Inhibition of the endosymbiont "Candidatus Midichloria mitochondrii" during 16S rRNA gene profiling reveals potential pathogens in Ixodes ticks from Australia

Ticks without borders: microbiome of immature neotropical tick species parasitizing migratory songbirds along northern Gulf of Mexico

Introduction

The long-distance, seasonal migrations of birds make them an effective ecological bridge for the movement of ticks. The introduction of exotic tick species to new geographical regions can cause the emergence of novel tick-borne pathogens. This study examined the prevalence of exotic tick species parasitizing migratory songbirds at stopover sites along the northern Gulf of Mexico using the mitochondrial 12S rRNA gene.

Methods

Overall, 421 individual ticks in the genera Amblyomma, Haemaphysalis, and Ixodes were recorded from 28 songbird species, of which Amblyomma and Amblyomma longirostre were the most abundant tick genera and species, respectively. A high throughput 16S ribosomal RNA sequencing approach characterized the microbial communities and identified pathogenic microbes in all tick samples.

Results and discussion

Microbial profiles showed that Proteobacteria was the most abundant phylum. The most abundant pathogens were Rickettsia and endosymbiont Francisella, Candidatus Midichloria, and Spiroplasma. Permutation multivariate analysis of variance revealed that the relative abundance of Francisella and Rickettsia drives microbial patterns across the tick genera. We also noted a higher percentage of positive correlations in microbe-microbe interactions among members of the microbial communities. Network analysis suggested a negative correlation between a) Francisella and Rickettsia and, b) Francisella and Cutibacterium. Lastly, mapping the distributions of bird species parasitized during spring migrations highlighted geographic hotspots where migratory songbirds could disperse ticks and their pathogens at stopover sites or upon arrival to their breeding grounds, the latter showing mean dispersal distances from 421-5003 kilometers. These findings spotlight the potential role of migratory birds in the epidemiology of tick-borne pathogens.

Nutritional symbiosis in ticks: singularities of the genus Ixodes

Symbiosis with intracellular bacteria is essential for the nutrition of ticks, particularly through the biosynthesis of B vitamins. Yet, ticks of the genus Ixodes, which include major vectors of human pathogens, lack the nutritional symbionts usually found in other tick genera. This paradox raises questions about the mechanisms that Ixodes ticks use to prevent nutritional deficiencies. Nonetheless, Ixodes ticks commonly harbor other symbionts belonging to the order Rickettsiales. Although these obligate intracellular bacteria are primarily known as human pathogens, Rickettsiales symbionts often dominate the Ixodes microbial community without causing diseases. They also significantly influence Ixodes physiology, synthesize key B vitamins, and are crucial for immatures. These findings underscore unique associations between Rickettsiales and Ixodes ticks distinct from other tick genera.

One Health Approach on Ehrlichia canis: Serosurvey of Owners and Dogs, Molecular Detection in Ticks, and Associated Risk Factors in Tick-Infested Households of Southern Brazil

Background: Ehrlichia canis has been the main hemopathogen affecting domestic dogs in Brazil. Even though tick-infested dogs may lead to household infestation and predispose human exposure and public health concern, no comprehensive study has surveyed humans, dogs, and environmental ticks altogether. Materials and Methods: Accordingly, the present study aimed to assess tick-infested households, identify tick species, perform serological (immunofluorescence assay) and molecular (PCR and q-PCR) detection of Ehrlichia in ticks, in the eighth biggest metropolitan area of Brazil. Results: Between 2007 and 2020, 233/5973 (3.9%) out of all complaints were from tick-infested households of 200 different addresses. Overall, 370/552 (67.0%) ticks were collected and identified as adult and 182/552 (33.0%) as immature forms of Rhipicephalus sanguineus s.l. complex; a single tick from one owner, a female tick of Amblyomma sculptum; and 395 ticks from dogs, 319/395 (80.8%) adult and 72/395 (18.2%) immature forms of Rhipicephalus spp., and 4/395 (1.01%) female Amblyomma aureolatum. Overall, 2/135 (1.5%) owners and 13/136 (9.6%) dogs were seropositive for E. canis. The DNA of Anaplasmataceae family was molecularly detected in 16/50 (32.0%) R. sanguineus s.l. As expected, the number of monthly tick infestation complaints were directly associated, and mean (p = 0.01), maximum (p = 0.011), and minimum (p = 0.008) temperature were statistically significant and had a low positive correlation (0.24, 0.23, and 0.24, respectively). In addition, complaints were highly associated to all socioeconomic variables (p < 0.001), with the exception of the presence of vacant lots. Conclusions: Despite low samplings and human negative results, areas with low-income with adequate temperature and urban agglomerations have been shown to be associated risks for tick infestations, predisposing tick-borne diseases. In conclusion, monitoring should always be conducted in such areas, including One Health approach with serosurvey of owners and dogs, along with identification and molecular screening of ticks.

Diversity of midgut microbiota in ticks collected from white-tailed deer (Odocoileus virginianus) from northern Mexico

Ticks host different pathogens as endosymbiont and nonpathogenic microorganisms and play an important role in reproductive fitness and nutrient provision. However, the bacterial microbiomes of white-tailed deer ticks have received minimal attention. This study aimed to examine the bacterial microbiome of ticks collected from Odocoileus virginianus on the Mexico-United States border to assess differences in microbiome diversity in ticks of different species, sexes, and localities. Five different tick species were collected: Rhipicephalus microplus, Dermacentor nitens, Otobius megnini, Amblyomma cajennense, and A. maculatum. The tick microbiomes were analyzed using next-generation sequencing. Among all tick species, the most predominant phylum was Proteobacteria, followed by Actinobacteria and Firmicutes. The ticks from Tamaulipas and Nuevo León presented the highest bacterial species diversity. Acinetobacter johnsonii and A. lwoffii were the common bacterial species in the microbiome of all ticks, Coxiella were present in R. microplus, and Dermacentor nitens also exhibited a Francisella-like endosymbiont. The microbiome of most females in D. nitens was less diverse than that of males, whereas R. microplus occurs in females, suggesting that microbiome diversity is influenced by sex. In the bacterial communities of A. maculatum and O. megnini, Candidatus Midichloria massiliensis, and Candidatus Endoecteinascidia fumentensis were the most predominant endosymbionts. These results constitute the initial report on these bacteria, and this is also the first study to characterize the microbiome of O. megnini.

Ticks without borders: Microbial communities of immature Neotropical tick species parasitizing migratory landbirds along northern Gulf of Mexico

The long-distance, seasonal migrations of birds make them an effective ecological bridge for the movement of ticks. The introduction of exotic tick species to new geographical regions can lead to the emergence of novel tick-borne pathogens or the re-emergence of previously eradicated ones. This study assessed the prevalence of exotic tick species parasitizing resident, short-distance, and long-distance songbirds during spring and autumn at stopover sites in the northern Gulf of Mexico using the mitochondrial 12S rDNA gene. Birds were captured for tick collection from six different sites from late August to early November in both 2018 and 2019. The highest number of ticks were collected in the 2019 season. Most ticks were collected off the Yellow-breasted Chat (Icteria virens) and Common Yellowthroat (Geothlypis trichas), and 54% of the total ticks collected were from Grand Chenier, LA. A high throughput 16S ribosomal RNA sequencing approach was followed to characterize the microbial communities and identify pathogenic microbes in all tick samples. Tick microbial communities, diversity, and community structure were determined using quantitative insight into microbial ecology (QIIME). The sparse correlations for compositional data (SparCC) approach was then used to construct microbial network maps and infer microbial correlations. A total of 421 individual ticks in the genera Amblyomma, Haemaphysalis, and Ixodes were recorded from 28 songbird species, of which Amblyomma and Amblyomma longirostre was the most abundant tick genus and species, respectively. Microbial profiles showed that Proteobacteria was the most abundant phylum. The most abundant bacteria include the pathogenic Rickettsia and endosymbiont Francisella, Candidatus Midichloria, and Spiroplasma. BLAST analysis and phylogenetic reconstruction of the Rickettsia sequences revealed the highest similarities to pathogenic spotted and non-spotted fever groups, including R. buchneri, R. conorii, R. prowazekii, R. bellii, R. australis, R. parkeri, R. monacensis, and R. monteiroi. Permutation multivariate analysis of variance revealed that the relative abundance of Francisella and Rickettsia drives microbial patterns across the tick genera. We also observed a higher percentage of positive correlations in microbe-microbe interactions among members of the microbial communities. Network analysis suggested a negative correlation between a) Francisella and Rickettsia and, b) Francisella and Cutibacterium. Lastly, mapping the distributions of bird species parasitized during spring migrations highlighted geographic hotspots where migratory songbirds could disperse ticks and their pathogens at stopover sites or upon arrival to their breeding grounds, the latter showing means dispersal distances from 421-5003 kilometers. These findings strongly highlight the potential role of migratory birds in the epidemiology of tick-borne pathogens.

