Identification of species and sources of Cryptosporidium oocysts in storm waters with a small-subunit rRNA-based diagnostic and genotyping tool

Zoonotic gastrointestinal parasites of shelter dogs in Israel

Dogs are potentially infected with a diverse spectrum of endoparasites, some which may affect their health or be of zoonotic concern. In Israel, no information exists on the prevalence and spatial distribution of endoparasitic infection among dogs. An investigation of the prevalence of endoparasite infection in Israel shelter dogs was performed by fecal flotation and molecular methods, with particular interest in parasites of zoonotic concern. Polymerase-chain reaction (PCR) was performed targeting the small subunit ribosomal RNA (rrnS) of Taenia spp.,-cox1 mitochondrial DNA of Strongyloides spp., and 18S rRNA of Cryptosporidium spp. The study included fecal samples of 393 dogs from six municipal shelters in different areas of Israel. Overall, 92 of 393 (23.4 %) dogs were infected with at least one endoparasite. According to fecal microscopy, 7.4 % were infected with Cystoisospora spp.; 7.1 % with Giardia intestinalis; 1.0 % with Toxocara canis; 3.1 % with Toxascaris leonina; 2.5 % with Sarcocystis spp.; 2.3 % shed taeniid eggs; 0.3 % Spirocerca lupi eggs; 0.3 % hookworm spp. eggs and 0.3 % shed Hammondia heydorni oocysts. PCR for Taenia spp. detected 1.8 % dogs with Taenia hydatigena, and 0.51 % dogs with Taenia spp. eggs. Several epidemiologically significant points were identified; Ta. leonina was more prevalent in dogs from the north of Israel, while Sarcocystis spp. and Taenia eggs were more prevalent in the south. In addition, infection with Ta. leonina was found to be significantly increased in summer compared to other seasons. This is the first large scale study of endoparasites in dogs from Israel, with results showing presence of potentially zoonotic parasites, T. canis, Giardia spp. and hookworms. These results should serve to increase awareness of veterinarians, human infectious disease specialists, and dog shelter personnel of relevant parasites to plan better prevention, diagnosis and treatment schemes in dog shelters and to look for suggestive signs of endoparasite-related disease in a One Health framework.

Environmental surveillance of Cryptosporidium and Giardia in surface supply water and treated sewage intended for reuse from an urban area in Brazil

Environmental monitoring of protozoa, with the potential to trigger diseases, is essential for decision-making by managing authorities and for the control of water surveillance. This study aimed to detect and quantify Cryptosporidium oocysts and Giardia cysts in surface water for drinking water supply and treated sewage for reuse in the city of São Paulo. Samples collected bimonthly for one year were concentrated using the USEPA 1623.1 and 1693 methods for surface water and treated effluents, respectively. Immunofluorescence and nucleic acid amplification techniques were used to detect and quantify (oo)cysts. The cloning technique followed by sequencing and phylogenetic analyses were performed to characterize species and genotypes. The immunofluorescence detected Cryptosporidium spp. and Giardia spp. in 69.2% (9/13) and 100% (13/13) of the surface water samples (0.1-41 oocysts/L and 7.2-354 cysts/L, respectively). In the reuse samples, 85.7% (12/14) were positive for both protozoa and the concentrations varied from 0.4 to 100.6 oocysts/L and 1.2 and 93.5 cysts/L. qPCR assays showed that 100% of surface water (0.1-14.6 oocysts/L and 0.3-639.8 cysts/L) and reused samples (0.1-26.6 oocysts/L and 0.3-92.5 cysts/L) were positive for both protozoa. Species C. parvum, C. hominis, and C. muris were identified using the 18S rRNA gene, demonstrating anthroponotic and zoonotic species in the samples. Multilocus SSU rRNAanalyses of the SSU rRNA, tpi, and gdh genes from Giardia intestinalis identified the AII, BII, and BIV assemblages, revealing that contamination in the different matrices comes from human isolates. The study showed the circulation of these protozoa in the São Paulo city area and the impairment of surface water supply in metropolitan regions impacted by the discharge of untreated or inadequately treated sewage regarding the removal of protozoa, emphasizing the need to implement policies for water safety, to prevent the spread of these protozoa in the population.

Cryptosporidium spp. in German wildlife: Detection, regional occurrence and diversity in wild boar, roe, red and fallow deer

Cryptosporidium is a cause of diarrheal infections responsible for a loss of human and animal welfare worldwide. The impact of the parasite is underestimated and the reported sources of infection are diverse, as it occurs in a wide variety of hosts. Wildlife has been reported as a notifiable source, but few studies are available on its occurrence in European wild boar and cervid species. To determine the occurrence of Cryptosporidium in game in Brandenburg, Germany, a molecular survey was conducted during the 2017 to 2020 hunting seasons. A total of 562 fecal samples from wild boar (Sus scrofa, n = 262), roe deer (Capreolus capreolus, n = 174), red deer (Cervus elaphus, n = 62), fallow deer (Dama, n = 51) and 13 samples of unspecified species were analyzed for both 18S ribosomal RNA (18S rRNA) and Cryptosporidium oocyst wall protein (COWP) gene sequence regions. PCR results showed that 21.2 % of the samples (n = 119/562) were positive for at least one target gene (18S rRNA: n = 114; COWP: n = 14), but differences in Cryptosporidium occurrence were observed within species and hunting seasons, with variations ranging from 1.8 % to 41.7 % (roe deer), respectively. Analysis of Sanger sequences of the 18S rRNA and COWP PCR products indicated that the C. sp. deer genotype was predominant in deer (roe deer: 86.7 %, red deer: 66.7 %, fallow deer: 58.8 %), while C. suis and C. scrofarum were mainly detected in wild boar (88.5 %). The human pathogenic species C. parvum was detected in only 1.2 % (n = 7) of the samples analyzed, but without a clear indication of a specific wild animal host. The highest Cryptosporidium diversity was found in wild boar and roe deer with five and four different species, respectively. Comparison of the 18S rRNA sequences with the designated reference revealed minor variations at several nucleotide positions in some isolates, possibly indicating evolutionary adaptations and the development of new subtypes. In conclusion, wildlife represents a reservoir for a diverse spectrum of Cryptosporidium species and may thus contribute to their environmental spread and the transmission to humans.

Development of the Intestinal Microbiota of Dairy Calves and Changes Associated with Cryptosporidium spp. Infection in Brazil

Cryptosporidium spp. is one of the most important pathogens infecting nursing calves worldwide. This study aimed to investigate the intestinal microbiota of dairy calves during the first month of life and the impact of diarrhea caused by Cryptosporidium on a Brazilian farm. Fecal samples from 30 calves were collected during the first month of life, and fecal scores were recorded. Samples from the second, third, and fourth days of life were analyzed by DNA sequencing of the 16S rRNA gene. In addition, samples of sixteen calves positive for Cryptosporidium spp. were retrospectively chosen according to the development of diarrhea: four and two days before diarrhea, at the onset of diarrhea, after four days of diarrhea, at the end of diarrhea, and after six days of diarrhea resolution. Diarrhea was observed in all calves (100%), starting at day 5 of life, and all calves tested positive for Cryptosporidium in at least one sample. The microbiota richness increased with age but was retarded by diarrhea. Compositional changes associated with Cryptosporidium infection included increases in Fusobacterium, Prevotella, and Peptostreptococcus, as well as decreases in Collinsella and Lachnospiraceae. In conclusion, Cryptosporidium infection has the potential to decrease richness and change the composition of the intestinal microbiota of dairy calves.

Cryptosporidium spp. in captive snakes from 26 provinces in China: Prevalence, molecular characterization, and symptoms

Snakes are sometimes regarded as pets and are used in traditional Chinese medicine. Cryptosporidium spp. are frequently identified in snakes, representing an important pathogen and causing gastrointestinal diseases. Current data indicate that risk factors for infection and patterns of clinical symptom presentation may differ among Cryptosporidium spp. To better understand the infection status by Cryptosporidium spp., fecal samples were collected from 603 asymptomatic and 147 symptomatic snakes in 26 provinces of China. These samples came from Elaphe guttata, Elaphe obsoleta, Pituophis melanoleucus, Thamnophis sirtalis, Lampropeltis getulus, and Heterodon nasicus. The partial small subunit (SSU) rRNA gene was amplified using nested polymerase chain reaction (PCR) to investigate the infection rate of Cryptosporidium spp., and to assess evolutionary relationships and genetic characterization. A prevalence of 20% was recorded in asymptomatic snakes, with age identified as a significant risk factor. In contrast, 70% of symptomatic snakes were positive for Cryptosporidium spp., with Cryptosporidium serpentis and Cryptosporidium varanii (syn. C. saurophilum). Further analysis revealed a potential association between C. serpentis and regurgitation, and C. varanii and diarrhea, while neither species was linked to flatulence. To our knowledge, this is the first study to report Cryptosporidium spp. and associated clinical signs in symptomatic snakes in China. This study aims to enhance the understanding of Cryptosporidium infections, risk factors, and clinical manifestations in snakes, providing data crucial for the control and prevention of cryptosporidiosis.

