Diversity of Cryptosporidium in brush-tailed rock-wallabies (Petrogale penicillata) managed within a species recovery programme

Zoonotic Cryptosporidium and Giardia in marsupials-an update

Marsupials, inhabiting diverse ecosystems, including urban and peri-urban regions in Australasia and the Americas, intersect with human activities, leading to zoonotic spill-over and anthroponotic spill-back of pathogens, including Cryptosporidium and Giardia. This review assesses the current knowledge on the diversity of Cryptosporidium and Giardia species in marsupials, focusing on the potential zoonotic risks. Cryptosporidium fayeri and C. macropodum are the dominant species in marsupials, while in possums, the host-specific possum genotype dominates. Of these three species/genotypes, only C. fayeri has been identified in two humans and the zoonotic risk is considered low. Generally, oocyst shedding in marsupials is low, further supporting a low transmission risk. However, there is some evidence of spill-back of C. hominis into kangaroo populations, which requires continued monitoring. Although C. hominis does not appear to be established in small marsupials like possums, comprehensive screening and analysis are essential for a better understanding of the prevalence and potential establishment of zoonotic Cryptosporidium species in small marsupials. Both host-specific and zoonotic Giardia species have been identified in marsupials. The dominance of zoonotic G. duodenalis assemblages A and B in marsupials may result from spill-back from livestock and humans and it is not yet understood if these are transient or established infections. Future studies using multilocus typing tools and whole-genome sequencing are required for a better understanding of the zoonotic risk from Giardia infections in marsupials. Moreover, much more extensive screening of a wider range of marsupial species, particularly in peri-urban areas, is required to provide a clearer understanding of the zoonotic risk of Cryptosporidium and Giardia in marsupials.

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.

Zoonotic infection by Cryptosporidium fayeri IVgA10G1T1R1 in a Western Australian human

In the present study, a 37-year-old immunosuppressed female in Western Australia (WA) was identified as positive for Cryptosporidium by microscopy and treated with nitazoxanide. Molecular analyses at the 18S ribosomal RNA (18S) and 60 kDa glycoprotein (gp60) loci identified C. fayeri subtype IVgA10G1T1R1, which had previously been identified in western grey kangaroos (Macropus fuliginosus) in WA. Next generation sequencing (NGS) of the gp60 locus confirmed the absence of mixed infections with other Cryptosporidium species. This is only the second report of C. fayeri in a human host highlighting the zoonotic potential of this wildlife-associated species. Routine diagnosis using molecular methods in laboratories is required to better understand the diversity and epidemiology of Cryptosporidium parasite.

Species and genotypes causing human cryptosporidiosis in New Zealand

Cryptosporidium is one of the most common causes of diarrhoea around the world. Successful management and prevention of this infectious disease requires knowledge of the diversity of species and subtypes causing human disease. We use sequence data from 2598 human faecal samples collected during an 11-year period (2009-2019) to better understand the impact of different species and subtypes on public health and to gain insights into the variation of human cryptosporidiosis in New Zealand. Human cryptosporidiosis in New Zealand is caused by a high diversity of species and subtypes. Six species cause human disease in New Zealand: C. hominis, C. parvum, C. cuniculus, C. erinacei, C. meleagridis and C. tyzzeri. Sequence analysis of the gp60 gene identified 16 subtype families and 101 subtypes. Cryptosporidium hominis IbA10G2 and C. parvum IIaA18G3R1 were the most frequent causes of human cryptosporidiosis with 27% and 29% of infections, respectively. Cryptosporidium hominis presented a peak of notified human cases during autumn (March-May) whereas most cases of human cryptosporidiosis caused by C. parvum are found during the calving and lambing season in spring (September-November). We also reported some subtypes that have been rarely detected in other countries such as IbA20G2 and IIoA13G1 and a low prevalence of the hypertransmissible and virulent IIaA15G2R1. This study provides insight into the variability of cryptosporidiosis in New Zealand essential for disease management and surveillance to prevent the introduction or spread of new species and subtypes in the country.

Identification of eukaryotic microorganisms with 18S rRNA next-generation sequencing in wastewater treatment plants, with a more targeted NGS approach required for Cryptosporidium detection

While some microbial eukaryotes can improve effluent quality in wastewater treatment plants (WWTPs), eukaryotic waterborne pathogens are a threat to public health. This study aimed to identify Eukarya, particularly faecal pathogens including Cryptosporidium, in different treatment stages (influent, intermediate and effluent) from four WWTPs in Western Australia (WA). Three WWTPs that utilise stabilisation ponds and one WWTP that uses activated sludge (oxidation ditch) treatment technologies were sampled. Eukaryotic 18S rRNA (18S) was targeted in the wastewater samples (n = 26) for next-generation sequencing (NGS), and a mammalian-blocking primer was used to reduce the amplification of mammalian DNA. Overall, bioinformatics analyses revealed 49 eukaryotic phyla in WWTP samples, and three of these phyla contained human intestinal parasites, which were primarily detected in the influent. These human intestinal parasites either had a low percent sequence composition or were not detected in the intermediate and effluent stages and included the amoebozoans Endolimax sp., Entamoeba sp. and Iodamoeba sp., the human pinworm Enterobius vermicularis (Nematoda), and Blastocystis sp. subtypes (Sarcomastigophora). Six Blastocystis subtypes and four Entamoeba species were identified by eukaryotic 18S NGS, however, Cryptosporidium sp. and Giardia sp. were not detected. Real-time polymerase chain reaction (PCR) also failed to detect Giardia, but Cryptosporidium-specific NGS detected Cryptosporidium in all WWTPs, and a total of nine species were identified, including five zoonotic pathogens. Although eukaryotic 18S NGS was able to identify some faecal pathogens, this study has demonstrated that more specific NGS approaches for pathogen detection are more sensitive and should be applied to future wastewater pathogen assessments.

