Human cryptosporidiosis diagnosed in Western Australia: a mixed infection with Cryptosporidium meleagridis, the Cryptosporidium mink genotype, and an unknown Cryptosporidium species

WHOLE GENOME TARGETED ENRICHMENT AND SEQUENCING OF HUMAN-INFECTING CRYPTOSPORIDIUM spp

Cryptosporidium spp. are protozoan parasites that cause severe illness in vulnerable human populations. Obtaining pure Cryptosporidium DNA from clinical and environmental samples is challenging because the oocysts shed in contaminated feces are limited in quantity, difficult to purify efficiently, may derive from multiple species, and yield limited DNA (<40 fg/oocyst). Here, we develop and validate a set of 100,000 RNA baits (CryptoCap_100k) based on six human-infecting Cryptosporidium spp. (C. cuniculus, C. hominis, C. meleagridis, C. parvum, C. tyzzeri, and C. viatorum) to enrich Cryptosporidium spp. DNA from a wide array of samples. We demonstrate that CryptoCap_100k increases the percentage of reads mapping to target Cryptosporidium references in a wide variety of scenarios, increasing the depth and breadth of genome coverage, facilitating increased accuracy of detecting and analyzing species within a given sample, while simultaneously decreasing costs, thereby opening new opportunities to understand the complex biology of these important pathogens.

WHOLE GENOME TARGETED ENRICHMENT AND SEQUENCING OF HUMAN-INFECTING CRYPTOSPORIDIUM spp

Cryptosporidium spp. are protozoan parasites that cause severe illness in vulnerable human populations. Obtaining pure Cryptosporidium DNA from clinical and environmental samples is challenging because the oocysts shed in contaminated feces are limited in quantity, difficult to purify efficiently, may derive from multiple species, and yield limited DNA (<40 fg/oocyst). Here, we develop and validate a set of 100,000 RNA baits (CryptoCap_100k) based on six human-infecting Cryptosporidium spp. ( C. cuniculus , C. hominis , C. meleagridis , C. parvum , C. tyzzeri , and C. viatorum ) to enrich Cryptosporidium spp. DNA from a wide array of samples. We demonstrate that CryptoCap_100k increases the percentage of reads mapping to target Cryptosporidium references in a wide variety of scenarios, increasing the depth and breadth of genome coverage, facilitating increased accuracy of detecting and analyzing species within a given sample, while simultaneously decreasing costs, thereby opening new opportunities to understand the complex biology of these important pathogens.

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.

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.

Different distribution of Cryptosporidium species between horses and donkeys

Few studies have been conducted on the distribution of Cryptosporidium species and subtypes in equine animals. In this study, 878 stool specimens were collected during 2015-2019 from 551 donkeys and 327 horses in Shandong, Xinjiang, and Inner Mongolia, China and screened for Cryptosporidium spp. by PCR analysis of the small subunit rRNA gene. The Cryptosporidium species presented were identified by sequence analysis of the PCR products and subtyped by sequence analysis of the 60 kDa glycoprotein gene. The infection rates of Cryptosporidium spp. in horses and donkeys were 3.1% (10/327) and 14.5% (80/551), respectively. Four Cryptosporidium species/genotypes were identified, including C. parvum (in 5 horses), C. hominis (in 75 donkeys), Cryptosporidium horse genotype (in 5 horses and 4 donkeys) and a new genotype that is genetically related to Cryptosporidium mink genotype (in 1 donkey). All C. parvum isolates were subtyped as IIdA19G1, C. hominis as IkA16G1, and horse genotype as VIaA15G4. Data from this study indicate that four Cryptosporidium species are circulating in horses and donkeys in the study areas, with C. hominis as a dominant Cryptosporidium species in only donkeys. Attention should be paid to reduce the transmission of these zoonotic Cryptosporidium spp.

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.