Novel strategy to quantify the viability of oocysts of Cryptosporidium parvum and C. hominis, a risk factor of the waterborne protozoan pathogens of public health concern

While waters might be contaminated by oocysts from >40 Cryptosporidium species, only viable oocysts of C. parvum and C. hominis truly pose the main health risk to the immunocompetent population. Oocyst viability is also an important but often neglected risk factor in monitoring waterborne parasites. However, commonly used methods in water monitoring and surveys cannot distinguish species (microscopic observation) or oocyst viability (PCR), as dead oocysts in water could retain gross structure and DNA content for weeks to months. Here, we report new TaqMan qRT-PCR/qPCR assays for quantitative detection of viable C. parvum and C. hominis oocysts. By targeting a hypothetical protein-encoding gene cgd6_3920 that is highly expressed in oocysts and variable between species, the qRT-PCR/qPCR assays achieve excellent analytical specificity and sensitivity (limit of quantification [LOQ] = 0.25 and 1.0 oocyst/reaction). Using calibration curves, the number and ratio of viable oocysts in specimens could be calculated. Additionally, we also establish a TaqMan-18S qPCR for cost-effective screening of pan-Cryptosporidium-positive specimens (LOQ = 0.1 oocyst/reaction). The assay feasibility is validated using field water (N = 43) and soil (79) specimens from 17 locations in Changchun, China, which detects four Cryptosporidium species from seven locations, including three gp60-subtypes (i.e., IIdA19G1, IIdA17G1 and IIdA24G2) of C. parvum oocysts showing varied viability ratios. These new TaqMan q(RT)-PCR assays supplement current methods in the survey of waters and other samples (e.g., surfaces, foods and beverages), and are applicable to assessing the efficiency of oocyst deactivation protocols.

Detection and molecular characterization of Cryptosporidium spp. in dairy calves in Lisbon and Tagus Valley, Portugal

Cryptosporidium is a protozoan parasite with worldwide distribution, infecting a wide range of hosts with some zoonotic species. Calves have been identified as one of the most common reservoirs of this parasite. However, little is known about the genetics of Cryptosporidium in calves in Portugal. This study aimed to molecularly characterize infections of Cryptosporidium in pre-weaned calves from the Lisbon and Tagus Valley (LTV) in Portugal. Fifty-two samples were collected from calves from eight dairy and two beef farms in LTV, Portugal. Cryptosporidium oocysts were detected by Modified Ziehl-Neelsen staining (MZN) and direct immunofluorescent assay (DFA). MZN and DFA revealed the presence of Cryptosporidium oocysts in 40.4% (21/52) and 67.3% (35/52) samples, respectively. Positive samples were analyzed by PCR-RFLP of the 18 s rRNA gene for species identification. DNA amplification of the 18S rRNA gene was successful for 88.6% (31/35) of samples. Cryptosporidium parvum was identified in 96.8% (30/31) of the samples, and from one sample Cryptosporidium bovis was identified. Cryptosporidium parvum positive samples were subtyped by sequencing the PCR product of a partial fragment of the 60 kDa glycoprotein (gp60) gene. Subtype analysis of the C. parvum isolates revealed that all isolates belonged to subtype family IIa. Four subtypes were recognized within this subtype family, including the hyper-transmissible IIaA15G2R1 subtype that is the most frequently reported worldwide (27/30), IIaA14G2R1 (1/30), IIaA16G2R1 (1/30) and IIaA19G2R1 (1/30). To our knowledge, this is the first report of C. bovis, and C. parvum subtypes IIaA14G2R1 and IIaA19G2R1 in cattle in LTV, Portugal. The presence of the zoonotic C. parvum subtype in this study suggests that pre-weaned calves are likely to be a significant reservoir of zoonotic C. parvum, highlighting the importance of animal-to-human infection transmission risk. Further molecular studies are required to better understand the epidemiology of cryptosporidiosis in Portugal.

Diagnosis of endoparasite species and subtypes of Cryptosporidium spp. with one health importance, in feces from captive snakes in Rio de Janeiro, Brazil

In captivity, snakes may present chronic infections with high mortality, such as those caused by Cryptosporidium serpentis, or they may be pseudoparasitized by species that present zoonotic potential. Thus, the aim of this study was to evaluate the frequency of helminths and protozoa in the feces of captive snakes, characterize the species and subtypes of Cryptosporidium spp. and correlate the parasites detected with other information obtained from these animals. Feces were collected from 189 snakes kept at the Vital Brazil Institute, Rio de Janeiro, including samples from Bothrops jararaca, Bothrops jararacussu, Bothrops moojeni, Bothrops atrox, Bothrops leucurus, Crotalus durissus and Lachesis muta. All the samples were subjected to microscopy techniques and the polymerase chain reaction (PCR) in association with sequencing, to identify Cryptosporidium spp.. Forms of parasites infecting the snakes were identified through microscopy in 50.8% of the samples. Helminths were detected more often than protozoa in the feces of these animals, mainly comprising eggs resembling Kalicephalus sp. and oocysts of Eimeria sp.. Pseudoparasites such as Syphacia sp., Aspiculuris sp. and Hymenolepis nana were also detected. Through correlating the results obtained from parasitological staining techniques and PCR, the total frequency of Cryptosporidium sp. was found to be 19%. The species C. tyzzeri and C. parvum were identified. Characterization using the target gp60 showed subtypes with high potential for zoonotic transmission, especially IIaA15G2R1 and IIaA14G2R1 of C. parvum and IXbA8 of C. tyzzeri. This study highlighted the need for more intensive health management in the Institute's serpentarium and, especially, in its bioterium where rodents are reared as a food source for these snakes.

Rapid detection of Cryptosporidium spp. in diarrheic cattle feces by isothermal recombinase polymerase amplification assays

As a zoonotic parasite, Cryptosporidium spp. could cause severe diarrhea mainly in calves and children globally. Monitoring and prevention of Cryptosporidium spp.'s prevalence is of great significance in both economy and public health aspects. In this study, specific primers and probes were designed within the conserved region of 18S rRNA gene for Cryptosporidium spp. and recombinase polymerase amplification assays based on the fluorescence monitoring (real-time RPA) as well as combined with a lateral flow strip (LFS RPA) were developed. Both of the two RPA assays allowed the exponential amplification of the target fragment within 20 min. After incubation on a metal bath at 42 °C, the LFS RPA results were displayed on the lateral flow strip within 5 min while real-time RPA allowed the real-time observation of the results in Genie III at 39 °C. The RPA assays showed high specificity for Cryptosporidium spp. without any cross-reaction with other tested pathogens causing diarrhea in cattle. With the recombinant plasmid DNA containing the 18S rRNA gene of Cryptosporidium spp. serving as a template, the limit of detection for real-time RPA and LFS RPA assays were 14.6 and 12.7 copies/reaction, respectively. Moreover, the RPA assays were validated by testing diarrheic cattle fecal samples and compared with a real-time PCR. The positive ratio of Cryptosporidium spp. was 24.04 % (44/183) and 26.23 % (48/183) in both RPA assays and real-time PCR assay, respectively, and the kappa coefficient value was 0.942. The diagnostic specificity and diagnostic sensitivity of both RPA assays were 100 % and 91.67 %, respectively. Forty-one of 48 positive samples were successfully sequenced and four Cryptosporidium species were detected, including C. parvum (n = 20), C. andersoni (n = 17), C. bovis (n = 3) and C. ryanae (n = 1). The developed RPA assays are easy to operate and faster to obtain the detection results, and they are suiting for the point-of-care detection and facilitating the prevention and control of Cryptosporidium spp. infections.

