Occurrence of Cryptosporidium suis and Cryptosporidium scrofarum on commercial swine farms in the Czech Republic and its associations with age and husbandry practices

Complete sequencing of the Cryptosporidium suis gp60 gene reveals a novel type of tandem repeats-Implications for surveillance

Cryptosporidiosis is an infectious enteric disease caused by species (some of them zoonotic) of the genus Cryptosporidium that in many countries are under surveillance. Typing assays critical to the surveillance of cryptosporidiosis typically involve characterization of Cryptosporidium glycoprotein 60 genes (gp60). Here, we characterized the gp60 of Cryptosporidium suis from two samples-a human and a porcine faecal sample-based on which a preliminary typing scheme was developed. A conspicuous feature of the C. suis gp60 was a novel type of tandem repeats located in the 5' end of the gene and that took up 777/1635 bp (48%) of the gene. The C. suis gp60 lacked the classical poly-serine repeats (TCA/TCG/TCT), which is usually subject to major genetic variation, and the length of the tandem repeat made a typing assay incorporating this region based on Sanger sequencing practically unfeasible. We therefore designed a typing assay based on the post-repeat region only and applied it to C. suis-positive samples from suid hosts from Norway, Denmark, and Spain. We were able to distinguish three different subtypes; XXVa-1, XXVa-2, and XXVa-3. Subtype XXVa-1 had a wider geographic distribution than the other subtypes and was also observed in the human sample. We think that the present data will inform future strategies to develop a C. suis typing assay that could be even more informative by including a greater part of the gene, including the tandem repeat region, e.g., by the use of long-read next-generation sequencing.

Cryptosporidium infections in asymptomatic calves up to 4 months in Poland: a cross-sectional population study

Cattle cryptosporidiosis is noted worldwide with varied frequency of infection prevalence depending on geographical, environmental and husbandry factors. In this study, the prevalence of Cryptosporidium infections in cattle was determined on the basis of molecular results obtained by testing 1601 faecal samples collected from calves up to 4 months of age housed in all Polish provinces from 2014 to 2018. Detection and identification of Cryptosporidium species was performed at the 18 small subunit ribosomal RNA (18S rRNA) locus by conducting PCR-RFLP analysis of the amplified DNA fragments. The prevalence of Cryptosporidium infections in the cattle population was 45.3% (CI 95%: 42.8-47.7; 725/1601). The infected animals were housed on 233/267 (87.3%) of monitored farms with regional prevalence ranging from 27.8 to 62%. The restriction pattern of 18S rRNA amplicons for positive samples was characteristic of C. parvum, C. bovis, C. ryanae, C. andersoni, and unexpectedly also of C. baileyi and C. suis. Infections of C. bovis and C. ryanae prevailed in the studied cattle population relegating C. parvum to third in prevalence. Likewise, mixed infections caused by C. bovis and C. ryanae as well as C. parvum and C. bovis were observed. A relationship between the infecting parasite species and animal breed was found. For instance, C. parvum prevailed in Black and White lowland breed, C. ryanae in Limousine cattle and C. andersoni in dairy animals of mixed dairy breeds. Furthermore, differences in prevalence of particular parasite species between cattle breeds were also shown.

Global prevalence of Cryptosporidium spp. in pigs: a systematic review and meta-analysis

Cryptosporidium spp. are significant opportunistic pathogens causing diarrhoea in humans and animals. Pigs are one of the most important potential hosts for Cryptosporidium. We evaluated the prevalence of Cryptosporidium in pigs globally using published information and a random-effects model. In total, 131 datasets from 36 countries were included in the final quantitative analysis. The global prevalence of Cryptosporidium in pigs was 16.3% (8560/64 809; 95% confidence interval [CI] 15.0–17.6%). The highest prevalence of Cryptosporidium in pigs was 40.8% (478/1271) in Africa. Post-weaned pigs had a significantly higher prevalence (25.8%; 2739/11 824) than pre-weaned, fattening and adult pigs. The prevalence of Cryptosporidium was higher in pigs with no diarrhoea (12.2%; 371/3501) than in pigs that had diarrhoea (8.0%; 348/4874). Seven Cryptosporidium species (Cryptosporidium scrofarum, Cryptosporidium suis, Cryptosporidium parvum, Cryptosporidium muris, Cryptosporidium tyzzeri, Cryptosporidium andersoni and Cryptosporidium struthioni) were detected in pigs globally. The proportion of C. scrofarum was 34.3% (1491/4351); the proportion of C. suis was 31.8% (1385/4351) and the proportion of C. parvum was 2.3% (98/4351). The influence of different geographic factors (latitude, longitude, mean yearly temperature, mean yearly relative humidity and mean yearly precipitation) on the infection rate of Cryptosporidium in pigs was also analysed. The results indicate that C. suis is the dominant species in pre-weaned pigs, while C. scrofarum is the dominant species in fattening and adult pigs. The findings highlight the role of pigs as possible potential hosts of zoonotic cryptosporidiosis and the need for additional studies on the prevalence, transmission and control of Cryptosporidium in pigs.

