Prevalence, genetic diversity and potential clinical impact of blood-borne and enteric protozoan parasites in native mammals from northern Australia

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.

'A flying start': Wildlife trypanosomes in tissues of Australian tabanids (Diptera: Tabanidae)

Tabanids (syn. horse flies) are biting-flies of medical and veterinary significance because of their ability to transmit a range of pathogens including trypanosomes - some species of which carry a combined health and biosecurity risk. Invertebrate vectors responsible for transmitting species of Trypanosoma between Australian wildlife remains unknown, thus establishing the role of potential vector candidates such as tabanids is of utmost importance. The current study aimed to investigate the presence of indigenous trypanosomes in tabanids from an endemic area of south-west Australia. A total of 148 tabanids were collected, with morphological analysis revealing two subgenera: Scaptia (Pseudoscione) and S. (Scaptia) among collected flies. A parasitological survey using an HRM-qPCR and sequencing approach revealed a high (105/148; 71%) prevalence of trypanosomatid DNA within collected tabanids. Individual tissues - proboscis (labrum, labium and mandibles, hypopharynx), salivary glands, proventriculus, midgut, and hindgut and rectum - were also tested from a subset of 20 tabanids (n = 140 tissues), confirming the presence of Trypanosoma noyesi in 31% of screened tissues, accompanied by T. copemani (3%) and T. vegrandis/T.gilletti (5%). An unconfirmed trypanosomatid sp. was also detected (9%) within tissues. The difference between tissues infected with T. noyesi compared with tissues infected with other trypanosome species was statistically significant (p < 0.05), revealing T. noyesi as the more frequent species detected in the tabanids examined. Fluorescence in situ hybridisation (FISH) and scanning electron microscopy (SEM) confirmed intact parasites within salivary glands and the proboscis respectively, suggesting that both biological and mechanical modes of transmission could occur. This study reveals the presence of Australian Trypanosoma across tabanid tissues and confirms intact parasites within tabanid salivary glands and the proboscis for the first time. Further investigations are required to determine whether tabanids have the vectorial competence to transmit Australian trypanosomes between wildlife.

Molecular Detection of Trypanosoma spp. in Questing and Feeding Ticks (Ixodidae) Collected from an Endemic Region of South-West Australia

A growing number of indigenous trypanosomes have been reported to naturally infect a variety of Australian wildlife with some species of Trypanosoma implicated in the population decline of critically endangered marsupials. However, the mode of transmission of Australian trypanosomes is unknown since their vectors remain unidentified. Here we aimed to fill this current knowledge gap about the occurrence and identity of indigenous trypanosomes in Australian invertebrates by conducting molecular screening for the presence of Trypanosoma spp. in native ticks collected from south-west Australia. A total of 231 ticks (148 collected from vegetation and 83 retrieved directly from 76 marsupial hosts) were screened for Trypanosoma using a High-Resolution Melt (HRM) qPCR assay. An overall Trypanosoma qPCR positivity of 37% (46/125) and 34% (26/76) was detected in questing ticks and host-collected (i.e., feeding) ticks, respectively. Of these, sequencing revealed 28% (35/125) of questing and 28% (21/76) of feeding ticks were infected with one or more of the five species of trypanosome previously reported in this region (T. copemani, T. noyesi, T. vegrandis, T. gilletti, Trypanosoma sp. ANU2). This work has confirmed that Australian ticks are capable of harbouring several species of indigenous trypanosome and likely serve as their vectors.

