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

Cryptosporidium occultus in disguise

As data accumulate in GenBank, the difficulties of delineating species of Cryptosporidium based on nuclear small subunit ribosomal RNA (ssu rRNA) gene information alone becomes increasingly evident. Here, we summarize currently available evidence suggesting that several ssu rDNA sequences primarily referred to as Cryptosporidium suis (some of them from non-suid hosts) should be considered Cryptosporidium occultus.

New records of Hepatozoon and Oswaldofilaria from saltwater crocodiles (Crocodylus porosus) in Australia

Diseases affecting wild Australian saltwater crocodiles (Crocodylus porosus) are rarely reported due to the difficulty in capturing animals and obtaining samples. In this investigation, we identified two haemoparasites (Hepatozoon and a filarial nematode) in saltwater crocodiles in Darwin, Australia. Light microscopic examination identified Hepatozoon in 7/7 (100%) wild crocodiles and in 2/20 (10%) of captive ones. When genomic DNAs from these same samples were further investigated using polymerase chain reaction (PCR)-based sequencing, we detected Hepatozoon in all 27 blood samples. Using both microscopy and PCR-based sequencing, we detected a filarial worm (proposed to be Oswaldofilaria) in one of 20 captive crocodiles. The sequence data were compared with sequence data available in public databases, and phylogenetic analyses indicated that the operational taxonomic units of Hepatozoon and Oswaldofilaria discovered here in these crocodiles are likely new species. This study is the first to use molecular tools to explore haemoparasites in Australian saltwater crocodiles and highlights the importance of health investigations in poorly studied vertebrate hosts.

Marked genetic diversity within Blastocystis in Australian wildlife revealed using a next generation sequencing-phylogenetic approach

Blastocystis is a genus of intestinal stramenopiles that infect vertebrates, and may cause disease of the alimentary tract. Currently, at least 40 genotypes ("subtypes") of Blastocystis are recognised worldwide based on sequence data for the small subunit of the nuclear ribosomal RNA (SSU-rRNA) gene. Despite the numerous studies of Blastocystis worldwide, very few studies have explored Blastocystis in wild animals, particularly in Australia. Here, we used a PCR-based next generation sequencing (NGS)-phylogenetic approach to genetically characterise and classify Blastocystis variants from selected wildlife in the Australian state of Victoria. In total, 1658 faecal samples were collected from nine host species, including eastern grey kangaroo, swamp wallaby, common wombat, deer, European rabbit, canines and emu. Genomic DNA was extracted from these samples, a 500 bp region of the SSU-rRNA gene amplified by polymerase chain reaction (PCR) and, then, a subset of samples sequenced using Illumina technology. Primary PCR detected Blastocystis in 482 of the 1658 samples (29%), with the highest percentage in fallow deer (63%). Subsequent, Illumina-based sequencing of a subset of 356 samples revealed 55 distinct amplicon sequence variants (ASVs) representing seven currently-recognised subtypes (STs) [ST13 (prominent in marsupials), ST10, ST14, ST21, ST23, ST24 and ST25 (prominent in deer)] and two novel STs (ST45 and ST46) in marsupials. Mixed infections of different STs were observed in macropods, deer, emu and canids (fox, feral dog or dingo), but no infection was detected in rabbits or wombats. This study reveals marked genetic diversity within Blastocystis in a small number of species of wild animals in Australia, suggesting complexity in the genetic composition and transmission patterns of members of the genus Blastocystis in this country.

The Prevalence of Cryptosporidium spp. and Giardia duodenalis in Marmota himalayana (Rodentia: Sciuridae) in the Qinghai Tibetan Plateau area, China

Background

Cryptosporidium and Giardia are well-known important intestinal zoonotic pathogens that can infect various hosts and cause diarrhoeal diseases. We aimed to determine the epidemiological prevalence and molecular characterization of Cryptosporidium and Giardia species in Himalayan marmot (Marmota himalayana, class Marmota) in the Qinghai Tibetan Plateau Area of Qinghai Province, Northwest China.

Methods

Overall, 243 Himalayan marmot fecal samples were collected in 2017 and in 2019 and a two-step nested PCR technique was performed to amplify the fragments of the SSU rRNA gene of Cryptosporidium and 18S ribosomal RNA gene of Giardia. Molecular characterization of Cryptosporidium was performed with the primary primers NDIAGF2 and N-DIAGR2, the secondary primers CPB-DIAGF and CPB-DIAGR. Similarly, molecular characterization of Giardia was used the first primers Gia2029 and Gia2150c, the secondary primers RH11 and RH4. The positive PCR products were sequenced and the sequences were processed by Clustal Omega and BLAST. Phylogenetic analysis was achieved by NJ method in MEGA.

Results

The infection rate of Cryptosporidium spp. and G. duodenalis was 4.9% (12/243) and 0.8% (2/243) in M. himalayana, respectively. Cryptosporidium spp. are characterized as novel genotypes Cryptosporidium marmot genotype I (n=3) and Cryptosporidium marmot genotype II (n=9); G. duodenalis assemblage A (n=2) was found in M. himalayana.

Conclusion

This is the first report of Cryptosporidium spp. and G. duodenalis infections in M. himalayana in Qinghai of Northwest China. The results indicate the existence of Cryptosporidium species and G. duodenalis infections that may have a potential public health significance.

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.

Mammal-related Cryptosporidium infections in endemic reptiles of New Zealand

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

Seasonal distribution of Cryptosporidium spp., Giardia duodenalis and Enterocytozoon bieneusi in Tibetan sheep in Qinghai, China

Background

Cryptosporidium spp., Giardia duodenalis and Enterocytozoon bieneusi can cause important intestinal diseases in ruminants. However, data on the distribution of these three protozoan pathogens in Tibetan sheep are limited.

Methods

We collected 761 fecal samples from Tibetan sheep across four seasons in Qinghai Province, China, and screened the samples for Cryptosporidium spp., G. duodenalis and E. bieneusi using PCR-based sequence analysis of the genes encoding 18S ribosomal RNA, triosephosphate isomerase and the internal transcribed spacer, respectively.

Results

The positivity rates of Cryptosporidium spp., G. duodenalis and E. bieneusi in Tibetan sheep were 3.68% (28/761 samples), 1.58% (12/761) and 6.44% (49/761), respectively. Four species of Cryptosporidium were identified: C. xiaoi (n = 13 samples), C. ubiquitum (n = 8), C. bovis (n = 6) and C. ryanae (n = 1). Two G. duodenalis assemblages, namely the A (n = 2 samples) and E (n = 10) assemblages, were detected. Five zoonotic E. bieneusi genotypes were found: BEB6 (n = 21 samples), COS-I (n = 14), CHS3 (n = 11) and CGS1 (n = 2) from group 2, and PIGEBITS5 (n = 1) from group 1. Geographic differences in the distribution of E. bieneusi, and seasonal differences for all the three protozoan pathogens were noted.