Prevalence of Swine Gastrointestinal Parasites in Two Free-Range Farms from Nord-West Region of Romania

Parasitic diseases cause significant economic losses in swine, including free-range swine farms, the number of which in Romania has increased in the last decades. The current study aimed to identify the parasitic profile of swine raised on two free-range (low-input) farms from Transylvania. Nine hundred sixty samples collected from weaners, fatteners, and sows were investigated by flotation, centrifugal sedimentation, modified Ziehl-Neelsen stained fecal smear, modified Blagg technique, and oocyst/egg cultures. The number of oocysts (OPG), cysts (CPG), and eggs (EPG) were counted per gram of fecal matter. The examination revealed parasitic infections with Balantidium coli, Eimeria spp., Ascaris suum, Trichuris suis, Oesophagostomum spp., Strongyloides ransomi and Cryptosporidium spp. Prevalence (P) and the mean intensity (MI) of the infections varied according to age, swine category, farm, and season. The overall prevalence in both free-range farms according to the age category was 63.2%—Eimeria spp., 70.31%—B. coli, 9.38%—Oesophagostomum spp., 3.75% S. ransomi, and 18.12% Cryptosporidium spp. in weaners. In fatteners Eimeria spp. revealed a prevalence of 50.93%, B. coli—72.5 %, A. suum—63.13%, T. suis—39.06%, and in sows Eimeria spp.—39.06%, B. coli—62.19%, A. suum—34.06%, Oesophagostomum spp.—27.19%, S. ransomi—1.56% and Cryptosporidium spp.—9.38%. The study revealed statistically significant (p < 0.05) differences between age groups, seasons, and farms for all diagnosed parasites. Further research is required to better understand the epidemiology of these infections in swine from Transylvania.

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.

Diarrhoea-causing enteric protist species in intensively and extensively raised pigs (Sus scrofa domesticus) in Southern Spain. Part I: Prevalence and genetic diversity

Numerous protist species are shared between humans and pigs. Among those, Giardia duodenalis, Cryptosporidium spp. and Balantioides coli have a clear public and animal health significance. For others such as Enterocytozoon bieneusi and Blastocystis sp., their impact on animal health has not been fully established. Little information is currently available on the molecular diversity of these protists in swine populations. To fill this gap, we molecularly assessed G. duodenalis, Cryptosporidium spp., B. coli, Blastocystis sp. and E. bieneusi in faecal samples from Iberian and Large White pigs raised under different (intensive and/or extensive) management systems in southern Spain. A total of 151 extensively raised Iberian pigs, 140 intensively raised Iberian pigs, and 184 intensively raised Large White pigs were investigated. Blastocystis sp. was the agent most prevalently found (47.8%), followed by B. coli (45.5%), G. duodenalis (10.7%), E. bieneusi (6.9%), and Cryptosporidium spp. (5.5%). Blastocystis sp. was significantly less prevalent in intensively raised Iberian pigs (22.9%) than in their extensively raised counterparts (51.0%) or in intensively raised Large White pigs (64.1%). A significantly higher prevalence was found for G. duodenalis, Cryptosporidium spp., and E. bieneusi in Large White pigs than Iberian pigs. Balantioides coli was similarly distributed (40.0-51.1%) in all three investigated swine populations. Sequence analyses revealed the presence of G. duodenalis assemblage E, two Cryptosporidium species (Cryptosporidium scrofarum and Cryptosporidium suis), B. coli (genotypes A and B), Blastocystis sp. (ST1, ST3, and ST5), and E. bieneusi (EbpA, EbpC, EbpD, O, and a novel genotype named PigSpEb2). Novel genotype PigSpEb2 was found alone or in combination with EbpA. Data suggest a widespread exposure to protist enteroparasites in domestic pig populations irrespectively of breed and raising management system. Many of the species/genotypes identified have a zoonotic potential and might represent a public health concern.