Decontamination protocols affect the internal microbiota of ticks

Studies on the microbiota of ticks have promoted hypotheses about the combined effects of the bacterial community, its functional contributions to the tick's physiology or probable competition effects with some tick-borne pathogens. However, knowledge on the origin of the microbiota of newly hatched larvae is missing. This study aimed to elucidate the source(s) of the microbiota in unfed tick larvae, addressing the composition of the "core microbiota" and the best ways to decontaminate eggs for microbiota studies. We applied laboratory degree bleach washes and/or ultraviolet light treatments on engorged Rhipicephalus australis females and/or their eggs. No significant effects of these treatments on the reproductive parameters of females and the hatching rates of eggs were observed. However, the different treatments did show striking effects on the composition of the microbiota. The results indicated that bleach washes disrupted the internal tick microbiota in females, implying that bleach may have entered the tick and subsequently affected the microbiota. Furthermore, the analyses of results demonstrated that the ovary is a main source of tick microbiota, while the contribution of Gené's organ (a part of the female reproductive system that secretes a protective wax coat onto tick eggs) or the male's spermatophore requires further investigation. Further studies are needed to identify best practice protocols for the decontamination of ticks for microbiota studies.

Metagenomic profile of the bacterial communities associated with Ixodes granulatus (Acari: Ixodidae): a potential vector of tick-borne diseases

Ixodes granulatus Supino, 1897 (Acari: Ixodida) is one of Malaysia's most common hard ticks and is a potential vector for tick-borne diseases (TBDs). Despite its great public health importance, research on I. granulatus microbial communities remains largely unexplored. Therefore, this study aimed to investigate the bacterial communities of on-host I. granulatus collected from three different recreational areas on the East Coast of Peninsular Malaysia using high throughput Next Generation Sequencing (NGS). A total of 9 females on-host I. granulatus were subjected to metabarcoding analysis targeting V3-V4 regions of 16S ribosomal RNA (rRNA) using the Illumina MiSeq platform. This study identified 15 bacterial phyla corresponding to 19 classes, 54 orders, and 90 families from 435 amplicon sequence variants (ASVs), revealing a diverse bacterial community profile. Together with 130 genera assigned, local I. granulatus harbored 4 genera of pathogens, i.e., Rickettsia da Rocha Lima, 1916 (Rickettsiales: Rickettsiaceae) (58.6%), Borrelia Swellengrebel 1907 (Spirochaetales: Borreliaceae) (31.6%), Borreliella Adeolu and Gupta 2015 (Spirochaetales: Borreliaceae) (0.6%), and Ehrlichia Cowdria Moshkovski 1947 (Rickettsiales: Ehrlichiaceae) (39.9%). Some endosymbiont bacteria, such as Coxiella (Philip, 1943) (Legionellales: Coxiellaceae), Wolbachia Hertig 1936 (Rickettsiales: Ehrlichiaceae), and Rickettsiella Philip, 1956 (Legionellales: Coxiellaceae), were also detected at very low abundance. Interestingly, this study reported the co-infection of Borrelia and Ehrlichia for the first time, instilling potential health concerns in the context of co-transmission to humans, especially in areas with a high population of I. granulatus. This study successfully characterized the tick microbiome and provided the first baseline data of I. granulatus bacterial communities in Malaysia. These results support the need for way-forward research on tick-associated bacteria using NGS, focusing on medically important species toward TBD prevention.

Changes in the Ixodes ricinus microbiome associated with artificial tick feeding

Artificial tick feeding systems (ATFS) can be used to study tick biology and tick-pathogen interactions. Due to the long feeding duration of hard ticks, antibiotics are commonly added to the in vitro blood meal to prevent the blood from decaying. This may affect the ticks' microbiome, including mutualistic bacteria that play an important role in tick biology. This effect was examined by the consecutive feeding of Ixodes ricinus larvae, nymphs, and adults in vitro with and without the supplementation of gentamicin and in parallel on calves. DNA extracted from unfed females was analyzed by 16S rRNA sequencing. The abundance of Candidatus Midichloria mitochondrii, Rickettsia helvetica and Spiroplasma spp. was measured by qPCR in unfed larvae, nymphs, and adults. Larvae and nymphs fed on calves performed significantly better compared to both in vitro groups. Adults fed on blood supplemented with gentamicin and B vitamins had a higher detachment proportion and weight compared to the group fed with B vitamins but without gentamicin. The detachment proportion and weights of females did not differ significantly between ticks fed on calves and in vitro with gentamicin, but the fecundity was significantly higher in ticks fed on calves. 16S rRNA sequencing showed a higher microbiome species richness in ticks fed on calves compared to ticks fed in vitro. A shift in microbiome composition, with Ca. Midichloria mitochondrii as dominant species in females fed as juveniles on calves and R. helvetica as the most abundant species in females previously fed in vitro was observed. Females fed in vitro without gentamicin showed significant lower loads of Ca. M. mitochondrii compared to females fed in vitro with gentamicin and ticks fed on calves. Spiroplasma spp. were exclusively detected in female ticks fed on cattle by qPCR, but 16S rRNA sequencing results also showed a low abundance in in vitro females exposed to gentamicin. In conclusion, the employed feeding method and gentamicin supplementation affected the ticks' microbiome composition and fecundity. Since these changes may have an impact on tick biology and vector competence, they should be taken into account in studies employing ATFS.

Using FlowCam and molecular techniques to assess the diversity of Cyanobacteria species in water used for food production

Globally, the occurrence of cyanobacteria in water currently remains an important subject as they produce cyanotoxins that pose threat to human health. Studies on the contamination of maize meals during mill grinding processes using cyanobacteria-contaminated water have not been conducted. The present study aimed to assess the diversity of cyanobacteria in the samples (process water, uncooked maize meal, and cooked maize meal (porridge)). Polymerized Chain Reaction (PCR) and Advanced digital flow cytometry (FlowCAM) were used to detect and identify cyanobacterial species available in these samples. 16S Primers (forward and reverse) tailed with Universal Sequences were used for amplification and sequencing of full-length 16S rRNA genes from cyanobacteria found in all samples. Cyanobacterial species from order Nostocales, Pseudanabaenales, Oscillatoriales Chroococcales, Synechococcales, and unclassified cyanobacterial order, some of which have the potential to produce cyanotoxins were amplified and identified in process water, raw maize meal and porridge samples using PCR. Images of the genus Microcystis, Phormidium, and Leptolyngbya were captured in process water samples using FlowCAM. These findings show the presence of cyanobacteria species in process water used for maize meal and the absence in cooked maize meal. The presence of cyanobacteria in process water is likely another route of human exposure to cyanotoxins.

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

In Australia, there is a paucity of data about the extent and impact of zoonotic tick-related illnesses. Even less is understood about a multifaceted illness referred to as Debilitating Symptom Complexes Attributed to Ticks (DSCATT). Here, we describe a research plan for investigating the aetiology, pathophysiology, and clinical outcomes of human tick-associated disease in Australia. Our approach focuses on the transmission of potential pathogens and the immunological responses of the patient after a tick bite. The protocol is strengthened by prospective data collection, the recruitment of two external matched control groups, and sophisticated integrative data analysis which, collectively, will allow the robust demonstration of associations between a tick bite and the development of clinical and pathological abnormalities. Various laboratory analyses are performed including metagenomics to investigate the potential transmission of bacteria, protozoa and/or viruses during tick bite. In addition, multi-omics technology is applied to investigate links between host immune responses and potential infectious and non-infectious disease causations. Psychometric profiling is also used to investigate whether psychological attributes influence symptom development. This research will fill important knowledge gaps about tick-borne diseases. Ultimately, we hope the results will promote improved diagnostic outcomes, and inform the safe management and treatment of patients bitten by ticks in Australia.

Quantitative microbial population study reveals geographical differences in bacterial symbionts of Ixodes ricinus

BACKGROUND

Ixodes ricinus ticks vector pathogens that cause serious health concerns. Like in other arthropods, the microbiome may affect the tick's biology, with consequences for pathogen transmission. Here, we explored the bacterial communities of I. ricinus across its developmental stages and six geographic locations by the 16S rRNA amplicon sequencing, combined with quantification of the bacterial load.

RESULTS

A wide range of bacterial loads was found. Accurate quantification of low microbial biomass samples permitted comparisons to high biomass samples, despite the presence of contaminating DNA. The bacterial communities of ticks were associated with geographical location rather than life stage, and differences in Rickettsia abundance determined this association. Subsequently, we explored the geographical distribution of four vertically transmitted symbionts identified in the microbiome analysis. For that, we screened 16,555 nymphs from 19 forest sites for R. helvetica, Rickettsiella spp., Midichloria mitochondrii, and Spiroplasma ixodetis. Also, the infection rates and distributions of these symbionts were compared to the horizontally transmitted pathogens Borrelia burgdorferi sensu lato, Anaplasma phagocytophilum, and Neoehrlichia mikurensis. The infection rates of all vertically transmitted symbionts differed between the study sites, and none of the symbionts was present in all tested ticks suggesting a facultative association with I. ricinus. The proportions in which symbionts occurred in populations of I. ricinus were highly variable, but geographically close study sites expressed similar proportions. These patterns were in contrast to what we observed for horizontally transmitted pathogens. Lastly, nearly 12% of tested nymphs were free of any targeted microorganisms, which is in line with the microbiome analyses.

CONCLUSIONS

Our results show that the microbiome of I. ricinus is highly variable, but changes gradually and ticks originating from geographically close forest sites express similar bacterial communities. This suggests that geography-related factors affect the infection rates of vertically transmitted symbionts in I. ricinus. Since some symbionts, such as R. helvetica can cause disease in humans, we propose that public health investigations consider geographical differences in its infection rates.