Epidemiology of Trypanosomiasis in Wildlife-Implications for Humans at the Wildlife Interface in Africa

While both human and animal trypanosomiasis continue to present as major human and animal public health constraints globally, detailed analyses of trypanosome wildlife reservoir hosts remain sparse. African animal trypanosomiasis (AAT) affects both livestock and wildlife carrying a significant risk of spillover and cross-transmission of species and strains between populations. Increased human activity together with pressure on land resources is increasing wildlife–livestock–human infections. Increasing proximity between human settlements and grazing lands to wildlife reserves and game parks only serves to exacerbate zoonotic risk. Communities living and maintaining livestock on the fringes of wildlife-rich ecosystems require to have in place methods of vector control for prevention of AAT transmission and for the treatment of their livestock. Major Trypanosoma spp. include Trypanosoma brucei rhodesiense, Trypanosoma brucei gambiense, and Trypanosoma cruzi, pathogenic for humans, and Trypanosoma vivax, Trypanosoma congolense, Trypanosoma evansi, Trypanosoma brucei brucei, Trypanosoma dionisii, Trypanosoma thomasbancrofti, Trypanosma elephantis, Trypanosoma vegrandis, Trypanosoma copemani, Trypanosoma irwini, Trypanosoma copemani, Trypanosoma gilletti, Trypanosoma theileri, Trypanosoma godfreyi, Trypansoma simiae, and Trypanosoma (Megatrypanum) pestanai. Wildlife hosts for the trypansomatidae include subfamilies of Bovinae, Suidae, Pantherinae, Equidae, Alcephinae, Cercopithecinae, Crocodilinae, Pteropodidae, Peramelidae, Sigmodontidae, and Meliphagidae. Wildlife species are generally considered tolerant to trypanosome infection following centuries of coexistence of vectors and wildlife hosts. Tolerance is influenced by age, sex, species, and physiological condition and parasite challenge. Cyclic transmission through Glossina species occurs for T. congolense, T. simiae, T. vivax, T. brucei, and T. b. rhodesiense, T. b. gambiense, and within Reduviid bugs for T. cruzi. T. evansi is mechanically transmitted, and T. vixax is also commonly transmitted by biting flies including tsetse. Wildlife animal species serve as long-term reservoirs of infection, but the delicate acquired balance between trypanotolerance and trypanosome challenge can be disrupted by an increase in challenge and/or the introduction of new more virulent species into the ecosystem. There is a need to protect wildlife, animal, and human populations from the infectious consequences of encroachment to preserve and protect these populations. In this review, we explore the ecology and epidemiology of Trypanosoma spp. in wildlife.

A review on application of next-generation sequencing methods for profiling of protozoan parasites in water: Current methodologies, challenges, and perspectives

The advancement in metagenomic techniques has provided novel tools for profiling human parasites in environmental matrices, such as water and wastewater. However, application of metagenomic techniques for the profiling of protozoan parasites in environmental matrices is not commonly reported in the literature. The key factors leading to the less common use of metagenomics are the complexity and large eukaryotic genome, the prevalence of small parasite populations in environmental samples compared to bacteria, difficulties in extracting DNA from (oo)cysts, and limited reference databases for parasites. This calls for further research to develop optimized methods specifically looking at protozoan parasites in the environment. This study reviews the current workflow, methods and provide recommendations for the standardization of techniques. The article identifies and summarizes the key methods, advantages, and limitations associated with metagenomic analysis, like sample pre-processing, DNA extraction, sequencing approaches, and analysis methods. The study enhances the understanding and application of standardized protocols for profiling of protozoan parasite community from highly complexe samples and further creates a resourceful comparison among datasets without any biases.

Meta-transcriptomic identification of Trypanosoma spp. in native wildlife species from Australia

Background

Wildlife species carry a remarkable diversity of trypanosomes. The detection of trypanosome infection in native Australian fauna is central to understanding their diversity and host-parasite associations. The implementation of total RNA sequencing (meta-transcriptomics) in trypanosome surveillance and diagnosis provides a powerful methodological approach to better understand the host species distribution of this important group of parasites.

Methods

We implemented a meta-transcriptomic approach to detect trypanosomes in a variety of tissues (brain, liver, lung, skin, gonads) sampled from native Australian wildlife, comprising four marsupials (koala, Phascolarctos cinereus; southern brown bandicoot, Isoodon obesulus; swamp wallaby, Wallabia bicolor; bare-nosed wombat, Vombatus ursinus), one bird (regent honeyeater, Anthochaera phrygia) and one amphibian (eastern dwarf tree frog, Litoria fallax). Samples corresponded to both clinically healthy and diseased individuals. Sequencing reads were de novo assembled into contigs and annotated. The evolutionary relationships among the trypanosomatid sequences identified were determined through phylogenetic analysis of 18S rRNA sequences.