Occurrence and genetic diversity of Cryptosporidium spp. in wild foxes, wolves, jackals, and bears in central Europe

Parasites of the genus Cryptosporidium Tyzzer, 1910 are one of the most common protistan parasites of vertebrates. Faecal samples from 179 red foxes (Vulpes vulpes [Linnaeus]), 100 grey wolves (Canis lupus Linnaeus), 11 golden jackals (Canis aureus Linnaeus), and 63 brown bears (Ursus arctos Linnaeus) were collected in the Czech Republic, Poland and Slovakia. Samples were examined for the presence of Cryptosporidium spp. using microscopy and PCR/sequence analysis. Phylogenetic analysis based on the small subunit ribosomal RNA (SSU), actin and 60-kDa glycoprotein (gp60) genes using the maximum likelihood method revealed the presence of Cryptosporidium tyzzeri Ren, Zhao, Zhang, Ning, Jian et al., 2012 (n = 1) and C. andersoni Lindsay, Upton, Owens, Morgan, Mead et Blackburn, 2000 (n = 2) in red foxes, C. canis Fayer, Trout, Xiao, Morgan, Lai et Dubey, 2001 (n = 2) and C. ubiquitum Fayer, Santín et Macarisin, 2010 (n = 2) in grey wolves, and C. galli Pavlásek, 1999 in brown bears (n = 1) and red foxes (n = 1). Subtyping of isolates of C. ubiquitum and C. tyzzeri based on sequence analysis of gp60 showed that they belong to the XIId and IXa families, respectively. The presence of specific DNA of C. tyzzeri, C. andersoni and C. galli, which primarily infect the prey of carnivores, is probably the result of their passage through the gastrointestinal tract of the carnivores. Finding C. ubiquitum XIId in wolves may mean broadening the host spectrum of this subtype, but it remains possible this is the result of infected prey passing through the wolf - in this case deer, which is a common host of this parasite. The dog genotype of C. canis was reported for the first time in wolves.

Molecular characterization of Cryptosporidium spp. from domestic pigs in Argentina

Cryptosporidiosis in pigs is caused by different Cryptosporidium species or genotypes, with C. suis and C. scrofarum considered porcine specific species. There is scarce information on Cryptosporidium infection in pigs in South America. A total of 520 individual faecal samples were obtained from 1, 2, 3 and 4 week old piglets (n = 130 from each age group), from 13 Argentinean intensive pig farms. The diagnosis of species of Cryptosporidium combined microscopy and molecular techniques. Genotyping from samples with Cryptosporidium oocysts at microscopy was performed by genus-specific and species-specific nested PCR targeting 18S rRNA gene fragments, and sequencing. Microscopic analysis detected Cryptosporidium oocysts in 47/520 (9%) faecal samples from 11/13 (85%) farms, with farm infection rates between 0 and 17.5%. Presence of Cryptosporidium oocysts was associated with diarrhea. The proportion of microscopically positive samples was not associated with piglet age. A total of 15/47 (32% of samples with oocyst compatible structures) were positive by genus and species-specific nested PCR. Species-specific PCR and sequencing showed presence of C. suis, C. scrofarum, and both species in 3, 8 and 4 samples, respectively. The proportion of positive samples on each specific PCR was similar between age groups, being C. suis proportion slightly higher in 4 week old piglets. The use of molecular tools allowed the confirmation of C. suis and C. scrofarum infection in Argentinean pigs. Cryptosporidiosis was widely distributed in the main pig husbandry area from Argentina, with a low to moderate intra farm infection rate.

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.

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.

High prevalence of Cryptosporidium infection caused by C. scrofarum and C. suis among pigs in Thailand

Cryptosporidium spp. is an important intestinal protozoan causing diarrhea among both healthy and immunocompromised patients especially those with HIV/AIDS. Cryptosporidium spp. can be transmitted via foodborne, waterborne and person-to-person routes. In addition, several Cryptosporidium species are zoonotic. This study aimed to determine the prevalence of Cryptosporidium infection among pigs raised in both smallholder (<50 heads/farm) and large scale farms (50-500 heads/farm) in Chonburi Province, eastern Thailand using nested PCR amplifying the small subunit of the ribosomal RNA (SSU-rRNA) gene. DNA sequencing was also performed to identify the species of Cryptosporidium. A total of 245 fecal samples were collected from 11 pig farms. The overall prevalence of Cryptosporidium infection was 20.8% (51/245) which were found in both smallholder and small large scale pig farms. The prevalence of Cryptosporidium infection among pigs aged ≤6 months was significantly higher than those aged >6 months (p < .001). Among 51 Cryptosporidium positive samples, Cryptosporidium scrofarum (42/51, 82.4%) and Cryptosporidium suis (9/51, 17.6%) were identified. The prevalence of C. scrofarum infection observed among pigs aged ≤6 months was significantly higher when compared with those aged >6 months (20.7% and 2.1%, respectively, p < .001). The high prevalence of C. scrofarum and C. suis infections among pigs could be a potential source of infection to humans.

Cryptosporidium infections in terrestrial ungulates with focus on livestock: a systematic review and meta-analysis

Background

Cryptosporidium spp. are causative agents of gastrointestinal diseases in a wide variety of vertebrate hosts. Mortality resulting from the disease is low in livestock, although severe cryptosporidiosis has been associated with fatality in young animals.