Conclusions

Our results elucidate the prevalence and genetic diversity of these three pathogens in Tibetan sheep across different regions and seasons, including zoonotic pathogens such as C. ubiquitum, C. ryanae, G. duodenalis assemblage A and five genotypes of E. bieneusi.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s13071-022-05442-0.

A molecular characterization of marsupial filarioid nematodes of the genus Breinlia

Here we present the genetic relationships of 26 specimens of the genus Breinlia (Nematoda: Filarioidea) from a range of Australian marsupials using markers in the small subunit of nuclear ribosomal RNA and mitochondrial cytochrome c oxidase subunit 1 (cox1) genes and compare them with morphological determinations. The molecular data support the validity of most of the morpho-species included in the study and provide provisional insights into the phylogeny of the genus in Australian mammals, with dasyuroid marsupials appearing to be the original hosts. The recent discovery of Breinlia annulipapillata in the eye of a human brings this genus of parasites into the group of emerging infectious parasitic diseases.

Intestinal Parasitic Infections Among Pediatric Patients in a Metropolitan City of Bangladesh With Emphasis on Cryptosporidiosis

Introduction

Gastrointestinal parasitic infections are one of the global health concerns in developing countries like Bangladesh. Among them, Cryptosporidium spp. plays an essential role in causing diarrhea, malnutrition, and poor cognitive function, especially in children. This study was conducted to identify the frequency of Cryptosporidium cases and other parasitic agents. 

Methods

A cross-sectional observational study was conducted among 219 hospitalized children with diarrhea. The conventional microscopic technique was applied for parasitic detection. Particular staining (modified Ziehl-Neelsen) procedure was performed to identify oocysts of Cryptosporidium spp. A polymerase chain reaction (PCR) was performed to determine the SSU rRNA and gp60 gene of Cryptosporidium. 

Results

Cysts of Giardia duodenalis (2.3%), ova of Ascaris lumbricoides (1.4%,), Trichuris trichiura (0.5%), and both A. lumbricoides and T. trichiura (0.9%) were identified in samples through wet mount preparation. The distribution of Cryptosporidium spp. as detected by the staining method and nested PCR was 1.4% and 4.1%, respectively. 

Conclusion

Factors independently associated with Cryptosporidium infection are unsafe water, lack of regular hand washing, and insufficiency of exclusive breastfeeding. This study reports, presumably for the first time, the detection of Cryptosporidium oocysts in Chattogram metropolitan city of Bangladesh.

Review of generic screening level assumptions for quantitative microbial risk assessment (QMRA) for estimating public health risks from Australian drinking water sources contaminated with Cryptosporidium by recreational activities

As urban communities continue to grow, demand for recreational access (including swimming) in drinking water sources have increased, yet relatively little is understood about the public health implications this poses for drinking water consumers. Preventative risk-based approaches to catchment management, informed by quantitative microbial risk assessment (QMRA), requires accurate input data to effectively model risks. A sound understanding of the knowledge gaps is also important to comprehend levels of uncertainty and help prioritise research needs. Cryptosporidium is one of the most important causes of waterborne outbreaks of gastroenteritis globally due to its resistance to chlorine. This review was undertaken by Water Research Australia to provide the most up-to-date information on current Cryptosporidium epidemiological data and underlying assumptions for exposure assessment, dose response and risk assessment for generic components of QMRA for Cryptosporidium and highlights priorities for common research. Key interim recommendations and guidelines for numerical values for relatively simple screening level QMRA modelling are provided to help support prospective studies of risks to drinking water consumers from Cryptosporidium due to body-contact recreation in source water. The review does not cover site-specific considerations, such as the levels of activity in the source water, the influence of dilution and inactivation in reservoirs, or water treatment. Although the focus is Australia, the recommendations and numerical values developed in this review, and the highlighted research priorities, are broadly applicable across all drinking source water sources that allow recreational activities.

Multilocus Genotyping of Giardia duodenalis in Alpine Musk Deer (Moschus chrysogaster) in China

Giardia duodenalis is the underlying cause of a significant number of outbreaks of gastrointestinal illness in humans and animals worldwide. The purpose of this study was to elucidate the prevalence and genetic diversity of G. duodenalis in captive alpine musk deer (Moschus chrysogaster) in China. A total of 202 fecal samples were collected from three farms in Gansu Province, China. Identification of G. duodenalis was conducted by nested PCR targeting the genes coding for SSU rRNA, β-giardin (bg), glutamate dehydrogenase (gdh) and triosephosphate isomerase (tpi). The overall prevalence of G. duodenalis in captive alpine musk deer in surveyed area was 19.3% (39/202). Two G. duodenalis genetic assemblages were identified, namely assemblage A and E. Mixed genotype infections (A+E) were found in 15.4% (6/39) of positive samples. Multilocus genotyping (MLG) analysis of G. duodenalis isolates revealed six novel assemblage A MLGs formed by two newly-described MLG-subtypes which belonged to sub-assemblage AI. To the best of our knowledge, this is the first report on MLG of G. duodenalis isolates in captive alpine musk deer in China. The presence of zoonotic assemblages and sub-assemblages of G. duodenalis in deer species suggests that these animals may potentially act as a reservoir of this protozoan for humans.

Variation in the Structure and Composition of Bacterial Communities within Drinking Water Fountains in Melbourne, Australia

Modern drinking water distributions systems (DWDSs) have been designed to transport treated or untreated water safely to the consumer. DWDSs are complex environments where microorganisms are able to create their own niches within water, biofilm or sediment. This study was conducted on twelve drinking fountains (of three different types, namely types A, B and C) within the Melbourne (Australia) city area with the aim to (i) characterize the water quality and viable and total counts at each fountain, (ii) compare the differences in the structure and diversity of the bacterial community between bulk water and biofilm and (iii) determine differences between the bacterial communities based on fountain type. Samples of water and biofilm were assessed using both culture-dependent and culture-independent techniques. Heterotrophic plate counts of water samples ranged from 0.5 to 107.5 CFU mL−1, and as expected, total cell counts (cells mL−1) were, on average, 2.9 orders of magnitude higher. Based on the mean relative abundance of operational taxonomic units (OTUs), ANOSIM showed that the structure of the bacterial communities in drinking water and biofilm varied significantly (R = 0.58, p = 0.001). Additionally, ANOSIM showed that across fountain types (in water), the bacterial community was more diverse in fountain type C compared to type A (p < 0.001) and type B (p < 0.001). 16S rRNA next-generation sequencing revealed that the bacterial communities in both water and biofilm were dominated by only seven phyla, with Proteobacteria accounting for 71.3% of reads in water and 68.9% in biofilm. The next most abundant phylum was Actinobacteria (10.4% water; 11.7% biofilm). In water, the genus with the highest overall mean relative abundance was Sphingomonas (24.2%), while Methylobacterium had the highest mean relative abundance in biofilm samples (54.7%). At the level of genus and higher, significant differences in dominance were found across fountain types. In water, Solirubrobacterales (order) were present in type C fountains at a relative abundance of 17%, while the mean relative abundance of Sphingomonas sp. in type C fountains was less than half that in types A (25%) and B (43%). In biofilm, the relative abundance of Sphingomonas sp. was more than double in type A (10%) fountains compared to types B (4%) and C (5%), and Sandarakinorhabdus sp. were high in type A fountains (6%) and low in types B and C (1%). Overall this research showed that there were significant differences in the composition of bacterial communities in water and biofilm from the same site. Furthermore, significant variation exists between microbial communities present in the fountain types, which may be related to age. Long-established environments may lead to a greater chance of certain bacteria gaining abilities such as increased disinfection resistance. Variations between the structure of the bacterial community residing in water and biofilm and differences between fountain types show that it is essential to regularly test samples from individual locations to determine microbial quality.