Molecular investigation of Cryptosporidium in farmed chickens in Hubei Province, China, identifies 'zoonotic' subtypes of C. meleagridis

BACKGROUND

Cryptosporidium is a key genus of parasitic protists that infect humans and other vertebrates (mammals and birds). Birds are typically infected with C. avium, C. baileyi, C. galli and/or C. meleagridis, the latter of which is recognised as being zoonotic. Stimulated by the previous finding of C. meleagridis subtypes IIIbA21G1R1, IIIbA22G1R1 and IIIbA26G1R1 in diarrhoeic children in Wuhan city and environs in Hubei Province, China, we performed a molecular epidemiological survey to explore whether these or similar subtypes might occur in farmed chickens in this province.

METHODS

PCR-coupled sequencing analyses of regions in the small subunit (SSU) of the nuclear ribosomal RNA and 60 kDa glycoprotein (gp60) genes were utilised to characterise Cryptosporidium in faecal samples from chickens (n = 471) from 14 farms from six distinct regions in Hubei Province.

RESULTS

Cryptosporidium baileyi (33/471; 7.0%) and C. meleagridis (15/471; 3.2%) were identified in chickens on eight farms in five of the six distinct geographical regions. No significant age-associated difference in the prevalence of C. baileyi was evident, whereas the prevalence of C. meleagridis was significantly higher in younger (≤ 4 months) than in older chickens (> 4 months). For C. meleagridis, two subtype families, IIIb and IIIe, were defined; some of the subtypes (i.e. IIIbA26G1R1b and IIIbA22G1R1c) characterised here matched those identified previously in diarrhoeic children in Wuhan.

CONCLUSIONS

This is the first molecular study reporting the genetic identity and prevalence of C. baileyi and C. meleagridis in chickens in Hubei. The findings suggest that C. meleagridis subtypes IIIbA26G1R1b and IIIbA22G1R1c are cross-transmissible between chickens and humans, raising awareness about the significance of birds as potential reservoirs of zoonotic variants of Cryptosporidium. Future studies might focus on investigating the prevalence of 'zoonotic' subtypes of Cryptosporidium meleagridis in various species of wild and domesticated birds, and on comparing them with those found in humans in China and other countries.

Cryptosporidium species and subtypes in animals inhabiting drinking water catchments in three states across Australia

As part of long-term monitoring of Cryptosporidium in water catchments serving Western Australia, New South Wales (Sydney) and Queensland, Australia, we characterised Cryptosporidium in a total of 5774 faecal samples from 17 known host species and 7 unknown bird samples, in 11 water catchment areas over a period of 30 months (July 2013 to December 2015). All samples were initially screened for Cryptosporidium spp. at the 18S rRNA locus using a quantitative PCR (qPCR). Positives samples were then typed by sequence analysis of an 825 bp fragment of the 18S gene and subtyped at the glycoprotein 60 (gp60) locus (832 bp). The overall prevalence of Cryptosporidium across the various hosts sampled was 18.3% (1054/5774; 95% CI, 17.3-19.3). Of these, 873 samples produced clean Sanger sequencing chromatograms, and the remaining 181 samples, which initially produced chromatograms suggesting the presence of multiple different sequences, were re-analysed by Next- Generation Sequencing (NGS) to resolve the presence of Cryptosporidium and the species composition of potential mixed infections. The overall prevalence of confirmed mixed infection was 1.7% (98/5774), and in the remaining 83 samples, NGS only detected one species of Cryptosporidium. Of the 17 Cryptosporidium species and four genotypes detected (Sanger sequencing combined with NGS), 13 are capable of infecting humans; C. parvum, C. hominis, C. ubiquitum, C. cuniculus, C. meleagridis, C. canis, C. felis, C. muris, C. suis, C. scrofarum, C. bovis, C. erinacei and C. fayeri. Oocyst numbers per gram of faeces (g^-1) were also determined using qPCR, with medians varying from 6021-61,064 across the three states. The significant findings were the detection of C. hominis in cattle and kangaroo faeces and the high prevalence of C. parvum in cattle. In addition, two novel C. fayeri subtypes (IVaA11G3T1 and IVgA10G1T1R1) and one novel C. meleagridis subtype (IIIeA18G2R1) were identified. This is also the first report of C. erinacei in Australia. Future work to monitor the prevalence of Cryptosporidium species and subtypes in animals in these catchments is warranted.