Methods

The goal of this systematic review and meta-analysis was to review the prevalence and molecular data on Cryptosporidium infections in selected terrestrial domestic and wild ungulates of the families Bovidae (bison, buffalo, cattle, goat, impala, mouflon sheep, sheep, yak), Cervidae (red deer, roe deer, white-tailed deer), Camelidae (alpaca, camel), Suidae (boar, pig), Giraffidae (giraffes) and Equidae (horses). Data collection was carried out using PubMed, Scopus, Science Direct and Cochran databases, with 429 papers being included in this systematic analysis.

Results

The results show that overall 18.9% of ungulates from the investigated species were infected with Cryptosporidium spp. Considering livestock species (cattle, sheep, goats, pigs, horses and buffaloes), analysis revealed higher Cryptosporidium infection prevalence in ungulates of the Cetartiodactyla than in those of the Perissodactyla, with cattle (29%) being the most commonly infected farm animal.

Conclusions

Overall, the investigated domestic ungulates are considered potential sources of Cryptosporidium contamination in the environment. Control measures should be developed to reduce the occurrence of Cryptosporidium infection in these animals. Furthermore, literature on wild populations of the named ungulate species revealed a widespread presence and potential reservoir function of wildlife.

Molecular identification and epidemiological comparison of Cryptosporidium spp. among different pig breeds in Tibet and Henan, China

Background

Cryptosporidium spp. are important zoonotic pathogens infecting a wide range of vertebrate hosts, and causing moderate to severe diarrhea in humans. Cryptosporidium infections are frequently reported in humans and animals worldwide, but little research has been done on local pig breeds such as Tibetan pigs and Yunan Black pigs and imported pig breeds such as Landrace pigs in China. Therefore, a total of 1089 pig fecal samples from four intensive farms in four areas of China, including Tibetan pigs from Gongbujiangda County (n = 180) and Mainling County (n = 434), Tibet, Yunan Black pigs from Sanmenxia, Henan Province (n = 246), and Landrace pigs from Kaifeng, Henan Province (n = 229), and were screened for the presence of Cryptosporidium with microscopy and nested PCR amplification of the small subunit rRNA gene.

Results

The total infection rate of Cryptosporidium in 1089 fecal samples of three different pig breeds was 2.11% (23/1089), and the infection rates of Tibetan pigs, Yunan Black pigs, and Landrace pigs were 0.49% (3/614), 0.41% (1/246), and 8.30% (19/229), respectively. The prevalence of Cryptosporidium infection was significantly higher in weaned piglets (1–2 months) (4.36%, 21/482) than in younger and older age groups (p < 0.01). Sequence analysis of positive samples revealed that there was no mixed infection in our study population, which included 12 cases of C. suis mono-infections (52.17%, 12/23) and 11 cases of C. scrofarum mono-infections (47.83%, 11/23). C. suis was identified in one pre-weaned piglet (< 1 month) and 11 weaned piglets (1–2 months), while C. scrofarum was only detected in 10 weaned piglets (1–2 months) and one finished pig (> 2 months).

Conclusions

This is the first report on the identification of Cryptosporidium spp. in Tibetan pigs, and our findings also elucidate the occurrence and distribution of Cryptosporidium in three different pig breeds in Tibet and Henan, China. More molecular epidemiological studies are required to better clarify the prevalence and public health significance of Cryptosporidium in different pigs.

Review of Cryptosporidium and Giardia in the eastern part of Europe, 2016

This paper reviews the current knowledge and understanding of Cryptosporidium spp. and Giardia spp. in humans, animals and the environment in 10 countries in the eastern part of Europe: Bosnia and Herzegovina, Croatia, Czech Republic, Estonia, Hungary, Latvia, Poland, Romania, Serbia and Slovenia. Methods: Published scientific papers and conference proceedings from the international and local literature, official national health service reports, national databases and doctoral theses in local languages were reviewed to provide an extensive overview on the epidemiology, diagnostics and research on these pathogens, as well as analyse knowledge gaps and areas for further research. Results: Cryptosporidium spp. and Giardia spp. were found to be common in eastern Europe, but the results from different countries are difficult to compare because of variations in reporting practices and detection methodologies used. Conclusion: Upgrading and making the diagnosis/detection procedures more uniform is recommended throughout the region. Public health authorities should actively work towards increasing reporting and standardising reporting practices as these prerequisites for the reported data to be valid and therefore necessary for appropriate control plans.