Multi-locus evaluation of gastrointestinal bacterial communities from Zalophus californianus pups in the Gulf of California, México

Background

The gastrointestinal (GI) bacterial communities of sea lions described to date have occasionally revealed large intraspecific variability, which may originate from several factors including different methodological approaches. Indeed, GI bacterial community surveys commonly rely on the use of a single hypervariable region (HR) of 16S rRNA, which may result in misleading structural interpretations and limit comparisons among studies. Here, we considered a multi-locus analysis by targeting six HRs of 16S rRNA with the aims of (i) comprehensively assessing the GI bacterial consortium in rectal samples from Zalophus californianus pups and (ii) elucidating structural variations among the tested HRs. In addition, we evaluated which HRs may be most suitable for identifying intrinsic, structurally related microbiome characteristics, such as geographic variations or functional capabilities.

Methods

We employed a Short MUltiple Regions Framework (SMURF) approach using the Ion 16S™ Metagenomic Kit. This kit provides different proprietary primers designed to target six HRs of the 16S rRNA gene. To date, the only analytical pipeline available for this kit is the Ion Reporter™ Software of Thermo Fisher Scientific. Therefore, we propose an in-house pipeline to use with open-access tools, such as QIIME2 and PICRUSt 2, in downstream bioinformatic analyses.

Results

As hypothesized, distinctive bacterial community profiles were observed for each analyzed HR. A higher number of bacterial taxa were detected with the V3 and V6-V7 regions. Conversely, the V8 and V9 regions were less informative, as we detected a lower number of taxa. The synergistic information of these HRs suggests that the GI microbiota of Zalophus californianus pups is predominated by five bacterial phyla: Proteobacteria (~50%), Bacteroidetes (~20%), Firmicutes (~18%), Fusobacteria (~7%), and Epsilonbacteraeota (~4%). Notably, our results differ at times from previously reported abundance profiles, which may promote re-evaluations of the GI bacterial compositions in sea lions and other pinniped species that have been reported to date. Moreover, consistent geographic differences were observed only with the V3, V4, and V6-V7 regions. In addition, these HRs also presented higher numbers of predicted molecular pathways, although no significant functional changes were apparent. Together, our results suggests that multi-locus analysis should be encouraged in GI microbial surveys, as single-locus approaches may result in misleading structural results that hamper the identification of structurally related microbiome features.

USING SURFACE WASHING TO REMOVE THE ENVIRONMENTAL COMPONENT FROM FLEA MICROBIOME ANALYSIS

Microbial metabarcoding is a common method to study the biology of blood-feeding arthropods and identify patterns of potential pathogen transmission. Before DNA extraction, specimens are often surface washed to remove environmental contaminants. While surface washing is common, its effects on microbial diversity remain unclear. We characterized the microbiome of the flea species Ceratophyllus idius, an avian ectoparasite, and a potential vector of pathogens, using high-throughput 16S rRNA sequencing. Half of the nests from which fleas were collected were subjected to an environmental manipulation in which nesting materials were periodically replaced. In a crossed study design we surface washed half of the flea samples from each environmental condition to produce 4 experimental conditions. Environmental manipulations resulted in significant differences in the diversity and structure of the flea microbiome, but these differences were unapparent when specimens were surface washed. Furthermore, differential abundance testing of the experimental groups revealed that surface washing predominantly affected the abundance of bacterial groups that are characterized as environmental contaminants. These findings suggest that environmental changes primarily affect the surface microbiome of arthropods and that surface washing is a useful tool to reduce the footprint of the external microbiome on analysis.

Novel symbionts and potential human pathogens excavated from argasid tick microbiomes that are shaped by dual or single symbiosis

Research on vector-associated microbiomes has been expanding due to increasing emergence of vector-borne pathogens and awareness of the importance of symbionts in the vector physiology. However, little is known about microbiomes of argasid (or soft-bodied) ticks due to limited access to specimens. We collected four argasid species (Argas japonicus, Carios vespertilionis, Ornithodoros capensis, and Ornithodoros sawaii) from the nests or burrows of their vertebrate hosts. One laboratory-reared argasid species (Ornithodoros moubata) was also included. Attempts were then made to isolate and characterize potential symbionts/pathogens using arthropod cell lines. Microbial community structure was distinct for each tick species. Coxiella was detected as the predominant symbiont in four tick species where dual symbiosis between Coxiella and Rickettsia or Coxiella and Francisella was observed in C. vespertilionis and O. moubata, respectively. Of note, A. japonicus lacked Coxiella and instead had Occidentia massiliensis and Thiotrichales as alternative symbionts. Our study found strong correlation between tick species and life stage. We successfully isolated Oc. massiliensis and characterized potential pathogens of genera Ehrlichia and Borrelia. The results suggest that there is no consistent trend of microbiomes in relation to tick life stage that fit all tick species and that the final interpretation should be related to the balance between environmental bacterial exposure and endosymbiont ecology. Nevertheless, our findings provide insights on the ecology of tick microbiomes and basis for future investigations on the capacity of argasid ticks to carry novel pathogens with public health importance.

The Symbiotic Continuum Within Ticks: Opportunities for Disease Control

Among blood-sucking arthropods, ticks are recognized as being of prime global importance because of their role as vectors of pathogens affecting human and animal health. Ticks carry a variety of pathogenic, commensal, and symbiotic microorganisms. For the latter, studies are available concerning the detection of endosymbionts, but their role in the physiology and ecology of ticks remains largely unexplored. This review paper focuses on tick endosymbionts of the genera Coxiella, Rickettsia, Francisella, Midichloria, and Wolbachia, and their impact on ticks and tick-pathogen interactions that drive disease risk. Tick endosymbionts can affect tick physiology by influencing nutritional adaptation, fitness, and immunity. Further, symbionts may influence disease ecology, as they interact with tick-borne pathogens and can facilitate or compete with pathogen development within the vector tissues. Rickettsial symbionts are frequently found in ticks of the genera of Ixodes, Amblyomma, and Dermacentor with relatively lower occurrence in Rhipicephalus, Haemaphysalis, and Hyalomma ticks, while Coxiella-like endosymbionts (CLEs) were reported infecting almost all tick species tested. Francisella-like endosymbionts (FLEs) have been identified in tick genera such as Dermacentor, Amblyomma, Ornithodoros, Ixodes, and Hyalomma, whereas Wolbachia sp. has been detected in Ixodes, Amblyomma, Hyalomma, and Rhipicephalus tick genera. Notably, CLEs and FLEs are obligate endosymbionts essential for tick survival and development through the life cycle. American dog ticks showed greater motility when infected with Rickettsia, indirectly influencing infection risk, providing evidence of a relationship between tick endosymbionts and tick-vectored pathogens. The widespread occurrence of endosymbionts across the tick phylogeny and evidence of their functional roles in ticks and interference with tick-borne pathogens suggests a significant contribution to tick evolution and/or vector competence. We currently understand relatively little on how these endosymbionts influence tick parasitism, vector capacity, pathogen transmission and colonization, and ultimately on how they influence tick-borne disease dynamics. Filling this knowledge gap represents a major challenge for future research.

Illuminating the bacterial microbiome of Australian ticks with 16S and Rickettsia-specific next-generation sequencing

Next-generation sequencing (NGS) studies show that mosquito and tick microbiomes influence the transmission of pathogens, opening new avenues for vector-borne pathogen control. Recent microbiological studies of Australian ticks highlight fundamental knowledge gaps of tick-borne agents. This investigation explored the composition, diversity and prevalence of bacteria in Australian ticks (n = 655) from companion animals (dogs, cats and horses). Bacterial 16S NGS was used to identify most bacterial taxa and a Rickettsia-specific NGS assay was developed to identify Rickettsia species that were indistinguishable at the V1-2 regions of 16S. Sanger sequencing of near full-length 16S was used to confirm whether species detected by 16S NGS were novel. The haemotropic bacterial pathogens Anaplasma platys, Bartonella clarridgeiae, “Candidatus Mycoplasma haematoparvum” and Coxiella burnetii were identified in Rhipicephalus sanguineus (s.l.) from Queensland (QLD), Western Australia, the Northern Territory (NT), and South Australia, Ixodes holocyclus from QLD, Rh. sanguineus (s.l.) from the NT, and I. holocyclus from QLD, respectively. Analysis of the control data showed that cross-talk compromises the detection of rare species as filtering thresholds for less abundant sequences had to be applied to mitigate false positives. A comparison of the taxonomic assignments made with 16S sequence databases revealed inconsistencies. The Rickettsia-specific citrate synthase gene NGS assay enabled the identification of Rickettsia co-infections with potentially novel species and genotypes most similar (97.9–99.1%) to Rickettsia raoultii and Rickettsia gravesii. “Candidatus Rickettsia jingxinensis” was identified for the first time in Australia. Phylogenetic analysis of near full-length 16S sequences confirmed a novel Coxiellaceae genus and species, two novel Francisella species, and two novel Francisella genotypes. Cross-talk raises concerns for the MiSeq platform as a diagnostic tool for clinical samples. This study provides recommendations for adjustments to Illuminaʼs 16S metagenomic sequencing protocol that help track and reduce cross-talk from cross-contamination during library preparation. The inconsistencies in taxonomic assignment emphasise the need for curated and quality-checked sequence databases.

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Bacterial pathogens identified in ticks from companion animals with 16S NGS.

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Sanger sequencing confirmed novel Coxiellaceae gen. sp. and Francisella.

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“Candidatus Rickettsia jingxinensis” was identified with Rickettsia-specific NGS.

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Comparison of taxonomic assignments in 16S sequence databases revealed errors.

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Modifications to the 16S metagenomic library protocol (Illumina) are provided.

