First Molecular Characterization of Theileria ornithorhynchi Mackerras, 1959: yet Another Challenge to the Systematics of the Piroplasms

Applying a modified streamlined disease risk analysis framework to a platypus conservation translocation, with special consideration for the conservation of ecto- and endoparasites

Platypuses are the world's most evolutionarily distinct mammal and have several host-specific ecto- and endoparasites. With platypus populations declining, consideration should also be given to preserving these high conservation priority parasites alongside their charismatic host. A disease risk analysis (DRA) was performed for a platypus conservation translocation, using a modified streamlined methodology that incorporated a parasite conservation framework. DRA frameworks rarely consider parasite conservation. Rather, parasites are typically considered myopically in terms of the potential harm they may cause their host. To address this, a previously proposed parasite conservation framework was incorporated into an existing streamlined DRA methodology. Incorporation of the two frameworks was achieved readily, although there is opportunity for further refinement of this process. This DRA is significant as it is the first performed for any monotreme species, and implements the emerging approach of balancing the health and disease risk of the host with parasite conservation.

First Detection of Theileria sinensis-like and Anaplasma capra in Ixodes kashmiricus: With Notes on cox1-Based Phylogenetic Position and New Locality Records

Ixodes ticks transmit Theileria and Anaplasma species to a wide range of animals. The spreading of ticks and tick-borne pathogens has been attributed to transhumant herds, and research on these uninvestigated issues has been neglected in many countries, including Pakistan. Recently, we used internal transcribed spacer (ITS) and 16S ribosomal DNA partial sequences to genetically characterize Ixodes kashmiricus ticks and their associated Rickettsia spp. However, the data on its cox1 sequence and associated Theileria spp. and Anaplasma spp. are missing. This study aimed to genetically characterize I. kashmiricus based on the cox1 sequence and their associated Theileria spp. and Anaplasma spp. The I. kashmiricus ticks were collected from small ruminants: sheep (Ovis aries) and goats (Capra hircus) of transhumant herds in district Shangla, Dir Upper and Chitral, Khyber Pakhtunkhwa (KP), Pakistan. Out of 129 examined hosts, 94 (72.87%) (56 sheep and 38 goats) were infested by 352 ticks, including adult females (175; 49.7%) followed by nymphs (115; 32.7%) and males (62; 17.6%). For molecular analyses, 121 ticks were subjected to DNA isolation and PCR for the amplification of the cox1 sequence for I. kashmiricus, 18S rDNA for Theileria spp. and 16S rDNA sequences for Anaplasma spp. The obtained cox1 sequence showed 89.29%, 88.78%, and 88.71% identity with Ixodes scapularis, Ixodes gibbosus, and Ixodes apronophorus, respectively. Phylogenetically, the present cox1 sequence clustered with the Ixodes ricinus complex. Additionally, the 18S rDNA sequence showed 98.11% maximum identity with Theileria cf. sinensis and 97.99% identity with Theileria sinensis. Phylogenetically, Theileria spp. clustered with the T. cf. sinensis and T. sinensis. In the case of Anaplasma spp., the 16S rDNA sequence showed 100% identity with Anaplasma capra and phylogenetically clustered with the A. capra. PCR-based DNA detection targeting the amplification of groEL and flaB sequences of Coxiella spp. and Borrelia spp., respectively, was unsuccessful. This is the first phylogenetic report based on cox1 and new locality records of I. kashmiricus, and the associated T. sinensis-like and A. capra. Significant tick surveillance studies are needed in order to determine the epidemiology of Ixodes ticks and their associated pathogens.

