fecal samples were purified using centrifugal sedimentation with ethyl acetate. They were then screened for Cryptosporidium spp. by malachite green negative staining and a nested PCR protocol targeting the 18S rRNA gene. Samples positive by microscopy or PCR were examined by PCR protocols targeting the actin, HSP-70, and GP60 genes. Amplicons from all PCR protocols were subjected to genetic sequencing. Microscopic screening and 18S rRNA gene-targeted PCR identified 0.25 % (1/401) and 0.5 % (2/401) of samples, respectively, as positive for Cryptosporidium spp. The genetic sequences of the 18S rRNA, HSP-70, actin, and GP60 genes showed genetic similarity to Cryptosporidium wrairi sequences of 99.07 %, 99.69 %, 99.57 %, and 91.51 %, respectively. Genetic sequencing and phylogenetic analyses identified the novel GP60 subtype family VIIbA13 of C. wrairi. In conclusion, we report in this study a low prevalence of the novel GP60 subtype family VIIbA13 of C. wrairi in free-living capybaras from urban areas of the state of Mato Grosso do Sul, Brazil. We propose that capybaras act as a novel host for C. wrairi.

Metabarcoding in gut protozoology

Next-generation sequencing (NGS) methods include whole-genome sequencing, metagenomic analysis, and amplicon-based NGS, all of which are gaining territory in parasitology. A modality of particular interest within the field of gut protozoology is exhaustive metabarcoding of ribosomal genes in a complex matrix such as faeces, by which method, amplicon-based NGS enables the detection and differentiation of both eukaryotic and prokaryotic organisms, circumventing Sanger sequencing-based limitations and representing a one-fits-most approach. Apart from being a tool to break the code of intracellular genetic variation and tell mixed species infections apart, metabarcoding can produce data that can serve to augment our understanding of the interplay between the organisms within the gut.

Rabbits as reservoirs: An updated perspective of the zoonotic risk from Cryptosporidium and Giardia

Rabbits are highly abundant in many countries and can serve as reservoirs of diseases for a diversity of pathogens including the enteric protozoan parasites, Cryptosporidium and Giardia. Both parasites shed environmentally robust environmental stages (oo/cysts) and have been responsible for numerous waterborne outbreaks of diseases. Cryptosporidium hominis and C. parvum are responsible for most infections in humans, while Giardia duodenalis assemblages A and B, cause most human cases of giardiasis. Cryptosporidium cuniculus, the dominant species infecting rabbits, is the only spceies other than C. hominis and C. parvum to have caused a waterborne outbreak of gastritis, which occurred in the United Kingdom in 2008. This review examines the prevalence of Cryptosporidium and Giardia species in rabbits to better understand the public health risks of contamination of water sources with Cryptosporidium and Giardia oo/cysts from rabbits. Despite the abundance of C. cuniculus in rabbits, reports in humans are relatively rare, with the exception of the United Kingdom and New Zealand, and reports of C. cuniculus in humans from the United Kingdom have declined substantially since the 2008 outbreak. Subtyping of C. cuniculus has supported the potential for zoonotic transmission. Relatively few studies have been conducted on Giardia, but assemblage B dominates. However, improved typing methods are required to better understand the transmission dynamics of Giardia assemblages in rabbits. Similarly, it is not well understood if pet rabbits or contaminated water are the main source of C. cuniculus infections in humans. Well-planned studies using high-resolution typing tools are required to understand the transmission dynamics better and quantify the public health risk of Cryptosporidium and Giardia from rabbits.

Cryptosporidium and agriculture: A review

Cryptosporidiosis is a significant contributor to global foodborne and waterborne disease burden. It is a widespread cause of diarrheal diseases that affect humans and animals worldwide. Agricultural environments can become a source of contamination with Cryptosporidium species through faecal material derived from humans and animals. This review aims to report the main findings of scientific research on Cryptosporidium species related to various agricultural sectors, and highlights the risks of cryptosporidiosis in agricultural production, the contamination sources, the importance of animal production in transmission, and the role of farmed animals as hosts of the parasites. Agricultural contamination sources can cause water pollution in groundwater and different surface waters used for drinking, recreational purposes, and irrigation. The application of contaminated manure, faecal sludge management, and irrigation with inadequately treated water are the main concerns associated with foodborne and waterborne cryptosporidiosis related to agricultural activities. The review emphasizes the public health implications of agriculture concerning the transmission risk of Cryptosporidium parasites and the urgent need for a new concept in the agriculture sector. Furthermore, the findings of this review provide valuable information for developing appropriate measures and monitoring strategies to minimize the risk of infection.