Medicinal plants as a source of antiparasitics: an overview of experimental studies

Despite advances in modern human and veterinary medicine, gastrointestinal (GI) parasitic infections remain a significant health issue worldwide, mainly in developing countries. Increasing evidence of the multi-drug resistance of these parasites and the side effects of currently available synthetic drugs have led to increased research on alternative medicines to treat parasitic infections. The exploration of potential botanical antiparasitics, which are inexpensive and abundant, may be a promising alternative in this context. This study summarizes the in vitro/in vivo antiparasitic efficacy of different medicinal plants and their components against GI parasites. Published literature from 1990-2020 was retrieved from Google Scholar, Web of Science, PubMed and Scopus. A total of 68 plant species belonging to 32 families have been evaluated as antiparasitic agents against GI parasites worldwide. The majority of studies (70%) were conducted in vitro. Most plants were from the Fabaceae family (53%, n = 18). Methanol (37%, n = 35) was the most used solvent. Leaf (22%, n = 16) was the most used plant part, followed by seed and rhizome (each 12%, n = 9). These studies suggest that herbal medicines hold a great scope for new drug discoveries against parasitic diseases and that the derivatives of these plants are useful structures for drug synthesis and bioactivity optimization.

Cryptosporidium parvum gp60 subtypes in diarrheic lambs and goat kids from Israel

Cryptosporidium parvum is the second-most prevalent Cryptosporidium species that infects humans worldwide. In European countries, it is the most prevalent species in sheep, suggesting that these animals are a source of zoonotic infection. Preweaned lambs and goats are particularly susceptible to infection by the parasite and may suffer from severe diarrhea whilst excreting large quantities of infectious oocysts. Fifty fecal samples from preweaned lambs and goats with diarrhea from 35 farms across Israel, found to be Cryptosporidium-positive by microscopy, were tested by PCR and sequence analyses to determine the infective species and subtypes. Cryptosporidium parvum DNA was detected in most samples from both lambs and goats (46/50). Cryptosporidium xiaoi DNA was detected in three samples from kids, with co-infection detected in a single sample. Eleven different C. parvum subtypes were found, 10 in lambs and 5 in goats. All subtypes were from the IIa and IId subtype families, with subtypes IIdA20G1 and IIaA15G2R1 being the most prevalent and widespread. These subtypes were previously found in calves and humans in Israel and are considered the most prevalent C. parvum subtypes in small ruminants globally. These results underline the zoonotic potential of C. parvum from small ruminants and the high subtype diversity compared to previous reports from other Middle Eastern countries. In addition, this is the first report of C. xiaoi in Israel.

The occurrence and zoonotic potential of Cryptosporidium species in freshwater biota

BACKGROUND

Protozoan pathogens from the genus Cryptosporidium cause the diarrhoeal disease cryptosporidiosis in humans and animals globally. Freshwater biota could act as potential reservoirs or zoonotic sources of Cryptosporidium infections for livestock and people, but Cryptosporidium occurrence in aquatic biota is largely unexplored. The aim of this study was to investigate the occurrence of Cryptosporidium in a range of freshwater organisms in upland rivers across England and Wales.

METHODS

Fish were sampled by electrofishing, invertebrate larvae by kick sampling and the otter Lutra lutra and mink Mustela vison through faecal samples collected opportunistically as part of a nation-wide study. PCR targeting the small subunit ribosomal RNA gene was used to detect Cryptosporidium species.

RESULTS

Cryptosporidium occurred in just 0.8% of all the samples and in none of 73 samples from nine invertebrate genera. Cryptosporidium was detected in two of 2/74 fish samples (2.7%), both salmonids, and in 2/92 otter faecal samples (2.17%), but there were no positive samples in mink (0/24) or the bullhead Cottus gobio (0/16).

CONCLUSIONS

Low detection rate of human-infective Cryptosporidium species in aquatic fauna indicates they may present a low risk of contamination of some upland freshwaters.

Mammal-related Cryptosporidium infections in endemic reptiles of New Zealand

New Zealand's endemic reptile fauna is highly threatened and pathogens causing infectious diseases may be a significant risk to already endangered species. Here, we investigate Cryptosporidium infection in captive endemic New Zealand reptiles. We found two mammal-related Cryptosporidium species (C. hominis and C. parvum) and six subtypes from three gp60 families (Ib, Ig and IIa) in 12 individuals of captive endemic Tuatara, Otago and Grand skinks, and Jewelled and Rough geckos. Cryptosporidium serpentis was identified in two Jewelled geckos using 18S. In New Zealand, C. hominis and C. parvum are associated with infections in humans and introduced domestic animals but have also been recently found in wildlife. Our finding of Cryptosporidium infection in endemic reptiles can help inform strategies to monitor the conservation of species and manage potential introductions of pathogens to in-situ and ex-situ populations.

Molecular and phylogenetic characterization of Cryptosporidium species in the saffron finch Sicalis flaveola

BACKGROUND

Cryptosporidium is the most common protozoan that can infect a wide variety of animals, including mammals and birds. Fecal samples of six saffron finches, Sicalis flaveola, from a commercial establishment were screened for the presence of Cryptosporidium by the modified Ziehl-Neelsen technique and nested PCR of the 18S rRNA gene followed by sequencing of the amplified fragments.

RESULTS

The species Cryptosporidium galli was identified in all six saffron fiches, in addition to Cryptosporidium andersoni in one of the birds, indicating a mixed infection. Only two birds had feathers that were ruffled and dirty with feces. Concomitant infection with Isospora spp. was observed in all birds.

CONCLUSIONS

Saffron finches are a possible host of C. andersoni and this is the first report of this species in a captive bird and the third report of parasitism by C. galli in Sicalis flaveola.

Molecular identification of Cryptosporidium species in Canadian post-weaned calves and adult dairy cattle

Cryptosporidium is a zoonotic protozoan parasite that is distributed globally and impacts both human and animal health. There are over 40 species of Cryptosporidium described to date, of which four (C. parvum, C. bovis, C. ryanae and C. andersoni) are routinely reported in cattle. The goal of this study was to identify the Cryptosporidium species infecting dairy cattle from across Canada using cow fecal samples and post-weaned calf rectal swabs obtained through the Canadian National Dairy Study. A total of 353 cattle samples (117 pooled rectal fecal swabs from post-weaned calves and 236 cow fecal samples) from 175 herds across the 10 Canadian provinces were analysed by targeting Cryptosporidium's small subunit ribosomal RNA (SSU rRNA or 18S) gene. Herd prevalence of Cryptosporidium was 27.4% nationally, ranging from 0% in Saskatchewan (SK) to 62% in Prince Edward Island (PE). The national prevalence of Cryptosporidium cattle infections was 15.4% in pooled rectal fecal swab samples from post-weaned calves and 16.1% in adult cows. Sanger sequence analysis of the SSU rRNA gene target revealed that C. bovis, C. andersoni and C. ryanae occurred in both adults and post-weaned calves, with C. bovis as the predominant species detected in pooled fecal swab samples of post-weaned calves (9/18, 50%) and C. andersoni as the predominant species in cows (25/38, 66%). Cryptosporidium parvum was not observed in any of the pooled rectal swab samples from post-weaned calves but was observed in one mixed infection of C. bovis/C. parvum in an adult cow. The fifth species identified in this study was C. muris and was present in two adult cows. Low concentrations of oocyst equivalents, as measured by quantitative real-time PCR (qPCR) of the SSU rRNA gene copy number, were observed in a subset of cattle samples. Cryptosporidium andersoni concentrations varied from province to province, with the widest range and highest counts in cows from PE. In conclusion, oocysts from Cryptosporidium species observed in this study are shed into the environment, contributing to the environmental load. However, the Cryptosporidium species in the post-weaned calves and cows found in this study pose a lower risk to the dairy cattle than if they were infected with C. parvum. Similarly, these Cryptosporidium species pose only a small risk to public health as the three species are infrequently reported in humans globally and have not been reported in Canadians to date.