Genomic Characterization of Theileria luwenshuni Strain Cheeloo

Theileria, a tick-borne intracellular protozoan, can cause infections of various livestock and wildlife around the world, posing a threat to veterinary health. Although more and more Theileria species have been identified, genomes have been available only from four Theileria species to date. Here, we assembled a whole genome of Theileria luwenshuni, an emerging Theileria, through next-generation sequencing of purified erythrocytes from the blood of a naturally infected goat. We designated it T. luwenshuni str. Cheeloo because its genome was assembled by the researchers at Cheeloo College of Medicine, Shandong University, China. The genome of T. lunwenshuni str. Cheeloo was the smallest in comparison with the other four Theileria species. T. luwenshuni str. Cheeloo possessed the fewest gene gains and gene family expansion. The protein count of each category was always comparable between T. luwenshuni str. Cheeloo and T. orientalis str. Shintoku in the Eukaryote Orthologs annotation, though there were remarkable differences in genome size. T. luwenshuni str. Cheeloo had lower counts than the other four Theileria species in most categories at level 3 of Gene Ontology annotation. Kyoto Encyclopedia of Genes and Genomes annotation revealed a loss of the c-Myb in T. luwenshuni str. Cheeloo. The infection rate of T. luwenshuni str. Cheeloo was up to 81.5% in a total of 54 goats from three flocks. The phylogenetic analyses based on both 18S rRNA and cox1 genes indicated that T. luwenshuni had relatively low diversity. The first characterization of the T. luwenshuni genome will promote better understanding of the emerging Theileria. IMPORTANCE Theileria has led to substantial economic losses in animal husbandry. Whole-genome sequencing data of the genus Theileria are currently limited, which has prohibited us from further understanding their molecular features. This work depicted whole-genome sequences of T. luwenshuni str. Cheeloo, an emerging Theileria species, and reported a high prevalence of T. luwenshuni str. Cheeloo infection in goats. The first assembly and characterization of T. luwenshuni genome will benefit exploring the infective and pathogenic mechanisms of the emerging Theileria to provide scientific basis for future control strategies of theileriosis.

Blood Parasites in Endangered Wildlife-Trypanosomes Discovered During a Survey of Haemoprotozoa from the Tasmanian Devil

The impact of emerging infectious diseases is increasingly recognised as a major threat to wildlife. Wild populations of the endangered Tasmanian devil, Sarcophilus harrisii, are experiencing devastating losses from a novel transmissible cancer, devil facial tumour disease (DFTD); however, despite the rapid decline of this species, there is currently no information on the presence of haemoprotozoan parasites. In the present study, 95 Tasmanian devil blood samples were collected from four populations in Tasmania, Australia, which underwent molecular screening to detect four major groups of haemoprotozoa: (i) trypanosomes, (ii) piroplasms, (iii) Hepatozoon, and (iv) haemosporidia. Sequence results revealed Trypanosoma infections in 32/95 individuals. Trypanosoma copemani was identified in 10 Tasmanian devils from three sites and a second Trypanosoma sp. was identified in 22 individuals that were grouped within the poorly described T. cyclops clade. A single blood sample was positive for Babesia sp., which most closely matched Babesia lohae. No other blood protozoan parasite DNA was detected. This study provides the first insight into haemoprotozoa from the Tasmanian devil and the first identification of Trypanosoma and Babesia in this carnivorous marsupial.

Sequence analyses at mitochondrial and nuclear loci reveal a novel Theileria sp. and aid in the phylogenetic resolution of piroplasms from Australian marsupials and ticks

