Cryptosporidium viatorum from the native Australian swamp rat Rattus lutreolus - An emerging zoonotic pathogen?

Rodent-adapted Cryptosporidium infection in humans: Seven new cases and review of the literature

Cases of cryptosporidiosis in humans have been reported with strong indication of transmission from rodents. Here, we report seven new human cases of cryptosporidiosis involving rodent-adapted species (Cryptosporidium ditrichi [n = 1], Cryptosporidium mortiferum [n = 4; previously known as Cryptosporidium chipmunk genotype I], Cryptosporidium tyzzeri [n = 1], and Cryptosporidium viatorum [n = 1]) and review cases of human infection caused by these four species published to date. The seven new cases were detected in Denmark within a period of twelve months from 2022 to 2023. Only the C. tyzzeri and C. viatorum cases were associated with travel outside Denmark. The total number of human cases of cryptosporidiosis due to C. ditrichi and C. tyzzeri documented to date globally are still limited (4 and 7, respectively), whereas cases involving C. viatorum and C. mortiferum have been detected to a larger extent (43 and 63 cases, respectively). The four new cases of C. mortiferum were all of the XIVaA20G2T1 subtype, which is the only subtype identified so far in Scandinavia, and which is a subtype not yet found outside of Scandinavia. The new C. viatorum case was identified as the XVaA3g subtype. The C. tyzzeri case was subtyped as IXbA6. No subtype data were produced for C. ditrichi due to lack of a subtype assay. Review of existing data suggests the presence of C. ditrichi and C. mortiferum primarily in northern countries and C. tyzzeri and C. viatorum primarily in warmer climates. While our data may further support the role of Cryptosporidium as a cause of zoonotic disease, case descriptions should be obtained where possible to determine if Cryptosporidium species primarily adapted to rodents are the likely cause of symptoms or just an incidental finding.

Molecular characterization of Cryptosporidium in wild rodents from the Inner Mongolian Autonomous Region and Liaoning Province, China: assessing host specificity and the potential for zoonotic transmission

Introduction

Wild rodents are key hosts for Cryptosporidium transmission, yet there is a dearth of information regarding their infection status in the Inner Mongolian Autonomous Region and Liaoning Province of China. Therefore, the present study was conducted to determine the prevalence and genetic characteristics of Cryptosporidium among wild rodents residing in these two provinces.

Methods

A total of 486 rodents were captured, and fresh feces were collected from each rodent's intestine for DNA extraction. Species identification of rodents was performed through PCR amplification of the vertebrate cytochrome b (cytb) gene. To detect the presence of Cryptosporidium in all fecal samples, PCR analysis and sequencing of the partial small subunit of the ribosomal RNA (rRNA) gene were performed.

Results

Four species of rodents were identified: Rattus norvegicus, Mus musculus, Apodemus agrarius, and Cricetulus barabensis. Positive results for Cryptosporidium were obtained for 9.2% (18/195), 6.6% (7/106), 5.6% (5/89), and 6.3% (6/96) of these rodents, respectively, with an average infection rate of 7.4% (36/486). The identification revealed the presence of five Cryptosporidium species, C. ubiquitum (n = 8), C. occultus (n = 5), C. muris (n = 2), C. viatorum (n = 1), and C. ratti (n = 1), along with two Cryptosporidium genotypes: Rat genotype III (n = 10) and Rat genotype IV (n = 9).

Discussion

Based on the molecular evidence presented, the wild rodents investigated were concurrently infected with zoonotic (C. muris, C. occultus, C. ubiquitum and C. viatorum) as well as rodent-adapted (C. ratti and Rat genotype III and IV) species/genotypes, actively participating in the transmission of cryptosporidiosis.

Enteric parasites Cyclospora cayetanensis and Cryptosporidium hominis in domestic and wildlife animals in Ghana

BACKGROUND

Enteric parasitic infections remain a major public health problem globally. Cryptosporidium spp., Cyclospora spp. and Giardia spp. are parasites that cause diarrhea in the general populations of both developed and developing countries. Information from molecular genetic studies on the speciation of these parasites and on the role of animals as vectors in disease transmission is lacking in Ghana. This study therefore investigated these diarrhea-causing parasites in humans, domestic rats and wildlife animals in Ghana using molecular tools.

METHODS

Fecal samples were collected from asymptomatic school children aged 9-12 years living around the Shai Hills Resource Reserve (tourist site), from wildlife (zebras, kobs, baboons, ostriches, bush rats and bush bucks) at the same site, from warthogs at the Mole National Park (tourist site) and from rats at the Madina Market (a popular vegetable market in Accra, Ghana. The 18S rRNA gene (18S rRNA) and 60-kDa glycoprotein gene (gp60) for Cryptosporidium spp., the glutamate dehydrogenase gene (gdh) for Giardia spp. and the 18S rDNA for Cyclospora spp. were analyzed in all samples by PCR and Sanger sequencing as markers of speciation and genetic diversity.

RESULTS

The parasite species identified in the fecal samples collected from humans and animals included the Cryptosporidium species C. hominis, C. muris, C. parvum, C. tyzzeri, C. meleagridis and C. andersoni; the Cyclopora species C. cayetanensis; and the Gardia species, G. lamblia and G. muris. For Cryptosporidium, the presence of the gp60 gene confirmed the finding of C. parvum (41%, 35/85 samples) and C. hominis (29%, 27/85 samples) in animal samples. Cyclospora cayetanensis was found in animal samples for the first time in Ghana. Only one human sample (5%, 1/20) but the majority of animal samples (58%, 51/88) had all three parasite species in the samples tested.

CONCLUSIONS

Based on these results of fecal sample testing for parasites, we conclude that animals and human share species of the three genera (Cryptosporidium, Cyclospora, Giardia), with the parasitic species mostly found in animals also found in human samples, and vice-versa. The presence of enteric parasites as mixed infections in asymptomatic humans and animal species indicates that they are reservoirs of infections. This is the first study to report the presence of C. cayetanensis and C. hominis in animals from Ghana. Our findings highlight the need for a detailed description of these parasites using high-throughput genetic tools to further understand these parasites and the neglected tropical diseases they cause in Ghana where such information is scanty.

