Metatranscriptomic profiling reveals diverse tick‐borne bacteria, protozoans and viruses in ticks and wildlife from Australia

Abstract

Tick-borne zoonoses are emerging globally due to changes in climate and land use.While the zoonotic threats associated with ticks are well studied elsewhere, in Australia, the diversity of potentially zoonotic agents carried by ticks and their significance to human and animal health is not sufficiently understood. To this end, we used untargeted metatranscriptomics to audit the prokaryotic, eukaryotic and viral biomes of questing ticks and wildlife blood samples from two urban and rural sites in New South Wales, Australia. Ixodes holocyclus and Haemaphysalis bancrofti were the main tick species collected, and blood samples from Rattus rattus, Rattus fuscipes, Perameles nasuta and Trichosurus vulpecula were also collected and screened for tick-borne microorganisms using metatranscriptomics followed by conventional targeted PCR to identify important microbial taxa to the species level. Our analyses identified 32 unique tick-borne taxa, including 10 novel putative species. Overall, a wide range of tick-borne microorganisms were found in questing ticks including haemoprotozoa such as Babesia, Theileria, Hepatozoon and Trypanosoma spp., bacteria such as Borrelia, Rickettsia, Ehrlichia, Neoehrlichia and Anaplasma spp., and numerous viral taxa including Reoviridiae (including two coltiviruses) and a novel Flaviviridae-like jingmenvirus. Of note, a novel hard tick-borne relapsing fever Borrelia sp. was identified in questing H. bancrofti ticks which is closely related to, but distinct from, cervid-associated Borrelia spp. found throughout Asia. Notably, all tick-borne microorganisms were phylogenetically unique compared to their relatives found outside Australia, and no foreign tick-borne human pathogens such as Borrelia burgdorferi s.l. or Babesia microti were found. This work adds to the growing literature demonstrating that Australian ticks harbour a unique and endemic microbial fauna, including potentially zoonotic agents which should be further studied to determine their relative risk to human and animal health.

Phylogenetic evidence for a clade of tick-associated trypanosomes

“…Possible transovarial transmission was reported once for T. rhipicephalis in artificially infected R. sanguineus [25], but we did not observe evidence of maternal transmission in I. ricinus, suggesting that this transmission route may be a biological trait variable between members of the T. pestanai clade. Transstadial transmission for members of the T. pestanai clade is probable at least in I. ricinus and A. oblongoguttatum since we detected infections in unfed ticks (meaning that they have digested their previous blood meals and have further moulted), a pattern also previously observed in I. ricinus, I. holocyclus, A. triguttatum and Haemaphysalis bancrofti [12,14,24].…”

“…Indeed, while I. ricinus is the tick species most commonly biting humans in Western Europe [41], in the present study, we found that 4% of field specimens were infected with a trypanosome of the T. pestanai clade. In Australia, a significant human-biting tick, I. holocyclus, was frequently found infected by T. giletti [24]. Humans are therefore exposed to bites of Trypanosoma-infected ticks without the risk of infection being documented to date.…”

“…Viable forms of T. copemani were also observed in faecal materials of Ixodes australiensis ticks, suggesting that transmission may be possible through the stercorarian route [21]. The molecular detection of trypanosomes from questing (unfed) ticks (e.g., Ixodes ricinus, I. holocyclus, Amblyomma triguttatum and Haemaphysalis bancrofti) that have already digested their previous blood meals, have further moulted (i.e., transstadial transmission), and are seeking vertebrates for their next blood meal further suggests that ecologically and taxonomically diverse ticks can acquire and maintain trypanosomes [12,14,24]. The in vitro isolation of viable trypanosomes from questing I. ricinus further corroborates this finding [14].…”

Jingmenviruses: Ubiquitous, understudied, segmented flavi-like viruses

“…Newport Tick virus (also named Ixodes holocyclus jingmenvirus) was identified in a metagenomics study of ticks from New South Wales in Australia ( Gofton et al, 2022 ). The sequences were detected in relatively high prevalence in I. holocylcus ticks from Kioloa and Sydney.…”

The Troublesome Ticks Research Protocol: Developing a Comprehensive, Multidiscipline Research Plan for Investigating Human Tick-Associated Disease in Australia

“…The answer may be that the native tick fauna are unique due to the continent's long geological isolation since the Gondwanan break-up some 130-135 million years ago [25,26]. Indeed, recent metagenomic and metatranscriptomic analyses have revealed a diverse microbiota in Australian ticks comprising known bacterial, viral, and protozoal genera and novel species that are related to, yet phylogenetically distinct from, northern hemisphere tick-borne pathogens [19,[27][28][29][30][31][32][33][34][35]. In other words, separate evolutionary and ecological pathways have resulted in not only a unique mammalian fauna but may also have impacted tick-associated microbial communities on the Australian continent.…”