The order Piroplasmida encompasses two main families: Babesiidae and Theileriidae, containing tick-borne pathogens of veterinary and medical importance worldwide. While only three genera (Babesia, Cytauxzoon and Theileria) comprising piroplasm parasites are currently recognised, phylogenetic studies at the 18S rRNA (18S) gene suggest that these organisms represent at least ten lineages, one of which comprises the relatively unique and highly diverse Theileria spp. from Australian marsupials and ticks. As an alternative to analysing 18S sequences alone, sequencing of mitochondrial genes has proven to be useful for the elucidation of evolutionary relationships amongst some groups of piroplasms. This research aimed to characterise piroplasms from Australian native mammals and ticks using multiple genetic markers (18S, cytochrome c, oxidase subunit III (cox3) and cytochrome B (cytB)) and microscopy. For this, nearly complete piroplasm-18S sequences were obtained from 32 animals belonging to six marsupial species: eastern bettong (Bettongia gaimardi), eastern quoll (Dasyurus viverrinus), eastern grey kangaroo (Macropus giganteus), swamp wallaby (Wallabia bicolor), quokka (Setonix brachyurus) and Gilbert’s potoroo (Potorous gilbertii). The organisms detected represented eight novel Theileria genotypes, which formed five sub-clades within the main marsupial clade containing previously reported Australian marsupial and tick-derived Theileria spp. A selection of both novel and previously described Australian piroplasms at the 18S were also successfully characterised, for the first time, at the cox3 and cytB loci, and corroborated the position of Australian native theilerias in a separate, well-supported clade. Analyses of the cox3 and cytB genes also aided in the taxonomic resolution within the clade of Australian Piroplasmida. Importantly, microscopy and molecular analysis at multiple loci led to the discovery of a unique piroplasm species that clustered with the Australian marsupial theilerias, for which we propose the name Theileria lupei n. sp.

Babesia Life Cycle - When Phylogeny Meets Biology

Although Babesia represents an important worldwide veterinary threat and an emerging risk to humans, this parasite has been poorly studied as compared to Plasmodium, its malaria-causing relative. In fact, Babesia employs highly specific survival strategies during its intraerythrocytic development and its intricate journey through the tick vector. This review introduces a substantially extended molecular phylogeny of the order Piroplasmida, challenging previous taxonomic classifications. The intriguing developmental proficiencies of Babesia are highlighted and compared with those of other haemoparasitic Apicomplexa. Molecular mechanisms associated with distinctive events in the Babesia life cycle are emphasized as potential targets for the development of Babesia-specific treatments.

Cysteine Proteinase C1A Paralog Profiles Correspond with Phylogenetic Lineages of Pathogenic Piroplasmids

Piroplasmid parasites comprising of Babesia, Theileria, and Cytauxzoon are transmitted by ticks to farm and pet animals and have a significant impact on livestock industries and animal health in tropical and subtropical regions worldwide. In addition, diverse Babesia spp. infect humans as opportunistic hosts. Molecular phylogeny has demonstrated at least six piroplasmid lineages exemplified by B. microti, B. duncani, C. felis, T. equi, Theileria sensu stricto (T. annulata, T. parva, and T. orientalis) and Babesia sensu stricto (B. bovis, B. bigemina, and B. ovis). C1A cysteine-proteinases (C1A-Cp) are papain-like enzymes implicated in pathogenic and vital steps of the parasite life cycle such as nutrition and host cell egress. An expansion of C1A-Cp of T. annulata and T. parva with respect to B. bovis and B. ovis was previously described. In the present work, C1A-Cp paralogs were identified in available genomes of species pertaining to each piroplasmid lineage. Phylogenetic analysis revealed eight C1A-Cp groups. The profile of C1A-Cp paralogs across these groups corroborates and defines the existence of six piroplasmid lineages. C. felis, T. equi and Theileria s.s. each showed characteristic expansions into extensive families of C1A-Cp paralogs in two of the eight groups. Underlying gene duplications have occurred as independent unique evolutionary events that allow distinguishing these three piroplasmid lineages. We hypothesize that C1A-Cp paralog families may be associated with the advent of the schizont stage. Differences in the invertebrate tick host specificity and/or mode of transmission in piroplasmid lineages might also be associated with the observed C1A-Cp paralog profiles.