Molecular Detection of Cryptosporidium cuniculus in Rabbits (Oryctolagus cuniculus) from Tenerife, Canary Islands, Spain

Cryptosporidium cuniculus is a zoonotic parasite responsible for cryptosporidiosis cases and outbreaks in both humans and rabbits. Since there are no molecular Cryptosporidium spp. infection data in rabbits (Oryctolagus cuniculus) from Spain, our aim was to gather information about this parasite in wild European rabbits from Tenerife, Canary Islands (Spain). A total of 100 faecal samples were collected from rabbits from eight municipalities of Tenerife. Microscopic analysis showed that 4.0% of the samples presented structures compatible with Cryptosporidium oocyst. A nested polymerase chain reaction (PCR) targeting 18S ribosomal RNA (rRNA) gene fragments was carried out, and sequencing confirmed the identity of C. cuniculus in one sample (1.0%). The sample was successfully subtyped using nested PCR analysis of the 60-kDa glycoprotein (gp60) gene as the subtype VbA26R3. This study confirms the presence of C. cuniculus in wild rabbits from Tenerife, providing new information on the occurrence of this zoonotic parasite. Further studies are required to better understand the epidemiology of Cryptosporidium spp. in wild rabbits in Spain and their possible public health repercussions.

Prevalence of Giardia duodenalis Among Dogs in China from 2001 to 2021: A Systematic Review and Meta-Analysis

Giardia duodenalis has a wide range of host species and is a common causative agent of diarrheal disease in humans and animals. This study conducted a systematic review and meta-analysis to evaluate the pooled prevalence of Giardia among dogs in China. We extracted 33 studies related to the prevalence of G. duodenalis in dogs, with samples taken from 2001 to 2021. The random-effect model was used to calculate pooled prevalence estimates with 95% confidence intervals, and the analyzed data were from 14 provinces in China. The estimated overall prevalence of G. duodenalis among dogs in China was 11.2%. The prevalence of Giardia was significantly higher in Northwestern China (35.7%) than in other regions. The prevalence in 2010 or later (11.8%) was significantly higher than in 2010 or before (6.9%). The estimated prevalence detected by microscopy (9.3%) was lower than molecular (12.3%) and serological (14.3%) ones. The prevalence was higher in dogs <1 year of age (12.2%) than that >1 year (5.4%). Among the genotype groups, the positive rate of assemblage A (5.2%) was significantly higher than that of other assemblages. Depending on the dog' type, the prevalence of G. duodenalis in stray dogs (3.5%) was lower than that in pet dogs (6.7%) and intensively breeding dogs (11.8%). In addition, no correlation was found between Giardia positive rate and the dogs' gender (p > 0.05). We also analyzed the effects of different geographic factor subgroups (longitude, latitude, precipitation, temperature, humidity, and altitude) on the prevalence of G. duodenalis in dogs in China. The results showed that giardiasis was widespread in dogs in China. It is suggested that corresponding control scheme and effective management measures should be formulated and applied to reduce the transmission of G. duodenalis according to the difference in geographical conditions in different areas.

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.

FIRST REPORT OF GENUS Cryptosporidium IN CERVIDS SPECIES: Mazama americana, Mazama nana AND Blastocerus dichotomus

We analyzed Cryptosporidium spp. in fecal samples of wild cervids (Ozotoceros bezoarticus, Blastocerus dichotomus, Mazama nana, Mazama americana, and Mazama bororo) from many Brazilian regions, a fact unprecedented in the literature. Sniffer dogs were used to collect 936 fecal samples of cervids from 14 Brazilian localities. Cervids species were identified using polymerase chain reaction (PCR) performed from genomic DNA extracted from 563 fecal samples of Ozotoceros bezoarticus, Blastocerus dichotomus, Mazama nana, Mazama americana, and Mazama bororo. Cryptosporidium spp. oocyst screening was performed using malachite green negative staining. Nested PCR (nPCR) protocols targeting the 18S rRNA and GP60 genes followed by genetic sequencing were performed for Cryptosporidium spp. detection and Cryptosporidium parvum subtyping, respectively. Nested PCR targeting actin gene and genetic sequencing were performed in samples with non-identified Cryptosporidium species by 18S rRNA amplicon sequencing. The association between the occurrence of Cryptosporidium and the presence of bovines in the same locality was evaluated using Fisher's exact test. The positivity rates of diagnostic methods were compared by McNemar test and the Kappa correlation coefficient. The prevalence rates of Cryptosporidium spp. in cervids were 1.42% (8/563) and 0.36% (2/563) by nPCR and malachite green negative staining, respectively. C. parvum IIaA16G3R1 isolate was identified in three fecal samples from M. americana, two from M. nana and one from B. dichotomus. Cryptosporidium ryanae were found in one sample from B. dichotomus. We identified a new Cryptosporidium genotype, named Cryptosporidium deer genotype BR, from one M. americana fecal sample.

Wildlife Is a Potential Source of Human Infections of Enterocytozoon bieneusi and Giardia duodenalis in Southeastern China

Wildlife is known to be a source of high-impact pathogens affecting people. However, the distribution, genetic diversity, and zoonotic potential of Cryptosporidium, Enterocytozoon bieneusi, and Giardia duodenalis in wildlife are poorly understood. Here, we conducted the first molecular epidemiological investigation of these three pathogens in wildlife in Zhejiang and Shanghai, China. Genomic DNAs were derived from 182 individual fecal samples from wildlife and then subjected to a nested polymerase chain reaction–based sequencing approach for detection and characterization. Altogether, 3 (1.6%), 21 (11.5%), and 48 (26.4%) specimens tested positive for Cryptosporidium species, E. bieneusi, and G. duodenalis, respectively. Sequence analyses revealed five known (BEB6, D, MJ13, SC02, and type IV) and two novel (designated SH_ch1 and SH_deer1) genotypes of E. bieneusi. Phylogenetically, novel E. bieneusi genotype SH_deer1 fell into group 6, and the other genotypes were assigned to group 1 with zoonotic potential. Three novel Cryptosporidium genotypes (Cryptosporidium avian genotype V-like and C. galli-like 1 and 2) were identified, C. galli-like 1 and 2 formed a clade that was distinct from Cryptosporidium species. The genetic distinctiveness of these two novel genotypes suggests that they represent a new species of Cryptosporidium. Zoonotic assemblage A (n = 36) and host-adapted assemblages C (n = 1) and E (n = 7) of G. duodenalis were characterized. The overall results suggest that wildlife act as host reservoirs carrying zoonotic E. bieneusi and G. duodenalis, potentially enabling transmission from wildlife to humans and other animals.