Molecular characterization of waterborne protozoa in surface water and sediment in Brazil: a taxonomic survey of ciliated protozoa and their correlation with Giardia duodenalis and Cryptosporidium spp

The detection of Giardia duodenalis and Cryptosporidium spp. was performed, along with the identification of the ciliated protozoa biodiversity, to evaluate the correlation between these protozoa in freshwater quality monitoring. Water and sediment samples from two sites in the Atibaia River (Campinas, São Paulo, Brazil) were collected monthly for 2 years (n = 96). Pathogenic protozoa in water and sediment were detected by using immunomagnetic separation, followed by visualization by immunofluorescence assay (IFA). All positive aliquots in IFA were subjected to DNA extraction and subsequently nested PCR. Qualitative (in vivo observation and silver impregnation) and quantitative (in vivo enumeration) analyses were performed for the ciliated protozoa. Giardia cysts were detected in 62.5% of the surface water samples and Cryptosporidium spp. in 25.0%. In the sediment, cysts were detected in 35.4% samples and oocysts in 16.6%. A total of 57 samples positive for Giardia cysts were subjected to sequencing, 40 of which were harboring G. duodenalis (24 were characterized as sub-assemblage AII). For ciliated protozoa, 73 taxa belonging to 53 genera were identified over the period of the study. These results revealed a high degree of contamination by waterborne protozoa in the main water source which supplies drinking water for more than one million people in Campinas (São Paulo), highlighting the need for continuous monitoring of this catchment site. In addition, the present study provides important data regarding the sources of the water body degradation, i.e., fecal contamination of human origin, in addition to the survey of the ciliated protozoa.

Point of care diagnostics for Cryptosporidium: new and emerging technologies

PURPOSE OF REVIEW

Although Cryptosporidium detection and typing techniques have improved dramatically in recent years, relatively little research has been conducted on point of care (POC) detection and typing tools. Therefore, the main purpose of the present review is to summarize and evaluate recent and emerging POC diagnostic methods for Cryptosporidium spp.

RECENT FINDINGS

Microscopy techniques such as light-emitting diode fluorescence microscopy with auramine-phenol staining (LED-AP), still have utility for (POC) diagnostics but require fluorescent microscopes and along with immunological-based techniques, suffer from lack of specificity and sensitivity. Molecular detection and typing tools offer higher sensitivity, specificity and speciation, but are currently too expensive for routine POC diagnostics. Isothermal amplification methods such as loop-mediated isothermal amplification (LAMP) or recombinase polymerase amplification (RPA) including a commercially available LAMP kit have been developed for Cryptosporidium but are prone to false positives. Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas diagnostic technologies (CRISPRDx) have recently been combined with isothermal amplification to increase its specificity and sensitivity for detection and typing. Other emerging technologies including amplification-free CRISPR detection methods are currently being developed for Cryptosporidium using a smartphone to read the results.

SUMMARY

Many challenges are still exist in the development of POC diagnostics for Cryptosporidium. The ideal POC tool would be able to concentrate the pathogen prior to detection and typing, which is complicated and research in this area is still very limited. In the short-term, CRISPR-powered isothermal amplification lateral flow tools offer the best opportunity for POC Cryptosporidium species and subtype detection, with a fully integrated autonomous biosensor for the long-term goal.

Well water sources simultaneous contamination with Cryptosporidium and Acanthamoeba in East-Southeast Asia and Acanthamoeba spp. in biofilms in the Philippines

Cryptosporidium is the leading agent of waterborne parasitic protozoan outbreaks and is the second leading cause of infant mortality due to diarrhoea worldwide. Acanthamoeba spp. causes Acanthamoeba keratitis (AK) and a life-threatening condition known as granulomatous amoebic encephalitis (GAE). The present study aimed to assess the water quality of an indigenous and a rural community for waterborne parasitic protozoan contamination. Aquatic samples (n = 22) were processed by filtration of 500 mL portion through a 1.2 μm pore size glass microfiber filter and eluted for light microscopy, culture in non-nutrient agar, and PCR analysis. Overall, 36% (8/22) of the investigated aquatic samples were positive for either Cryptosporidium spp. oocysts (13%; 3/22) or Acanthamoeba spp., (36%; 8/22) or both (13%; 3/22). Cryptosporidium spp. oocysts were detected in 27% (3/11) of wet season samples only while Acanthamoeba spp. were detected in 18% (2/11) and 55% (6/11) of wet and dry season samples, respectively. Subsequently, molecular detection for Acanthamoeba species identified A. lenticulata and A. hatchetti with 98-99% BLAST similarity. This is the first report on the simultaneous contamination of Cryptosporidium and Acanthamoeba in well water sources in East-Southeast Asia, the first detection of Acanthamoeba spp. in biofilms in the Philippines, and the longest viability demonstrated for A. lenticulata in two-year-old water samples stored at room temperature.