Molecular detection and genetic characterizations of Cryptosporidium spp. in farmed foxes, minks, and raccoon dogs in northeastern China

Cryptosporidium spp. are common intestinal protozoa causing diarrhea in humans and a variety of animal species. With the recent development of fur industry, a large number of fur animals are farmed worldwide, especially in China. The existence of identical Cryptosporidium species/genotypes in humans and fur animals suggests zoonotic potential. In order to assess the presence of zoonotic Cryptosporidium species and/or genotypes in farmed fur animals, 367 fecal specimens were collected from 213 foxes, 114 minks and 40 raccoon dogs farmed in Heilongjiang, Jilin, and Liaoning provinces, northeastern China, during the period from June 2014 to October 2016. By PCR and sequencing of the partial small subunit (SSU) rRNA gene of Cryptosporidium, 20 of 367 (5.4%) animal samples were found to be infected, corresponding to 12 of 213 fox samples (5.6%) and 8 of 114 mink samples (7.0%) screened. Three Cryptosporidium species/genotypes were identified: C. canis (n = 17), C. meleagridis (n = 1) and Cryptosporidium mink genotype (n = 2). Two host-adapted C. canis types (C. canis dog genotype and C. canis fox genotype) were found. By PCR and sequencing of the partial 60 kDa glycoprotein (gp60) encoding gene, one mink genotype isolate was successfully subtyped as XcA5G1R1. The three Cryptosporidium species/genotypes identified in this study have been previously reported in humans suggesting that fur animals infected with Cryptosporidium spp. may pose a risk of zoonotic transmission of cryptosporidiosis, especially for the people working in fur animal farming and processing industry.

Foodborne cryptosporidiosis

Foodborne illness, the majority of which is caused by enteric infectious agents, costs global economies billions of dollars each year. The protozoan parasite Cryptosporidium is particularly suited to foodborne transmission and is responsible for >8 million cases of foodborne illness annually. Procedures have been developed for sensitive detection of Cryptosporidium oocysts on fresh produce and molecular diagnostic assays have been widely used in case linkages and infection source tracking, especially during outbreak investigations. The integrated use of advanced diagnostic techniques with conventional epidemiological studies is essential to improve our understanding of the occurrence, source and epidemiology of foodborne cryptosporidiosis. The implementation of food safety management tools such as Good Hygienic Practices (GHP), Hazard Analysis and Critical Control Points (HACCP), and Quantitative Microbial Risk Assessment (QMRA) in industrialised nations and Water, Sanitation, and Hygiene (WASH) in developing countries is central for prevention and control and foodborne cryptosporidiosis in the future.

Cryptosporidium in humans and animals-a one health approach to prophylaxis

Cryptosporidium is a major cause of moderate-to-severe diarrhoea in humans worldwide, second only to rotavirus. Due to the wide host range and environmental persistence of this parasite, cryptosporidiosis can be zoonotic and associated with foodborne and waterborne outbreaks. Currently, 31 species are recognized as valid, and of these, Cryptosporidium hominis and Cryptosporidium parvum are responsible for the majority of infections in humans. The immune status of the host, both innate and adaptive immunity, has a major impact on the severity of the disease and its prognosis. Immunocompetent individuals typically experience self-limiting diarrhoea and transient gastroenteritis lasting up to 2 weeks and recover without treatment, suggesting an efficient host antiparasite immune response. Immunocompromised individuals can suffer from intractable diarrhoea, which can be fatal. Effective drug treatments and vaccines are not yet available. As a result of this, the close cooperation and interaction between veterinarians, health physicians, environmental managers and public health operators is essential to properly control this disease. This review focuses on a One Health approach to prophylaxis, including the importance of understanding transmission routes for zoonotic Cryptosporidium species, improved sanitation and better risk management, improved detection, diagnosis and treatment and the prospect of an effective anticryptosporidial vaccine.