The bacterial biome of ticks and their wildlife hosts at the urban-wildland interface

Advances in sequencing technologies have revealed the complex and diverse microbial communities present in ticks (Ixodida). As obligate blood-feeding arthropods, ticks are responsible for a number of infectious diseases that can affect humans, livestock, domestic animals and wildlife. While cases of human tick-borne diseases continue to increase in the northern hemisphere, there has been relatively little recognition of zoonotic tick-borne pathogens in Australia. Over the past 5 years, studies using high-throughput sequencing technologies have shown that Australian ticks harbour unique and diverse bacterial communities. In the present study, free-ranging wildlife (n=203), representing ten mammal species, were sampled from urban and peri-urban areas in New South Wales (NSW), Queensland (QLD) and Western Australia (WA). Bacterial metabarcoding targeting the 16S rRNA locus was used to characterize the microbiomes of three sample types collected from wildlife: blood, ticks and tissue samples. Further sequence information was obtained for selected taxa of interest. Six tick species were identified from wildlife: Amblyomma triguttatum, Ixodes antechini, Ixodes australiensis, Ixodes holocyclus, Ixodes tasmani and Ixodes trichosuri. Bacterial 16S rRNA metabarcoding was performed on 536 samples and 65 controls, generating over 100 million sequences. Alpha diversity was significantly different between the three sample types, with tissue samples displaying the highest alpha diversity (P<0.001). Proteobacteria was the most abundant taxon identified across all sample types (37.3 %). Beta diversity analysis and ordination revealed little overlap between the three sample types (P<0.001). Taxa of interest included Anaplasmataceae, Bartonella, Borrelia, Coxiellaceae, Francisella, Midichloria, Mycoplasma and Rickettsia. Anaplasmataceae bacteria were detected in 17.7% (95/536) of samples and included Anaplasma, Ehrlichia and Neoehrlichia species. In samples from NSW, 'Ca. Neoehrlichia australis', 'Ca. Neoehrlichia arcana', Neoehrlichia sp. and Ehrlichia sp. were identified. A putative novel Ehrlichia sp. was identified from WA and Anaplasma platys was identified from QLD. Nine rodent tissue samples were positive for a novel Borrelia sp. that formed a phylogenetically distinct clade separate from the Lyme Borrelia and relapsing fever groups. This novel clade included recently identified rodent-associated Borrelia genotypes, which were described from Spain and North America. Bartonella was identified in 12.9% (69/536) of samples. Over half of these positive samples were obtained from black rats (Rattus rattus), and the dominant bacterial species identified were Bartonella coopersplainsensis and Bartonella queenslandensis. The results from the present study show the value of using unbiased high-throughput sequencing applied to samples collected from wildlife. In addition to understanding the sylvatic cycle of known vector-associated pathogens, surveillance work is important to ensure preparedness for potential zoonotic spillover events.

Discovery and Surveillance of Tick-Borne Pathogens

Within the past 30 yr molecular assays have largely supplanted classical methods for detection of tick-borne agents. Enhancements provided by molecular assays, including speed, throughput, sensitivity, and specificity, have resulted in a rapid increase in the number of newly characterized tick-borne agents. The use of unbiased high throughput sequencing has enabled the prompt identification of new pathogens and the examination of tick microbiomes. These efforts have led to the identification of hundreds of new tick-borne agents in the last decade alone. However, little is currently known about the majority of these agents beyond their phylogenetic classification. Our article outlines the primary methods involved in tick-borne agent discovery and the current status of our understanding of tick-borne agent diversity.

Temporal patterns in Ixodes ricinus microbial communities: an insight into tick-borne microbe interactions

BACKGROUND

Ticks transmit pathogens of medical and veterinary importance and are an increasing threat to human and animal health. Assessing disease risk and developing new control strategies requires identifying members of the tick-borne microbiota as well as their temporal dynamics and interactions.

METHODS

Using high-throughput sequencing, we studied the Ixodes ricinus microbiota and its temporal dynamics. 371 nymphs were monthly collected during three consecutive years in a peri-urban forest. After a Poisson lognormal model was adjusted to our data set, a principal component analysis, sparse network reconstruction, and differential analysis allowed us to assess seasonal and monthly variability of I. ricinus microbiota and interactions within this community.

RESULTS

Around 75% of the detected sequences belonged to five genera known to be maternally inherited bacteria in arthropods and to potentially circulate in ticks: Candidatus Midichloria, Rickettsia, Spiroplasma, Arsenophonus and Wolbachia. The structure of the I. ricinus microbiota varied over time with interannual recurrence and seemed to be mainly driven by OTUs commonly found in the environment. Total network analysis revealed a majority of positive partial correlations. We identified strong relationships between OTUs belonging to Wolbachia and Arsenophonus, evidence for the presence of the parasitoid wasp Ixodiphagus hookeri in ticks. Other associations were observed between the tick symbiont Candidatus Midichloria and pathogens belonging to Rickettsia. Finally, more specific network analyses were performed on TBP-infected samples and suggested that the presence of pathogens belonging to the genera Borrelia, Anaplasma and Rickettsia may disrupt microbial interactions in I. ricinus.

CONCLUSIONS

We identified the I. ricinus microbiota and documented marked shifts in tick microbiota dynamics over time. Statistically, we showed strong relationships between the presence of specific pathogens and the structure of the I. ricinus microbiota. We detected close links between some tick symbionts and the potential presence of either pathogenic Rickettsia or a parasitoid in ticks. These new findings pave the way for the development of new strategies for the control of ticks and tick-borne diseases. Video abstract.

An integrated overview of the bacterial flora composition of Hyalomma anatolicum, the main vector of CCHF

The microbial flora associated with Hyalomma anatolicum ticks was investigated using culture-dependent (CD) and independent (next generation sequencing, NGS) methods. The bacterial profiles of different organs, development stages, sexes, and of host cattle skins were analyzed using the CD method. The egg and female gut microbiota were investigated using NGS. Fourteen distinct bacterial strains were identified using the CD method, of which Bacillus subtilis predominated in eggs, larval guts and in adult female and male guts, suggesting probable transovarial transmission. Bacillus velezensis and B. subtilis were identified in cattle skin and tick samples, suggesting that skin is the origin of tick bacteria. H.anatolicum males harbour lower bacterial diversity and composition than females. The NGS analysis revealed five different bacterial phyla across all samples, Proteobacteria contributing to >95% of the bacteria. In all, 56611sequences were generated representing 6,023 OTUs per female gut and 421 OTUs per egg. Francisellaceae family and Francisella make up the vast majority of the OTUs. Our findings are consistent with interference between Francisella and Rickettsia. The CD method identified bacteria, such B. subtilis that are candidates for vector control intervention approaches such paratransgenesis whereas NGS revealed high Francisella spp. prevalence, indicating that integrated methods are more accurate to characterize microbial community and diversity.

Molecular characterization of bacterial communities of two neotropical tick species (Amblyomma aureolatum and Ornithodoros brasiliensis) using rDNA 16S sequencing

Ticks are one of the main vectors of pathogens for humans and animals worldwide. However, they harbor non-pathogenic microorganisms that are important for their survival, facilitating both their nutrition and immunity. We investigated the bacterial communities associated with two neotropical tick species of human and veterinary potential health importance from Brazil: Amblyomma aureolatum and Ornithodoros brasiliensis. In A. aureolatum (adult ticks collected from wild canids from Southern Brazil), the predominant bacterial phyla were Proteobacteria (98.68%), Tenericutes (0.70%), Bacteroidetes (0.14%), Actinobacteria (0.13%), and Acidobacteria (0.05%). The predominant genera were Francisella (97.01%), Spiroplasma (0.70%), Wolbachia (0.51%), Candidatus Midichloria (0.25%), and Alkanindiges (0.13%). The predominant phyla in O. brasiliensis (adults, fed and unfed nymphs collected at the environment from Southern Brazil) were Proteobacteria (90.27%), Actinobacteria (7.38%), Firmicutes (0.77%), Bacteroidetes (0.44%), and Planctomycetes (0.22%). The predominant bacterial genera were Coxiella (87.71%), Nocardioides (1.73%), Saccharopolyspora (0.54%), Marmoricola (0.42%), and Staphylococcus (0.40%). Considering the genera with potential importance for human and animal health which can be transmitted by ticks, Coxiella sp. was found in all stages of O. brasiliensis, Francisella sp. in all stages of A. aureolatum and in unfed nymphs of O. brasiliensis, and Rickettsia sp. in females of A. aureolatum from Banhado dos Pachecos (BP) in Viamão municipality, Brazil, and in females and unfed nymphs of O. brasiliensis. These results deepen our understanding of the tick-microbiota relationship in Ixodidae and Argasidae, driving new studies with the focus on the manipulation of tick microbiota to prevent outbreaks of tick-borne diseases in South America.