Multilocus Sequence Typing as a Useful Tool for the Study of the Genetic Diversity and Population Structure of Cryptosporidium Spp

One of the most important aquatic parasites in industrialized countries, Cryptosporidium spp., is a major cause of diarrheal disease in humans and animals worldwide. The contingent evolution of cryptosporidia with hosts, host adaptation, and geographic variation contributed to the creation of species subtypes, thereby shaping their population genetic structures. Multilocus typing tools for population genetic characterizations of transmission dynamics and delineation of mechanisms for the emergence of virulent subtypes have played an important role in improving our understanding of the transmission of this parasite. However, to better understand the significance of different subtypes with clinical disease manifestations and transmission risks, a large number of samples and preferably from different geographical areas need to be analyzed. This review provides an analysis of genetic variation through multilocus sequence typing, provides an overview of subtypes, typing gene markers for Cryptosporidium parvum, Cryptosporidium hominis, Cryptosporidium muris and Cryptosporidium andersoni genotypes and an overview of the hosts of these parasites.

Clustering of Cryptosporidium species infections among sheep and cattle but not children in remote highland communities of Madagascar

Background

The aim of this study was to identify local transmission patterns of Cryptosporidium spp. infections among livestock and humans in four extremely rural and remote highland communities in Madagascar.

Methods

In this cross-sectional study, households were randomly sampled throughout a 1-year study period, with one feces sample collected from each child (≤ 5 years old), sheep and cattle. Cryptosporidium spp. were identified using a nested PCR assay targeting the 18S ribosomal RNA gene. All samples positive for Cryptosporidium hominis were further subtyped by sequencing the 60-kDa glycoprotein gene (gp60). Spatial clustering methods were applied to analyze potential transmission patterns.

Results

In total, 252 households participated in the study, and samples from 197 children, 862 cattle and 334 sheep were collected and included in the study. Of the samples collected, 11 (5.6%) from children, 30 (3.5%) from cattle and 42 (12.6%) from sheep tested positive for Cryptosporidium spp. Very little overlap in the species distribution between human and animal infections was found. Global (overall) and local (spatially defined) clustering was observed for Cryptosporidium spp. infections in sheep and for Cryptosporidium xiaoi/bovis infections among sheep and cattle.

Discussion

The results of this analysis do not support the occurrence of defined disease outbreaks, rather they point to a continuous series of transmission events that are spatially aggregated. Despite the close coexistence between humans, sheep and cattle in the study area, mutual transmission was not observed. Hence, the study underlines the importance of sustained sanitation and hygiene measures to prevent cryptosporidiosis transmission among infants, since asymptomatic children serve as an infection reservoir. Similarly, the study highlights the importance of improving hygiene to reduce the transmission of Cryptosporidium spp. in livestock, an infection with serious consequences, especially in newborn calves.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s13071-022-05434-0.

Genetic diversity of Cryptosporidium species in Njoro Sub County, Nakuru, Kenya

Cryptosporidium spp. cause cryptosporidiosis in humans through zoonotic and anthroponotic transmission. Previous studies illustrated the significance of domestic animals as reservoirs of this parasite. Cryptosporidium occurs in Njoro River; a main source of water to humans and animals. However, there is no information on the Cryptosporidium spp. and genotypes circulating in Njoro Sub County. A total of 2174 samples from humans, cattle, chickens, sheep and goats were assessed for the presence of Cryptosporidium spp. Thirty-three positive samples were subsequently successfully sequenced and compared to Cryptosporidium sequences in the GenBank repository using NCBI's (National Center for Biotechnology Information) online BLAST (Basic Local Alignment Search Tool) algorithmic program. Sequence alignment was done using the Clustal W program and phylogenetic analysis was executed in MEGA X (Molecular Evolutionary Genetics Analysis version X). The prevalence of cryptosporidiosis in Njoro Sub County is 6.99%. Cryptosporidium spp. present in the watershed showed great genetic diversity and nine Cryptosporidium species were recorded: Cryptosporidium parvum, Cryptosporidium hominis, Cryptosporidium ubiquitum, Cryptosporidium meleagridis, Cryptosporidium andersoni, Cryptosporidium baileyi, Cryptosporidium muris, Cryptosporidium xiaoi and Cryptosporidium viatorum. This is the first study to report the presence of C. viatorum in Kenya. Cattle is the major reservoir of zoonotic Cryptosporidium spp. while goats harbored the lowest number of species. Humans and domestic animals drink the contaminated water from Njoro River, humans are therefore, exposed to a high cryptosporidiosis risk.

A survey of Cryptosporidium prevalence among birds in two zoos in China

BACKGROUND

Cryptosporidiosis is an important zoonotic protozoan disease worldwide, but few studies on this disease have been performed in wild birds; thus, our knowledge of this disease is insufficient, even in zoo birds. Animals in zoos are possible zoonotic disease reservoirs, potentially resulting in zoonotic agent spillover to humans; accordingly, our understanding of such phenomena should be improved.

METHODS

A total of 263 fresh fecal samples from 43 avian species were randomly collected from the Beijing Zoo and Harbin North Forest Zoo and screened for the prevalence of Cryptosporidium by 18S rRNA gene sequencing. Cryptosporidium species were distinguished based on the combined results of phylogenetic tree and genetic distance analyses conducted with the inclusion of seven avian Cryptosporidium species and 13 avian Cryptosporidium genotypes. The genetic diversity of Cryptosporidium parvum among different hosts, including humans, cattle, dogs, and birds, and the genetic diversity of avian C. parvum among avian hosts in China, Iraq and Brazil were determined based on C. parvum 18S rRNA haplotypes.