Molecular epidemiologic tools for waterborne pathogens Cryptosporidium spp. and Giardia duodenalis

Molecular diagnostic tools have played an important role in improving our understanding of the transmission of Cryptosporidium spp. and Giardia duodenalis, which are two of the most important waterborne parasites in industrialized nations. Genotyping tools are frequently used in the identification of host-adapted Cryptosporidium species and G. duodenalis assemblages, allowing the assessment of infection sources in humans and public health potential of parasites found in animals and the environment. In contrast, subtyping tools are more often used in case linkages, advanced tracking of infections sources, and assessment of disease burdens attributable to anthroponotic and zoonotic transmission. More recently, multilocus typing tools have been developed for population genetic characterizations of transmission dynamics and delineation of mechanisms for the emergence of virulent subtypes. With the recent development in next generation sequencing techniques, whole genome sequencing and comparative genomic analysis are increasingly used in characterizing Cryptosporidium spp. and G. duodenalis. The use of these tools in epidemiologic studies has identified significant differences in the transmission of Cryptosporidium spp. in humans between developing countries and industrialized nations, especially the role of zoonotic transmission in human infection. Geographic differences are also present in the distribution of G. duodenalis assemblages A and B in humans. In contrast, there is little evidence for widespread zoonotic transmission of giardiasis in both developing and industrialized countries. Differences in virulence have been identified among Cryptosporidium species and subtypes, and possibly between G. duodenalis assemblages A and B, and genetic recombination has been identified as one mechanism for the emergence of virulent C. hominis subtypes. These recent advances are providing insight into the epidemiology of waterborne protozoan parasites in both developing and developed countries.

Molecular Analysis of the Enteric Protozoa Associated with Acute Diarrhea in Hospitalized Children

Pediatric diarrhea is a common cause of death among children under 5 years of age. In the current study, we investigated the frequency of intestinal parasites among 580 pediatric patients with chronic diarrhea. Parasitic protozoa (all species combined) were detected by molecular tools in 22.9% of the children and the most common parasite was Cryptosporidium spp. (15.1%). Blastocystis hominis was detected in 4.7%, Dientamoeba fragilis in 4%, Giardia duodenalis in 1.7%, and Entamoeba histolytica in 0.17%. Protozoan infections were observed among all regional groups, but prevalence was highest among Qatari subjects and during the winter season. Typing of Cryptosporidium spp. revealed a predominance of Cryptosporidium parvum in 92% of cases with mostly the IIdA20G1 subtype. Subtypes IIdA19G2, IIdA18G2, IIdA18G1, IIdA17G1, IIdA16G1, and IIdA14G1 were also detected. For Cryptosporidium hominis, IbA10G2 and IbA9G3 subtypes were identified. This study provides supplementary information for implementing prevention and control strategies to reduce the burden of these pediatric protozoan infections. Further analyses are required to better understand the local epidemiology and transmission of Cryptosporidium spp. in Qatar.

Molecular diagnosis and characterization of Cryptosporidium spp. in turkeys and chickens in Germany reveals evidence for previously undetected parasite species