Identification of Theileria fuliginosa-like species in Ixodes australiensis ticks from western grey kangaroos (Macropus fuliginosus) in Western Australia

Piroplasms, including the genera Babesia and Theileria, are intra-erythrocytic protozoa that are generally transmitted by ticks and are the aetiological agents for piroplasmosis in animals, as well as humans, worldwide. In Australia, numerous studies have been conducted on piroplasms in domestic animals; however, less is known about these protozoa in ticks from native wildlife. The present study characterised piroplasms in Ixodes australiensis (n = 119) and Amblyomma triguttatum (n = 35) ticks collected from kangaroos in Western Australia (WA). Approximately 7.6% (9/119) (95% CI 2.8-12.2) of the I. australiensis ticks were positive for piroplasms using nested-PCR at the 18S rRNA locus, whereas no piroplasm 18S rDNA was detected in the A. triguttatum ticks. All sequences from I. australiensis ticks were identical. Using a 852 bp multiple nucleotide alignment at the 18S rRNA variable region, sequences shared 97.6%, 94.3%, 93.5% and 93.4% pairwise identity with Theileria fuliginosa, Theileria brachyuri, Theileria penicillata, and a Theileria sp. (K1), derived from a burrowing bettong or boodie (Bettongia lesueur), respectively. Phylogenetic analysis revealed that the Theileria sp. from I. australiensis clustered together in the marsupial-associated Theileria group, with T. fuliginosa as closest sister species. Hence, we conclude that this is the first observation of T. fuliginosa-like species in I. australiensis ticks parasitising kangaroos in WA.

Molecular survey on the occurrence of arthropod-borne pathogens in wild brown hares (Lepus europaeus) from Central Italy

Data about the spreading of arthropod-borne pathogens among hare populations are very scant, so the aim of the present preliminary study was to investigate, through molecular analysis, the occurrence of Anaplasma phagocytophilum, Bartonella sp., Borrelia burgdorferi sensu lato, Coxiella burnetii, Francisella tularensis, Leishmania spp. and piroplasms DNA in blood of 51 wild hares (Lepus europaeus) living in protected areas in Tuscany. All hares resulted negative for A. phagocytophilum, Bartonella sp., B. burgdorferi s.l., C. burnetii and F. tularensis. Five animals (9.8%) were positive for Leishmania and one hare (1.9%) tested positive for piroplasms. Sequencing of this sample showed a piroplasm similar to one Babesia isolate from the same animal species in Turkey. Therefore, to the best of our knowledge, this is the first molecular report of piroplasms occurring in wild hares from Italy, and the second worldwide. The examined hares appeared to be in good health status, corroborating the hypothesis of a chronic carrier state of some vector borne agents for this animal species.

Wildlife parasitology in Australia: past, present and future

Wildlife parasitology is a highly diverse area of research encompassing many fields including taxonomy, ecology, pathology and epidemiology, and with participants from extremely disparate scientific fields. In addition, the organisms studied are highly dissimilar, ranging from platyhelminths, nematodes and acanthocephalans to insects, arachnids, crustaceans and protists. This review of the parasites of wildlife in Australia highlights the advances made to date, focussing on the work, interests and major findings of researchers over the years and identifies current significant gaps that exist in our understanding. The review is divided into three sections covering protist, helminth and arthropod parasites. The challenge to document the diversity of parasites in Australia continues at a traditional level but the advent of molecular methods has heightened the significance of this issue. Modern methods are providing an avenue for major advances in documenting and restructuring the phylogeny of protistan parasites in particular, while facilitating the recognition of species complexes in helminth taxa previously defined by traditional morphological methods. The life cycles, ecology and general biology of most parasites of wildlife in Australia are extremely poorly understood. While the phylogenetic origins of the Australian vertebrate fauna are complex, so too are the likely origins of their parasites, which do not necessarily mirror those of their hosts. This aspect of parasite evolution is a continuing area for research in the case of helminths, but remains to be addressed for many other parasitic groups.