RESULTS

The results of PCR targeting the 18S rRNA gene revealed that 1.9% (5/263) of the samples were Cryptosporidium-positive. Four of the five Cryptosporidium-positive samples originated from white cranes (Grus leucogeranus), and one originated from a flamingo (Phoenicopteridae). Avian C. parvum isolates, including the isolates examined in the present study, showed gene flow with other isolates from different types of hosts, including humans, cattle and dogs, indicating that zoo birds potentially pose zoonotic and pathogenic risks to humans and animals. Additionally, gene flow between avian C. parvum isolates from China and Brazil was detected.

CONCLUSIONS

To the best of our knowledge, our results demonstrate C. parvum infection in a flamingo (Phoenicopteridae) and white cranes (Grus leucogeranus) for the first time. The results of our study provide an important reference for understanding the host range, biological characteristics, and molecular epidemiology of C. parvum.

Public health and ecological significance of rodents in Cryptosporidium infections

Cryptosporidium is one of the most important genera of intestinal zoonotic pathogens that cause diarrhea in both humans and animals. Rodents are common and important hosts or carriers of pathogens with public health importance, and rodents play an important role in the ecology of zoonotic transmission. The overall worldwide prevalence of Cryptosporidium spp. in rodents is 19.8% (4589/23142). Twenty-five known Cryptosporidium species and 43 genotypes have been identified, and C. parvum is the dominant species in rodents worldwide. Rodents transfer pathogens to humans by the direct route or by serving as intermediate hosts transmitting the pathogens to other animals. We review the epidemiology, diversity, and transmission routes of Cryptosporidium spp. in rodents. The main purpose of this review is to highlight Cryptosporidium infection in rodents and its transmission, associated risk factors, and prevention; in addition, we assess the public health and ecological significance of Cryptosporidium infections from the One Health perspective.

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Review of the epidemiology and diversity of Cryptosporidium in rodents.

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The overall worldwide prevalence is 19.8% (4589/23142), C. parvum is the dominant species.

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Public health and ecological significance of rodent-borne Cryptosporidium at “One Health” perspective.

Molecular Detection of Cryptosporidium spp. and Enterocytozoon bieneusi Infection in Wild Rodents From Six Provinces in China

Enterocytozoon (E.) bieneusi and Cryptosporidium spp. are the most important zoonotic enteric pathogens associated with diarrheal diseases in animals and humans. However, it is still not known whether E. bieneusi and Cryptosporidium spp. are carried by wild rodents in Shanxi, Guangxi, Zhejiang, Shandong, and Inner Mongolia, China. In the present study, a total of 536 feces samples were collected from Rattus (R.) norvegicus, Mus musculus, Spermophilus (S.) dauricus, and Lasiopodomys brandti in six provinces of China, and were detected by PCR amplification of the SSU rRNA gene of Cryptosporidium spp. and ITS gene of E. bieneusi from June 2017 to November 2020. Among 536 wild rodents, 62 (11.6%) and 18 (3.4%) samples were detected as E. bieneusi- and Cryptosporidium spp.-positive, respectively. Differential prevalence rates of E. bieneusi and Cryptosporidium spp. were found in different regions. E. bieneusi was more prevalent in R. norvegicus, whereas Cryptosporidium spp. was more frequently identified in S. dauricus. Sequence analysis indicated that three known Cryptosporidium species/genotypes (Cryptosporidium viatorum, Cryptosporidium felis, and Cryptosporidium sp. rat genotype II/III) and two uncertain Cryptosporidium species (Cryptosporidium sp. novel1 and Cryptosporidium sp. novel2) were present in the investigated wild rodents. Meanwhile, 5 known E. bieneusi genotypes (XJP-II, EbpC, EbpA, D, and NCF7) and 11 novel E. bieneusi genotypes (ZJR1 to ZJR7, GXM1, HLJC1, HLJC2, and SDR1) were also observed. This is the first report for existence of E. bieneusi and Cryptosporidium spp. in wild rodents in Shanxi, Guangxi, Zhejiang, and Shandong, China. The present study also demonstrated the existence of E. bieneusi and Cryptosporidium spp. in S. dauricus worldwide for the first time. This study not only provided the basic data for the distribution of E. bieneusi and Cryptosporidium genotypes/species, but also expanded the host range of the two parasites. Moreover, the zoonotic E. bieneusi and Cryptosporidium species/genotypes were identified in the present study, suggesting wild rodents are a potential source of human infections.

Cryptosporidium spp. in wild murids (Rodentia) from Corsica, France

Cryptosporidium spp. are worldwide protozoan parasites that can affect to a broad range of vertebrate hosts, including rodents. In the island of Corsica (France), there are no previous data about these protozoa infecting wild rodents. To estimate the distribution and occurrence, a total of 117 wild murine rodents of the species Rattus rattus (84), Mus musculus domesticus (21), Apodemus sylvaticus (11), and Rattus norvegicus (1) were captured in 24 different biotopes. Fecal samples were screened for Cryptosporidium spp. by nested PCR to amplify an 830 bp fragment of the 18S rRNA gene. As general occurrence, 15.4% of the rodents analyzed were positive for Cryptosporidium spp., being detected widely distributed along the island in R. rattus (17.6%) and M. m. domesticus (14.3%). Cryptosporidium viatorum, Cryptosporidium sp. rat genotype II, and Cryptosporidium sp. rat genotype III were successfully identified in R. rattus. The results herein reported provide the first data on Cryptosporidium spp. in wild murine species from a Mediterranean island and constitute the first report of the zoonotic species C. viatorum in R. rattus. Although a low occurrence of Cryptosporidium spp. in murids was obtained and only in one animal the zoonotic species C. viatorum was identified, our results highlight that wild murine rodents from Corsica could mediate in the maintenance and transmission of this protozoan to the environment and other hosts including humans and animals. Further studies are required to better understand the epidemiology of Cryptosporidium spp. in wild rodents from Corsica and their possible public health repercussions.