Evaluation of Next-Generation Sequencing Applied to Cryptosporidium parvum and Cryptosporidium hominis Epidemiological Study

Background. Nowadays, most of the C. parvum and C. hominis epidemiological studies are based on gp60 gene subtyping using the Sanger sequencing (SgS) method. Unfortunately, SgS presents the limitation of being unable to detect mixed infections. Next-Generation Sequencing (NGS) seems to be an interesting solution to overcome SgS limits. Thus, the aim of our study was to (i) evaluate the reliability of NGS as a molecular typing tool for cryptosporidiosis, (ii) investigate the genetic diversity of the parasite and the frequency of mixed infections, (iii) assess NGS usefulness in Cryptosporidium sp. outbreak investigations, and (iv) assess an interpretation threshold of sequencing data. Methods. 108 DNA extracts from positive samples were sequenced by NGS. Among them, two samples were used to validate the reliability of the subtyping obtained by NGS and its capacity to detect DNA mixtures. In parallel, 106 samples from French outbreaks were used to expose NGS to epidemic samples. Results. NGS proved suitable for Cryptosporidium sp. subtyping at the gp60 gene locus, bringing more genetic information compared to SgS, especially by working on many samples simultaneously and detecting more diversity. Conclusions. This study confirms the usefulness of NGS applied to C. hominis and C. parvum epidemiological studies, especially aimed at detecting minority variants.

First report of rodent-adapted Cryptosporidium wrairi in an immunocompetent child, Spain

Cryptosporidiosis is a leading cause of childhood diarrhoea. Two species, Cryptosporidium hominis and Cryptosporidium parvum, are responsible for most confirmed cases globally. Close contact with pet animals can be an unnoticed source of children infections. We describe a case of infection by rodent-adapted Cryptosporidium wrairi in a 22-month-old immunocompetent toddler with no clinical manifestations in close contact with a pet guinea pig and poor personal hygiene practices in Majadahonda (Madrid, Spain). Attempts to determine the C. wrairi genotype family at the 60-kDa glycoprotein marker failed repeatedly. This is the first description of C. wrairi in a human host. Although a spurious infection cannot be completely ruled out, data presented here suggest that C. wrairi can be transmitted zoonotically.

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.

Molecular Detection of Cryptosporidium cuniculus in Rabbits (Oryctolagus cuniculus) from Tenerife, Canary Islands, Spain

Cryptosporidium cuniculus is a zoonotic parasite responsible for cryptosporidiosis cases and outbreaks in both humans and rabbits. Since there are no molecular Cryptosporidium spp. infection data in rabbits (Oryctolagus cuniculus) from Spain, our aim was to gather information about this parasite in wild European rabbits from Tenerife, Canary Islands (Spain). A total of 100 faecal samples were collected from rabbits from eight municipalities of Tenerife. Microscopic analysis showed that 4.0% of the samples presented structures compatible with Cryptosporidium oocyst. A nested polymerase chain reaction (PCR) targeting 18S ribosomal RNA (rRNA) gene fragments was carried out, and sequencing confirmed the identity of C. cuniculus in one sample (1.0%). The sample was successfully subtyped using nested PCR analysis of the 60-kDa glycoprotein (gp60) gene as the subtype VbA26R3. This study confirms the presence of C. cuniculus in wild rabbits from Tenerife, providing new information on the occurrence of this zoonotic parasite. Further studies are required to better understand the epidemiology of Cryptosporidium spp. in wild rabbits in Spain and their possible public health repercussions.

Association of Common Zoonotic Pathogens With Concentrated Animal Feeding Operations

Animal farming has intensified significantly in recent decades, with the emergence of concentrated animal feeding operations (CAFOs) in industrialized nations. The congregation of susceptible animals in CAFOs can lead to heavy environmental contamination with pathogens, promoting the emergence of hyper-transmissible, and virulent pathogens. As a result, CAFOs have been associated with emergence of highly pathogenic avian influenza viruses, hepatitis E virus, Escherichia coli O157:H7, Streptococcus suis, livestock-associated methicillin-resistant Staphylococcus aureus, and Cryptosporidium parvum in farm animals. This has led to increased transmission of zoonotic pathogens in humans and changes in disease patterns in general communities. They are exemplified by the common occurrence of outbreaks of illnesses through direct and indirect contact with farm animals, and wide occurrence of similar serotypes or subtypes in both humans and farm animals in industrialized nations. Therefore, control measures should be developed to slow down the dispersal of zoonotic pathogens associated with CAFOs and prevent the emergence of new pathogens of epidemic and pandemic potential.