Results

We detected trypanosome sequences in all six species of vertebrates sampled, with positive samples in multiple organs and tissues confirmed by PCR. Phylogenetic analysis indicated that the trypanosomes infecting marsupials were related to those previously detected in placental and marsupial mammals, while the trypanosome in the regent honeyeater grouped with avian trypanosomes. In contrast, we provide the first evidence for a trypanosome in the eastern dwarf tree frog that was phylogenetically distinct from those described in other amphibians.

Conclusions

To our knowledge, this is the first meta-transcriptomic analysis of trypanosomes in native Australian wildlife, expanding the known genetic diversity of these important parasites. We demonstrated that RNA sequencing is sufficiently sensitive to detect low numbers of Trypanosoma transcripts and from diverse hosts and tissues types, thereby representing an effective means to detect trypanosomes that are divergent in genome sequence.

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.

BASELINE HEALTH AND DISEASE ASSESSMENT OF FOUNDER EASTERN QUOLLS (DASYURUS VIVERRINUS) DURING A CONSERVATION TRANSLOCATION TO MAINLAND AUSTRALIA

We evaluated the health of 31 (eight males, 23 females) founder eastern quolls (Dasyurus viverrinus), translocated to a fenced reserve in the Australian Capital Territory between February 2016 and July 2017. Quolls were wild caught in Tasmania (16 animals) or captive bred at Mount Rothwell Biodiversity Interpretation Centre, Victoria (15 animals). Quolls were assessed for the presence of selected potential pathogens (Toxoplasma gondii, herpesviruses, Salmonella serovars, hemoprotozoa, and ectoparasites). We assessed the relationships among sex, provenance (captive or free ranging), T. gondii or herpesvirus infection, weight, and hematologic and biochemical variables. Six of 21 quolls (29%) tested were seropositive for antibodies to T. gondii. Seropositive quolls weighed significantly more and had significantly lower potassium levels, anion gaps, and urea and triglyceride levels than seronegative quolls had. Eighteen of 31 (58%) combined conjunctival-pharyngeal-cloacal swabs collected from quolls were PCR positive for a newly identified gammaherpesvirus, tentatively named dasyurid gammaherpesvirus 3. There were no significant differences among hematologic and biochemical variables or body weights from PCR-positive and PCR-negative quolls. Eighteen of 18 (100%) of rectal-swab samples were culture negative for Salmonella serovars. Three species of tick (Ixodes tasmani, Ixodes fecialis, and Ixodes holocyclus), two species of mite (Andreacus radfordi, one unidentified), and four species of flea (Pygiopsylla hoplia, Acanthopsylla rothschildi rothschildi, Uropsylla tasmanica, and Stephanocircus dasyuri), were detected on wild-caught quolls, whereas a fifth species of flea, Echidnophaga myremecobii, was detected only on captive-bred quolls. Five of 15 blood samples (33%) were positive for hemoprotozoan DNA via PCR, a novel Hepatozoon species, a novel Theileria species, Theileria paparinii, and Trypanosoma copemani were detected. Despite the presence of several potential pathogens known to be associated with disease in other marsupials, the quolls were considered to be in good general health, suitable for translocation, and a viable population was subsequently established.

A new method for quantitative detection of Lactobacillus casei based on casx gene and its application

Background

The traditional method of bacterial identification based on 16S rRNA is a widely used and very effective detection method, but this method still has some deficiencies, especially in the identification of closely related strains. A high homology with little differences is mostly observed in the 16S sequence of closely related bacteria, which results in difficulty to distinguish them by 16S rRNA-based detection method. In order to develop a rapid and accurate method of bacterial identification, we studied the possibility of identifying bacteria with other characteristic fragments without the use of 16S rRNA as detection targets.