An Update on Zoonotic Cryptosporidium Species and Genotypes in Humans

The enteric parasite, Cryptosporidium is a major cause of diarrhoeal illness in humans and animals worldwide. No effective therapeutics or vaccines are available and therefore control is dependent on understanding transmission dynamics. The development of molecular detection and typing tools has resulted in the identification of a large number of cryptic species and genotypes and facilitated our understanding of their potential for zoonotic transmission. Of the 44 recognised Cryptosporidium species and >120 genotypes, 19 species, and four genotypes have been reported in humans with C. hominis, C. parvum, C. meleagridis, C. canis and C. felis being the most prevalent. The development of typing tools that are still lacking some zoonotic species and genotypes and more extensive molecular epidemiological studies in countries where the potential for transmission is highest are required to further our understanding of this important zoonotic pathogen. Similarly, whole-genome sequencing (WGS) and amplicon next-generation sequencing (NGS) are important for more accurately tracking transmission and understanding the mechanisms behind host specificity.

An annotated checklist of the eukaryotic parasites of humans, exclusive of fungi and algae

The classification of "parasites" in the medical field is a challenging notion, a group which historically has included all eukaryotes exclusive of fungi that invade and derive resources from the human host. Since antiquity, humans have been identifying and documenting parasitic infections, and this collective catalog of parasitic agents has expanded considerably with technology. As our understanding of species boundaries and the use of molecular tools has evolved, so has our concept of the taxonomy of human parasites. Consequently, new species have been recognized while others have been relegated to synonyms. On the other hand, the decline of expertise in classical parasitology and limited curricula have led to a loss of awareness of many rarely encountered species. Here, we provide a comprehensive checklist of all reported eukaryotic organisms (excluding fungi and allied taxa) parasitizing humans resulting in 274 genus-group taxa and 848 species-group taxa. For each species, or genus where indicated, a concise summary of geographic distribution, natural hosts, route of transmission and site within human host, and vectored pathogens are presented. Ubiquitous, human-adapted species as well as very rare, incidental zoonotic organisms are discussed in this annotated checklist. We also provide a list of 79 excluded genera and species that have been previously reported as human parasites but are not believed to be true human parasites or represent misidentifications or taxonomic changes.

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.

Prevalence and Characterization of Cryptosporidium Species in Tibetan Antelope (Pantholops hodgsonii)

Cryptosporidium is an enteric apicomplexan parasite, which can infect multiple mammals including livestock and wildlife. Tibetan Antelope (Pantholops hodgsonii) is one of the most famous wildlife species, that belongs to the first class protected wild animals in China. However, it has not been known whether Tibetan Antelope is infected with Cryptosporidium so far. The objective of the present study was to determine the prevalence and characterization of Cryptosporidium species infection in Tibetan Antelope and the corresponding species by using molecular biological method. In the current study, a total of 627 fecal samples were randomly collected from Tibetan Antelope in the Tibet Autonomous Region (2019–2020), and were examined by PCR amplification of the small subunit ribosomal RNA (SSU rRNA) gene. Among 627 samples, 19 (3.03%, 19/627) were examined as Cryptosporidium-positive, with 7 (2.33%, 7/300) in females and 12 (3.67%, 12/327) in males. The analysis of SSU rRNA gene sequence suggested that only two Cryptosporidium species, namely, C. xiaoi and C. ubiquitum, were identified in this study. This is the first evidence for an existence of Cryptosporidium in Tibetan Antelope. These findings extend the host range for Cryptosporidium spp. and also provide important data support for prevention and control of Cryptosporidium infection in Tibetan Antelope.

Molecular Identification of Cryptosporidium viatorum Infection in a Patient Suffering from Unusual Cryptosporidiosis in West Bengal, India

In this study, we have collected and screened a total of 268 stool samples from diarrheal patients admitted to an Infectious disease hospital in Kolkata for the presence of Cryptosporidium spp. The initial diagnosis was carried out by microscopy followed by genus specific polymerase chain reaction assays based on 70 kDa heat shock proteins (HSP70). DNA sequencing of the amplified locus has been employed for determination of genetic diversity of the local isolates. Out of 268 collected samples, 12 (4.48%) were positive for Cryptosporidium spp. Sequences analysis of 70 kDa heat shock proteins locus in 12 Cryptosporidium local isolates revealed that 2.24% and 1.86% of samples were showing 99% to 100% identity with C. parvum and C. hominis. Along with the other 2 major species one recently described globally distributed pathogenic species Cryptosporidium viatorum has been identified. The HSP70 locus sequence of the isolate showed 100% similarity with a previously described isolate of C. viatorum (Accession No. JX978274.1, JX978273.1, and JN846706.1) present in GenBank.

Surface Waters and Urban Brown Rats as Potential Sources of Human-Infective Cryptosporidium and Giardia in Vienna, Austria

Cryptosporidium and Giardia are waterborne protozoa that cause intestinal infections in a wide range of warm-blooded animals. Human infections vary from asymptomatic to life-threatening in immunocompromised people, and can cause growth retardation in children. The aim of our study was to assess the prevalence and diversity of Cryptosporidium and Giardia in urban surface water and in brown rats trapped in the center of Vienna, Austria, using molecular methods, and to subsequently identify their source and potential transmission pathways. Out of 15 water samples taken from a side arm of the River Danube, Cryptosporidium and Giardia (oo)cysts were detected in 60% and 73% of them, with concentrations ranging between 0.3-4 oocysts/L and 0.6-96 cysts/L, respectively. Cryptosporidium and Giardia were identified in 13 and 16 out of 50 rats, respectively. Eimeria, a parasite of high veterinary importance, was also identified in seven rats. Parasite co-ocurrence was detected in nine rats. Rat-associated genotypes did not match those found in water, but matched Giardia previously isolated from patients with diarrhea in Austria, bringing up a potential role of rats as sources or reservoirs of zoonotic pathogenic Giardia. Following a One Health approach, molecular typing across potential animal and environmental reservoirs and human cases gives an insight into environmental transmission pathways and therefore helps design efficient surveillance strategies and relevant outbreak responses.