Unbiased Characterization of the Microbiome and Virome of Questing Ticks

Due to their vector capacity, ticks are ectoparasites of medical and veterinary significance. Modern sequencing tools have facilitated tick-associated microbiota studies, but these have largely focused on bacterial pathogens and symbionts. By combining 16S rRNA gene sequencing with total RNA-sequencing methods, we aimed to determine the complete microbiome and virome of questing, female Ixodes holocyclus recovered from coastal, north-eastern New South Wales (NSW), Australia. We present, for the first time, a robust and unbiased method for the identification of novel microbes in ticks that enabled us to identify bacteria, viruses, fungi and eukaryotic pathogens. The dominant bacterial endosymbionts were Candidatus Midichloria sp. Ixholo1 and Candidatus Midichloria sp. Ixholo2. Candidatus Neoehrlichia australis and Candidatus Neoehrlichia arcana were also recovered, confirming that these bacteria encompass I. holocyclus’ core microbiota. In addition, seven virus species were detected—four previously identified in I. holocyclus and three novel species. Notably, one of the four previously identified virus species has pathogenic potential based on its phylogenetic relationship to other tick-associated pathogens. No known pathogenic eukaryotes or fungi were identified. This study has revealed the microbiome and virome of female I. holocyclus from the environment in north-eastern NSW. We propose that future tick microbiome and virome studies utilize equivalent methods to provide an improved representation of the microbial diversity in ticks globally.

The Prevalence of Coxiella burnetii in Hard Ticks in Europe and Their Role in Q Fever Transmission Revisited-A Systematic Review

The zoonosis Q fever is caused by the obligate intracellular bacterium Coxiella burnetii. Besides the main transmission route via inhalation of contaminated aerosols, ticks are discussed as vectors since the first isolation of the pathogen from a Dermacentor andersonii tick. The rare detection of C. burnetii in ticks and the difficult differentiation of C. burnetii from Coxiella-like endosymbionts (CLEs) are questioning the relevance of ticks in the epidemiology of Q fever. In this review, literature databases were systematically searched for recent prevalence studies concerning C. burnetii in ticks in Europe and experimental studies evaluating the vector competence of tick species. A total of 72 prevalence studies were included and evaluated regarding DNA detection methods and collection methods, country, and tested tick species. Specimens of more than 25 different tick species were collected in 23 European countries. Overall, an average prevalence of 4.8% was determined. However, in half of the studies, no Coxiella-DNA was detected. In Southern European countries, a significantly higher prevalence was observed, possibly related to the abundance of different tick species here, namely Hyalomma spp. and Rhipicephalus spp. In comparison, a similar proportion of studies used ticks sampled by flagging and dragging or tick collection from animals, under 30% of the total tick samples derived from the latter. There was no significant difference in the various target genes used for the molecular test. In most of the studies, no distinction was made between C. burnetii and CLEs. The application of specific detection methods and the confirmation of positive results are crucial to determine the role of ticks in Q fever transmission. Only two studies were available, which assessed the vector competence of ticks for C. burnetii in the last 20 years, demonstrating the need for further research.

Clinical Manifestations Associated with Bartonella henselae Infection in a Tropical Region

Bartonella henselae is a zoonotic Gram-negative Bacillus associated with self-limited regional lymphadenopathy. In recent decades, an expanding spectrum of clinical manifestations has been described, in part, due to improved diagnostics. However, updated epidemiological data are sparse. We retrospectively reviewed the clinical features of 31 patients with B. henselae infection over 15 years from 2005 to 2019, in the tropical Top End of Australia. Our annual disease incidence of 1.3 cases per 100,000 population is lower than that in the national database surveillances in the United States, but the hospitalization incidence of 0.9 per 100,000 population in our region is higher than those reported in the literature, with an average length of stay of 9 days. Patients were more commonly male, aboriginal, and aged less than 14 years (median age: 7 years), living in a rural setting with presentation during our monsoon season. The disease spectrum included lymph node disease (74%), organ peliosis, endocarditis, cutaneous lesions, parapharyngeal abscess, parotitis, and neurologic and ocular syndromes. Lymph node disease was far commoner in children than the more serious systemic B. henselae infections associated with adults (P = 0.074). Although no deaths were reported, significant morbidities were observed. Two endocarditis cases presented with glomerulonephritis, and hematological and neurological features mimicking vasculitis, and consequently received immunosuppressants. One case was only diagnosed after representation with serial embolic strokes. Given the heterogeneity of disease manifestations with nonspecific symptoms and significant consequences, a timely and accurate diagnosis is needed to avoid unnecessary treatments or interventions.

Morphological identification of ticks and molecular detection of tick-borne pathogens from bare-nosed wombats (Vombatus ursinus)

BACKGROUND

Ticks are obligate haematophagous ectoparasites of vertebrate hosts and transmit the widest range of pathogenic organisms of any arthropod vector. Seven tick species are known to feed on bare-nosed wombats (Vombatus ursinus), in addition to the highly prevalent Sarcoptes scabiei mite which causes fatal sarcoptic mange in most bare-nosed wombat populations. Little is known about the pathogens carried by most wombat ticks or how they may impact wombats and wombat handlers.

METHODS

Wombat ticks were sourced from wildlife hospitals and sanctuaries across Australia and identified to species level using taxonomic keys. Genomic DNA was extracted from a subsample, and following the amplification of the bacterial 16S rRNA gene V3-V4 hypervariable region, next-generation sequencing (NGS) on the Illumina MiSeq platform was used to assess the microbial composition.

RESULTS

A total of 447 tick specimens were collected from 47 bare-nosed wombats between January 2019 and January 2020. Five species of ticks were identified comprising wombat tick Bothriocroton auruginans (n = 420), wallaby tick Haemaphysalis bancrofti (n = 8), bush tick Haemaphysalis longicornis (n = 3), common marsupial tick Ixodes tasmani (n = 12), and Australian paralysis tick Ixodes holocyclus (n = 4). Tick infestations ranged from one to 73 ticks per wombat. The wombat tick was the most prevalent tick species comprising 94% of the total number of samples and was present on 97.9% (46/47) of wombat hosts. NGS results revealed the 16S rRNA gene diversity profile was predominantly Proteobacteria (55.1%) followed by Firmicutes (21.9%) and Actinobacteria (18.4%). A species of Coxiella sharing closest sequence identity to Coxiella burnetii (99.07%), was detected in 72% of B. auruginans and a Rickettsiella endosymbiont dominated the bacterial profile for I. tasmani.

CONCLUSIONS

A new host record for H. longicornis is the bare-nosed wombat. One adult male and two engorged adult female specimens were found on an adult male wombat from Coolagolite in New South Wales, and more specimens should be collected to confirm this host record. The most prevalent tick found on bare-nosed wombats was B. auruginans, confirming previous records. Analysis of alpha-diversity showed high variability across both sample locations and instars, similar to previous studies. The detection of various Proteobacteria in this study highlights the high bacterial diversity in native Australian ticks.

Parasites of wombats (family Vombatidae), with a focus on ticks and tick-borne pathogens

Ticks (Arachnida: Acari) are vectors for pathogens and the biggest threat to animal health. Many Australian ticks are associated with pathogens that impact humans, domestic animals and livestock. However, little is known about the presence or impact of tick-borne pathogens in native Australian wildlife. Wombats are particularly susceptible to the effects of the ectoparasite Sarcoptes scabiei which causes sarcoptic mange, the reason for which is unknown. Factors such as other ectoparasites and their associated pathogens may play a role. A critical understanding of the species of ectoparasites that parasitise wombats and their pathogens, and particularly ticks, is therefore warranted. This review describes the ectoparasites of wombats, pathogens known to be associated with those ectoparasites, and related literature gaps. Pathogens have been isolated in most tick species that typically feed on wombats; however, there are minimal molecular studies to determine the presence of pathogens in any other wombat ectoparasites. The development of next-generation sequencing (NGS) technologies allows us to explore entire microbial communities in ectoparasite samples, allowing fast and accurate identification of potential pathogens in many samples at once. These new techniques have highlighted the diversity and uniqueness of native ticks and their microbiomes, including pathogens of potential medical and veterinary importance. An increased understanding of all ectoparasites that parasitise wombats, and their associated pathogens, requires further investigation.

Update on the intricate tango between tick microbiomes and tick-borne pathogens

The recent development of high-throughput NGS technologies, (ie, next-generation sequencing) has highlighted the complexity of tick microbial communities-which include pathogens, symbionts, and commensals-and also their dynamic variability. Symbionts and commensals can confer crucial and diverse benefits to their hosts, playing nutritional roles or affecting fitness, development, nutrition, reproduction, defence against environmental stress and immunity. Nonpathogenic tick bacteria may also play a role in modifying tick-borne pathogen colonization and transmission, as relationships between microorganisms existing together in one environment can be competitive, exclusive, facilitating or absent, with many potential implications for both human and animal health. Consequently, ticks represent a compelling yet challenging system in which to investigate the composition and both the functional and ecological implications of tick bacterial communities, and thus merits greater attention. Ultimately, deciphering the relationships between microorganisms carried by ticks as well as symbiont-tick interactions will garner invaluable information, which may aid in some future arthropod-pest and vector-borne pathogen transmission control strategies. This review outlines recent research on tick microbiome composition and dynamics, highlights elements favouring the reciprocal influence of the tick microbiome and tick-borne agents and finally discusses how ticks and tick-borne diseases might potentially be controlled through tick microbiome manipulation in the future.

Microbial community of Hyalomma lusitanicum is dominated by Francisella-like endosymbiont

Exploring tick associations with complex microbial communities and single-microbial partners, especially intracellular symbionts, has become crucial to understand tick biology. Of particular interest are the underlying interactions with biological consequences i.e. tick fitness, vector competence. In this study, we first sequenced the 16S rRNA bacterial phylogenetic marker in adult male ticks of Hyalomma lusitanicum collected from 5 locations in the province of Cáceres to explore the composition of its microbial community. Overall, 16S rRNA sequencing results demonstrated that the microbial community of H. lusitanicum is mostly dominated by Francisella-like endosymbionts (FLEs) (ranging from 52% to 99% of relative abundance) suggesting it is a key taxon within the microbial community and likely a primary endosymbiont. However, further research is required to explore the mechanisms underlying the interaction between FLEs and H. lusitanicum.