Results

We analyzed the potential of using cas (CRISPR-associated proteins) gene as a target for bacteria detection. We found that certain fragment located in the casx gene was species-specific and could be used as a specific target gene. Based on these fragments, we established a TaqMan MGB Real-time PCR method for detecting bacteria. We found that the method used in this study had the advantages of high sensitivity and good specificity.

Conclusions

The casx gene-based method of bacterial identification could be used as a supplement to the conventional 16 s rRNA-based detection method. This method has an advantage over the 16 s rRNA-based detection method in distinguishing the genetic relationship between closely-related bacteria, such as subgroup bacteria, and can be used as a supplement to the 16 s rRNA-based detection method.

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.

Sporothrix humicola (Ascomycota: Ophiostomatales) - A soil-borne fungus with pathogenic potential in the eastern quoll (Dasyurus viverrinus)

The genus Sporothrix contains both species pathogenic to humans and animals as well as environmental fungi. S. humicola, a member of the latter S. pallida clade, has previously been reported only from soil. We have isolated this dimorphic fungus from multiple cutaneous lesions in two endangered marsupials native to Tasmania. Clinical appearance resembled cutaneous sporotrichosis, highlighting the principle pathogenic potential. Identification was based on partial ITS, β-tubulin and calmodulin gene sequencing.

Anthropozoonotic significance, risk factors and spatial distribution of Giardia spp. infections in quenda (Isoodon obesulus) in the greater Perth region, Western Australia

Giardia spp. infections in wildlife populations have been linked to anthropogenic sources of infection and public health risk in a diversity of wildlife species and ecological locations worldwide. Quenda (Isoodon obesulus) remain in many urbanised areas of Perth, Western Australia, and can be gregarious in their interactions with humans and domestic animals. In a previous study, a high prevalence of Giardia spp. infection was identified amongst quenda trapped in urbanised environments and bushland in Perth, Western Australia. This study aimed to expand on that finding, by: identifying and estimating the prevalence of particular species of Giardia infecting quenda, and thus clarifying their anthropozoonotic/public health significance; identifying risk factors for Giardia spp. infection; and investigating putative associations between infection and indicators of ill health. Giardia spp. infections in Perth quenda are overwhelmingly of the host-adapted, non-zoonotic Giardia peramelis (apparent prevalence 22.2%; 95% CI 17.7–27.4%), indicating that quenda are not a substantial veterinary public health risk regarding this parasite genus. However, one case each of Giardia duodenalis and Giardia canis genotype D were identified in quenda trapped in urbanised environments (apparent prevalences 0.4%; 95% CI 0.1–1.9%). In quenda, Giardia spp. infection is associated with Cryptosporidium infection and flea infection intensity, which may reflect host population density, or regarding Cryptosporidium spp., similar transmission pathways or synergistic interactions between these taxa within the host. Giardia spp. infection is not associated with the measured indicators of ill health in Perth quenda, but this finding is representative of Giardia peramelis only, given the apparent rarity of other Giardia sp. infections in this study.

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Giardia spp. infections in Perth quenda are rarely of anthropozoonotic species.

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Anthropozoonotic Giardia spp. only found in quenda in urbanised environments.

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Quenda Giardia spp. infection risk is associated with Cryptosporidium spp.

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No association identified between G. peramelis infection and ill health indicators.

Molecular surveillance of piroplasms in ticks from small and medium-sized urban and peri-urban mammals in Australia