Ocular Filariasis in Human Caused by Breinlia (Johnstonema) annulipapillata Nematode, Australia

We report a human case of ocular filariasis, caused by a species of Breinlia nematode, from Queensland, Australia. Morphological and molecular evidence indicated that the nematode Breinlia (Johnstonema) annulipapillata, or a closely related taxon, likely transmitted from a macropodid marsupial host was involved, which might represent an accidental finding or an emerging zoonosis.

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.

Enterocytozoon bieneusi of animals-With an 'Australian twist'

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

Polarization of microbial communities between competitive and cooperative metabolism

Resource competition and metabolic cross-feeding are among the main drivers of microbial community assembly. Yet the degree to which these two conflicting forces are reflected in the composition of natural communities has not been systematically investigated. Here, we use genome-scale metabolic modelling to assess the potential for resource competition and metabolic cooperation in large co-occurring groups (up to 40 members) across thousands of habitats. Our analysis reveals two distinct community types, which are clustered at opposite ends of a spectrum in a trade-off between competition and cooperation. At one end are highly cooperative communities, characterized by smaller genomes and multiple auxotrophies. At the other end are highly competitive communities, which feature larger genomes and overlapping nutritional requirements, and harbour more genes related to antimicrobial activity. The latter are mainly present in soils, whereas the former are found in both free-living and host-associated habitats. Community-scale flux simulations show that, whereas competitive communities can better resist species invasion but not nutrient shift, cooperative communities are susceptible to species invasion but resilient to nutrient change. We also show, by analysing an additional data set, that colonization by probiotic species is positively associated with the presence of cooperative species in the recipient microbiome. Together, our results highlight the bifurcation between competitive and cooperative metabolism in the assembly of natural communities and its implications for community modulation.

Prevalence and Characterization of Cryptosporidium Species and Genotypes in Four Farmed Deer Species in the Northeast of China

Cryptosporidiosis is a major public health problem in humans and animals. Information on the prevalence and molecular diversity of Cryptosporidium in farmed deer in northeastern China is limited. In this study, the prevalence of these parasites was investigated in four farmed deer species, including 125 reindeer, 109 red deer, 86 sika deer, and 18 Siberian roe deer by nested PCR amplification of the partial small subunit of ribosomal RNA (SSU rRNA) gene. C. ubiquitum isolates were subtyped using nested PCR and sequence analysis of the 60-kDa glycoprotein (gp60) gene. The overall prevalence of Cryptosporidium was 7.1%, with 15.1% for sika deer, 4.0% for reindeer, 4.6% for red deer, and 5.6% for roe deer. C. ubiquitum (n = 4), C. xiaoi (n = 2), and Cryptosporidium deer genotype (n = 18) were identified. All four C. ubiquitum isolates belonged to the XIIa subtype (n = 4). This study confirms that Cryptosporidium deer genotype is widely occurring in deer in the investigated areas. Presence of zoonotic C. ubiquitum XIIa subtype indicates that farmed deer represent potential source of zoonotic cryptosporidia and might pose a threat to human health.

Disseminated protozoal infection in a wild feathertail glider (Acrobates pygmaeus) in Australia

This is the first report of a disseminated protozoal infection in a wild feathertail glider (Acrobates pygmaeus) from south-eastern Australia. The glider was found dead in poor body condition. Histologically, large numbers of zoites were seen predominantly in macrophages in the liver, spleen and lung, with protozoal cysts present in the liver. Molecular and phylogenetic analyses inferred that the protozoan parasite belongs to the family Sarcocystidae and is closely related to previously identified apicomplexans found in yellow-bellied gliders (Petaurus australis) in Australia and southern mouse opossums (Thylamys elegans) in Chile.

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A novel apicomplexan parasite caused a disseminated fatal disease in a wild feathertail glider.

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The apicomplexan parasite is a member of the family Sarcocystidae.

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It is most closely related to parasites previously identified in yellow-bellied gliders in Australia and southern mouseopossums in Chile.

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

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

Longitudinal analysis of Giardia duodenalis assemblages in animals inhabiting drinking water catchments in New South Wales and Queensland - Australia (2013-2015)

Giardia duodenalis is one of the most common waterborne zoonotic parasites worldwide, and its occurrence in the environment and catchment reservoir water has serious implications for management of drinking water. The aim of the present study was to use molecular tools to identify the Giardia spp. infecting animals inhabiting five drinking water catchments across two states in Australia; New South Wales and Queensland, to better understand the potential health risks they pose. We used quantitative PCR to screen a total of 2174 faecal samples collected from dominant host species in catchment areas for the presence of G. duodenalis. All samples positive for G. duodenalis were further characterized and subtyped at tpi and gdh loci, respectively. The overall prevalence of G. duodenalis was 15.3% (332/2174, 95%CI; 13.8-16.9), and two zoonotic assemblages (assemblages A and B) and one potentially zoonotic assemblage (E) were detected in various host species. Additional subtyping of a subset of samples (n = 76) identified four human infectious sub-assemblages including AI, AII, BII-like and BIV-like, all of which have been previously reported in humans in Australia. The finding of zoonotic assemblages of G. duodenalis in the present study necessitates continued identification of the sources/carriers of human pathogenic strains in drinking water catchment areas for more accurate risk assessment and optimal catchment management.

Prevalence and molecular characterization of Cryptosporidium spp. in Père David's deer (Elaphurus davidianus) in Jiangsu, China

Cryptosporidium is a zoonotic parasite that causes diarrhea in a broad range of animals, including deer. Little is known about the prevalence and genotype of Cryptosporidium spp. in Père David's deer. In this study, 137 fecal samples from Père David's deer were collected between July 2017 and August 2018 in the Dafeng Reserve and analyzed for Cryptosporidium spp. by nested-PCR based on the small subunit ribosomal RNA (SSU rRNA) gene, followed by sequence analyses to determine the species. The 60 kDa glycoprotein (gp60) gene was used to characterize Cryptosporidium spp. Among 137 samples, 2 (1.46%) were positive for Cryptosporidium spp. according to SSU rRNA gene sequencing results. Both samples belonged to the Cryptosporidium deer genotype, with two nucleotide deletions and one nucleotide substitution. The prevalence data and molecular characterization of this study provide basic knowledge for controlling and preventing Cryptosporidium infections in Père David's deer in this area.