Defining the aetiology of amoebic diseases of aquatic animals: trends, hurdles and best practices

Disease caused by parasitic amoebae impacts a range of aquatic organisms including finfish, crustaceans, echinoderms and molluscs. Despite the significant economic impact caused in both aquaculture and fisheries, the aetiology of most aquatic amoebic diseases is uncertain, which then affects diagnosis, treatment and prevention. The main factors hampering research effort in this area are the confusion around amoeba taxonomy and the difficulty proving that a particular species causes specific lesions. These issues stem from morphological and genetic similarities between cryptic species and technical challenges such as establishing and maintaining pure amoeba cultures, scarcity of Amoebozoa sequence data, and the inability to trigger pathogenesis under experimental conditions. This review provides a critical analysis of how amoebae are commonly identified and defined as aetiological agents of disease in aquatic animals and highlights gaps in the available knowledge regarding determining pathogenic Amoebozoa.

Screening for Rickettsia, Coxiella and Borrelia Species in Ticks from Queensland, Australia

Tick bites in Australia are linked to the transmission of a variety of infectious diseases in humans, livestock and wildlife. Despite this recognition, little is currently known about the variety of potential pathogens that are carried and transmitted by Australian ticks. In this study, we attempted to expand knowledge of Australian tick-borne bacterial pathogens by analyzing various tick species from the state of Queensland for potential human pathogens belonging to the Rickettsia, Coxiella and Borrelia genera. A total of 203 ticks, comprising of four genera and nine different tick species, were screened by specific qPCR assays. An overall Rickettsia qPCR positivity of 6.4% (13/203) was detected with rickettsial DNA found in four tick species (Ixodes holocyclus, I. tasmani, Amblyommatriguttatum, and Haemaphysalis longicornis). Amplification and analysis of several rickettsial genes from rickettsial qPCR positive samples identified sequences closely related to but genetically distinct from several previously described cultured and uncultured rickettsial species in the Rickettsia spotted fever subgroup. No ticks were positive for either Coxiella or Borrelia DNA. This work suggests that a further diversity of rickettsiae remain to be described in Australian ticks with the full importance of these bacteria to human and animal health yet to be elucidated.

General Microbiota of the Soft Tick Ornithodoros turicata Parasitizing the Bolson Tortoise (Gopherus flavomarginatus) in the Mapimi Biosphere Reserve, Mexico

The general bacterial microbiota of the soft tick Ornithodoros turicata found on Bolson tortoises (Gopherus flavomarginatus) were analyzed using next generation sequencing. The main aims of the study were to establish the relative abundance of bacterial taxa in the tick, and to document the presence of potentially pathogenic species for this tortoise, other animals, and humans. The study was carried-out in the Mapimi Biosphere Reserve in the northern-arid part of Mexico. Bolson tortoises (n = 45) were inspected for the presence of soft ticks, from which 11 tortoises (24.4%) had ticks in low loads (1–3 ticks per individual). Tick pools (five adult ticks each) were analyzed through 16S rRNA V3–V4 region amplification in a MiSeq Illumina, using EzBioCloud as a taxonomical reference. The operational taxonomic units (OTUs) revealed 28 phyla, 84 classes, 165 orders, 342 families, 1013 genera, and 1326 species. The high number of taxa registered for O. turicata may be the result of the variety of hosts that this tick parasitizes as they live inside G. flavomarginatus burrows. While the most abundant phyla were Proteobacteria, Actinobacteria, and Firmicutes, the most abundant species were two endosymbionts of ticks (Midichloria-like and Coxiella-like). Two bacteria documented as pathogenic to Gopherus spp. were registered (Mycoplasma spp. and Pasteurella testudinis). The bovine and ovine tick-borne pathogens A. marginale and A. ovis, respectively, were recorded, as well as the zoonotic bacteria A. phagocytophilum,Coxiella burnetii, and Neoehrlichia sp. Tortoises parasitized with O. turicata did not show evident signs of disease, which could indicate a possible ecological role as a reservoir that has yet to be demonstrated. In fact, the defense mechanisms of this tortoise against the microorganisms transmitted by ticks during their feeding process are still unknown. Future studies on soft ticks should expand our knowledge about what components of the microbiota are notable across multiple host–microbe dynamics. Likewise, studies are required to better understand the host competence of this tortoise, considered the largest terrestrial reptile in North America distributed throughout the Chihuahuan Desert since the late Pleistocene.

Application of 16S rRNA next generation sequencing in ticks in Greece

Tick-borne bacteria pose a significant threat to human and veterinary public health. Greece is a Mediterranean country with rich tick fauna and the most commonly detected tick-borne bacterial pathogens are members of the Rickettsia and Anaplasma species. The variable V2–V4 and V6–V9 regions of 16S rRNA gene of seven ticks belonging to four genera representative in Greece (Ixodes, Rhipicephalus, Dermacentor, Haemophyssalis) were analysed using multiple primer pairs by next generation sequencing (NGS). Nine bacterial phyla corresponding to 95 families, 116 genera and 172 species were identified. Proteobacteria was the predominant phylum in five of the seven ticks, followed by Actinobacteria, which predominated in two ticks. The tick-borne bacteria included Rickettsia and Anaplasma species, while “Candidatus Midichloria mitochondrii” were detected in high abundance in I. ricinus ticks and less in Rhipicephalus bursa; Coxiella-like endosymbionts were detected in Rh. sanguineus, H. parva, and less in Rh. bursa ticks. Co-infections with Rickettsia and Anaplasma were also observed. 16S rRNA NGS is a powerful tool to investigate the tick bacteriome and can improve the strategies for prevention and control of tick-borne diseases.

Biotic Factors Influence Microbiota of Nymph Ticks from Vegetation in Sydney, Australia

Ticks are haematophagous ectoparasites of medical and veterinary significance due to their excellent vector capacity. Modern sequencing techniques enabled the rapid sequencing of bacterial pathogens and symbionts. This study’s aims were two-fold; to determine the nymph diversity in Sydney, and to determine whether external biotic factors affect the microbiota. Tick DNA was isolated, and the molecular identity was determined for nymphs at the cox1 level. The tick DNA was subjected to high throughput DNA sequencing to determine the bacterial profile and the impact of biotic factors on the microbiota. Four nymph tick species were recovered from Sydney, NSW: Haemaphysalis bancrofti, Ixodes holocyclus, Ixodes trichosuri and Ixodes tasmani. Biotic factors, notably tick species and geography, were found to have a significance influence on the microbiota. The microbial analyses revealed that Sydney ticks display a core microbiota. The dominating endosymbionts among all tick species were Candidatus Midichloria sp. Ixholo1 and Candidatus Midichloria sp. Ixholo2. A novel Candidatus Midichloria sp. OTU_2090 was only found in I. holocyclus ticks (nymph: 96.3%, adult: 75.6%). Candidatus Neoehrlichia australis and Candidatus Neoehrlichia arcana was recovered from I. holocyclus and one I. trichosuri nymph ticks. Borrelia spp. was absent from all ticks. This study has shown that nymph and adult ticks carry different bacteria, and a tick bite in Sydney, Australia will result in different bacterial transfer depending on tick life stage, tick species and geography.

Taxon Appearance From Extraction and Amplification Steps Demonstrates the Value of Multiple Controls in Tick Microbiota Analysis

Background

The development of high-throughput sequencing technologies has substantially improved analysis of bacterial community diversity, composition, and functions. Over the last decade, high-throughput sequencing has been used extensively to identify the diversity and composition of tick microbial communities. However, a growing number of studies are warning about the impact of contamination brought along the different steps of the analytical process, from DNA extraction to amplification. In low biomass samples, e.g., individual tick samples, these contaminants may represent a large part of the obtained sequences, and thus generate considerable errors in downstream analyses and in the interpretation of results. Most studies of tick microbiota either do not mention the inclusion of controls during the DNA extraction or amplification steps, or consider the lack of an electrophoresis signal as an absence of contamination. In this context, we aimed to assess the proportion of contaminant sequences resulting from these steps. We analyzed the microbiota of individual Ixodes ricinus ticks by including several categories of controls throughout the analytical process: homogenization, DNA extraction, and DNA amplification.

Results

Controls yielded a significant number of sequences (1,126-13,198 mean sequences, depending on the control category). Some operational taxonomic units (OTUs) detected in these controls belong to genera reported in previous tick microbiota studies. In this study, these OTUs accounted for 50.9% of the total number of sequences in our samples, and were considered contaminants. Contamination levels (i.e., the percentage of sequences belonging to OTUs identified as contaminants) varied with tick instar and sex: 76.3% of nymphs and 75% of males demonstrated contamination over 50%, while most females (65.7%) had rates lower than 20%. Contamination mainly corresponded to OTUs detected in homogenization and extraction reagent controls, highlighting the importance of carefully controlling these steps.

Conclusion

Here, we showed that contaminant OTUs from sample laboratory processing steps can represent more than half the total sequence yield in sequencing runs, and lead to unreliable results when characterizing tick microbial communities. We thus strongly advise the routine use of negative controls in tick microbiota studies, and more generally in studies involving low biomass samples.