Humans and Hoofed Livestock Are the Main Sources of Fecal Contamination of Rivers Used for Crop Irrigation: A Microbial Source Tracking Approach

Freshwater bodies receive waste, feces, and fecal microorganisms from agricultural, urban, and natural activities. In this study, the probable sources of fecal contamination were determined. Also, antibiotic resistant bacteria (ARB) were detected in the two main rivers of central Chile. Surface water samples were collected from 12 sampling sites in the Maipo (n = 8) and Maule Rivers (n = 4) every 3 months, from August 2017 until April 2019. To determine the fecal contamination level, fecal coliforms were quantified using the most probable number (MPN) method and the source of fecal contamination was determined by Microbial Source Tracking (MST) using the Cryptosporidium and Giardia genotyping method. Separately, to determine if antimicrobial resistance bacteria (AMB) were present in the rivers, Escherichia coli and environmental bacteria were isolated, and the antibiotic susceptibility profile was determined. Fecal coliform levels in the Maule and Maipo Rivers ranged between 1 and 130 MPN/100-ml, and 2 and 30,000 MPN/100-ml, respectively. Based on the MST results using Cryptosporidium and Giardia host-specific species, human, cattle, birds, and/or dogs hosts were the probable sources of fecal contamination in both rivers, with human and cattle host-specific species being more frequently detected. Conditional tree analysis indicated that coliform levels were significantly associated with the river system (Maipo versus Maule), land use, and season. Fecal coliform levels were significantly (p < 0.006) higher at urban and agricultural sites than at sites immediately downstream of treatment centers, livestock areas, or natural areas. Three out of eight (37.5%) E. coli isolates presented a multidrug-resistance (MDR) phenotype. Similarly, 6.6% (117/1768) and 5.1% (44/863) of environmental isolates, in Maipo and Maule River showed and MDR phenotype. Efforts to reduce fecal discharge into these rivers should thus focus on agriculture and urban land uses as these areas were contributing the most and more frequently to fecal contamination into the rivers, while human and cattle fecal discharges were identified as the most likely source of this fecal contamination by the MST approach. This information can be used to design better mitigation strategies, thereby reducing the burden of waterborne diseases and AMR in Central Chile.

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.

Diagnosis, risk factors analysis and first molecular characterization of Cryptosporidium spp. in horses from Rio de Janeiro, Brazil

An analysis was made of the frequency of Cryptosporidium spp. in fecal samples from horses raised on farms in the Teresópolis city, state of Rio de Janeiro, Brazil, and the risk factors that favored this infection. Between 2019 and 2020, 314 samples of equine feces were collected, 287 of which came from English Thoroughbred horses and 27 from ponies. Information on the horses and their management were retrieved from a stud book and forms filled out by trainers. The fecal samples were subjected to macroscopic analysis, modified Sheather's and Lutz parasitological techniques, safranin staining, and to enzyme-linked immunosorbent assay (ELISA) for the detection of coproantigens. All the samples that tested positive by these techniques underwent partial sequence analysis of the 18S rRNA gene to characterize the protozoan species. Cryptosporidium spp. was identified in 35 (11.1%) of the samples, 34 from English Thoroughbred horses and one from a pony. Based on a logistic regression model, it was found that the presence of dogs and small ruminants on the farms, and drinking water from a spring, were significantly associated with the animals' infection by the protozoan (p < 0.05). Eight of the English Thoroughbred horse samples underwent molecular characterization, which revealed the presence of Cryptosporidium felis in one sample and Cryptosporidium parvum in seven. The seven samples containing C. parvum were subjected to gp60 gene analysis, based on which nucleotide sequences typical of the IIa family were identified, which are usually transmitted from animals to humans. In addition, the genotype IIaA15G2R1, which is considered to have the highest profile of zoonotic transmissibility, was identified in one Thoroughbred horse. This is the first study conducted in the state of Rio de Janeiro that molecularly characterized Cryptosporidium spp. in horses, and the first on the American continent to detect C. felis in the feces of these animals.

Validation of a one-tube nested real-time PCR assay for the detection of Cryptosporidium spp. in avian fecal samples

The aim of this study was to validate a one-tube nested real-time PCR assay followed by genetic sequencing to detect and identify Cryptosporidium species and genotypes in birds. A total of 443 genomic DNA extracted from avian fecal samples were analyzed by one-tube nested real-time PCR and conventional nested PCR. By one-tube nested real-time PCR, 90/443 (20.3%) samples were positive for Cryptosporidium spp. In contrast, 36/443 (8.1%) samples were positive for Cryptosporidium spp. by conventional nested PCR. The analytical sensitivity test showed that one-tube nested real-time PCR detects approximately 0.5 oocyst (2 sporozoites) per reaction. An evaluation of analytical specificity did not reveal amplification of microorganisms that commonly present nonspecific amplification with primers used for the diagnosis of Cryptosporidium spp. The repeatability analysis showed the same result in 27 out of 30 samples (90%). As for the reproducibility of one-tube nested real-time PCR, 24 of the 30 samples examined (80%) showed the same result. All the 90 samples amplified by one-tube real-time nested PCR were successfully sequenced, leading to the identification of C. baileyi, C. galli, C. meleagridis, C. proventriculi, and Cryptosporidium avian genotype I. Genetic sequencing of conventional nested PCR amplicons was successful in 10/36 (27.8%) of positive samples.

Comparison of three diagnostic methods in the diagnosis of cryptosporidiosis and gp60 subtyping of Cryptosporidium parvum in diarrheic calves in Central Anatolia Region of Turkey

The aim of this study was to compare three diagnostic methods for the diagnosis of cryptosporidiosis and to detect subtypes ofCryptosporidium parvum by sequences analyses of gp60 gene in diarrheic calves in several herds in Konya province located in Central Anatolia Region of Turkey. Fecal samples were collected from a total of 194 pre-weaned calves (n=158, ≤15 days old, and n=36, 15 to 40 days old), with diarrhoea. For comparative diagnosis, all samples were examined by modified Ziehl-Neelsen staining of fecal smears for the presence of oocyst, nested PCR-RFLP of SSU rRNA and TaqMan qPCR for the detection of Cryptosporidium DNA. A total of 92 (47.4%) and 104 (53.6%) out of the examined samples were found positive by microscopic examination and molecular tools, respectively. The diagnostic sensitivity and specificity of microscopic identification were determined as 88.5% and 100.0%, respectively compared to molecular assays. Cryptosporidium parvum was the only detected species in all positive samples by species-specific qPCR and nested PCR-RFLP assays. Species identifications were further confirmed by sequence analyses of the SSU rRNA PCR products. There was no statistically significant difference in C. parvum prevalence between early pre-weaned calves and calves older than 15 days. The sequence analyses of the gp60 gene of C. parvum isolates revealed a one subtype IIaA13G2R1 belonging to zoonotic family IIa in diarrheic calves

CryptoGenotyper: A new bioinformatics tool for rapid Cryptosporidium identification

Cryptosporidium is a protozoan parasite that is transmitted to both humans and animals through zoonotic or anthroponotic means. When a host is infected with this parasite, it causes a gastrointestinal disease known as cryptosporidiosis. To understand the transmission dynamics of Cryptosporidium, the small subunit (SSU or 18S) rRNA and gp60 genes are commonly studied through PCR analysis and conventional Sanger sequencing. However, analyzing sequence chromatograms manually is both time consuming and prone to human error, especially in the presence of poorly resolved, heterozygous peaks and the absence of a validated database. For this study, we developed a Cryptosporidium genotyping tool, called CryptoGenotyper, which has the capability to read raw Sanger sequencing data for the two common Cryptosporidium gene targets (SSU rRNA and gp60) and classify the sequence data into standard nomenclature. The CryptoGenotyper has the capacity to perform quality control and properly classify sequences using a high quality, manually curated reference database, saving users' time and removing bias during data analysis. The incorporated heterozygous base calling algorithms for the SSU rRNA gene target resolves double peaks, therefore recovering data previously classified as inconclusive. The CryptoGenotyper successfully genotyped 99.3% (428/431) and 95.1% (154/162) of SSU rRNA chromatograms containing single and mixed sequences, respectively, and correctly subtyped 95.6% (947/991) of gp60 chromatograms without manual intervention. This new, user-friendly tool can provide both fast and reproducible analyses of Sanger sequencing data for the two most common Cryptosporidium gene targets.

Molecular Identification of Cryptosporidium spp., Enterocytozoon bieneusi, and Giardia duodenalis in Captive Pet Birds in Henan Province, Central China

Cryptosporidium spp., Enterocytozoon bieneusi, and Giardia duodenalis are common enteric pathogens that are capable of infecting humans and animals. Total of 1,005 fecal samples from captive pet birds were collected from seven locations in Henan Province, China. The results demonstrated that 9.9% (99/1,005) of the captive birds were infected with one of these three pathogens. Enterocytozoon bieneusi was the most prevalent species among the birds (45/1,005, 4.5%) followed by G. duodenalis (33/1,005, 3.3%) and Cryptosporidium spp. (21/1,005, 2.1%). Five Cryptosporidium species were identified, namely, C. baileyi (10), C. galli (5), C. meleagridis (4), C. andersoni (1), and C. parvum (1). Two known E. bieneusi genotypes were identified: Peru 6 (44) was identified in pigeons (34) and European turtle doves (10); whereas, the genotype PtEb I (1) was only identified in a pigeon. Only G. duodenalis assemblage E (33) was identified in some pet birds. To the best of our knowledge, this study is the first to undertake the molecular identification of G. duodenalis in birds in China. The identification of potentially zoonotic species/genotypes of the pathogens suggests that exposure to the excreta of these birds, either directly or via food and water, may pose a threat to human health.