Cryptosporidium hominis infections in non-human animal species: revisiting the concept of host specificity

Parasites in the genus Cryptosporidium, phylum Apicomplexa, are found worldwide in the intestinal tract of many vertebrate species and in the environment. Driven by sensitive PCR methods, and the availability of abundant sequence data and reference genomes, the taxonomic complexity of the genus has steadily increased; 38 species have been named to date. Due to its public health importance, Cryptosporidium hominis has long attracted the interest of the research community. This species was initially described as infectious to humans only. This perception has persisted in spite of an increasing number of observations of natural and experimental infections of animals with this species. Here we summarize and discuss this literature published since 2000 and conclude that the host range of C. hominis is broader than originally described. The evolving definition of the C. hominis host range raises interesting questions about host specificity and the evolution of Cryptosporidium parasites.

Multiplex PCRs for the specific identification of marsupial and deer species from faecal samples as a basis for non-invasive epidemiological studies of parasites

Background

The specific identification of animals through the analysis of faecal DNA is important in many areas of scientific endeavour, particularly in the field of parasitology.

Methods

Here, we designed and assessed two multiplex PCR assays using genetic markers in a mitochondrial cytochrome b (cytb) gene region for the unequivocal identification and discrimination of animal species based on the specific amplification of DNA from faecal samples collected from water catchment areas in Victoria, Australia. One of these assays differentiates three marsupial species (eastern grey kangaroo, swamp wallaby and common wombat) and the other distinguishes three deer species (fallow, red and sambar deer). We tested these two assays using a total of 669 faecal samples, collected as part of an ongoing programme to monitor parasites and microorganisms in these animals.

Results

These two PCR assays are entirely specific for these animal species and achieve analytical sensitivities of 0.1–1.0 picogram (pg). We tested 669 faecal samples and found that some previous inferences of species based on faecal morphology were erroneous. We were able to molecularly authenticate all of the 669 samples.

Conclusions

We have established PCR assays that accurately distinguish the faecal samples of some of the prominent large mammalian herbivores found within a water catchment system in the state of Victoria, Australia. The multiplex assays for marsupials and deer produce amplicons that are easily differentiable based on their size on an agarose gel, and can be readily sequenced for definitive species authentication. Although established for marsupials and deer, the methodology used here can be applied to other host-parasite study systems to ensure data integrity.

Prevalence and Genotype Distribution of Giardia duodenalis in Rabbits in Shandong Province, Eastern China

Giardia duodenalis is a zoonotic enteric parasite that can infect humans and a number of animal species including rabbits with a worldwide distribution. Infection with G. duodenalis can cause serious public health problems and significant economic losses to animal husbandry. So accurate understanding of the prevalence and genotype distribution of G. duodenalis in rabbits is necessary. In the present study, a total of 616 fecal samples were collected from rabbits in Shandong province, eastern China, and examined in G. duodenalis prevalence and genotypes by nested PCR amplification of β-giardin (bg), glutamate dehydrogenase (gdh), and triosephosphate isomerase (tpi) gene loci of G. duodenalis. Sixty-nine (11.2%) of the examined rabbit fecal samples were G. duodenalis-positive. Of them, the prevalence of G. duodenalis is 8.4% (41/490) in Rizhao city and 22.2% (28/126) in Weihai city. Breeds, region, and feeding modes were highly correlated with G. duodenalis infection in rabbits. Moreover, three genotypes (assemblages A, B, and E) were identified in rabbits at three gene loci, and the assemblage E was the dominant genotype, while the assemblage A was reported in rabbits in China for the first time. It is noticeable that two rabbits were found to be infected with two different G. duodenalis assemblages (assemblages A and E, assemblages B and E, respectively). These findings enrich the genotype distribution of G. duodenalis in rabbits and provide baseline data for preventing and controlling G. duodenalis infection in rabbits in eastern China.

Host-associated microbiomes are predicted by immune system complexity and climate

BACKGROUND

Host-associated microbiomes, the microorganisms occurring inside and on host surfaces, influence evolutionary, immunological, and ecological processes. Interactions between host and microbiome affect metabolism and contribute to host adaptation to changing environments. Meta-analyses of host-associated bacterial communities have the potential to elucidate global-scale patterns of microbial community structure and function. It is possible that host surface-associated (external) microbiomes respond more strongly to variations in environmental factors, whereas internal microbiomes are more tightly linked to host factors.

RESULTS

Here, we use the dataset from the Earth Microbiome Project and accumulate data from 50 additional studies totaling 654 host species and over 15,000 samples to examine global-scale patterns of bacterial diversity and function. We analyze microbiomes from non-captive hosts sampled from natural habitats and find patterns with bioclimate and geophysical factors, as well as land use, host phylogeny, and trophic level/diet. Specifically, external microbiomes are best explained by variations in mean daily temperature range and precipitation seasonality. In contrast, internal microbiomes are best explained by host factors such as phylogeny/immune complexity and trophic level/diet, plus climate.

CONCLUSIONS

Internal microbiomes are predominantly associated with top-down effects, while climatic factors are stronger determinants of microbiomes on host external surfaces. Host immunity may act on microbiome diversity through top-down regulation analogous to predators in non-microbial ecosystems. Noting gaps in geographic and host sampling, this combined dataset represents a global baseline available for interrogation by future microbial ecology studies.

Prevalence and phylogenetic analysis of Cryptosporidium infections in Yezo sika deer (Cervus nippon yesoensis) in the Tokachi sub-prefecture of Hokkaido, Japan

The Yezo sika deer (Cervus nippon yesoensis) on the island of Hokkaido, Japan are currently recognized as overabundant. Hunting is used to control the deer population, and this has increased the supply of game meat, which is associated with a high risk of various food-borne infections. Additionally, the sub-prefecture Tokachi has a dense population of livestock, which are potentially at risk of cross-species infections from the deer. In this study, we undertook the first analysis of the incidence of Cryptosporidium infection in the Yezo sika deer in the Tokachi area using polymerase chain reaction testing and phylogenetic analysis. Polymerase chain reaction analysis showed Cryptosporidium species present in 7.5% of fecal samples (13/173) collected from deer hunted between 2016 and 2017. However, the zoonotic Cryptosporidium paruvm parasite was not detected in the phylogenetic analysis; when sequenced, all species in the positive samples matched the Cryptosporidium deer genotype. However, deer may act as a reservoir of the zoonotic Cryptosporidium parvum parasite, which affects both humans and livestock. Therefore, we recommend the continuation of surveys of the incidence of Cryptosporidium infections in Yezo sika deer.