A total of 256 fecal specimens were randomly collected from farmed poultry in Germany and screened for the presence of Cryptosporidium spp. by PCR and further characterized by direct automated DNA sequencing. Using a nested PCR amplifying approximately 830 bp 18S rDNA fragment, 7.03% (n = 18) of the samples were Cryptosporidium-positive. In detail, Cryptosporidium was detected in 9.3% (8/86) of turkeys, 5.7% (9/158) of broilers and 8.3% (1/12) of layers. After DNA sequencing, Cryptosporidium parvum the most frequently observed species was identified in 5.1% (13/256) of all poultry species, including 8.1% (7/86) of turkeys, 3.2% (5/158) of broilers and 8.3% (1/12) of layers. Cryptosporidium baileyi was detected in 1.3% (2/256) of the broilers only. Three novel unclassified Cryptosporidium spp. were detected in 1.2% (1/86) of turkeys and 1.3% (2/158) of broilers. The infection rate was high in 13-20 week old turkeys, 1-6 weeks old broilers and >20 weeks old layers but differences between age groups were not significant. This is the first study in Germany uses molecular methods for the detection of Cryptosporidium in poultry. The results indicate that Cryptosporidium parasites are common among broilers and turkeys in Germany. Considering the large size of the poultry industry, the large amount of poultry meat that is consumed and the fact that C. parvum is also the most common Cryptosporidium parasite in humans, poultry might also be a source of human infections.

Zoonotic Cryptosporidium Species in Animals Inhabiting Sydney Water Catchments

Cryptosporidium is one of the most common zoonotic waterborne parasitic diseases worldwide and represents a major public health concern of water utilities in developed nations. As animals in catchments can shed human-infectious Cryptosporidium oocysts, determining the potential role of animals in dissemination of zoonotic Cryptosporidium to drinking water sources is crucial. In the present study, a total of 952 animal faecal samples from four dominant species (kangaroos, rabbits, cattle and sheep) inhabiting Sydney's drinking water catchments were screened for the presence of Cryptosporidium using a quantitative PCR (qPCR) and positives sequenced at multiple loci. Cryptosporidium species were detected in 3.6% (21/576) of kangaroos, 7.0% (10/142) of cattle, 2.3% (3/128) of sheep and 13.2% (14/106) of rabbit samples screened. Sequence analysis of a region of the 18S rRNA locus identified C. macropodum and C. hominis in 4 and 17 isolates from kangaroos respectively, C. hominis and C. parvum in 6 and 4 isolates respectively each from cattle, C. ubiquitum in 3 isolates from sheep and C. cuniculus in 14 isolates from rabbits. All the Cryptosporidium species identified were zoonotic species with the exception of C. macropodum. Subtyping using the 5' half of gp60 identified C. hominis IbA10G2 (n = 12) and IdA15G1 (n = 2) in kangaroo faecal samples; C. hominis IbA10G2 (n = 4) and C. parvum IIaA18G3R1 (n = 4) in cattle faecal samples, C. ubiquitum subtype XIIa (n = 1) in sheep and C. cuniculus VbA23 (n = 9) in rabbits. Additional analysis of a subset of samples using primers targeting conserved regions of the MIC1 gene and the 3' end of gp60 suggests that the C. hominis detected in these animals represent substantial variants that failed to amplify as expected. The significance of this finding requires further investigation but might be reflective of the ability of this C. hominis variant to infect animals. The finding of zoonotic Cryptosporidium species in these animals may have important implications for the management of drinking water catchments to minimize risk to public health.

Cryptosporidium and Giardia taxa in faecal samples from animals in catchments supplying the city of Melbourne with drinking water (2011 to 2015)

BACKGROUND

In a long-term program to monitor pathogens in water catchments serving the City of Melbourne in the State of Victoria in Australia, we detected and genetically characterised Cryptosporidium and Giardia in faecal samples from various animals in nine water reservoir areas over a period of 4 years (July 2011 to November 2015).

METHODS

This work was conducted using PCR-based single-strand conformation polymorphism (SSCP) and phylogenetic analyses of portions of the small subunit of ribosomal RNA (SSU) and 60 kDa glycoprotein (gp60) genes for Cryptosporidium, and triose-phosphate isomerase (tpi) gene for Giardia.