Molecular characterization of Cryptosporidium isolates from humans in Ontario, Canada

BACKGROUND

Cryptosporidiosis is a gastrointestinal disease with global distribution. It has been a reportable disease in Canada since 2000; however, routine molecular surveillance is not conducted. Therefore, sources of contamination are unknown. The aim of this project was to identify species and subtypes of Cryptosporidium in clinical cases from Ontario, the largest province in Canada, representing one third of the Canadian population, in order to understand transmission patterns.

METHODS

A total of 169 frozen, banked, unpreserved stool specimens that were microscopy positive for Cryptosporidium over the period 2008-2017 were characterized using molecular tools. A subset of the 169 specimens were replicate samples from individual cases. DNA was extracted directly from the stool and nested PCR followed by Sanger sequencing was conducted targeting the small subunit ribosomal RNA (SSU) and glycoprotein 60 (gp60) genes.

RESULTS

Molecular typing data and limited demographic data were obtained for 129 cases of cryptosporidiosis. Of these cases, 91 (70.5 %) were due to Cryptosporidium parvum and 24 (18.6%) were due to Cryptosporidium hominis. Mixed infections of C. parvum and C. hominis occurred in four (3.1%) cases. Five other species observed were Cryptosporidium ubiquitum (n = 5), Cryptosporidium felis (n = 2), Cryptosporidium meleagridis (n = 1), Cryptosporidium cuniculus (n = 1) and Cryptosporidium muris (n = 1). Subtyping the gp60 gene revealed 5 allelic families and 17 subtypes of C. hominis and 3 allelic families and 17 subtypes of C. parvum. The most frequent subtype of C. hominis was IbA10G2 (22.3%) and of C. parvum was IIaA15G2R1 (62.4%).

CONCLUSIONS

The majority of isolates in this study were C. parvum, supporting the notion that zoonotic transmission is the main route of cryptosporidiosis transmission in Ontario. Nonetheless, the observation of C. hominis in about a quarter of cases suggests that anthroponotic transmission is also an important contributor to cryptosporidiosis pathogenesis in Ontario.

Cryptosporidium Genotyping for Epidemiology Tracking

Cryptosporidium genotyping has made significant contributions to the species structure and population genetics of Cryptosporidium spp. In addition, the standardized method has shown utility in epidemiologic investigations identifying case linkages and contamination sources that could not be determined with traditional epidemiologic tools. The standardized method for Cryptosporidium genotyping from stool specimens described here comprises multiple individual protocols to amplify and sequence regions of the SSU rRNA and gp60 genes of Cryptosporidium.

Prevalence of intestinal parasite infections in stray and farm dogs from Spain

Dogs play a potential role as reservoirs for zoonotic parasites, being especially problematic uncontrolled dog populations such as stray and farm dogs with access to populated areas. In order to investigate the prevalence of canine intestinal parasites in at-risk dog populations, we tested a total of 233 faecal samples shed by stray and dairy farm dogs from northern Spain. Telemann method was used to detect the presence of eggs and (oo)cysts of common dog intestinal parasites and Cryptosporidium was detected by PCR. One hundred and forty eight out of 233 samples (63.5%) were positive for at least one intestinal parasite, being Ancylostomidae (35.6%; 83/233) and Trichuris (35.2%; 82/233) the parasites most frequently identified. Cryptosporidium DNA was not detected in any of the faecal samples analysed. The overall prevalence was significantly higher in stray dogs than in farm dogs (72.5% vs 58.8%). Specifically, stray dogs had a significantly higher prevalence of Ancylostomatidae, Toxocara, Toxascaris and Taenidae. These dog populations are an important source of environmental contamination with intestinal parasite forms, which could be of significance to animal and human health.

Dairy Calves in Uruguay Are Reservoirs of Zoonotic Subtypes of Cryptosporidium parvum and Pose a Potential Risk of Surface Water Contamination

Cryptosporidium parvum, a major cause of diarrhea in calves, is of concern given its zoonotic potential. Numerous outbreaks of human cryptosporidiosis caused by C. parvum genetic subtypes are reported yearly worldwide, with livestock or water being frequently identified sources of infection. Although cryptosporidiosis has been reported from human patients in Uruguay, particularly children, epidemiologic information is scant and the role of cattle as reservoirs of zoonotic subtypes of C. parvum has not been explored. In this study, we aimed to (a)-identify C. parvum subtypes infecting dairy calves in Uruguay (including potentially zoonotic subtypes), (b)-assess their association with calf diarrhea, (c)-evaluate their spatial clustering, and (d)-assess the distance of infected calves to surface watercourses draining the farmlands and determine whether these watercourses flow into public water treatment plants. Feces of 255 calves that had tested positive for Cryptosporidium spp. by antigen ELISA were selected. Samples had been collected from 29 dairy farms in seven Uruguayan departments where dairy farming is concentrated and represented 170 diarrheic and 85 non-diarrheic calves. Selected samples were processed by nested PCRs targeting the 18S rRNA and gp60 genes followed by sequencing to identify C. parvum subtypes. Of seven C. parvum subtypes detected in 166 calves, five (identified in 143 calves on 28/29 farms) had been identified in humans elsewhere and have zoonotic potential. Subtype IIaA15G2R1 was the most frequent (53.6%; 89/166), followed by IIaA20G1R1 (24.1%; 40/166), IIaA22G1R1 (11.4%; 19/166), IIaA23G1R1 (3.6%; 6/166), IIaA17G2R1 (3%; 5/166), IIaA21G1R1 (2.4%; 4/166), and IIaA16G1R1 (1.8%; 3/166). There were no significant differences in the proportions of diarrheic and non-diarrheic calves infected with any of the C. parvum subtypes. Two spatial clusters were detected, one of which overlapped with Uruguay's capital city and its main water treatment plant (Aguas Corrientes), harvesting surface water to supply ~1,700,000 people. Infected calves on all farms were within 20–900 m of a natural surface watercourse draining the farmland, 10 of which flowed into six water treatment plants located 9–108 km downstream. Four watercourses flowed downstream into Aguas Corrientes. Calves are reservoirs of zoonotic C. parvum subtypes in Uruguay and pose a public health risk.

Detection and molecular characterisation of Cryptosporidium spp. in Swedish pigs

Background

Cryptosporidium is a genus of apicomplexan parasites that cause enteric disease in vertebrates. In pigs, infections are most often asymptomatic, but may result in diarrhoea and poor growth. The most common species detected in pigs are C. suis and C. scrofarum with low zoonotic potential. C. parvum, with higher zoonotic potential, may also be found. As previous knowledge on the occurrence of Cryptosporidium in Swedish pigs is scarce, this was investigated in our study. Faecal samples from 13 pig herds were collected and a total of 222 pooled pen samples, from suckling piglets (n = 48), growers, aged 6–12 weeks (n = 57), fatteners, aged 13–24 weeks (n = 67) and adult animals (n = 50) were included. Samples were analysed using microscopy and positive samples were further analysed using polymerase chain reaction and sequencing of the 18S rRNA gene and the 28S rRNA gene to determine species.

Results

Cryptosporidium spp. were detected in all sampled herds and in 25% (56/222) of the individual pen samples. Infections were most common in growers and fatteners with 51% (29/57) and 35% (20/67) positive samples in each group, respectively. The piglets had 8% (4/48) positive samples and adults had 6% (3/50). Species determination showed C. suis and C. scrofarum in piglets and growers, C. scrofarum in the fatteners, and C. suis and C. parvum in the adults. Although no mixed infections could be confirmed we saw signs of double peaks in the 28S rRNA gene chromatograms, possibly indicating more than one species present per sample.

Conclusion

Cryptosporidium spp. were detected on every sampled farm and in 25% of the individual pen samples in our study. We therefore conclude that Cryptosporidium spp. are present and likely common in Swedish pig herds, where pigs are loose and reared on solid floors. However, none of the farms reported any problems with poor weight gain, diarrhoea, or reduced appetite in their pig herds. The pig adapted C. suis and C. scrofarum were the predominant species identified. Two samples were positive for the more zoonotic C. parvum, and pigs should hence not be disregarded as a possible source of zoonotic cryptosporidiosis.