Molecular detection of Cryptosporidium and Enterocytozoon bieneusi in dairy calves and sika deer in four provinces in Northern China

The protistan pathogens Cryptosporidium and Enterocytozoon bieneusi can cause significant intestinal diseases in animals and humans. However, limited information is available regarding prevalence and molecular characterization of Cryptosporidium and E. bieneusi in ruminants in Northern China. In this study, the overall prevalence of Cryptosporidium and E. bieneusi was 19.3% (62/321) and 28.97% (93/321) in dairy calves and 1.10% (9/818) and 13.57% (111/818) in sika deer (Cervus nippon) in four provinces in Northern China, respectively. The prevalence of Cryptosporidium and E. bieneusi in different factor groups was various. Five Cryptosporidium species/genotypes were identified, of which C. parvum, C. ryanae, C. bovis, and C. andersoni were only found in dairy calves, and only Cryptosporidium deer genotype was found in sika deer. Moreover, J, I, and BEB4 ITS genotypes of E. bieneusi were found in dairy calves, and six known genotypes (JLD-III, JLD-IX, JLD-VII, EbpC, BEB6, and I) and ten novel genotypes (namely LND-I and JLD-XV to JLD-XXIII) were found in sika deer in this study. Cryptosporidium parvum and E. bieneusi genotype J were identified as the predominant species/genotypes in dairy calves, whereas the predominance of Cryptosporidium spp. and E. bieneusi in sika deer was Cryptosporidium deer genotype and BEB6, respectively. The present study reported the prevalence and genotypes of Cryptosporidium and E. bieneusi in dairy calves and sika deer in four provinces in northern China. The present findings also suggest that investigated dairy calves and sika deer may play an important role in the transmission of E. bieneusi and Cryptosporidium to humans and other animals, and also in an effort to better understand the epidemiology of these enteric pathogens in China.

Molecular epidemiology of giardiasis from a veterinary perspective

A total of eight Giardia species are accepted. These include: Giardia duodenalis (syn. Giardia intestinalis and Giardia lamblia), which infects humans and animals, Giardia agilis, Giardia ardeae, Giardia psittaci, Giardia muris, Giardia microti, Giardia peramelis and G. cricetidarum, which infect non-human hosts including amphibians, birds, rodents and marsupials. Giardia duodenalis is a species complex consisting of eight assemblages (A-H), with assemblages A and B the dominant assemblages in humans. Molecular studies to date on the zoonotic potential of Giardia in animals are problematic and are hampered by lack of concordance between loci. Livestock (cattle, sheep, goats and pigs) are predominantly infected with G. duodenalis assemblage E, which has recently been shown to be zoonotic, followed by assemblage A. In cats and dogs, assemblages A, B, C, D and F are commonly reported but relatively few studies have conducted molecular typing of humans and their pets and the results are contradictory with some studies support zoonotic transmission but the majority of studies suggesting separate transmission cycles. Giardia also infects a broad range of wildlife hosts and although much less well studied, host-adapted species as well as G. duodenalis assemblages (A-H) have been identified. Fish and other aquatic wildlife represent a source of infection for humans with Giardia via water contamination and/or consumption of undercooked fish and interestingly, assemblage B and A predominated in the two molecular studies conducted to date. Our current knowledge of the transmission dynamics of Giardia is still poor and the development of more discriminatory typing tools such as whole genome sequencing (WGS) of Giardia isolates is therefore essential.

Detection of Cryptosporidium and Giardia in the slaughterhouse, sewage and river waters of the Qinghai Tibetan plateau area (QTPA), China

The occurrence of Cryptosporidium and Giardia species in slaughter, sewage and river waters of the Qinghai Tibetan Plateau Area (QTPA), China, was investigated. A total of 456 samples were collected from different locations in the QTPA to study the contamination rates of Cryptosporidium spp. and Giardia via PCR and subsequent sequence analysis. Ten samples were Cryptosporidium positive, and 97 were Giardia positive, as confirmed by PCR amplification of the SSU rRNA gene. The percentages of positive Cryptosporidium and Giardia detection were 2.2% (10/456) and 21.3% (97/456), respectively. Cryptosporidium was detected in only sewage and river waters. Six species of Cryptosporidium were identified: Cryptosporidium hominis (n = 5), C. andersoni (n = 1), C. environmental (n = 1), C. struthionis (n = 1), C. canis (n = 1), and C. parvum (n = 1). G. duodenalis assemblage A was identified in almost all positive samples (n = 96), and one sample harboured G. duodenalis assemblage E. The results suggest that Cryptosporidium and Giardia species circulate through the aqueous environment and different hosts. Therefore, we strongly recommend that the local government and health authorities in China undertake control measures to reduce the contamination of water sources by these protozoa to protect the health of humans and animals.

First cross-sectional, molecular epidemiological survey of Cryptosporidium, Giardia and Enterocytozoon in alpaca (Vicugna pacos) in Australia

BACKGROUND

Eukaryotic pathogens, including Cryptosporidium, Giardia and Enterocytozoon, have been implicated in neonatal diarrhoea, leading to marked morbidity and mortality in the alpaca (Vicugna pacos) and llama (Lama glama) around the world. Australia has the largest population of alpacas outside of South America, but very little is known about these pathogens in alpaca populations in this country. Here, we undertook the first molecular epidemiological survey of Cryptosporidium, Giardia and Enterocytozoon in V. pacos in Australia.

METHODS

A cross-sectional survey of 81 herds, comprising alpacas of 6 weeks to 26 years of age, were sampled from the six Australian states (Queensland, New South Wales, Victoria, South Australia, Tasmania and Western Australia) across the four seasons. PCR-based sequencing was employed, utilising genetic markers in the small subunit of the nuclear ribosomal RNA (SSU) and 60-kilodalton glycoprotein (gp60) genes for Cryptosporidium, triose-phosphate isomerase (tpi) gene for Giardia duodenalis and the internal transcribed spacer region (ITS) for Enterocytozoon bieneusi.

RESULTS

PCR-based analyses of 81 faecal DNA samples representing 1421 alpaca individuals detected Cryptosporidium, Giardia and/or Enterocytozoon on 15 farms in New South Wales, Victoria and South Australia, equating to 18.5% of all samples/herds tested. Cryptosporidium was detected on three (3.7%) farms, G. duodenalis on six (7.4%) and E. bieneusi on eight (9.9%) in two or all of these three states, but not in Queensland, Tasmania or Western Australia. Molecular analyses of selected faecal DNA samples from individual alpacas for Cryptosporidium, Giardia and/or Enterocytozoon consistently showed that alpacas of ≤ 6 months of age harboured these pathogens.

CONCLUSIONS

This first molecular investigation of Cryptosporidium, Giardia and Enterocytozoon in alpaca subpopulations in Australia has identified species and genotypes that are of likely importance as primary pathogens of alpacas, particularly young crias, and some genotypes with zoonotic potential. Although the prevalence established here in the alpaca subpopulations studied is low, the present findings suggest that crias are likely reservoirs of infections to susceptible alpacas and/or humans. Future studies should focus on investigating pre-weaned and post-weaned crias, and on exploring transmission patterns to establish what role particular genotypes play in neonatal or perinatal diarrhoea in alpacas and in zoonotic diseases in different states of Australia.