Natural landscape alterations as a consequence of urbanisation are one of the main drivers in the movements of wildlife into metropolitan and peri-urban areas. Worldwide, these wildlife species are highly adaptable and may be responsible for the transmission of tick-borne pathogens including piroplasms (Babesia, Theileria and Cytauxzoon spp.) that cause piroplasmosis in animals and occasionally in humans. Little is known about piroplasms in the ticks of urban wildlife in Australia. Ticks from long-nosed bandicoots (Perameles nasuta; n = 71), eastern-barred bandicoots (Perameles gunnii; n = 41), northern-brown bandicoots (Isoodon macrourus; n = 19), southern-brown bandicoots (Isoodon obesulus; n = 4), bandicoot sp. (n = 2), flying foxes (Pteropus sp.; n = 3), black rats (Rattus rattus; n = 7), bush rats (Rattus fuscipes; n = 4), brushtail possums (Trichosurus vulpecula; n = 19), ringtail possums (Pseudocheirus peregrinus; n = 12), short-eared possums (Trichosurus caninus; n = 6), possum sp. (Trichosurus sp.; n = 8), and red foxes (Vulpes vulpes; n = 12) were analysed using piroplasm-specific 18S primers and Sanger sequencing. Seven Ixodes tasmani ticks from long-nosed bandicoots and bandicoots sp., three I. tasmani ticks and one Ixodes holocyclus tick from brushtail possums, and one Haemaphysalis longicornis tick from a red fox were positive for piroplasms. New genotypes, with sequences sharing 98% nucleotide similarities with Theileria sp. K1 detected in a burrowing bettong (Bettongia lesueur), were identified from bandicoot ticks. New genotypes were detected in ticks from brushtail possums, which shared 98% similarity with a Babesia sp. (JQ682877) previously identified in marsupials. Theileria orientalis was identified in the H. longicornis tick from the red fox. Babesia and Theileria spp. in the ticks parasitizing bandicoots and brushtail possums clustered closely with respective Babesia and Theileria clades derived from Australian marsupials. This represents the first detection of piroplasms in ticks parasitizing brushtail possums and a red fox in Australia.

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First characterisation of novel Babesia sp. in ticks from brushtail possums in Australia.

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First detection of Theileria orientalis in tick on a red fox in Australia.

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Theileria sp. derived from Australian marsupials form a unique clade.

Increased genetic diversity and prevalence of co-infection with Trypanosoma spp. in koalas (Phascolarctos cinereus) and their ticks identified using next-generation sequencing (NGS)

Infections with Trypanosoma spp. have been associated with poor health and decreased survival of koalas (Phascolarctos cinereus), particularly in the presence of concurrent pathogens such as Chlamydia and koala retrovirus. The present study describes the application of a next-generation sequencing (NGS)-based assay to characterise the prevalence and genetic diversity of trypanosome communities in koalas and two native species of ticks (Ixodes holocyclus and I. tasmani) removed from koala hosts. Among 168 koalas tested, 32.2% (95% CI: 25.2–39.8%) were positive for at least one Trypanosoma sp. Previously described Trypanosoma spp. from koalas were identified, including T. irwini (32.1%, 95% CI: 25.2–39.8%), T. gilletti (25%, 95% CI: 18.7–32.3%), T. copemani (27.4%, 95% CI: 20.8–34.8%) and T. vegrandis (10.1%, 95% CI: 6.0–15.7%). Trypanosoma noyesi was detected for the first time in koalas, although at a low prevalence (0.6% 95% CI: 0–3.3%), and a novel species (Trypanosoma sp. AB-2017) was identified at a prevalence of 4.8% (95% CI: 2.1–9.2%). Mixed infections with up to five species were present in 27.4% (95% CI: 21–35%) of the koalas, which was significantly higher than the prevalence of single infections 4.8% (95% CI: 2–9%). Overall, a considerably higher proportion (79.7%) of the Trypanosoma sequences isolated from koala blood samples were identified as T. irwini, suggesting this is the dominant species. Co-infections involving T. gilletti, T. irwini, T. copemani, T. vegrandis and Trypanosoma sp. AB-2017 were also detected in ticks, with T. gilletti and T. copemani being the dominant species within the invertebrate hosts. Direct Sanger sequencing of Trypanosoma 18S rRNA gene amplicons was also performed and results revealed that this method was only able to identify the genotypes with greater amount of reads (according to NGS) within koala samples, which highlights the advantages of NGS in detecting mixed infections. The present study provides new insights on the natural genetic diversity of Trypanosoma communities infecting koalas and constitutes a benchmark for future clinical and epidemiological studies required to quantify the contribution of trypanosome infections on koala survival rates.