Occurrence, Molecular Characterization, and Assessment of Zoonotic Risk of Cryptosporidium spp., Giardia duodenalis, and Enterocytozoon bieneusi in Pigs in Henan, Central China

Cryptosporidium spp., Giardia duodenalis, and Enterocytozoon bieneusi are common gastrointestinal pathogens in humans and animals. Little is known about them and the range of species/assemblages/genotypes occurring in domestic pigs in China. Here, we present data on the occurrence and molecular diversity of these pathogens detected in the feces from farms in Henan, central China. Of 897 fecal samples tested, 28 (3.1%), 15 (1.7%), and 408 (45.5%) samples were positive for Cryptosporidium, G. duodenalis, and E. bieneusi, respectively. Cryptosporidium and G. duodenalis were most frequently detected in piglets, while E. bieneusi was markedly more prevalent in fattening pigs. Sequence analysis of SSU rRNA gene revealed that positive Cryptosporidium strains belonged to C. suis (n = 18) and C. scrofarum (n = 10). Giardia duodenalis assemblages E (n = 9), assemblages A (n = 3), and assemblages C (n = 3) were characterized based on the sequence analysis of tpi gene. Thirteen E. bieneusi genotypes comprising four novel (pigHN-I to pigHN-IV) and nine known (EbpC, EbpA, pigEbITS5, LW1, H, CM8, G, CHG19, and CHS5) genotypes were identified by ITS sequence analysis of a large proportion (n = 200) of E. bieneusi-positive samples. EbpC was the most frequent genotype, detected in 60 specimens. All 13 genotypes identified in this study clustered in zoonotic Group 1. The findings indicate that the presence of zoonotic species/assemblages/genotypes of these pathogens poses a threat to public health, suggesting that pigs in Henan province could be a significant source of human infection and water pollution.

Identification of pig-specific Cryptosporidium species in mixed infections using Illumina sequencing technology

Nowadays molecular methods are widely used in epidemiological studies of Cryptosporidium infections in humans and animals. However to gain better understanding of parasite species or genotypes, especially when mixed infections are noticed, highly sensitive tools with adequate resolution power need to be employed. In this article, we report an application of the next generation sequencing method (NGS) for detection and characterisation of Cryptosporidium species concurrently present in pig faeces. A mixture of Cryptosporidium DNA obtained from two faecal samples was amplified at the 18 SSU rRNA gene locus and the resulting amplicons were subsequently used for MiSeq sequencing. Although initial molecular analyses indicated the possible presence of another Cryptosporidium species other than Cryptosporidium scrofarum and Cryptosporidium suis, deep sequencing only confirmed the presence of pig-specific Cryptosporidium.

Rodents as a reservoir of infection caused by multiple zoonotic species/genotypes of C. parvum, C. hominis, C. suis, C. scrofarum, and the first evidence of C. muskrat genotypes I and II of rodents in Europe

Cryptosporidium spp. is an important causative agent of intestinal parasitoses-induced diarrhoea in humans and animals worldwide. Rodents (small mammals), the main reservoir of infections, are globally expanded and overpopulated, which increases the risk of transfer of human and zoonotic pathogens from the genus Cryptosporidium. In this study, Cryptosporidium was detected in wild immunocompetent asymptomatic small mammals. Altogether 262 fecal samples were collected from five areas in Eastern Slovakia from four different rodent species (Myodes glareolus, Apodemus agrarius, Apodemus flavicollis, Rattus norvegicus), eight samples originated from two insectivore species (Sorex araneus, Crocidura suaveolens), and two sample from a carnivore Mustela nivalis. The samples were examined using a method modified in our laboratory, based on the use of specific primers on a small subunit rRNA (18S rRNA) gene for species identification, and amplification of GP60 gene coding 60-kDa glycoprotein for genotype determination. The following species were identified: Cryptosporidium parvum (n=15), genotypes IIaA18G3R1 (n=11; KU311673), IIaA10G1R1 (n=1; KU311670), IIcA5G3a (n=1; KU311669), IIiA10 (n=2; KU311672); Cryptosporidium suis (n=4; KU311671); Cryptosporidium scrofarum (n=28); Cryptosporidium environment sp. (n=12; KU311677); Cryptosporidium muskrat genotype I (n=3; KU311675); Cryptosporidium muskrat genotype II (n=3; KU311676). From one of the rodent, the species Cryptosporidium hominis genotype IbA10G2 (KU311668) was identified for the first time. The results of this study indicate low host specificity of the detected Cryptosporidium species and imply the importance of free-living small mammals in urban and suburban habitats as a potential source of human cryptosporidiosis.