Taxonomy and molecular epidemiology of Cryptosporidium and Giardia - a 50 year perspective (1971-2021)

The protozoan parasites Cryptosporidium and Giardia are significant causes of diarrhoea worldwide and are responsible for numerous waterborne and foodborne outbreaks of diseases. Over the last 50 years, the development of improved detection and typing tools has facilitated the expanding range of named species. Currently at least 44 Cryptosporidium spp. and >120 genotypes, and nine Giardia spp., are recognised. Many of these Cryptosporidium genotypes will likely be described as species in the future. The phylogenetic placement of Cryptosporidium at the genus level is still unclear and further research is required to better understand its evolutionary origins. Zoonotic transmission has long been known to play an important role in the epidemiology of cryptosporidiosis and giardiasis, and the development and application of next generation sequencing tools is providing evidence for this. Comparative whole genome sequencing is also providing key information on the genetic mechanisms for host specificity and human infectivity, and will enable One Health management of these zoonotic parasites in the future.

Molecular analysis of cryptosporidiosis cases in Western Australia in 2019 and 2020 supports the occurrence of two swimming pool associated outbreaks and reveals the emergence of a rare C. hominis IbA12G3 subtype

Cryptosporidium is an important protozoan parasite and due to its resistance to chlorine is a major cause of swimming pool-associated gastroenteritis outbreaks. The present study combined contact tracing and molecular techniques to analyse cryptosporidiosis cases and outbreaks in Western Australia in 2019 and 2020. In the 2019 outbreak, subtyping at the 60 kDa glycoprotein (gp60) gene identified 89.0% (16/18) of samples were caused by the C. hominis IdA15G1 subtype. Amplicon next generation sequencing (NGS) at the gp60 locus identified five C. hominis IdA15G1 subtype samples that also had C. hominis IdA14 subtype DNA, while multi locus sequence typing (MLST) analysis on a subset (n = 14) of C. hominis samples identified three IdA15G1 samples with a 6 bp insertion at the end of the trinucleotide repeat region of the cp47 gene. In 2020, 88.0% (73/83) of samples typed were caused by the relatively rare C. hominis subtype IbA12G3. Four mixed infections were observed by NGS with three IdA15G1/ IdA14 mixtures and one C. parvum IIaA18G3R1 sample mixed with IIaA16G3R1. No genetic diversity using MLST was detected. Epidemiological and molecular data indicates that the outbreaks in 2019 and 2020 were each potentially from swimming pool point sources and a new C. hominis subtype IbA12G3 is emerging in Australia. The findings of the present study are important for understanding the introduction and transmission of rare Cryptosporidium subtypes to vulnerable populations.

Molecular Characterisation of Cryptosporidium spp. in Mozambican Children Younger than 5 Years Enrolled in a Matched Case-Control Study on the Aetiology of Diarrhoeal Disease

Cryptosporidium is a leading cause of childhood diarrhoea and associated physical and cognitive impairment in low-resource settings. Cryptosporidium-positive faecal samples (n = 190) from children aged ≤ 5 years enrolled in the Global Enteric Multicenter Study (GEMS) in Mozambique detected by ELISA (11.5%, 430/3754) were successfully PCR-amplified and sequenced at the gp60 or ssu rRNA loci for species determination and genotyping. Three Cryptosporidium species including C. hominis (72.6%, 138/190), C. parvum (22.6%, 43/190), and C. meleagridis (4.2%, 8/190) were detected. Children ≤ 23 months were more exposed to Cryptosporidium spp. infections than older children. Both C. hominis and C. parvum were more prevalent among children with diarrhoeal disease compared to those children without it (47.6% vs. 33.3%, p = 0.007 and 23.7% vs. 11.8%, p = 0.014, respectively). A high intra-species genetic variability was observed within C. hominis (subtype families Ia, Ib, Id, Ie, and If) and C. parvum (subtype families IIb, IIc, IIe, and IIi) but not within C. meleagridis (subtype family IIIb). No association between Cryptosporidium species/genotypes and child's age was demonstrated. The predominance of C. hominis and C. parvum IIc suggests that most of the Cryptosporidium infections were anthroponotically transmitted, although zoonotic transmission events also occurred at an unknown rate. The role of livestock, poultry, and other domestic animal species as sources of environmental contamination and human cryptosporidiosis should be investigated in further molecular epidemiological studies in Mozambique.