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

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

Using host species traits to understand the consequences of resource provisioning for host-parasite interactions

Supplemental food provided to wildlife by human activities can be more abundant and predictable than natural resources, and subsequent changes in wildlife ecology can have profound impacts on host-parasite interactions. Identifying traits of species associated with increases or decreases in infection outcomes with resource provisioning could improve assessments of wildlife most prone to disease risks in changing environments. We conducted a phylogenetic meta-analysis of 342 host-parasite interactions across 56 wildlife species and three broad taxonomic groups of parasites to identify host-level traits that influence whether provisioning is associated with increases or decreases in infection. We predicted dietary generalists that capitalize on novel food would show greater infection in provisioned habitats owing to population growth and food-borne exposure to contaminants and parasite infectious stages. Similarly, species with fast life histories could experience stronger demographic and immunological benefits from provisioning that affect parasite transmission. We also predicted that wide-ranging and migratory behaviours could increase infection risks with provisioning if concentrated and non-seasonal foods promote dense aggregations that increase exposure to parasites. We found that provisioning increased infection with bacteria, viruses, fungi and protozoa (i.e. microparasites) most for wide-ranging, dietary generalist host species. Effect sizes for ectoparasites were also highest for host species with large home ranges but were instead lowest for dietary generalists. In contrast, the type of provisioning was a stronger correlate of infection outcomes for helminths than host species traits. Our analysis highlights host traits related to movement and feeding behaviour as important determinants of whether species experience greater infection with supplemental feeding. These results could help prioritize monitoring wildlife with particular trait profiles in anthropogenic habitats to reduce infectious disease risks in provisioned populations.

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.

Molecular characterization of Cryptosporidium and Giardia from the Tasmanian devil (Sarcophilus harrisii)

The Tasmanian devil (Sarcophilus harrisii) is a carnivorous marsupial found only in the wild in Tasmania, Australia. Tasmanian devils are classified as endangered and are currently threatened by devil facial tumour disease, a lethal transmissible cancer that has decimated the wild population in Tasmania. To prevent extinction of Tasmanian devils, conservation management was implemented in 2003 under the Save the Tasmanian Devil Program. This study aimed to assess if conservation management was altering the interactions between Tasmanian devils and their parasites. Molecular tools were used to investigate the prevalence and diversity of two protozoan parasites, Cryptosporidium and Giardia, in Tasmanian devils. A comparison of parasite prevalence between wild and captive Tasmanian devils showed that both Cryptosporidium and Giardia were significantly more prevalent in wild devils (p < 0.05); Cryptosporidium was identified in 37.9% of wild devils but only 10.7% of captive devils, while Giardia was identified in 24.1% of wild devils but only 0.82% of captive devils. Molecular analysis identified the presence of novel genotypes of both Cryptosporidium and Giardia. The novel Cryptosporidium genotype was 98.1% similar at the 18S rDNA to Cryptosporidium varanii (syn. C. saurophilum) with additional samples identified as C. fayeri, C. muris, and C. galli. Two novel Giardia genotypes, TD genotype 1 and TD genotype 2, were similar to G. duodenalis from dogs (94.4%) and a Giardia assemblage A isolate from humans (86.9%). Giardia duodenalis BIV, a zoonotic genotype of Giardia, was also identified in a single captive Tasmanian devil. These findings suggest that conservation management may be altering host-parasite interactions in the Tasmanian devil, and the presence of G. duodenalis BIV in a captive devil points to possible human-devil parasite transmission.

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.

Public health significance of zoonotic Cryptosporidium species in wildlife: Critical insights into better drinking water management

Cryptosporidium is an enteric parasite that is transmitted via the faecal-oral route, water and food. Humans, wildlife and domestic livestock all potentially contribute Cryptosporidium to surface waters. Human encroachment into natural ecosystems has led to an increase in interactions between humans, domestic animals and wildlife populations. Increasing numbers of zoonotic diseases and spill over/back of zoonotic pathogens is a consequence of this anthropogenic disturbance. Drinking water catchments and water reservoir areas have been at the front line of this conflict as they can be easily contaminated by zoonotic waterborne pathogens. Therefore, the epidemiology of zoonotic species of Cryptosporidium in free-ranging and captive wildlife is of increasing importance. This review focuses on zoonotic Cryptosporidium species reported in global wildlife populations to date, and highlights their significance for public health and the water industry.