Occurrence, clinical involvement and zoonotic potential of endoparasites infecting Swiss pigs

In order to estimate the diversity, clinical involvement and zoonotic potential of parasites in pigs submitted for diagnosis to the PathoPig project of the Swiss Federal Food Safety and Veterinary Office, faeces (n=125) from suckling piglets (n=39), weaners (n=60) and piglets beginning fattening (n=26) from 74 Swiss farms were examined by 3 coproscopical methods (i.e. sedimentation/zinc chloride-flotation; SAFC and Ziehl-Neelsen staining). Samples microscopically positive for Cryptosporidium were further tested by PCR/sequencing for species assessment. The most frequently detected parasite was Balantidium coli, a facultative pathogenic ciliate with zoonotic potential, in 5.1, 36.7 and 50.0% of suckling, weaners and fatteners and 43.2% of farms; however, no association with disease was observed. Isospora (syn. Cystoisospora) suis infections were detected in 13.3 and 11.1% of suckling piglets with and without diarrhoea, and in 10.0 and 13.3% of weaners and fatteners with diarrhoea, respectively, and were significant associated with emaciation. Cryptosporidium infections were detected in 10.3, 15.0 and 19.2% of sucklings, weaners and fatteners, respectively, and in 18.9% of the farms. Interestingly, two age-related species were identified: C. suis in younger piglets (2 to 6weeks) and C. scrofarum in older ones (6 to 17weeks). None of the pigs infected with C. scrofarum (n=8), but 3 of 4 piglets infected with C. suis (co-infection with I. suis in 2 cases) had diarrhoea. The zoonotic species C. parvum was not detected, nevertheless, sporadic cases of human infection with the porcine-adapted species have been reported. Ascaris suum, Trichuris suis and Strongylida were rarely detected (<4%) in all age categories.

Molecular testing for clinical diagnosis and epidemiological investigations of intestinal parasitic infections

Over the past few decades, nucleic acid-based methods have been developed for the diagnosis of intestinal parasitic infections. Advantages of nucleic acid-based methods are numerous; typically, these include increased sensitivity and specificity and simpler standardization of diagnostic procedures. DNA samples can also be stored and used for genetic characterization and molecular typing, providing a valuable tool for surveys and surveillance studies. A variety of technologies have been applied, and some specific and general pitfalls and limitations have been identified. This review provides an overview of the multitude of methods that have been reported for the detection of intestinal parasites and offers some guidance in applying these methods in the clinical laboratory and in epidemiological studies.

Cryptosporidium and Giardia in Danish organic pig farms: Seasonal and age-related variation in prevalence, infection intensity and species/genotypes

Although pigs are commonly infected with Cryptosporidium spp. and Giardia duodenalis, including potentially zoonotic species or genotypes, little is known about age-related infection levels, seasonal differences and genetic variation in naturally infected pigs raised in organic management systems. Therefore, the current study was conducted to assess seasonal and age-related variations in prevalence and infection intensity of Cryptosporidium and Giardia, evaluate zoonotic potential and uncover correlations between species/genotypes, infection intensity and faecal consistency. Shedding of oocysts and cysts ((oo-)cysts) was monitored at quarterly intervals (September 2011-June 2012) in piglets (n = 152), starter pigs (n = 234), fatteners (n = 230) and sows (n = 240) from three organic farms in Denmark. (oo-)Cysts were quantified by immunofluorescence microscopy; and 56/75 subsamples from Cryptosporidium infected pigs were successfully analysed by PCR amplification and partial sequencing of the small subunit (SSU) 18S rRNA and hsp70genes, while 13/67 Giardia subsamples were successfully analysed by amplification and partial sequencing of the 18S rRNA and the gdh genes. Altogether, Cryptosporidium or Giardia infections were observed in 40.9% (350/856) and 14.0% (120/856) of the pigs, respectively, including 8.2% (70/856) infected with both parasites. Prevalence, intensity of infections and presence of Cryptosporidium species varied significantly between age-groups; 53.3% piglets, 72.2% starter pigs, 40.4% fatteners and 2.9% sows were infected with Cryptosporidium, whereas 2.0% piglets, 27.4% starter pigs, 17.8% fatteners and 5.0% sows were infected with Giardia. The overall prevalence was stable throughout the year, except for dual-infections that were more prevalent in September and December (p < 0.05). The infection intensity was age-related for both parasites, and dual-infected pigs tended to excrete lower levels of oocysts compared to pigs harbouring only Cryptosporidium. Likewise, pigs infected with Cryptosporidium scrofarum excreted fewer oocysts (mean CPG: 54,848 ± 194,508CI: 9085-118,781) compared to pigs infected with Cryptosporidium suis (mean OPG: 351,035 ± 351,035CI: 67,953-634,117). No correlation between faecal consistency and (oo-)cyst excretion levels was observed. Of the successfully genotyped isolates, 38/56 (67.9%) were C. scrofarum and 18/56 (32.1%) were C. suis, while the livestock specific G. duodenalis Assemblage E was detected in 11/13 (84.6%) isolates and the potentially zoonotic Assemblage A was identified in 2/13 (15.4%) isolates. Piglets exclusively hosted C. suis, with one exception, while starter pigs and fatteners predominantly hosted C. scrofarum. As organic pigs are partly reared outdoors, environmental contamination with Cryptosporidium and Giardia is inevitable. Nevertheless, the present data indicate that the potential public health risk associated with both of these parasites in Danish organic pig production seems to be negligible.

