Pathogen profiling of Australian rabbits by metatranscriptomic sequencing

Abstract

Australia is known for its long history of using biocontrol agents, such as myxoma virus (MYXV) and rabbit haemorrhagic disease virus (RHDV), to manage wild European rabbit populations. Interestingly, while undertaking RHDV surveillance of rabbits that were found dead, we observed that approximately 40% of samples were negative for RHDV. To investigate whether other infectious agents are responsible for killing rabbits in Australia, we subjected a subset of these RHDV‐negative liver samples to metatranscriptomic sequencing. In addition, we investigated whether the host transcriptome data could provide additional differentiation between likely infectious versus non‐infectious causes of death. We identified transcripts from several Clostridia species, Pasteurella multocida, Pseudomonas spp., and Eimeria stiedae, in liver samples of several rabbits that had died suddenly, all of which are known to infect rabbits and are capable of causing disease and mortality. In addition, we identified Hepatitis E virus and Cyniclomyces yeast in some samples, both of which are not usually associated with severe disease. In one‐third of the sequenced total liver RNAs, no infectious agent could be identified. While metatranscriptomic sequencing cannot provide definitive evidence of causation, additional host transcriptome analysis provided further insights to distinguish between pathogenic microbes and commensals or environmental contaminants. Interestingly, three samples where no pathogen could be identified showed evidence of up‐regulated host immune responses, while immune response pathways were not up‐regulated when E. stiedae, Pseudomonas, or yeast were detected. In summary, although no new putative rabbit pathogens were identified, this study provides a robust workflow for future investigations into rabbit mortality events.

First Detection of Benign Rabbit Caliciviruses in Chile

“…A total of eight duodenum samples positive for rabbit caliciviruses were processed for total RNA sequencing. Libraries were prepared for metatranscriptomic sequencing, as previously described [ 44 ]. Briefly, total RNA was subject to an rRNA depletion step using the NEBNext rRNADepletion Kit (Human/Mouse/Rat) (New England Biolabs, Ipswich, MA, USA).…”

Rabbits as a Reservoir of Multidrug-Resistant Escherichia coli: Clonal Lineages and Public Health Impact

“…Regarding domestic rabbits and pet rabbits, the dissemination of resistant bacteria can occur in different ways. In pet species, the close human-animal interface poses a potential public health risk for the transmission of zoonotic diseases from rabbits to their owners, particularly when good hygiene practices are not followed [20]. In meat rabbits, transmission can occur from rabbit to human and from rabbit to other animal through bacterial transmission (and vice versa) if biosecurity practices are poor.…”

Neglected Spleen Transcriptional Profile Reveals Inflammatory Disorder Conferred by Rabbit Hemorrhagic Disease Virus 2 Infection

“…A few early studies focused on the liver tropism of RHDV2, virus burdens, and the serology dynamic during the infection and vaccine cross-protection [ 21 , 22 ]. Molecular pathways for virus entry, replication, and perturbation of inflammatory activities were highlighted by multi-omics analysis, which indicated the interactive networks of antigen recognition and presentation by MPS in early and late RHDV2 infection [ 18 , 23 , 24 ]. It was speculated that lagoviruses might trade with immune cells to escape innate and adaptive immunity through specific, unexplained mechanisms.…”