RESULTS

The prevalence of Cryptosporidium was 1.62 % (69 of 4,256 samples); 25 distinct sequence types were defined for pSSU, and six for gp60 which represented C. hominis (genotype Ib - subgenotype IbA10G2), C. cuniculus (genotype Vb - subgenotypes VbA26, and VbA25), and C. canis, C. fayeri, C. macropodum, C. parvum, C. ryanae, Cryptosporidium sp. "duck" genotype, C. suis and C. ubiquitum as well as 12 novel SSU sequence types. The prevalence of Giardia was 0.31 % (13 of 4,256 samples); all three distinct tpi sequence types defined represented assemblage A of G. duodenalis.

CONCLUSIONS

Of the 34 sequence types (genotypes) characterized here, five and one have been recorded previously for Cryptosporidium and Giardia, respectively, from humans. Novel genotypes of Cryptosporidium and Giardia were recorded for SSU (n = 12), gp60 (n = 4) and tpi (n = 1); the zoonotic potential of these novel genotypes is presently unknown. Future work will continue to monitor the prevalence of Cryptosporidium and Giardia genotypes in animals in these catchments, and expand investigations to humans. Nucleotide sequences reported in this paper are available in the GenBank database under accession nos. KU531647-KU531718.

First report of Cryptosporidium canis in foxes (Vulpes vulpes) and raccoon dogs (Nyctereutes procyonoides) and identification of several novel subtype families for Cryptosporidium mink genotype in minks (Mustela vison) in China

Despite the rapid and extensive advances in molecular epidemiology of Cryptosporidium in humans and a variety of animals, the prevalence and genetic traits of the parasite in wildlife bred in captivity and the role of the neglected hosts in zoonotic transmission of human cryptosporidiosis are rarely understood. This study investigated the prevalence, species/genotype, and subtype of Cryptosporidium in farmed fur animals in China and assessed the possibility of zoonotic transmission. Three of 191 (1.6%) foxes (Vulpes vulpes), 17 of 162 (10.5%) raccoon dogs (Nyctereutes procyonoides), and 48 of 162 (29.6%) minks (Mustela vison) were positive for Cryptosporidium by nested PCRs targeting the small subunit rRNA gene. Sequence analysis indicated the presence of only Cryptosporidium canis in foxes and raccoon dogs. There is no significant difference in prevalence between young and adult foxes (or raccoon dogs). Three Cryptosporidium species or genotype including C. canis, Cryptosporidium meleagridis, and mink genotype were determined in minks aged five to six months. Subtyping based on nucleotide and amino acid sequence polymorphisms of the 60kDa glycoprotein facilitated identification of three novel subtype families named as Xb to Xd for Cryptosporidium mink genotype. The presence of zoonotic C. canis, C. meleagridis, and Cryptosporidium mink genotype in captive-bred fur animals is of public health concerns. The findings expanded the host ranges of C. canis and C. meleagridis and confirmed genetic diversity at the subtype level in Cryptosporidium mink genotype. This is the first study reporting Cryptosporidium infections in foxes and raccoon dogs in China.

Emergence of Cryptosporidium hominis Monkey Genotype II and Novel Subtype Family Ik in the Squirrel Monkey (Saimiri sciureus) in China

A single Cryptosporidium isolate from a squirrel monkey with no clinical symptoms was obtained from a zoo in Ya'an city, China, and was genotyped by PCR amplification and DNA sequencing of the small-subunit ribosomal RNA (SSU rRNA), 70-kDa heat shock protein (HSP70), Cryptosporidium oocyst wall protein, and actin genes. This multilocus genetic characterization determined that the isolate was Cryptosporidium hominis, but carried 2, 10, and 6 nucleotide differences in the SSU rRNA, HSP70, and actin loci, respectively, which is comparable to the variations at these loci between C. hominis and the previously reported monkey genotype (2, 3, and 3 nucleotide differences). Phylogenetic studies, based on neighbor-joining and maximum likelihood methods, showed that the isolate identified in the current study had a distinctly discordant taxonomic status, distinct from known C. hominis and also from the monkey genotype, with respect to the three loci. Restriction fragment length polymorphisms of the SSU rRNA gene obtained from this study were similar to those of known C. hominis but clearly differentiated from the monkey genotype. Further subtyping was performed by sequence analysis of the gene encoding the 60-kDa glycoprotein (gp60). Maximum homology of only 88.3% to C. hominis subtype IdA10G4 was observed for the current isolate, and phylogenetic analysis demonstrated that this particular isolate belonged to a novel C. hominis subtype family, IkA7G4. This study is the first to report C. hominis infection in the squirrel monkey and, based on the observed genetic characteristics, confirms a new C. hominis genotype, monkey genotype II. Thus, these results provide novel insights into genotypic variation in C. hominis.