Molecular detection and characterisation of Babesia and Theileria in Australian hard ticks

Babesia and Theileria are intraerythrocytic protozoans of the phylum Apicomplexa. These species are capable of infecting wild and domestic animals and have historically caused great economic loss in the agricultural industry. In recent years human babesiosis has been deemed an emerging zoonosis in North America, Europe and Asia. The first locally acquired case of babesiosis in Australia, caused by Babesia microti, was reported in March 2012. A number of native Babesia and Theileria species have been identified in Australian marsupials, however their associated tick vectors and threat to human health is unknown. In the present study DNA was extracted from 1154 ticks collected from across Australia. PCR was used to amplify a Babesia and Theileria-specific partial region of the 18S ribosomal RNA gene. Positive samples were sequenced and phylogenetic analysis was performed. Twenty-nine sequences were obtained from ticks belonging to the genera Ixodes, Haemaphysalis and Bothriocroton. The sequences were closely related to Babesia macropus, and Theileria recently identified in marsupials and monotremes. Bayesian inference and maximum likelihood methods showed that Australian Babesia and Theileria species form monophyletic groups.

A novel Ehrlichia species in blood and Ixodes ornithorhynchi ticks from platypuses (Ornithorhynchus anatinus) in Queensland and Tasmania, Australia

Worldwide, Ehrlichia spp. are emerging infectious organisms of domestic animals and people, however, most Ehrlichia spp. naturally infect wildlife reservoirs causing mainly asymptomatic infections. Australian ecosystems have been under-explored for these potentially pathogenic organisms, and recent studies have identified a range of novel Ehrlichia, and their sister genera, Anaplasma and 'Candidatus Neoehrlichia' species, from native Australian ticks. We used bacterial 16S rRNA (16S) next-generation sequencing and genus-specific PCR to profile the bacterial communities in platypus (Ornithorhynchus anatinus) blood samples and platypus ticks (Ixodes ornithorhynchi), and identified a high prevalence of Ehrlichia sequences. We also observed Ehrlichia-like intra-neutrophilic inclusions (morulae) in PCR-positive stained platypus blood films that were consistent in morphology with other Ehrlichia spp. Bayesian phylogenetic analysis of 16S (1343 bp), gltA (1004 bp), and groEL (1074 bp) gene sequences group the platypus Ehrlichia with 'Candidatus Ehrlichia khabarensis' from far-eastern Russia, and demonstrate that the platypus Ehrlichia is clearly distinct from all other Ehrlichia spp. Enough genetic divergence exists to delineate this platypus Ehrlichia as a separate species that we propose to designate 'Candidatus Ehrlichia ornithorhynchi'. There is no evidence that 'Candidatus Ehrlichia ornithorhynchi' causes disease in wild platypuses, however, the organism does seem to be widespread in Australia, being found in both Queensland and Tasmania. 'Candidatus Ehrlichia ornithorhynchi' is the second native Australian Ehrlichia described and adds to the rapidly growing diversity of recently described native Australian tick-borne bacteria.

Deep-sequencing to resolve complex diversity of apicomplexan parasites in platypuses and echidnas: Proof of principle for wildlife disease investigation

The short-beaked echidna (Tachyglossus aculeatus) and the platypus (Ornithorhynchus anatinus) are iconic egg-laying monotremes (Mammalia: Monotremata) from Australasia. The aim of this study was to demonstrate the utility of diversity profiles in disease investigations of monotremes. Using small subunit (18S) rDNA amplicon deep-sequencing we demonstrated the presence of apicomplexan parasites and confirmed by direct and cloned amplicon gene sequencing Theileria ornithorhynchi, Theileria tachyglossi, Eimeria echidnae and Cryptosporidium fayeri. Using a combination of samples from healthy and diseased animals, we show a close evolutionary relationship between species of coccidia (Eimeria) and piroplasms (Theileria) from the echidna and platypus. The presence of E. echidnae was demonstrated in faeces and tissues affected by disseminated coccidiosis. Moreover, the presence of E. echidnae DNA in the blood of echidnas was associated with atoxoplasma-like stages in white blood cells, suggesting Hepatozoon tachyglossi blood stages are disseminated E. echidnae stages. These next-generation DNA sequencing technologies are suited to material and organisms that have not been previously characterised and for which the material is scarce. The deep sequencing approach supports traditional diagnostic methods, including microscopy, clinical pathology and histopathology, to better define the status quo. This approach is particularly suitable for wildlife disease investigation.