Prevalence and Genotypes of Cryptosporidium in Wildlife Populations Co-Located in a Protected Watershed in the Pacific Northwest, 2013 to 2016

Between October 2013 and May 2016, 506 scat samples were collected from 22 species of wildlife located in a protected watershed of a major municipal water supply in the Pacific Northwest, USA. Overall prevalence of Cryptosporidium in the wildlife scat was 13.8% (70/506), with 15 species of wildlife found positive for Cryptosporidium. Prevalence of Cryptosporidium varied among species of wildlife, with higher prevalences observed in cougars (50.0%), mountain beavers (40.0%), and bobcats (33.3%), but none of these species are riparian-dependent. Genotyping of Cryptosporidium by sequencing PCR amplicons from the 18S rRNA gene were successful for seven species of wildlife, including bobcat, unknown predator, black-tailed deer, deer mouse, snowshoe hare, mountain beaver, and western spotted skunk. BLAST and phylogenetic analyses indicated that multiple species and genotypes of Cryptosporidium were present, with some isolates possibly co-circulating within and between wildlife populations in this protected watershed. Evidence of oocyst exchange between infected prey and their predators was also found. During the study period, several zoonotic Cryptosporidium species and genotypes that are uncommon in humans were detected in bobcat (99.58% identical to Cryptosporidium felis), unknown predator (100% identical to Cryptosporidium canis), snowshoe hare (100% identical to Cryptosporidium sp. skunk genotype), and mountain beaver (100% identical to Cryptosporidium ubiquitum). Novel sequences were also found in mountain beaver. To our knowledge, this is the first published report of a unique genotype or species of Cryptosporidium in mountain beaver (Aplodontia rufa).

Cryptosporidium and Giardia in locally harvested clams in Iqaluit, Nunavut

High prevalences of Cryptosporidium and Giardia were recently found in enteric illness patients in the Qikiqtaaluk region of Nunavut, Canada, with a foodborne, waterborne or animal source of parasites suspected. Clams (Mya truncata) are a commonly consumed, culturally important and nutritious country food in Iqaluit; however, shellfish may concentrate protozoan pathogens from contaminated waters. The goal of this work was to investigate clams as a potential source of Cryptosporidium and Giardia infections in residents in Iqaluit, Nunavut. The objectives were to estimate the prevalence and genetically characterize Cryptosporidium and Giardia in locally harvested clams. Clams (n = 404) were collected from Iqaluit harvesters in September 2016. Haemolymph (n = 328) and digestive gland (n = 390) samples were screened for Cryptosporidium and Giardia via PCR, and amplified products were further processed for sequence analyses for definitive confirmation. Giardia DNA was found in haemolymph from 2 clams, while Cryptosporidium was not detected. The two Giardia sequences were identified as zoonotic Giardia enterica assemblage B. The overall prevalence of Giardia in clams near Iqaluit was low (0.6%) compared with other studies in southern Canada and elsewhere. The presence of Giardia DNA in clams suggests human or animal faecal contamination of coastal habitat around Iqaluit in shellfish harvesting waters. Results from this study are intended to inform public health practice and planning in Inuit Nunangat.

Cryptosporidium Diagnostic Assays: Molecular Detection

Molecular diagnostic assays for Cryptosporidium are usually based on PCR and may detect the entire genus or target specified species. Of the ~40 species, fewer than half have been reported from humans, and most human cases of cryptosporidiosis are caused by Cryptosporidium parvum or Cryptosporidium hominis. Here we describe a nested PCR for the detection of all Cryptosporidium spp. that can then be differentiated by sequencing the PCR amplicons, and a duplex, real-time PCR for the simultaneous detection and differentiation of C. parvum and C. hominis.

Austwickiosis in Captive African Spurred Tortoises (Geochelone sulcata) Co-infected with Cryptosporidium ducismarci

Dermatophilosis has been described in many animals since it was first reported in 1915. In 2010, the genus and species associated with chelonid dermatophilosis was reclassified as Austwickia chelonae. Here we discuss a series of four submissions consisting of eight juvenile African spurred tortoises (Geochelone sulcata) from a large breeding facility. Submissions began in December 2016 and continued to June 2017 and then again in November 2018. Clinical signs were originally noted in December of 2015 and consisted of facial swelling and mandibular necrosis that led to complete disarticulation of the mandibles from the skull. Affected animals were emaciated with minimal gastrointestinal contents and several had soft faeces. The facial and head lesions were caused by A. chelonae. Additionally, co-infection with Cryptosporidium ducismarci was discovered within the small intestine. This report gives information on the pathology and pathogenicity of A. chelonae and characterizes the first reported cases of cryptosporidiosis in African spurred tortoises.

Molecular identification and phylogenetic analysis of Cryptosporidium, Hepatozoon and Spirometra in snakes from central China

Snakes are popular as food and traditional medicine in China. However, information about parasitic and bacterial infections in snakes from China is scarce. We investigated the prevalence of selected zoonotic agents including Cryptosporidium, Hepatozoon and Spirometra, in snakes in central China from June to October in 2018 by PCR amplification using parasite-specific primers. PCR amplification and DNA sequencing showed that 10.1% (15/149) of snakes were positive for Cryptosporidium spp., while 2.7% (4/149) were positive for Hepatozoon. Additionally, we found 36.9% (55/149) of snakes were infected with Spirometra erinaceieuropaei. The spargana burden per infected snake ranged from 1 to 26. BLAST and phylogenetic analysis of small subunit ribosomal RNA (SSU rRNA) gene and 60-kDa glycoprotein (gp60) gene showed that the parasites belonged to Cryptosporidium parvum genotype IIdA15G1, C. baileyi, C. serpentis and a Hepatozoon species. We conclude that intensively farmed snakes excrete C. parvum and C. baileyi oocysts due to ingestion of infected feeder animals, and that wild snakes in central China were commonly infected with S. erinaceieuropaei, suggesting that eating improperly cooked snakes could be risky to human health.

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Cryptosporidium parvum and C. baileyi were reported in farmed snakes in China for the first time.

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C. serpentis was detected for the first time in Ptyas dhumnades and Gloydius brevicaudus.

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A tentative new Hapatozoon species was first time recorded in wild Lycodon rufozonatus and G. brevicaudus.

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Spirometra erinaceieuropaei infection was found common in wild snakes from central China.

Molecular Epizootiology of Toxoplasma gondii and Cryptosporidium parvum in the Eastern Oyster (Crassostrea virginica) from Maine (USA)

Shellfish are known as a potential source of Toxoplasma gondii (responsible for toxoplasmosis), and Cryptosporidium parvum, which is one of the major causes of gastroenteritis in the world. Here we performed a comprehensive qPCR-based monthly survey for T. gondii and C. parvum during 2016 and 2017 in oysters (Crassostrea virginica) (n = 1440) from all six sites along the coast of Maine (USA). Pooled samples (mantle, gills, and rectum) from individual oysters were used for DNA extraction and qPCR. Our study resulted in detections of qPCR positives oysters for T. gondii and C. parvum at each of the six sites sampled (in 31% and 10% of total oysters, respectively). The prevalence of T. gondii was low in 2016, and in September 2017 several sites peaked in prevalence with 100% of the samples testing positive. The prevalence of C. parvum was very low except in one estuarine location (Jack's Point) in June 2016 (58%), and in October of 2016, when both prevalence and density of C. parvum at most of the sampling sites were among the highest values detected. Statistical analysis of environmental data did not identify clear drivers of retention, but there were some notable statistically significant patterns including current direction and nitrate along with the T. gondii prevalence. The major C. parvum retention event (in October 2016) corresponded with the month of highest dissolved oxygen measurements as well as a shift in the current direction revealed by nearby instrumentation. This study may guide future research to locate any contributing parasite reservoirs and evaluate the potential risk to human consumption.

First study of Cryptosporidium spp. occurrence in eared doves (Zenaida auriculata)

Cryptosporidium is a protozoan parasite with a wide range of hosts, including humans. However, only a few Cryptosporidium species have been described in birds (C. meleagridis, C. baileyi, C. galli and C. avium). The aim of this study was to investigate the occurrence of Cryptosporidium spp. in feces of eared doves (Zenaida auriculata), followed by molecular characterization of the parasite. A total of 196 animals of both sexes were trap-captured; the animals were culled and the intestinal contents were collected for DNA extraction. After extraction, a nested-PCR (nPCR), which amplifies a fragment of the 18S rRNA gene of Cryptosporidium spp., was performed. The amplicons obtained were purified and sequenced. PCR analysis revealed that 30 animals (15.3%) were positive for Cryptosporidium spp. There was no significant sex-dependent enrichment of Cryptosporidium occurrence (p > 0.05). Only 15 out of the 30 positive samples were successfully sequenced and their species determined, of which, 13 (86.7%) and 2 (13.3%) were C. meleagridis and C. galli, respectively. Herein, we present for the first time a molecular characterization of Cryptosporidium from feces of eared doves (Z. auriculata) and propose that these birds are a potential source of C. meleagridis infection in humans.