Genetic analysis of Giardia and Cryptosporidium from people in Northern Australia using PCR-based tools

To date, there has been limited genetic study of the gastrointestinal pathogens Giardia and Cryptosporidium in northern parts of Australia. Here, PCR-based methods were used for the genetic characterization of Giardia and Cryptosporidium from 695 people with histories of gastrointestinal disorders from the tropical North of Australia. Genomic DNAs from fecal samples were subjected to PCR-based analyses of regions from the triose phosphate isomerase (tpi), small subunit (SSU) of the nuclear ribosomal RNA and/or the glycoprotein (gp60) genes. Giardia and Cryptosporidium were detected in 13 and four of the 695 samples, respectively. Giardia duodenalis assemblages A and B were found in 4 (31%) and 9 (69%) of the 13 samples in persons of <9 years of age. Cryptosporidium hominis (subgenotype IdA18), Cryptosporidium mink genotype (subgenotype IIA16R1) and C. felis were also identified in single patients of 11-21 years of age. Future studies might focus on a comparative study of these and other protists in rural communities in Northern Australia.

Selected Zoonoses

Human risks of acquiring a zoonotic disease from animals used in biomedical research have declined over the last decade because higher quality research animals have defined microbiologic profiles. Even with diminished risks, the potential for exposure to infectious agents still exists, especially from larger species such as nonhuman primates, which may be obtained from the wild, and from livestock, dogs, ferrets, and cats, which are generally not raised in barrier facilities and are not subject to the intensive health monitoring performed routinely on laboratory rodents and rabbits. Additionally, when laboratory animals are used as models for infectious disease studies, exposure to microbial pathogens presents a threat to human health. Also, with the recognition of emerging diseases, some of which are zoonotic, constant vigilance and surveillance of laboratory animals for zoonotic diseases are still required.

Occurrence of novel and rare subtype families of Cryptosporidium in bamboo rats (Rhizomys sinensis) in China

This report is the first to describe Cryptosporidium infection in bamboo rats (Rhizomys sinensis). Ninety-two fresh fecal specimens were collected from a pet market in Ya'an City, China. One Cryptosporidium isolate from an asymptomatic host and two isolates from separate hosts with diarrhea were obtained by using Sheather's sucrose flotation technique and modified acid-fast staining. The Cryptosporidium spp. were genotyped by nested PCR and nucleotide sequencing of the small subunit rRNA (SSU rRNA), 70-kDa heat shock protein (HSP70), oocyst wall protein (COWP), and actin genes: isolates were identified as Cryptosporidium parvum with minor nucleotide differences at all four loci. Further subtyping was performed by PCR amplification and DNA sequence analysis of the 60-kDa glycoprotein (gp60) gene: two subtype families were detected, including a novel C. parvum subtype IIpA9 and a rare subtype IIoA13G1 (only reported in diarrheal patients of Sweden). Our results suggest that the bamboo rat is a reservoir host of C. parvum. Significantly, we discovered that the rare C. parvum subtype family IIo is also a zoonotic subtype and confirmed C. parvum subtype IIpA9 as a novel subtype family.