High Diversity of Cryptosporidium Species and Subtypes Identified in Cryptosporidiosis Acquired in Sweden and Abroad

The intestinal protozoan parasite Cryptosporidium is an important cause of diarrheal disease worldwide. The aim of this study was to expand the knowledge on the molecular epidemiology of human cryptosporidiosis in Sweden to better understand transmission patterns and potential zoonotic sources. Cryptosporidium-positive fecal samples were collected between January 2013 and December 2014 from 12 regional clinical microbiology laboratories in Sweden. Species and subtype determination was achieved using small subunit ribosomal RNA and 60 kDa glycoprotein gene analysis. Samples were available for 398 patients, of whom 250 (63%) and 138 (35%) had acquired the infection in Sweden and abroad, respectively. Species identification was successful for 95% (379/398) of the samples, revealing 12 species/genotypes: Cryptosporidium parvum (n = 299), C. hominis (n = 49), C. meleagridis (n = 8), C. cuniculus (n = 5), Cryptosporidium chipmunk genotype I (n = 5), C. felis (n = 4), C. erinacei (n = 2), C. ubiquitum (n = 2), and one each of C. suis, C. viatorum, C. ditrichi, and Cryptosporidium horse genotype. One patient was co-infected with C. parvum and C. hominis. Subtyping was successful for all species/genotypes, except for C. ditrichi, and revealed large diversity, with 29 subtype families (including 4 novel ones: C. parvum IIr, IIs, IIt, and Cryptosporidium horse genotype Vic) and 81 different subtypes. The most common subtype families were IIa (n = 164) and IId (n = 118) for C. parvum and Ib (n = 26) and Ia (n = 12) for C. hominis. Infections caused by the zoonotic C. parvum subtype families IIa and IId dominated both in patients infected in Sweden and abroad, while most C. hominis cases were travel-related. Infections caused by non-hominis and non-parvum species were quite common (8%) and equally represented in cases infected in Sweden and abroad.

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.

Molecular Epidemiology of Human Cryptosporidiosis in Low- and Middle-Income Countries

Cryptosporidiosis is one of the most important causes of moderate to severe diarrhea and diarrhea-related mortality in children under 2 years of age in low- and middle-income countries. In recent decades, genotyping and subtyping tools have been used in epidemiological studies of human cryptosporidiosis. Results of these studies suggest that higher genetic diversity of Cryptosporidium spp. is present in humans in these countries at both species and subtype levels and that anthroponotic transmission plays a major role in human cryptosporidiosis. Cryptosporidium hominis is the most common Cryptosporidium species in humans in almost all the low- and middle-income countries examined, with five subtype families (namely, Ia, Ib, Id, Ie, and If) being commonly found in most regions. In addition, most Cryptosporidium parvum infections in these areas are caused by the anthroponotic IIc subtype family rather than the zoonotic IIa subtype family. There is geographic segregation in Cryptosporidium hominis subtypes, as revealed by multilocus subtyping. Concurrent and sequential infections with different Cryptosporidium species and subtypes are common, as immunity against reinfection and cross protection against different Cryptosporidium species are partial. Differences in clinical presentations have been observed among Cryptosporidium species and C. hominis subtypes. These observations suggest that WASH (water, sanitation, and hygiene)-based interventions should be implemented to prevent and control human cryptosporidiosis in low- and middle-income countries.

Molecular Diversity of Giardia duodenalis, Cryptosporidium spp., and Blastocystis sp. in Symptomatic and Asymptomatic Schoolchildren in Zambézia Province (Mozambique)

Infections by the protist enteroparasites Giardia duodenalis, Cryptosporidium spp., and, to a much lesser extent, Blastocystis sp. are common causes of childhood diarrhoea in low-income countries. This molecular epidemiological study assesses the frequency and molecular diversity of these pathogens in faecal samples from asymptomatic schoolchildren (n = 807) and symptomatic children seeking medical attention (n = 286) in Zambézia province, Mozambique. Detection and molecular characterisation of pathogens was conducted by polymerase chain reaction (PCR)-based methods coupled with Sanger sequencing. Giardia duodenalis was the most prevalent enteric parasite found [41.7%, 95% confidence interval (CI): 38.8‒44.7%], followed by Blastocystis sp. (14.1%, 95% CI: 12.1‒16.3%), and Cryptosporidium spp. (1.6%, 95% CI: 0.9‒2.5%). Sequence analyses revealed the presence of assemblages A (7.0%, 3/43) and B (88.4%, 38/43) within G. duodenalis-positive children. Four Cryptosporidium species were detected, including C. hominis (30.8%; 4/13), C. parvum (30.8%, 4/13), C. felis (30.8%, 4/13), and C. viatorum (7.6%, 1/13). Four Blastocystis subtypes were also identified including ST1 (22.7%; 35/154), ST2 (22.7%; 35/154), ST3 (45.5%; 70/154), and ST4 (9.1%; 14/154). Most of the genotyped samples were from asymptomatic children. This is the first report of C. viatorum and Blastocystis ST4 in Mozambique. Molecular data indicate that anthropic and zoonotic transmission (the latter at an unknown rate) are important spread pathways of diarrhoea-causing pathogens in Mozambique.

Enterocytozoon bieneusi of animals-With an 'Australian twist'

Enterocytozoon bieneusi is a microsporidian microorganism that causes intestinal disease in animals including humans. E. bieneusi is an obligate intracellular pathogen, typically causing severe or chronic diarrhoea, malabsorption and/or wasting. Currently, E. bieneusi is recognised as a fungus, although its exact classification remains contentious. The transmission of E. bieneusi can occur from person to person and/or animals to people. Transmission is usually via the faecal-oral route through E. bieneusi spore-contaminated water, environment or food, or direct contact with infected individuals. Enterocytozoon bieneusi genotypes are usually identified and classified by PCR-based sequencing of the internal transcribed spacer region (ITS) of nuclear ribosomal DNA. To date, ~600 distinct genotypes of E. bieneusi have been recorded in ~170 species of animals, including various orders of mammals and reptiles as well as insects in >40 countries. Moreover, E. bieneusi has also been found in recreational water, irrigation water, and treated raw- and waste-waters. Although many studies have been conducted on the epidemiology of E. bieneusi, prevalence surveys of animals and humans are scant in some countries, such as Australia, and transmission routes of individual genotypes and related risk factors are poorly understood. This article/chapter reviews aspects of the taxonomy, biology and epidemiology of E. bieneusi; the diagnosis, treatment and prevention of microsporidiosis; critically appraises the naming system for E. bieneusi genotypes as well as the phylogenetic relationships of these genotypes; provides new insights into the prevalence and genetic composition of E. bieneusi populations in animals in parts of Australia using molecular epidemiological tools; and proposes some areas for future research in the E. bieneusi/microsporidiosis field.