Comparative analysis of the midgut microbiota of two natural tick vectors of Rickettsia rickettsii

Although the ticks Amblyomma sculptum and Amblyomma aureolatum are important vectors of Rickettsia rickettsii, causative agent of the life-threatening Rocky Mountain spotted fever, A. aureolatum is considerably more susceptible to infection than A. sculptum. As the microbiota can interfere with the colonization of arthropod midgut (MG) by pathogens, in the current study we analyzed the MG microbiota of both tick species. Our results revealed that the MG of A. aureolatum harbors a prominent microbiota, while A. sculptum does not. Remarkably, a significant reduction of the bacterial load was recorded in R. rickettsii-infected A. aureolatum. In addition, the taxonomy analysis of the MG bacterial community of A. aureolatum revealed a dominance of the genus Francisella, suggesting an endosymbiosis. This study is the first step in getting insights into the mechanisms underlying the interactions among Amblyomma species, their microbiota and R. rickettsii. Additional studies to better understand these mechanisms are required and may help the development of novel alternatives to block rickettsial transmission.

A Host-Specific Blocking Primer Combined with Optimal DNA Extraction Improves the Detection Capability of a Metabarcoding Protocol for Canine Vector-Borne Bacteria

Bacterial canine vector-borne diseases are responsible for some of the most life-threatening conditions of dogs in the tropics and are typically poorly researched with some presenting a zoonotic risk to cohabiting people. Next-generation sequencing based methodologies have been demonstrated to accurately characterise a diverse range of vector-borne bacteria in dogs, whilst also proving to be more sensitive than conventional PCR techniques. We report two improvements to a previously developed metabarcoding tool that increased the sensitivity and diversity of vector-borne bacteria detected from canine blood. Firstly, we developed and tested a canine-specific blocking primer that prevents cross-reactivity of bacterial primer amplification on abundant canine mitochondrial sequences. Use of our blocking primer increased the number of canine vector-borne infections detected (five more Ehrlichia canis and three more Anaplasma platys infections) and increased the diversity of bacterial sequences found. Secondly, the DNA extraction kit employed can have a significant effect on the bacterial community characterised. Therefore, we compared four different DNA extraction kits finding the Qiagen DNeasy Blood and Tissue Kit to be superior for detection of blood-borne bacteria, identifying nine more A. platys, two more E. canis, one more Mycoplasma haemocanis infection and more putative bacterial pathogens than the lowest performing kit.

Bacterial community profiling highlights complex diversity and novel organisms in wildlife ticks

Ticks Acari:Ixodida transmit a greater variety of pathogens than any other blood-feeding group of arthropods. While numerous microbes have been identified inhabiting Australian Ixodidae, some of which are related to globally important tick-borne pathogens, little is known about the bacterial communities within ticks collected from Australian wildlife. In this study, 1,019 ticks were identified on 221 hosts spanning 27 wildlife species. Next-generation sequencing was used to amplify the V1-2 hypervariable region of the bacterial 16S rRNA gene from 238 ticks; Amblyomma triguttatum (n = 6), Bothriocroton auruginans (n = 11), Bothriocroton concolor (n = 20), Haemaphysalis bancrofti (n = 10), Haemaphysalis bremneri (n = 4), Haemaphysalis humerosa (n = 13), Haemaphysalis longicornis (n = 4), Ixodes antechini (n = 29), Ixodes australiensis (n = 26), Ixodes fecialis (n = 13), Ixodes holocyclus (n = 37), Ixodes myrmecobii (n = 1), Ixodes ornithorhynchi (n = 10), Ixodes tasmani (n = 51) and Ixodes trichosuri (n = 3). After bioinformatic analyses, over 14 million assigned bacterial sequences revealed the presence of recently described bacteria 'Candidatus Borrelia tachyglossi', 'Candidatus Neoehrlichia australis', 'Candidatus Neoehrlichia arcana' and 'Candidatus Ehrlichia ornithorhynchi'. Furthermore, three novel Anaplasmataceae species were identified in the present study including; a Neoehrlichia sp. in I. australiensis and I. fecialis collected from quenda (Isoodon fusciventer) (Western Australia), an Anaplasma sp. from one B. concolor from echidna (Tachyglossus aculeatus) (New South Wales), and an Ehrlichia sp. from a single I. fecialis parasitising a quenda (WA). This study highlights the diversity of bacterial genera harboured within wildlife ticks, which may prove to be of medical and/or veterinary importance in the future.

Assessment of a metabarcoding approach for the characterisation of vector-borne bacteria in canines from Bangkok, Thailand

BACKGROUND

Globally, bacterial vector-borne disease (VBD) exerts a large toll on dogs in terms of morbidity and mortality but nowhere is this more pronounced than in the tropics. Tropical environments permit a burgeoning diversity and abundance of ectoparasites some of which can transmit an extensive range of infectious agents, including bacteria, amongst others. Although some of these vector-borne bacteria are responsible for both animal and human diseases in the tropics, there is a scarcity of epidemiological investigation into these pathogens' prevalence. The situation is further exacerbated by frequent canine co-infection, complicating symptomatology that regular diagnostic techniques may miss or be unable to fully characterise. Such limitations draw attention to the need to develop screening tools capable of detecting a wide range of pathogens from a host simultaneously.

RESULTS

Here, we detail the employment of a next-generation sequencing (NGS) metabarcoding methodology to screen for the spectrum of bacterial VBD that are infecting semi-domesticated dogs across temple communities in Bangkok, Thailand. Our NGS detection protocol was able to find high levels of Ehrlichia canis, Mycoplasma haemocanis and Anaplasma platys infection rates as well as less common pathogens, such as "Candidatus Mycoplasma haematoparvum", Mycoplasma turicensis and Bartonella spp. We also compared our high-throughput approach to conventional endpoint PCR methods, demonstrating an improved detection ability for some bacterial infections, such as A. platys but a reduced ability to detect Rickettsia.

CONCLUSIONS

Our methodology demonstrated great strength at detecting coinfections of vector-borne bacteria and rare pathogens that are seldom screened for in canines in the tropics, highlighting its advantages over traditional diagnostics to better characterise bacterial pathogens in environments where there is a dearth of research.

Cryptic species diversity in ticks that transmit disease in Australia

Ticks are important vectors of a broad range of pathogens in Australia. Many tick species are morphologically similar and are therefore difficult to identify using morphology alone, particularly when collected in the larval and nymphal life stages. We report here the application of molecular methods to examine the species diversity of ixodid ticks at two sites in southern New South Wales, Australia. Our taxon sampling included six morphologically characterised adult stage voucher specimens of Ixodes trichosuri, Ixodes tasmani, Ixodes fecialis and Ixodes holocyclus (the paralysis tick) and ~250 field collected specimens that were in the larva or nymph stage and thus not morphologically identifiable. One nuclear and two mitochondrial amplicons were sequenced using a combination of Sanger and Illumina MiSeq sequencing. Phylogenetic relationships were estimated using both maximum likelihood and Bayesian methods. Two clades with strong bootstrap and Bayesian support were observed across trees estimated from each of three markers and from an analysis of the concatenated sequences. One voucher specimen of I. trichosuri was located in one of these clades, while the other I. trichosuri voucher specimen was in a second clade with the remaining three identified species, suggesting these morphologically similar ticks may represent different cryptic species. Unidentified specimens were found across both clades, and molecular divergence of many of these is equal to or greater than that observed between identified species, suggesting additional unidentified species may exist. Further studies are required to understand the taxonomic status of ticks in Australia, and how this species diversity impacts disease risk for livestock, domestic animals, wildlife and humans.

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Ticks genetically closely related had distinct morphological features.

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Remarkable genetic diversity of tick species collected.

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Rapid evolution of morphological characters in Ixodes.

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Understanding tick relationships could improve control of disease risk.

The Not-so-Sterile Womb: Evidence That the Human Fetus Is Exposed to Bacteria Prior to Birth

The human microbiome includes trillions of bacteria, many of which play a vital role in host physiology. Numerous studies have now detected bacterial DNA in first-pass meconium and amniotic fluid samples, suggesting that the human microbiome may commence in utero. However, these data have remained contentious due to underlying contamination issues. Here, we have used a previously described method for reducing contamination in microbiome workflows to determine if there is a fetal bacterial microbiome beyond the level of background contamination. We recruited 50 women undergoing non-emergency cesarean section deliveries with no evidence of intra-uterine infection and collected first-pass meconium and amniotic fluid samples. Full-length 16S rRNA gene sequencing was performed using PacBio SMRT cell technology, to allow high resolution profiling of the fetal gut and amniotic fluid bacterial microbiomes. Levels of inflammatory cytokines were measured in amniotic fluid, and levels of immunomodulatory short chain fatty acids (SCFAs) were quantified in meconium. All meconium samples and most amniotic fluid samples (36/43) contained bacterial DNA. The meconium microbiome was dominated by reads that mapped to Pelomonas puraquae. Aside from this species, the meconium microbiome was remarkably heterogeneous between patients. The amniotic fluid microbiome was more diverse and contained mainly reads that mapped to typical skin commensals, including Propionibacterium acnes and Staphylococcus spp. All meconium samples contained acetate and propionate, at ratios similar to those previously reported in infants. P. puraquae reads were inversely correlated with meconium propionate levels. Amniotic fluid cytokine levels were associated with the amniotic fluid microbiome. Our results demonstrate that bacterial DNA and SCFAs are present in utero, and have the potential to influence the developing fetal immune system.