Giardia spp. and Cryptosporidium spp. removal efficiency of a combined fixed-film system treating domestic wastewater receiving hospital effluent

Giardia and Cryptosporidium have caused numerous outbreaks of diarrhea as a result of the ingestion of water contaminated with sewage. In Brazil, the efficiency of Giardia and Cryptosporidium removal by combined fixed-film systems has rarely been studied. The aims of the present study were therefore to verify the removal efficiency of Giardia and Cryptosporidium by a combined system (anaerobic/anoxic filter and aerated submerged biofilter) and to perform the genetic characterization of these parasites. The (oo)cysts were detected by centrifuge concentration and membrane filtration from raw sewage, effluents, adhered biomass, and sludge samples. Immunofluorescence assay and differential interference contrast microscopy were used for the visualization of the (oo)cysts. Nested PCR was applied to confirm Giardia and Cryptosporidium. Giardia and Cryptosporidium were detected in 27% and 5.5% of the 144 analyzed samples of raw sewage and effluents, respectively. A total of 33,000 cysts/L were recovered in the adhered biomass samples (n = 25) from different points of the aerated submerged biofilter, while 6000 oocysts/L were registered in a single point. An average of 11,800 cysts/L were found in the sludge samples (n = 5). The combined system exhibited a removal efficiency of Giardia cysts of 1.8 ± 1.0 log removal. The C and BIV assemblages of Giardia were identified in the raw sewage while AII was found in the treated effluent sample. It was not possible to calculate the removal efficiency of Cryptosporidium oocysts by the combined system. The combined system exhibited some potential as a suitable treatment for the removal of parasites from sewage.

Identification of Cryptosporidium bat genotypes XVI-XVIII in bats from Brazil

Cryptosporidiosis is an emergent zoonotic disease caused by the globally distributed protozoa Cryptosporidium spp. Although several Cryptosporidium studies related to humans and many animal species have been published, there are still limited studies on the epidemiology of Cryptosporidium infection in bats. The aim of this study was to determine the occurrence of Cryptosporidium spp. and to perform the molecular characterization of Cryptosporidium species and genotypes in fecal samples from bats in an urban area of the municipality of Araçatuba, state of São Paulo, Brazil. Nested PCR targeting the 18S rRNA, actin, and HSP-70 genes was performed to screen 141 fecal samples from bats and detected Cryptosporidium spp. in 16.3% (23/141) of the samples. Bidirectional sequencing identified three novel Cryptosporidium bat genotypes (XVI, XVII, and XVIII) and a new genotype (18SH) genetically similar to Cryptosporidium avium in six species of bats. This is the first report on the occurrence and molecular characterization of Cryptosporidium spp. in Brazilian bats. Zoonotic Cryptosporidium species were not found in fecal samples from bats living in an urban area in the municipality of Araçatuba, state of São Paulo, Brazil.

Cryptosporidium Incidence and Surface Water Influence of Groundwater Supplying Public Water Systems in Minnesota, USA

Regulations for public water systems (PWS) in the U.S. consider Cryptosporidium a microbial contaminant of surface water supplies. Groundwater is assumed free of Cryptosporidium unless surface water is entering supply wells. We determined the incidence of Cryptosporidium in PWS wells varying in surface water influence. Community and noncommunity PWS wells ( n = 145) were sampled ( n = 964) and analyzed for Cryptosporidium by qPCR and immunofluorescence assay (IFA). Surface water influence was assessed by stable isotopes and the expert judgment of hydrogeologists using site-specific data. Fifty-eight wells (40%) and 107 samples (11%) were Cryptosporidium-positive by qPCR, and of these samples 67 were positive by IFA. Cryptosporidium concentrations measured by qPCR and IFA were significantly correlated ( p < 0.001). Cryptosporidium incidence was not associated with surface water influence as assessed by stable isotopes or expert judgment. We successfully sequenced 45 of the 107 positive samples to identify species, including C. parvum (41), C. andersoni (2), and C. hominis (2), and the predominant subtype was C. parvum IIa A17G2R1. Assuming USA regulations for surface water-supplied PWS were applicable to the study wells, wells positive for Cryptosporidium by IFA would likely be required to add treatment. Cryptosporidium is not uncommon in groundwater, even when surface water influence is absent.

Odds, challenges and new approaches in the control of helminthiasis, an Asian study

The time is passing, and the worms are still a major struggle for local people in Asian countries, especially the less empowered and in a situation of social vulnerability. We are working in the field in Laos, Thailand, and the Philippines where the usual control programs based only on human treatment are partially effective. Areas with mass drug administration could diminish, but not eliminate STHs of endemic areas. The persistence of helminthic NTDs in the environment and animal hosts makes the eradication a very difficult task. Great changes in the landscapes of endemic areas, such as construction of dams, can change the fauna and the lifestyle of local people. Those changes can improve infrastructure, but it can also lead to social vulnerability. The challenge, then, is to conceive new and directed control programs for helminthiasis based on multi- and transdisciplinary approaches diminishing the health gap in a globalized world. In this short review, we summarize the actual scenario concerning the main helminths in Southeast Asia and how an environmental DNA approach and the use of GIS could contribute to surveillance and control programs.

Profiling the diversity of Cryptosporidium species and genotypes in wastewater treatment plants in Australia using next generation sequencing

Wastewater recycling is an increasingly popular option in worldwide to reduce pressure on water supplies due to population growth and climate change. Cryptosporidium spp. are among the most common parasites found in wastewater and understanding the prevalence of human-infectious species is essential for accurate quantitative microbial risk assessment (QMRA) and cost-effective management of wastewater. The present study conducted next generation sequencing (NGS) to determine the prevalence and diversity of Cryptosporidium species in 730 raw influent samples from 25 Australian wastewater treatment plants (WWTPs) across three states: New South Wales (NSW), Queensland (QLD) and Western Australia (WA), between 2014 and 2015. All samples were screened for the presence of Cryptosporidium at the 18S rRNA (18S) locus using quantitative PCR (qPCR), oocyst numbers were determined directly from the qPCR data using DNA standards calibrated by droplet digital PCR, and positives were characterized using NGS of 18S amplicons. Positives were also screened using C. parvum and C. hominis specific qPCRs. The overall Cryptosporidium prevalence was 11.4% (83/730): 14.3% (3/21) in NSW; 10.8% (51/470) in QLD; and 12.1% (29/239) in WA. A total of 17 Cryptosporidium species and six genotypes were detected by NGS. In NSW, C. hominis and Cryptosporidium rat genotype III were the most prevalent species (9.5% each). In QLD, C. galli, C. muris and C. parvum were the three most prevalent species (7.7%, 5.7%, and 4.5%, respectively), while in WA, C. meleagridis was the most prevalent species (6.3%). The oocyst load/Litre ranged from 70 to 18,055 oocysts/L (overall mean of 3426 oocysts/L: 4746 oocysts/L in NSW; 3578 oocysts/L in QLD; and 3292 oocysts/L in WA). NGS-based profiling demonstrated that Cryptosporidium is prevalent in the raw influent across Australia and revealed a large diversity of Cryptosporidium species and genotypes, which indicates the potential contribution of livestock, wildlife and birds to wastewater contamination.

Comparison of freeze-thaw cycles for nucleic acid extraction and molecular detection of Cryptosporidium parvum and Toxoplasma gondii oocysts in environmental matrices

Freeze-thaw DNA extraction methods and PCR primers were compared to optimize detection of Cryptosporidium parvum and Toxoplasma gondii oocysts in different matrices. Increasing FT cycles did not increase parasite DNA detection, and primers targeting the 18S ssrRNA gene yielded the most sensitive detection of C. parvum oocysts.