First genetic analysis of Cryptosporidium from humans from Tasmania, and identification of a new genotype from a traveller to Bali

Little is known about the molecular composition of Cryptosporidium species from humans living in the insular state of Tasmania, Australia. In the present study, we genetically characterized 82 samples of Cryptosporidium from humans following conventional coproscopic testing in a routine, diagnostic laboratory. Using a PCR-coupled single-strand conformation polymorphism (SSCP) technique, targeting portions of the small subunit rRNA (SSU), and 60 kDa glycoprotein (gp60) loci, we identified two species of Cryptosporidium, including C. hominis (subgenotypes IbA10G2, IdA16, IeA12G3T3, and IfA19G1) and C. parvum (IIaA16G1R1 and IIaA18G3), and a new operational taxonomic unit (OTU) that genetically closely resembled C. wrairi. This OTU was further characterized using markers in the actin, Cryptosporidium oocyst wall protein (COWP), and 70 kDa heat shock protein (hsp70) genes. This study provides the first characterization of species and genotypes of Cryptosporidium from Tasmania, and presents clear genetic evidence, using five independent genetic loci, for a new genotype or species of Cryptosporidium in a Tasmanian person with a recent history of travelling to Bali, Indonesia. It would be interesting to undertake detailed molecular-based studies of Cryptosporidium in Indonesia and neighbouring countries, in conjunction with morphological and experimental investigations of new genotypes.

Population structure of natural and propagated isolates of Cryptosporidium parvum, C. hominis and C. meleagridis

The three protozoan species Cryptosporidium parvum, C. meleagridis and C. hominis (phylum Apicomplexa) are enteric pathogens of humans. The former two species are zoonotic and the latter is thought to infect only humans. To better characterize the structure and transmission of natural and laboratory-propagated isolates, we analyzed a collection of archived human and animal isolates of these three species by deep-sequencing polymerase chain reaction products amplified from a polymorphic sequence on chromosome 1. Thousands of screened 200-nucleotide sequences were analyzed to compare the diversity among samples, to assess the impact of laboratory propagation on population complexity and to identify taxonomically mixed isolates. Contrary to our expectation, repeated propagation in animals did not reduce intra-isolate diversity nor was diversity associated with host species. Significantly, in most samples, sequences characteristic of a different species were identified. The presence of C. hominis alleles in C. parvum and C. meleagridis isolates confirms earlier reports of mixed isolates and raises the possibility that the host range of C. hominis is broader than typically assumed. In a genetically divergent isolate of C. parvum, a majority of sequences was found to be recombinant, suggesting that this genotype originated from a C. parvum × C. hominis recombination event.

Multilocus genotype and subtype analysis of Cryptosporidium andersoni derived from a Bactrian camel (Camelus bactrianus) in China

Fecal specimens from two Bactrian camels were collected in the Ya'an city zoo of China and were examined for Cryptosporidium by centrifugal flotation. One specimen was found to be parasitized by Cryptosporidium via microscopy, and the oocysts were measured to have an average size of 7.03 × 5.50 μm (n > 50). The isolate was genotyped by polymerase chain reaction (PCR) amplification and DNA sequence analysis of the partial 18S rRNA, COWP, and A135 genes, and was confirmed to be Cryptosporidium andersoni with minor nucleotide differences. Multilocus sequence typing (MLST) analysis indicated that the subtype of the camel-derived C. andersoni isolate was A4, A4, A4, and A1 at the four minisatellite loci (MS1, MS2, MS3, and MS16, respectively). Therefore, this isolate belongs to the most common MLST subtype reported in cattle in China and is distinct from two other known camel C. andersoni MLST subtypes (A6, A4, A2, A1 and A6, A5, A2, A1). Animal transmission experiments demonstrated that the C. andersoni isolate was not infectious to immunosuppressed or immunocompetent Kun-ming mice, Sprague-Dawley rats, and hamsters but was biologically similar to most bovine C. andersoni isolates characterized so far. Therefore, transmission of this camel-derived C. andersoni isolate is very likely to occur between camels and bovine.