Identification of Uncommon Cryptosporidium viatorum (a Novel Subtype XVcA2G1c) and Cryptosporidium andersoni as Well as Common Giardia duodenalis Assemblages A and B in Humans in Myanmar

Cryptosporidium and Giardia are two important zoonotic intestinal protozoa responsible for diarrheal diseases in humans and animals worldwide. Feces from infected hosts, water and food contaminated by Cryptosporidium oocysts and Giardia cysts as well as predictors such as poverty have been involved in their transmission. Myanmar is one of the world’s most impoverished countries. To date, there are few epidemiological studies of Cryptosporidium and Giardia in humans. To understand the prevalence and genetic characterization of Cryptosporidium spp. and Giardia duodenalis in humans in Myanmar, a molecular epidemiological investigation of the two protozoa was conducted in four villages of Shan State. 172 fecal specimens were collected from Wa people (one each) and identified for the presence of Cryptosporidium spp. and G. duodenalis by sequence analysis of their respective small subunit ribosomal RNA genes. 1.74% of investigated people were infected with Cryptosporidium spp.—C. andersoni (n = 2) and C. viatorum (n = 1) while 11.05% infected with G. duodenalis—assemblages A (n = 6) and B (n = 13). By sequence analysis of 60-kDa glycoprotein gene, the C. viatorum isolate belonged to a novel subtype XVcA2G1c. DNA preparations positive for G. duodenalis were further subtyped. Five of them were amplified and sequenced successfully: different assemblage B sequences (n = 2) at the triosephosphate isomerase (tpi) locus; sub-assemblage AII sequence (n = 1) and identical assemblage B sequences (n = 2) at the β-giardin (bg) locus. This is the first molecular epidemiological study of Cryptosporidium spp. and G. duodenalis in humans in Myanmar at both genotype and subtype levels. Due to unclear transmission patterns and dynamics of Cryptosporidium spp. and G. duodenalis, future research effort should focus on molecular epidemiological investigations of the two parasites in humans and animals living in close contact in the investigated areas, even in whole Myanmar. These data will aid in making efficient control strategies to intervene with and prevent occurrence of both diseases.

Comparative analyses and structural insights of new class glutathione transferases in Cryptosporidium species

Cryptosporidiosis, caused by protozoan parasites of the genus Cryptosporidium, is estimated to rank as a leading cause in the global burden of neglected zoonotic parasitic diseases. This diarrheal disease is the second leading cause of death in children under 5 years of age. Based on the C. parvum transcriptome data, glutathione transferase (GST) has been suggested as a drug target against this pathogen. GSTs are diverse multifunctional proteins involved in cellular defense and detoxification in organisms and help pathogens to alleviate chemical and environmental stress. In this study, we performed genome-wide data mining, identification, classification and in silico structural analysis of GSTs in fifteen Cryptosporidium species. The study revealed the presence three GSTs in each of the Cryptosporidium species analyzed in the study. Based on the percentage identity and comprehensive comparative phylogenetic analysis, we assigned Cryptosporidium species GSTs to three new GST classes, named Vega (ϑ), Gamma (γ) and Psi (ψ). The study also revealed an atypical thioredoxin-like fold in the C. parvum GST1 of the Vega class, whereas C. parvum GST2 of the Gamma class and C. melagridis GST3 of the Psi class has a typical thioredoxin-like fold in the N-terminal region. This study reports the first comparative analysis of GSTs in Cryptosporidium species.

Cryptosporidium cf. avium in an inland-bearded dragon (Pogona vitticeps) - A case report and review of the literature

Here, we report the first case of Cryptosporidium cf. avium from an inland bearded dragon (Pogona vitticeps) from a wildlife sanctuary in Victoria, Australia. Molecular characterisation was conducted by PCR-coupled sequencing of regions in the small subunit of nuclear RNA (SSU), actin and large subunit of nuclear RNA (LSU) genes. The sequences obtained grouped with those of C. ornithophilus and other C. avium genotypes/variants originating from reptiles or birds. We discuss this case in relation to the current state of knowledge of C. avium of birds and reptiles, considering provenance and environment (agricultural, pet industry, wildlife, zoo or wildlife park) as well as clinical context, and pathological changes associated with cryptosporidiosis in these host animals.

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Characterisation of Cryptosporidium cf. avium from an inland bearded dragon (Pogona vitticeps).

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Molecular differentiation of C. cf. avium from other members of the C. avium clade.

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Pathogenicity of C. cf. avium seems higher than other members of this clade.

Diversity of Cryptosporidium spp. in wild rodents from the Canary Islands, Spain

BACKGROUND

Cryptosporidium spp. are worldwide protozoan parasites which include species that can lead to cryptosporidiosis in humans. Different animal species can serve as reservoirs and sources of dissemination of the disease, such as rodent species due their potential in transmitting zoonotic pathogens to humans and other animals. In the Canary Islands (Spain), Cryptosporidium parvum and Cryptosporidium hominis have been identified in patients with diarrhea. However, the occurrence of Cryptosporidium spp. in possible reservoirs in this archipelago remains unclear. Considering the zoonotic potential of these protozoans, the aim of the present study was to determine the presence of Cryptosporidium spp. in peridomestic wild rodents and the possible role of these mammals as a source of transmission of these protozoans in Canary Islands.

METHODS

A total of 179 rodents belonging to Rattus rattus and Mus musculus domesticus from four Canary Islands, La Palma, El Hierro, Tenerife and Lanzarote, were analyzed. Feces were screened for Cryptosporidium spp. by nested PCR of the 18S ribosomal RNA fragment and the sequences used for phylogenetic analyses.