Parasite infection of public databases: a data mining approach to identify apicomplexan contaminations in animal genome and transcriptome assemblies

Background

Contaminations from various exogenous sources are a common problem in next-generation sequencing. Another possible source of contaminating DNA are endogenous parasites. On the one hand, undiscovered contaminations of animal sequence assemblies may lead to erroneous interpretation of data; on the other hand, when identified, parasite-derived sequences may provide a valuable source of information.

Results

Here we show that sequences deriving from apicomplexan parasites can be found in many animal genome and transcriptome projects, which in most cases derived from an infection of the sequenced host specimen. The apicomplexan sequences were extracted from the sequence assemblies using a newly developed bioinformatic pipeline (ContamFinder) and tentatively assigned to distinct taxa employing phylogenetic methods. We analysed 920 assemblies and found 20,907 contigs of apicomplexan origin in 51 of the datasets. The contaminating species were identified as members of the apicomplexan taxa Gregarinasina, Coccidia, Piroplasmida, and Haemosporida. For example, in the platypus genome assembly, we found a high number of contigs derived from a piroplasmid parasite (presumably Theileria ornithorhynchi). For most of the infecting parasite species, no molecular data had been available previously, and some of the datasets contain sequences representing large amounts of the parasite’s gene repertoire.

Conclusion

Our study suggests that parasite-derived contaminations represent a valuable source of information that can help to discover and identify new parasites, and provide information on previously unknown host-parasite interactions. We, therefore, argue that uncurated assembly data should routinely be made available in addition to the final assemblies.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3504-1) contains supplementary material, which is available to authorized users.

Mitochondrial Genome Sequences and Structures Aid in the Resolution of Piroplasmida phylogeny

The taxonomy of the order Piroplasmida, which includes a number of clinically and economically relevant organisms, is a hotly debated topic amongst parasitologists. Three genera (Babesia, Theileria, and Cytauxzoon) are recognized based on parasite life cycle characteristics, but molecular phylogenetic analyses of 18S sequences have suggested the presence of five or more distinct Piroplasmida lineages. Despite these important advancements, a few studies have been unable to define the taxonomic relationships of some organisms (e.g. C. felis and T. equi) with respect to other Piroplasmida. Additional evidence from mitochondrial genome sequences and synteny should aid in the inference of Piroplasmida phylogeny and resolution of taxonomic uncertainties. In this study, we have amplified, sequenced, and annotated seven previously uncharacterized mitochondrial genomes (Babesia canis, Babesia vogeli, Babesia rossi, Babesia sp. Coco, Babesia conradae, Babesia microti-like sp., and Cytauxzoon felis) and identified additional ribosomal fragments in ten previously characterized mitochondrial genomes. Phylogenetic analysis of concatenated mitochondrial and 18S sequences as well as cox1 amino acid sequence identified five distinct Piroplasmida groups, each of which possesses a unique mitochondrial genome structure. Specifically, our results confirm the existence of four previously identified clades (B. microti group, Babesia sensu stricto, Theileria equi, and a Babesia sensu latu group that includes B. conradae) while supporting the integration of Theileria and Cytauxzoon species into a single fifth taxon. Although known biological characteristics of Piroplasmida corroborate the proposed phylogeny, more investigation into parasite life cycles is warranted to further understand the evolution of the Piroplasmida. Our results provide an evolutionary framework for comparative biology of these important animal and human pathogens and help focus renewed efforts toward understanding the phylogenetic relationships within the group.