Reduction of Cryptosporidium, Giardia, and Fecal Indicators by Bardenpho Wastewater Treatment

Increased demand for water reuse and reclamation accentuates the importance for optimal wastewater treatment to limit protozoa in effluents. Two wastewater treatment plants utilizing advanced Bardenpho were investigated over a 12-month period to determine the incidence and reduction of Cryptosporidium, Giardia, Cyclospora, and fecal indicators. Results were compared to facilities that previously operated in the same geographical area. Protozoa (oo)cysts were concentrated using an electronegative filter and subsequently detected by fluorescent microscopy and/or PCR methods. Cryptosporidium and Giardia were frequently detected in raw sewage, but Cyclospora was not detected in any wastewater samples. Facilities with Bardenpho treatment exhibited higher removals of (oo)cysts than facilities utilizing activated sludge or trickling filters. This was likely due to Bardenpho systems having increased solid wasting rates; however, this mechanism cannot be confirmed as sludge samples were not analyzed. Use of dissolved-air-flotation instead of sedimentation tanks did not result in more efficient removal of (oo)cysts. Concentrations of protozoa were compared with each other, Escherichia coli, somatic coliphage, and viruses (pepper mild mottle virus, Aichi virus 1, adenovirus, and polyomaviruses JC and BK). Although significant correlations were rare, somatic coliphage showed the highest potential as an indicator for the abundance of protozoa in wastewaters.

Distribution of Giardia duodenalis (Assemblages A and B) and Cryptosporidium parvum amongst migrant workers in Peninsular Malaysia

The influx of low skilled workers from socioeconomically deprived neighbouring countries to Malaysia has raised concerns about the transmission of communicable gastrointestinal diseases such as giardiasis and cryptosporidiosis to the local population. Therefore, a cross sectional study was conducted to investigate the prevalence of both diseases and the genetic diversity of these pathogens in the migrant population. Microscopic examination of faecal samples from 388 migrant workers involved in five working sectors were screened and 10.8% (n = 42) were found to be positive with Giardia spp. and 3.1% (n = 12) with Cryptosporidium spp. infections. PCR amplicons at the triosephosphate isomerase (tpi) gene were successfully obtained for Giardia duodenalis from 30 (30/388; 7.73%) samples with assemblages AII and B in 13 (13/30; 43.3%) and 17 (17/30; 56.7%) positive samples, respectively. Nine samples (9/388; 2.3%) were identified as Cryptosporidium parvum using PCR-RFLP analysis. Country of origin, duration of residence in Malaysia and working sectors significantly influenced G. duodenalis assemblage AII infections amongst the targeted population. Meanwhile, C. parvum infection was significantly associated with those working in the food service sector. Despite the low presence of pathogenic G. duodenalis and C. parvum in the study population, the results highlight the risk of anthroponotic foodborne and waterborne transmission and therefore call for implementation of control strategies through improvements in personal hygiene and sanitation standards.

Occurrence and molecular characterization of Giardia duodenalis cysts and Cryptosporidium oocysts in raw water samples from the Rímac River, Peru

Giardia and Cryptosporidium are potentially pathogenic protozoa which are ubiquitous in ambient surface water. The present study included 60 samples of surface water from three sampling sites from the Rímac River, Lima and Callao, Peru, to detect the occurrence of Giardia spp. and Cryptosporidium spp. and to perform molecular characterization of specimens found. Water samples were concentrated using the membrane filtration technique, and following elution, cysts and oocysts were visualized by direct immunofluorescence assay (IFA). For molecular characterization, tpi and bg gene fragments and 18S rRNA were amplified by nested PCR for Giardia and Cryptosporidium, respectively, followed by sequencing and phylogenetic analysis. Giardia cysts were found in 93.3% of the analyzed samples, whereas Cryptosporidium oocysts were detected in 15%. The positivity of the Giardia cysts was 86.6% (n = 26) in 2014, while Cryptosporidium oocysts were not detected. In 2015, both protozoa were found in raw water samples, with all 30 samples collected positive for Giardia cysts (100.0%) and 9 positive for Cryptosporidium oocysts (30.0%). Oocysts were detected in 20.0% of water samples from sites 1 (mean 5.25 oocysts/L) and 2 (mean 52.3 oocysts/L), while at site 3, oocysts were detected in 50.0% of raw water samples (mean 193.6 oocysts/L). The presence of Giardia duodenalis assemblage A was confirmed in several samples by the phylogenetic positioning of the bg and tpi genes, and the sub-assemblage AII was predominant (8/9). Sequencing for Cryptosporidium resulted in profiles compatible with Cryptosporidium hominis, Cryptosporidium meleagridis, and Cryptosporidium baileyi. This is the first time that the presence of G. duodenalis assemblage A/sub-assemblage AII and Cryptosporidium species has been reported in surface water samples in Peru. These Cryptosporidium species and the Giardia duodenalis assemblage are associated with human disease which highlights the potential risk to public health and the need to increase environmental monitoring measures to protect this water body.

Detection of natural occurrence of Tritrichomonas foetus in cats in Araçatuba, São Paulo, Brazil

ABSTRACT: The aim of this study was to investigate the occurrence of Tritrichomonas foetus in cats in the area surrounding the city of Araçatuba municipality, State of São Paulo, Brazil. Fecal samples from 129 cats were collected by rectal flush technique. It was compared two diagnosis methods, direct examination of feces and PCR. The presence of T. foetus DNA was verified using PCR by amplification of 347-bp fragment from the primers TFR3 and TFR4 and amplicons of positive cases were sequenced. Statistical analyses were performed investigating the associations between T. foetus infection with gender, age, breed, presence of diarrhea and/or history of diarrhea, previous treatment, lifestyle, origin, environment, and co-infection. T. foetus was observed in one sample (n=129) by direct microscopic examination of feces while PCR was positive in five samples (3.9%). Giardia species and Cryptosporidium species co-infection was also observed. Statistical analyses showed no significant associations between T. foetus infection and all listed factors, although most positive cats were asymptomatic and lived in multi-cat household. The isolates of T. foetus showed 100% identical sequences with other T. foetus isolates from cats around the world. So, the occurrence of T. foetus was confirmed in cats in Araçatuba city (Brazil). This parasite must be considered as a differential diagnosis in cats with diarrhea and also in asymptomatic carriers as source of infection in multi-cat environments.

Detection and characterization of Cryptosporidium species and genotypes in three chicken production systems in Brazil using different molecular diagnosis protocols

The objective of this study was to determine the occurrence of Cryptosporidium spp. in domestic chickens raised in different chicken production systems in Brazil using three nested PCR protocols. The purification and concentration of oocysts present in 190 fecal samples from chickens raised in extensive, semi-intensive and intensive production systems were accomplished by centrifugal flotation in Sheather's solution and were followed by the extraction of genomic DNA. The detection and molecular characterization of Cryptosporidium species and genotypes were performed using three nested polymerase chain reaction (nested PCR) protocols targeting the 18S rRNA gene followed by sequencing of the amplified fragments. Subgenotyping of C. meleagridis was performed using a nested PCR reaction targeting the gp60 gene. Sample identified as Cryptosporidium sp. genetically similar to Cryptosporidium xiaoi and Cryptosporidium bovis by 18S rRNA gene sequencing were further analyzed by nested PCR targeting the actin gene and subsequent sequencing of the amplified fragment. Positive amplification for Cryptosporidium spp. was observed in 12.6% (24/190) of the samples, including C. baileyi (9.8%; 18/190), C. meleagridis (0.5%, 1/190), C. parvum (2.1%; 4/190) and Cryptosporidium sp. (0.5%; 1/190). Subgenotyping of C. meleagridis revealed the presence of the zoonotic subtype IIIgA23G3R1. Sequencing of the 18S rRNA gene and the actin gene fragments revealed a Cryptosporidium genotype in an extensive poultry system genetically related to C. xiaoi and C. bovis. There was no significant difference in the frequency of positive results obtained by the three nested PCR protocols (p > 0.05); additionally, the agreement obtained by Kappa index ranged from substantial (0.70) to almost perfect (0.9).

DNA barcoding of Cryptosporidium

Cryptosporidium spp. (Apicomplexa) causing cryptosporidiosis are of medical and veterinary significance. The genus Cryptosporidium has benefited from the application of what is considered a DNA-barcoding approach, even before the term 'DNA barcoding' was formally coined. Here, the objective to define the DNA barcode diversity of Cryptosporidium infecting mammals is reviewed and considered to be accomplished. Within the Cryptosporidium literature, the distinction between DNA barcoding and DNA taxonomy is indistinct. DNA barcoding and DNA taxonomy are examined using the latest additions to the growing spectrum of named Cryptosporidium species and within-species and between-species identity is revisited. Ease and availability of whole-genome DNA sequencing of the relatively small Cryptosporidium genome offer an initial perspective on the intra-host diversity. The opportunity emerges to apply a metagenomic approach to purified field/clinical Cryptosporidum isolates. The outstanding question remains a reliable definition of Cryptosporidium phenotype. The complementary experimental infections and metagenome approach will need to be applied simultaneously to address Cryptosporidium phenotype with carefully chosen clinical evaluations enabling identification of virulence factors.