Metagenomic profiling of ticks: Identification of novel rickettsial genomes and detection of tick-borne canine parvovirus

Abstract

BackgroundAcross the world, ticks act as vectors of human and animal pathogens. Ticks rely on bacterial endosymbionts, which often share close and complex evolutionary links with tick-borne pathogens. As the prevalence, diversity and virulence potential of tick-borne agents remain poorly understood, there is a pressing need for microbial surveillance of ticks as potential disease vectors.Methodology/Principal FindingsWe developed a two-stage protocol that includes 16S-amplicon screening of pooled samples of hard ticks collected from dogs, sheep and camels in Palestine, followed by shotgun metagenomics on individual ticks to detect and characterise tick-borne pathogens and endosymbionts. Two ticks isolated from sheep yielded an abundance of reads from the genus Rickettsia, which were assembled into draft genomes. One of the resulting genomes was highly similar to Rickettsia massiliae strain MTU5. Analysis of signature genes showed that the other represents the first genome sequence of the potential pathogen Candidatus Rickettsia barbariae. Ticks from a dog and a sheep yielded draft genome sequences of Coxiella strains. A sheep tick yielded sequences from the sheep pathogen Anaplasma ovis, while Hyalomma ticks from camels yielded sequences belonging to Francisella-like endosymbionts. From the metagenome of a dog tick from Jericho, we generated a genome sequence of a canine parvovirus.SignificanceHere, we have shown how a cost-effective two-stage protocol can be used to detect and characterise tick-borne pathogens and endosymbionts. In recovering genome sequences from an unexpected pathogen (canine parvovirus) and a previously unsequenced pathogen (Candidatus Rickettsia barbariae), we demonstrate the open-ended nature of metagenomics. We also provide evidence that ticks can carry canine parvovirus, raising the possibility that ticks might contribute to the spread of this troublesome virus.

Microbial communities associated with the camel tick, Hyalomma dromedarii: 16S rRNA gene-based analysis

“…Enterobacteriaceae was the most abundant bacterial family in R. microplus ticks collected from cattle whereas Rickettsiaceae, Oxalobacteraceae, and Micrococcaceae were abundant in the R. turanicus ticks infesting goats 41 . Furthermore, the results of this study differ from Ravi et al 60 who reported four www.nature.com/scientificreports/ bacterial families: Coxiellaceae, Francisellaceae, Rickettsiaceae and Anaplasmataceae in H. dromedarii, Rhipicephalus sanguineus and Haemaphysalis concinna. The differences among families could be attributed to host specific factors.…”

“…Therefore, the genus level identifications presented in the current study are provided as preliminary baseline data, which may require further confirmation. Our results indicated that Acinetobacter and Corynebacterium were the two most abundant genera detected in the microbiota of H. dromedarii from all locations with high sequence ratios 47 and Saudi Arabia 48 . We found significant associations between Acinetobacter, Escherichia and Francisella and between these three genera and several other genera.…”

“…Furthermore, the results of this study differ from Ravi et al . 60 who reported four bacterial families: Coxiellaceae , Francisellaceae , Rickettsiaceae and Anaplasmataceae in H. dromedarii , Rhipicephalus sanguineus and Haemaphysalis concinna . The differences among families could be attributed to host specific factors.…”

“…Nonetheless, so far there are no published records on the microbial communities in H. dromedarii ticks in the UAE. Two studies, one from West Bank, Palestine 47 , and second from Saudi Arabia 48 investigated microbial communities in H. dromedarii . The objectives of this study were to (i) characterize the microbiota associated with H. dromedarii ticks in the UAE and (ii) determine temporal patterns of richness and evenness in microbial communities in H .…”

Targeted Metagenomics Offers Insights into Potential Tick-Borne Pathogens

“…It is reassuring that targeted metagenomics sequencing of the >13,000 samples that they had found as many or more of each species, but still unknown if any of the Borrelia-specific PCR positive samples were not able to be detected by targeted metagenomics. shown to work in principal to identify pathogens transmitted by ticks both from human specimens (12,13) as well as direct testing of ticks (14,15). However, the lack of a targeted sequence requires substantially more sequencing depth and interpretation of data can be much more challenging.…”