Molecular characterisation of Cryptosporidium (Apicomplexa) in children and cattle in Romania

To investigate the transmission of species of Cryptosporidium Tyzzer, 1907 in Timis County, Romania, 48 isolates of Cryptosporidium coccidia from 11 children, 29 calves and eight pigs were characterised by molecular analysis of two loci (SSU rRNA and 60-kDa glycoprotein gene). Overall, 22 isolates were amplified and sequence analyses revealed that all isolates were Cryptosporidium parvum Tyzzer, 1912. Two subtype families were identified, IIa and IId. Subtype IIdA22G1 (n = 4) was the single C. parvum subtype found in children. Subtypes found in calves included IIdA27G1 (n = 8), a novel subtype, IIdA25G1 (n = 5), IIdA22G1 (n = 2), IIdA21G1a (n = 1), and IIaA16G1R1 (n = 1). Subtype IIdA26G1 was found in a pig. These results were significantly different from previous Romanian reports, as the five subtypes of family IId identified in this study were never identified previously in this country. Thus, cattle may be a source of Cryptosporidium infections for humans and the transmission dynamics of C. parvum in Romania is more complex than previously believed.

Occurrence, source, and human infection potential of Cryptosporidium and Enterocytozoon bieneusi in drinking source water in Shanghai, China, during a pig carcass disposal incident

In March 2013, thousands of domestic pig carcasses were found floating in the Huangpu River, a drinking source water in Shanghai, China. To investigate the impact of the pig carcass incident on microbial water quality, 178 river water samples were collected from the upper Huangpu River from March 2013 to March 2014. Samples were concentrated by calcium carbonate flocculation and examined for host-adapted Cryptosporidium and Enterocytozoon bieneusi by ploymerase chain reaction (PCR). Positive PCR products were sequenced to determine Cryptosporidium species and E. bieneusi genotypes. A total of 67 (37.6%) and 56 (31.5%) samples were PCR-positive for Cryptosporidium and E. bieneusi, respectively. The occurrence rates of Cryptosporidium and E. bieneusi in March 2013 (83.3%; 41.7%) and May 2013 (73.5%; 44.1%) were significantly higher than rates in later sampling times. Among the 13 Cryptosporidium species/genotypes identified, C. andersoni and C. suis were the most common species, being found in 38 and 27 samples, respectively. Seventeen E. bieneusi genotypes were found, belonging to 11 established genotypes (EbpC, EbpA, D, CS-8, PtEb IX, Peru 8, Peru 11, PigEBITS4, EbpB, G, O) and six new ones (RWSH1 to RWSH6), most of which belonged to pig-adapted Groups 1d and 1e. EbpC was the most common genotype, being found in 37 samples. The distribution of Cryptosporidium species and E. bieneusi genotypes suggest that dead pigs contributed significantly to Cryptosporidium and E. bieneusi contamination in the Huangpu River. Although most Cryptosporidium species found in river water were not major human pathogens, the majority of E. bieneusi genotypes detected were endemic in China. Data from this study should be useful in the development of strategies in addressing future contamination events in drinking water supplies.

Cryptosporidiumspecies in humans and animals: current understanding and research needs

Cryptosporidiumis increasingly recognized as one of the major causes of moderate to severe diarrhoea in developing countries. With treatment options limited, control relies on knowledge of the biology and transmission of the members of the genus responsible for disease. Currently, 26 species are recognized as valid on the basis of morphological, biological and molecular data. Of the nearly 20Cryptosporidiumspecies and genotypes that have been reported in humans,Cryptosporidium hominisandCryptosporidium parvumare responsible for the majority of infections. Livestock, particularly cattle, are one of the most important reservoirs of zoonotic infections. Domesticated and wild animals can each be infected with severalCryptosporidiumspecies or genotypes that have only a narrow host range and therefore have no major public health significance. Recent advances in next-generation sequencing techniques will significantly improve our understanding of the taxonomy and transmission ofCryptosporidiumspecies, and the investigation of outbreaks and monitoring of emerging and virulent subtypes. Important research gaps remain including a lack of subtyping tools for manyCryptosporidiumspecies of public and veterinary health importance, and poor understanding of the genetic determinants of host specificity ofCryptosporidiumspecies and impact of climate change on the transmission ofCryptosporidium.