New operational taxonomic units of Enterocytozoon in three marsupial species

Background

Enterocytozoon bieneusi is a microsporidian, commonly found in animals, including humans, in various countries. However, there is scant information about this microorganism in Australasia. In the present study, we conducted the first molecular epidemiological investigation of E. bieneusi in three species of marsupials (Macropus giganteus, Vombatus ursinus and Wallabia bicolor) living in the catchment regions which supply the city of Melbourne with drinking water.

Methods

Genomic DNAs were extracted from 1365 individual faecal deposits from these marsupials, including common wombat (n = 315), eastern grey kangaroo (n = 647) and swamp wallaby (n = 403) from 11 catchment areas, and then individually tested using a nested PCR-based sequencing approach employing the internal transcribed spacer (ITS) and small subunit (SSU) of nuclear ribosomal DNA as genetic markers.

Results

Enterocytozoon bieneusi was detected in 19 of the 1365 faecal samples (1.39%) from wombat (n = 1), kangaroos (n = 13) and wallabies (n = 5). The analysis of ITS sequence data revealed a known (designated NCF2) and four new (MWC_m1 to MWC_m4) genotypes of E. bieneusi. Phylogenetic analysis of ITS sequence data sets showed that MWC_m1 (from wombat) clustered with NCF2, whereas genotypes MWC_m2 (kangaroo and wallaby), MWC_m3 (wallaby) and MWC_m4 (kangaroo) formed a new, divergent clade. Phylogenetic analysis of SSU sequence data revealed that genotypes MWC_m3 and MWC_m4 formed a clade that was distinct from E. bieneusi. The genetic distinctiveness of these two genotypes suggests that they represent a new species of Enterocytozoon.

Conclusions

Further investigations of Enterocytozoon spp. from macropods and other animals will assist in clarifying the taxonomy and epidemiology of these species in Australia and elsewhere, and in assessing the public health risk of enterocytozoonosis.

Electronic supplementary material

The online version of this article (10.1186/s13071-018-2954-x) contains supplementary material, which is available to authorized users.

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.

Comparison of current methods used to detect Cryptosporidium oocysts in stools

In this review all of the methods that are currently in use for the investigation of Cryptosporidium in stool material are highlighted and critically discussed. It appears that more qualifications and background knowledge in this field regarding the diagnosis of the Cryptosporidium parasite is required. Furthermore, there is no standardization for the protocols that are commonly used to either detect oocysts in faeces or to diagnose the Cryptosporidium infection. It is therefore necessary to initiate further education and research that will assist in improving the accuracy of the diagnosis of Cryptosporidium oocysts in the faecal micro-cosmos. Where ambient concentrations of oocysts are low in stool material, detection becomes a formidable task. Procedures for ring tests and the standardization of multi-laboratory testing are recommended. It is also necessary to enhance the routine surveillance capacity of cryptosporidiosis and to improve the safety against it, considering the fact that this disease is under diagnosed and under reported. This review is intended to stimulate research that could lead to future improvements and further developments in monitoring the diagnostic methodologies that will assist in harmonizing Cryptosporidium oocysts in stool diagnosis.

Prevalence and molecular characterization of Cryptosporidium spp. and Giardia duodenalis in 1-2-month-old highland yaks in Qinghai Province, China

Cryptosporidium and Giardia are ubiquitous parasites that infect humans and animals. Few reports are available on the prevalence of these two protozoan parasites in yaks (Bos grunniens). In this study, 344 faecal samples were collected from yaks with diarrhoea in the Chenduo and Nangqian counties of Qinghai Province, China. Cryptosporidium spp. and Giardia duodenalis were detected by light and immunofluorescence microscopy and nested PCR (nPCR). Fifteen samples were positive (4.5%) by Kinyoun staining, 40 (11.6%) samples were positive by immunofluorescence test (IFT), and 39 (11.3%) samples were positive by nPCR for Cryptosporidium spp., Cryptosporidium bovis (11/39, 28.2%) was the most prevalent species, followed by C. ryanae (6/39, 15.4%), C. andersoni (5/39, 12.8%), C. struthionis (5/39, 12.8%), C. parvum (5/39, 12.8%), C. hominis (4/39, 10.3%) and C. canis (3/39, 7.7%). Thirteen out of 344 (3.8%) samples were positive for Giardia by simple microscopy, 20 (5.8%) by IFT and 18 samples (5.2%) yak faecal samples were Giardia positive by nPCR. Two G. duodenalis assemblages (B, E) were detected in this study. Nine positive samples for G. duodenalis assemblage E were from the towns of Xiewu (8/9, 4.9%) and Xiangda (1/9, 1.3%), and nine positive samples (9/9, 8.5%) for G. duodenalis assemblage B were from the town of Zhenqin. This report provides information about infection with Cryptosporidium species and G. duodenalis assemblages in domesticated 1-2-month-old highland yaks living in the Qinghai-Tibet Plateau region of China.

Prevalence and molecular characterization of Cryptosporidium spp. and Giardia duodenalis in deer in Henan and Jilin, China

Background

Little is known about the prevalence and zoonotic potential of Cryptosporidium spp. and Giardia duodenalis in deer in China. In this study, 662 fecal samples were collected from 11 farms in Henan and Jilin Provinces between July 2013 and August 2014, and were screened for the presence of Cryptosporidium and G. duodenalis with genotyping and subtyping methods.

Results

Cryptosporidium spp. and G. duodenalis were detected in 6.80% (45/662) and 1.21% (5/662) of samples, respectively. Six Cryptosporidium species/genotypes were identified based on the small subunit ribosomal ribonucleic acid (SSU rRNA) gene: C. parvum (n = 11); C. andersoni (n = 5); C. ubiquitum (n = 3); C. muris (n = 1); C. suis-like (n = 1); and Cryptosporidium deer genotype (n = 24). When five of the 11 C. parvum isolates were subtyped by sequencing the 60 kDa glycoprotein (gp60) gene, zoonotic subtypes IIaA15G2R2 (n = 4) and IIdA19G1 (n = 1) were found. According to a subtype analysis, three C. ubiquitum isolates belonged to XIIa subtype 2. In contrast, only assemblage E was detected in the five Giardia-positive samples with small subunit ribosomal ribonucleic acid (SSU rRNA) gene sequencing.

Conclusions

To our knowledge, this is the first study to report C. andersoni, as well as C. parvum zoonotic subtypes IIaA15G2R2 and IIdA19G1 in cervids. These data, though limited, suggest that cervids may be a source of zoonotic Cryptosporidium and Giardia. Cervids in the present study are likely to be of low zoonotic potential to humans, and more molecular epidemiological studies are required to clarify the prevalence and public health significance of Cryptosporidium and G. duodenalis in cervids throughout China.

Prevalence and risk factors of Giardia duodenalis in domestic rabbbits (Oryctolagus cuniculus) in Jilin and Liaoning province, northeastern China

BACKGROUND

Giardia duodenalis is one of the most important intestinal parasites that can infect virtually all animals, including rabbits and humans. However, there is little information regarding the prevalence and genotypes of G. duodenalis in domestic rabbits in China.