RESULTS

Cryptosporidium spp. were found widely distributed with an overall prevalence of 12.30% in rodents (13.86% for R. rattus and 10.25% for M. m. domesticus). The overall prevalence by island was 19.60% for Tenerife, 7.14% for La Palma, 5.71% for El Hierro and 0% for Lanzarote. Cryptosporidium tyzzeri, Cryptosporidium meleagridis, Cryptosporidium muris and Cryptosporidium sp. rat genotype I and II/III were successfully identified, in addition to two unidentified Cryptosporidium genotypes.

CONCLUSIONS

This study contributes to the knowledge of the biodiversity and distribution of Cryptosporidium spp. in wild rodents from the Canary Islands, highlighting the presence of three zoonotic species, C. tyzzeri, C. meleagridis and C. muris, being the first detection of these three species in wild rodents in the Canary Islands and the first report of C. meleagridis in R. rattus. Given the results obtained in our study, future studies in non-sampled areas are required to better understand the epidemiology of these protozoans in wild rodents in the archipelago.

Occurrence and genetic characteristics of Cryptosporidium spp. and Enterocytozoon bieneusi in pet red squirrels (Sciurus vulgaris) in China

Cryptosporidium spp. and Enterocytozoon bieneusi are two well-known protist pathogens which can result in diarrhea in humans and animals. To examine the occurrence and genetic characteristics of Cryptosporidium spp. and E. bieneusi in pet red squirrels (Sciurus vulgaris), 314 fecal specimens were collected from red squirrels from four pet shops and owners in Sichuan province, China. Cryptosporidium spp. and E. bieneusi were examined by nested PCR targeting the partial small subunit rRNA (SSU rRNA) gene and the ribosomal internal transcribed spacer (ITS) gene respectively. The infection rates were 8.6% (27/314) for Cryptosporidium spp. and 19.4% (61/314) for E. bieneusi. Five Cryptosporidium species/genotypes were identified by DNA sequence analysis: Cryptosporidium rat genotype II (n = 8), Cryptosporidium ferret genotype (n = 8), Cryptosporidium chipmunk genotype III (n = 5), Cryptosporidium rat genotype I (n = 4), and Cryptosporidium parvum (n = 2). Additionally, a total of five E. bieneusi genotypes were revealed, including three known genotypes (D, SCC-2, and SCC-3) and two novel genotypes (RS01 and RS02). Phylogenetic analysis revealed that genotype D fell into group 1, whereas the remaining genotypes clustered into group 10. To our knowledge, this is the first study to report Cryptosporidium spp. and E. bieneusi in pet red squirrels in China. Moreover, C. parvum and genotype D of E. bieneusi, previously identified in humans, were also found in red squirrels, suggesting that red squirrels may give rise to cryptosporidiosis and microsporidiosis in humans through zoonotic transmissions. These results provide preliminary reference data for monitoring Cryptosporidium spp. and E. bieneusi infections in pet red squirrels and humans.

First report of Cryptosporidium viatorum and Cryptosporidium occultus in humans in China, and of the unique novel C. viatorum subtype XVaA3h

BACKGROUND

Cryptosporidium is a genus of common intestinal protozoa, members of which cause diarrhea in a wide variety of hosts. Previous studies on Cryptosporidium in China have mainly focused on diarrhea sufferers, children, and immunodeficient individuals such as HIV/AIDS patients. However, the epidemiological characteristics of Cryptosporidium in the population in rural areas remain unclear. Herein, we investigated the prevalence of, and risk factors for, Cryptosporidium in rural areas of Binyang County, Guangxi Zhuang Autonomous Region, China, and genetically characterized the Cryptosporidium isolates we obtained.

METHODS

From August to December 2016, two villages in Binyang County, Guangxi, were sampled using a random cluster sampling method. Fresh fecal samples were collected from all eligible residents (residence time > 6 months). Molecular characterization of Cryptosporidium was carried out based on its SSU rRNA, gp60, actin and hsp70 gene sequences. Fisher's exact test were conducted to assess the risk factors for Cryptosporidium infection.

RESULTS

A total of 400 fecal samples were collected from 195 males (48.8%) and 205 females (51.2%). Two samples (0.5%) were positive for Cryptosporidium and were identified as C. viatorum and C. occultus respectively. Moreover, a new C. viatorum subtype XVaA3h was identified based on the sequence of the gp 60 gene.

CONCLUSIONS

To our knowledge, this is the first report of C. viatorum and C. occultus infections in humans in China and of C. viatorum subtype XVaA3h. The findings provide important information on the prevalence of Cryptosporidium in the Chinese population, and expand the range of Cryptosporidium species known to infect people in China.

Identification of Cryptosporidium viatorum XVa subtype family in two wild rat species in China

Background

Cryptosporidium viatorum is a minor Cryptosporidium pathogen in humans. Currently, there is limited information regarding the prevalence and genotypes of C. viatorum in animals in China.

Methods

In this study, 228 faecal samples were collected from two wild rat species (Leopoldamys edwardsi and Berylmys bowersi) in Chongqing Municipality and Guangdong Province, China. These specimens were analyzed for C. viatorum and then subtyped it using PCR and sequence analysis of the small subunit ribosomal RNA (SSU rRNA) and 60-kilodalton glycoprotein (gp60) genes, respectively.

Results

A total of 25 (11.0%) faecal samples were tested positive for C. viatorum by SSU rRNA assay. Of these samples, 4 (3.6%) came from L. edwardsi and 21 (18.0%) from B. bowersi. Of the 25 C. viatorum-positive samples, 17 were successfully amplified at the gp60 gene locus, which represented four subtypes belonging to two subtype families, including XVa (XVaA6, XVaA3g, XVaA3h) and XVc (XVcA2G1). Phylogenetic analysis based on the gp60 amino acid sequences indicated that all of the C. viatorum isolates grouped together, supporting the conclusion that C. viatorum from the wild rats represent two subtype families.