Validation of fragment analysis by capillary electrophoresis to resolve mixed infections by Cryptosporidium parvum subpopulations

The potential of capillary electrophoresis (CE)-based DNA fragment analysis to identify mixed infections by Cryptosporidium parvum subpopulations was validated using high-resolution slab-gel electrophoresis. A selection of genomic DNA samples from C. parvum isolates with CE electropherogram profiles indicative of two concurrent alleles at one or more of six mini and microsatellite loci (MSB, MS5, ML1, ML2, TP14, 5B12) were analysed. These loci were PCR-amplified and products separated on precast Spreadex EL600 slab gels. ML1 PCR products differing by as little as 3 bp in length were visible after Spreadex gel electrophoresis and fragments were clearly separated for all but the ML2 and 5B12 loci, which generated stutter bands. No stuttering was seen for the remaining markers, having three or more nucleotide motifs in the repeat region. For each sample, the two bands of interest were excised separately, DNA extracted and re-amplified by PCR. Sequencing of these PCR products revealed the expected sequences for both alleles at most samples, except for the longest ML2 and 5B12 alleles which generated indeterminate sequences. Two novel MS5 alleles were successfully sequenced after PCR re-amplification. These findings demonstrate the utility of high-resolution Spreadex gels for analysing the polymorphism of satellite markers of Cryptosporidium isolates and support the validity of CE as a reliable and sensitive tool for detecting mixed Cryptosporidium subpopulations in a single-host infection.

Cryptosporidium suis and Cryptosporidium scrofarum in Eurasian wild boars (Sus scrofa) in Central Europe

From 2011 to 2012, to identify Cryptosporidium spp. occurrence in Eurasian wild boars (Sus scrofa) 29 randomly selected localities (both forest areas and enclosures) across the Central European countries of Austria, the Czech Republic, Poland, and the Slovak Republic were investigated. Cryptosporidium oocysts were microscopicaly detected in 11 out of 460 faecal samples examined using aniline-carbol-methyl violet staining. Sixty-one Cryptosporidium infections, including the 11 infections that were detected by microscopy, were detected using genus- or species-specific nested PCR amplification of SSU rDNA. This represents a 5.5 fold greater sensitivity for PCR relative to microscopy. Combining genus- and species-specific PCR tools significantly changes the perspective on the occurrence of Cryptosporidium spp. in wild boars. While RFLP and direct sequencing of genus specific PCR-amplified products revealed 56 C. suis (20) and C. scrofarum (36) monoinfections and only 5 mixed infections of these species, species-specific molecular tools showed 44 monoinfections and 17 mixed infections with these species. PCR analysis of the gp60 gene did not reveal any other Cryptosporidium infections. Similar to domestic pigs, C. scrofarum was detected as a dominant species infecting adult Eurasian wild boars (Sus scrofa). Cryptosporidium infected wild boars did not show signs of clinical disease. This report is perhaps the most comprehensive survey of cryptosporidial infection in wild boars.

Equine cryptosporidial infection associated with Cryptosporidium hedgehog genotype in Algeria

Faecal samples from two horse farms in Algeria keeping Arabian, Thoroughbred, and Barb horses were examined for the presence of Cryptosporidium in 2010-2011. A total of 138 faecal samples (16 from a farm keeping 50 animals and 122 from a farm with 267 horses) were screened for Cryptosporidium spp. infection using molecular tools. DNA was extracted from all samples. Nested PCR was performed to amplify fragments of the SSU rDNA and gp60 genes to determine the presence of Cryptosporidium species and genotypes. Sequence analyses of SSU and gp60 genes revealed four animals positive for the presence of subtype XIIIa A22R9 of the Cryptosporidium hedgehog genotype. The infections were not associated with diarrhoea. This study reports, for the first time, the occurrence of Cryptosporidium in Algeria and the first occurrence of the hedgehog genotype in horses. These findings support the potential role of infected horses in sylvatic-domestic transmission of Cryptosporidium.

Looking for Cryptosporidium: the application of advances in detection and diagnosis

The protozoan Cryptosporidium is a major public and animal health concern. Young children, immunocompromised people, and pre-weaning animals are especially vulnerable, but treatment options are limited and there is no vaccine. A laboratory diagnosis is required to confirm cases of cryptosporidiosis, and species and genotype determination is essential in distinguishing human from non-human sources, understanding transmission, and strengthening the epidemiological evidence for causative links in outbreaks. However, testing is not consistent, as demonstrated by investigation of a significant increase in cases in some European countries during 2012. Many methods employed are laborious and time-consuming; recent advances, translated into diagnostic assays, can improve testing and facilitate typing to support clinical and environmental investigations.