METHODS

A total of 426 rabbit fecal samples (136 from Shenyang City, 174 from Changchun City, and 116 from Jilin City) were examined by Lugol's iodine staining with microscopy analysis, and the positive samples were genotyped at the triosephosphate isomerase (tpi) and the beta giardin (bg) gene loci using nested PCR.

RESULTS

Forty-two (9.86%) out of 426 rabbit fecal samples were G. duodenalis-positive under microscopy analysis, and the highest G. duodenalis infection rate was 23.08% on farm 6. The prevalence of G. duodenalis in rabbits from different cities ranged from 1.47% to 14.37%. Among different age groups, G. duodenalis prevalence in rabbits ranged from 5.41% to 12.58%. The prevalence of G. duodenalis in outdoor rabbits and indoor rabbits was 14.29% and 6.77%, respectively. In the present study, region and farming mode were highly correlated with G. duodenalis infection in rabbits. All 42 G. duodenalis isolates were successfully amplified and sequenced at the tpi and bg loci, and only G. duodenalis assemblage B were identified.

CONCLUSION

This study not only further confirmed the dominance of G. duodenalis assemblage B in rabbits, but also further improved the foundation data concerning the distribution of G. duodenalis assemblages in China.

The first report of Cryptosporidium spp. in Microtus fuscus (Qinghai vole) and Ochotona curzoniae (wild plateau pika) in the Qinghai-Tibetan Plateau area, China

Cryptosporidium is one of the most important genera of intestinal zoonotic pathogens, which can infect various hosts and cause diarrhoea. There is little available information about the molecular characterisation and epidemiological prevalence of Cryptosporidium spp. in Microtus fuscus (Qinghai vole) and Ochotona curzoniae (wild plateau pika) in the Qinghai-Tibetan Plateau area of Qinghai Province, Northwest China. Therefore, the aim of this study was to determine Cryptosporidium species/genotypes and epidemiological prevalence in these mammals by detecting the SSU rRNA gene by PCR amplification. The Cryptosporidium spp. infection rate was 8.9% (8/90) in Qinghai voles and 6.25% (4/64) in wild plateau pikas. Positive samples were successfully sequenced, and the following Cryptosporidium species were found: C. parvum, C. ubiquitum, C. canis and a novel genotype in Qinghai voles and C. parvum and a novel genotype in wild plateau pikas. This is the first report of Cryptosporidium infections in M. fuscus and wild O. curzoniae in Northwest China. The results suggest the possibility of Cryptosporidium species transmission among these two hosts, the environment, other animals and humans and provide useful molecular epidemiological data for the prevention and control of Cryptosporidium infections in wild animals and the surrounding environments. The results of the present study indicate the existence of Cryptosporidium species infections that have potential public health significance. This is the first report of Cryptosporidium multi-species infections in these animal hosts.

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

Cryptosporidium viatorum is a globally distributed pathogenic species of Cryptosporidium that has only ever been recorded from humans, until now. For the first time, we molecularly characterised a novel subtype of C. viatorum (subtype XVbA2G1) from the endemic Australian swamp rat (Rattus lutreolus) using the small subunit of nuclear ribosomal RNA (SSU) gene and then subtyped it using the 60-kilodalton glycoprotein (gp60) gene. In total, faecal samples from 21 swamp rats (three were positive for C. viatorum), three broad toothed rats (Mastacomys fuscus) and two bush rats (Rattus fuscipes) were tested for Cryptosporidium. The long-term, isolated nature of the swamp rat population in Melbourne's drinking water catchment system (where public access is prohibited), the lack of C. viatorum from other mammals and birds living within the vicinity of this system and its genetic distinctiveness in both the SSU and gp60 gene sequences from other species of Cryptosporidium collectively suggest that C. viatorum might be endemic to native rats in Australia. The current state of knowledge of epidemiological surveys of Cryptosporidium of rats and the zoonotic potential are further discussed in light of the finding of C. viatorum. Long-term studies, with the capacity to repetitively sample a variety of hosts in multiple localities, in different seasons and years, will allow for greater insight into the epidemiological patterns and zoonotic potential of rare Cryptosporidium species such as C. viatorum.

Use of a bioinformatic-assisted primer design strategy to establish a new nested PCR-based method for Cryptosporidium

BACKGROUND

The accurate tracking of Cryptosporidium in faecal, water and/or soil samples in water catchment areas is central to developing strategies to manage the potential risk of cryptosporidiosis transmission to humans. Various PCR assays are used for this purpose. Although some assays achieve specific amplification from Cryptosporidium DNA in animal faecal samples, some do not. Indeed, we have observed non-specificity of some oligonucleotide primers in the small subunit of nuclear ribosomal RNA gene (SSU), which has presented an obstacle to the identification and classification of Cryptosporidium species and genotypes (taxa) from faecal samples.

RESULTS

Using a novel bioinformatic approach, we explored all available Cryptosporidium genome sequences for new and diagnostically-informative, multi-copy regions to specifically design oligonucleotide primers in the large subunit of nuclear ribosomal RNA gene (LSU) as a basis for an effective nested PCR-based sequencing method for the identification and/or classification of Cryptosporidium taxa.

CONCLUSION

This newly established PCR, which has high analytical specificity and sensitivity, is now in routine use in our laboratory, together with other assays developed by various colleagues. Although the present bioinformatic workflow used here was for the specific design of primers in nuclear DNA of Cryptosporidium, this approach should be broadly applicable to many other microorganisms.

Giardia duodenalis Infections in Humans and Other Animals in China

Giardia duodenalis is an important zoonotic pathogen in both public and veterinary health, and has been genotyped into at least eight assemblages (A-H), each with a distinct host range. In recent years, this intestinal protozoan parasite has been identified widely in humans and various other animals, and has even been recorded in environmental contaminants. Along with whole genome sequencing of G. duodenalis, multilocus sequence typing is increasingly being used to characterize G. duodenalis isolates. Here, we review the epidemiology, genotyping, and subtyping of G. duodenalis from humans and a wide range of other animals, as well as from wastewater, in China.

Is Cryptosporidium from the common wombat (Vombatus ursinus) a new species and distinct from Cryptosporidium ubiquitum?

The emerging zoonotic pathogen Cryptosporidium ubiquitum has been found in a variety of mammalian hosts, including humans, throughout the world. Advances in the molecular characterization of this parasite using the sequence of the 60kDa glycoprotein (gp60) gene have allowed the classification of "subtypes". Sequences derived from faecal samples from the common wombat (Vombatus ursinus) have identified a novel gp60 subtype designated here as C. ubiquitum XIIg. Phylogenetic analysis suggests that subtypes of C. ubiquitum can be divided into generalist and specialist groups, which is important when considering the zoonotic potential of C. ubiquitum in the context of drinking water safety.