Conclusions

These results indicate an occurrence of C. viatorum XVa subtype family from rats which is genetically identical to those found in humans. Our findings suggest that wild rats may be a potential source of human cryptosporidiosis.

Prevalence and diversity of Cryptosporidium spp. in bamboo rats (Rhizomys sinensis) in South Central China

Cryptosporidium is one of the most prevalent zoonotic parasites and is responsible for the high burden of diarrheal disease across the globe. Rodents are globally overpopulated and are reservoirs for a variety of zoonotic pathogens. Bamboo rats are a common species of rodent that are bred for meat and wool in China. However, the genetic characterization of Cryptosporidium in bamboo rats in China is limited. The aim of this study was to determine the occurrence and genetic characterization of Cryptosporidium in bamboo rats from South Central China. From February2017to February 2018, 435 fecal samples were collected from bamboo rats in 13 farms located in 12 cities in South Central China. All fecal specimens were examined for Cryptosporidium by PCR, and through sequencing the partial small subunit of ribosomal DNA (SSU rRNA). C. parvum-positive samples were further subtyped through analysis of the 60-kDa glycoprotein (gp60) gene sequence. Meanwhile, all the new Cryptosporidium genotypes samples were selected for further sequence characterization at the 70-kDa heat shock protein (HSP70) gene and oocyst wall protein (COWP) gene as well as gp60 gene. Infection rates of 2.1% (9/435) were recorded for Cryptosporidium. Sequence analysis confirmed the presence of two Cryptosporidium species including C. parvum (n = 2), C. occultus (n = 1) and two new Cryptosporidium genotypes termed Cryptosporidium bamboo rat genotype I (n = 5) and Cryptosporidium bamboo rat genotype II (n = 1). Two subtypes of C. parvum were identified including IIdA15G1 and IIpA19 (one each).The discovery of zoonotic Cryptosporidium species/genotypes in bamboo rats suggests they have significant zoonotic potential and pose a threat to human health. The novel sequences discovered provide new insight into genotypic variations in Cryptosporidium in bamboo rats.

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This is the first report of the identification of Cryptosporidium in farmed bamboo rats in South Central China.

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2.1% (9/435) bamboo rats were PCR-positive for Cryptosporidium.

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Cryptosporidium parvum, C. occultus, Cryptosporidium bamboo rats I and II were identified.

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The possibility of transmission of Cryptosporidium between bamboo rats and humans was suggested.

Retrospective analysis of Cryptosporidium species in Western Australian human populations (2015-2018), and emergence of the C. hominis IfA12G1R5 subtype

Cryptosporidium species are a major cause of diarrhoea worldwide. In the present study, a retrospective analysis of 109 microscopically Cryptosporidium-positive faecal specimens from Western Australian patients, collected between 2015 and 2018 was conducted. Sequence analysis of the 18S rRNA and the 60 kDa glycoprotein (gp60) gene loci identified four Cryptosporidium species: C. hominis (86.2%, 94/109), C. parvum (11.0%, 12/109), C. meleagridis (1.8%, 2/109) and C. viatorum (0.9%, 1/109). Subtyping at the gp60 locus identified a total of 11 subtypes including the emergence of the previously rare C. hominis IfA12G1R5 subtype in 2017 as the dominant subtype (46.7%, 21/45). This subtype has also recently emerged as the dominant subtype in the United States but the reasons for its emergence are unknown. This is also the first report of C. viatorum in humans in Australia and a novel subtype (XVaA3g) was identified in the one positive patient.

Cryptosporidium spp. in wild rats (Rattus spp.) from the Hainan Province, China: Molecular detection, species/genotype identification and implications for public health

Wild rats (Rattus spp.) carry many zoonotic pathogens including Cryptosporidium. Due to the close proximity of rats to humans in urban environments, the potential for disease transmission is high. Cryptosporidium is a protozoan parasite which when ingested causes serious human illness. Despite its importance, genetic characterization of Cryptosporidium in wild rats in the Hainan province of China has not been performed. In this study, we analyzed the occurrence and genetics of Cryptosporidium in wild rats from Hainan, China. From December 2017 to October 2018, 150 wild rats were captured and fresh fecal material was collected from intestinal sections. Rat species were identified by PCR-based amplification and analysis of the vertebrate cytochrome b (cytb) gene. Cryptosporidium was examined by PCR amplification of the partial small subunit of ribosomal DNA (SSU rDNA). C. viatorum were subtyped by PCR analysis of the gp60 gene. A total of four rat species were identified including Asian house rats (Rattus tanezumi) (n = 46), brown rats (Rattus norvegicus) (n = 56), Edward's long-tailed rats (Leopoldamys edwardsi) (n = 38) and muridae (Niviventer fulvescens) (n = 10), with Cryptosporidium positive rates of 73.9%, 28.6%, 55.3% and 40.0%, respectively (average infection rate: 50.0%, 75/150. Sequence analysis confirmed the presence of four Cryptosporidium species and two genotypes including C. viatorum (n = 11); C. occultus (n = 2); C. muris (n = 1); and C. erinacei (n = 1); rat genotypes III (n = 13) and IV (n = 47). Three novel subtypes of C. viatorum were identified in 6 of the 11 infected Edward's long-tailed rats: XVcA2G1a (n = 4), XVcA2G1b (n = 1) and XVdA3 (n = 1). The identification of human pathogenic C. viatorum and zoonotic C. occultus, C. muris and C. erinacei, suggested that wild rats infected with Cryptosporidium pose a threat to human health. Taken together, these findings highlight the need to control the rat population in Hainan, China. The need to improve the public awareness of the risk of disease transmission from wild rats to humans is also highlighted.

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This is the first report of the identification of Cryptosporidium in wild rats in Hainan Province, China.

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A total of 75 out of 150 (50.0%) specimens were PCR-positive for Cryptosporidium.

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Six known species or genotypes and three novel subtypes of C. viatorum were identified.

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The possibility of transmission of Cryptosporidium between wild rats and humans was suggested.