Surface sterilization methods impact measures of internal microbial diversity in ticks

BACKGROUND

Ticks are obligate blood feeders transmitting major pathogens worldwide. Over the past few years, considerable research efforts have focused on the diversity, distribution and impact of gut and intracellular bacterial symbionts on tick development and tick-borne pathogen transmission. The study of this internal microbiome requires the use of a sterilization method to remove external (i.e. cuticular) microbes present on the tick's surface and to avoid any further contamination. Several sterilization methods exist, including ethanol- or bleach-based treatments that are both effective in killing microbes but with different potential effects on DNA denaturation.

METHODS

We examined how these different sterilization methods impact the measure of internal microbial diversity hosted by the Cayenne tick Amblyomma cajennense (sensu stricto). Bacterial barcoding investigations based on 16S rRNA gene sequences were conducted on two batches of 50 individuals each: Ticks of the first batch were sterilized with bleach diluted at 1% and the second batch with 70% ethanol. Tick external microbiome was also determined from cuticle smearing and water samples used for tick washing.

RESULTS

Bacterial barcoding investigations showed major differences between ethanol- and bleach-treated specimens. Both methods led to the detection of major intracellular bacteria associated with A. cajennense (s.s.) but ethanol-treated ticks always harbored a higher bacterial diversity than bleach-treated ticks. Further examinations of tick gut and tick external microbiome revealed that ethanol-based surface sterilization method is inefficient to eliminate the DNA of external bacteria.

CONCLUSIONS

We herein provide evidence that studies investigating the internal microbiome of ticks should consider bleach as the gold standard to efficiently remove cuticular bacterial DNA. Indeed, this method does not impact the internal bacterial diversity hosted by ticks and is thus a better method than the ethanol-based one for studying the internal microbiome.

Effects of temperature on bacterial microbiome composition in Ixodes scapularis ticks

Ixodes scapularis, the blacklegged deer tick, is the principal vector of Lyme disease in North America. Environmental factors are known to influence regional and seasonal incidence of Lyme disease and possibly the endemicity of the disease to the northeastern and upper mid-western regions of the United States. With a goal to understand the impact of environmental temperature on microbial communities within the tick, we investigated the bacterial microbiome of colony-reared I. scapularis ticks statically incubated at different temperatures (4, 20, 30, and 37°C) at a constant humidity in a controlled laboratory setting by comparison of sequenced amplicons of the bacterial 16S V4 rRNA gene to that of the untreated baseline controls. The microbiomes of colony-reared I. scapularis males were distinct than that of females, which were entirely dominated by Rickettsia. In silico removal of Rickettsia sequences from female data revealed the underlying bacterial community, which is consistent in complexity with those seen among male ticks. The bacterial community composition of these ticks changes upon incubation at 30°C for a week and 37°C for more than 5 days. Moreover, the male ticks incubated at 30 and 37°C exhibited significantly different bacterial diversity compared to the initial baseline microbiome, and the change in bacterial diversity was dependent upon duration of exposure. Rickettsia-free data revealed a significantly different bacterial diversity in female ticks incubated at 37°C compared to that of 4 and 20°C treatments. These results provide experimental evidence that environmental temperature can impact the tick bacterial microbiome in a laboratory setting.

Investigation of the performance of serological assays used for Lyme disease testing in Australia

Spirochaetes of the Borrelia burgdorferi sensu lato complex, which includes those that cause Lyme disease, have not been identified in Australia. Nevertheless, Australian patients exist, some of whom have not left the country, who have symptoms consistent with so-called “chronic Lyme disease”. Blood specimens from these individuals may be tested in Australian laboratories and in specialist laboratories outside Australia and sometimes conflicting results are obtained. Such discrepancies cause the patients to question the results from the Australian laboratories and seek assistance from the Australian Government in clarifying why the discrepancies occur. The aim of this study was to determine the level of agreement in results between commonly used B. burgdorferi serology assays in specimens of known status, and between results reported by different laboratories when they use the same serology assay. Five immunoassays and five immunoblots used in Australia and elsewhere were examined for the detection of IgG antibodies to Borrelia burgdorferi sensu lato. Predominantly, archived specimens previously tested for Lyme disease were used for the study and included 639 contributed by seven clinical laboratories located either in Australia or in areas endemic for Lyme disease. Also included were 308 prospectively collected Australian blood donor specimens. All clinical specimens were tested in all 10 assays whereas blood donor specimens were tested in all immunoassays and a subset was tested on immunoblots. With the exception of one immunoblot, the results between the assays agreed with each other in a known positive specimen population ≥ 77% of the time and in a known negative population, 88% of the time or greater. The test results obtained during the study were different from the participating laboratory’s less than 2% of the time when the same assay was used. These findings suggest that discordance in results between laboratories is more likely due to variation in algorithms or in the use of assays with different sensitivities or specificities rather than conflicting results being reported from the same assay in different laboratories. In the known negative population, specificities of the immunoassays ranged between 87.7% and 99.7%. In Australia’s low prevalence population, this would translate to a positive predictive value of < 4%.

Metagenomic Approach to Characterizing Disease Epidemiology in a Disease-Endemic Environment in Northern Thailand

In this study, we used a metagenomic approach to analyze bacterial communities from diverse populations (humans, animals, and vectors) to investigate the role of these microorganisms as causative agents of disease in human and animal populations. Wild rodents and ectoparasites were collected from 2014 to 2018 in Nan province, Thailand where scrub typhus is highly endemic. Samples from undifferentiated febrile illness (UFI) patients were obtained from a local hospital. A total of 200 UFI patient samples were obtained and 309 rodents and 420 pools of ectoparasites were collected from rodents (n = 285) and domestic animals (n = 135). The bacterial 16S rRNA gene was amplified and sequenced with the Illumina. Real-time PCR and Sanger sequencing were used to confirm the next-generation sequencing (NGS) results and to characterize pathogen species. Several pathogens were detected by NGS in all populations studied and the most common pathogens identified included Bartonella spp., Rickettsia spp., Leptospira spp., and Orientia tsutsugamushi. Interestingly, Anaplasma spp. was detected in patient, rodent and tick populations, although they were not previously known to cause human disease from this region. Candidatus Neoehrlichia, Neorickettsia spp., Borrelia spp., and Ehrlichia spp. were detected in rodents and their associated ectoparasites. The same O. tsutsugamushi genotypes were shared among UFI patients, rodents, and chiggers in a single district indicating that the chiggers found on rodents were also likely responsible for transmitting to people. Serological testing using immunofluorescence assays in UFI samples showed high prevalence (IgM/IgG) of Rickettsia and Orientia pathogens, most notably among samples collected during September–November. Additionally, a higher number of seropositive samples belonged to patients in the working age population (20–60 years old). The results presented in this study demonstrate that the increased risk of human infection or exposure to chiggers and their associated pathogen (O. tsutsugamushi) resulted in part from two important factors; working age group and seasons for rice cultivation and harvesting. Evidence of pathogen exposure was shown to occur as there was seropositivity (IgG) in UFI patients for bartonellosis as well as for anaplasmosis. Using a metagenomic approach, this study demonstrated the circulation and transmission of several pathogens in the environment, some of which are known causative agents of illness in human populations.

Human Tick-Borne Diseases in Australia

There are 17 human-biting ticks known in Australia. The bites of Ixodes holocyclus, Ornithodoros capensis, and Ornithodoros gurneyi can cause paralysis, inflammation, and severe local and systemic reactions in humans, respectively. Six ticks, including Amblyomma triguttatum, Bothriocroton hydrosauri, Haemaphysalis novaeguineae, Ixodes cornuatus, Ixodes holocyclus, and Ixodes tasmani may transmit Coxiella burnetii, Rickettsia australis, Rickettsia honei, or Rickettsia honei subsp. marmionii. These bacterial pathogens cause Q fever, Queensland tick typhus (QTT), Flinders Island spotted fever (FISF), and Australian spotted fever (ASF). It is also believed that babesiosis can be transmitted by ticks to humans in Australia. In addition, Argas robertsi, Haemaphysalis bancrofti, Haemaphysalis longicornis, Ixodes hirsti, Rhipicephalus australis, and Rhipicephalus sanguineus ticks may play active roles in transmission of other pathogens that already exist or could potentially be introduced into Australia. These pathogens include Anaplasma spp., Bartonella spp., Burkholderia spp., Francisella spp., Dera Ghazi Khan virus (DGKV), tick-borne encephalitis virus (TBEV), Lake Clarendon virus (LCV), Saumarez Reef virus (SREV), Upolu virus (UPOV), or Vinegar Hill virus (VINHV). It is important to regularly update clinicians' knowledge about tick-borne infections because these bacteria and arboviruses are pathogens of humans that may cause fatal illness. An increase in the incidence of tick-borne infections of human may be observed in the future due to changes in demography, climate change, and increase in travel and shipments and even migratory patterns of birds or other animals. Moreover, the geographical conditions of Australia are favorable for many exotic ticks, which may become endemic to Australia given an opportunity. There are some human pathogens, such as Rickettsia conorii and Rickettsia rickettsii that are not currently present in Australia, but can be transmitted by some human-biting ticks found in Australia, such as Rhipicephalus sanguineus, if they enter and establish in this country. Despite these threats, our knowledge of Australian ticks and tick-borne diseases is in its infancy.

Extensive Diversity of RNA Viruses in Australian Ticks

Each year a growing number of individuals along the east coast of Australia experience debilitating disease following tick bites. As there is no evidence for the presence of the causative agent of Lyme disease, Borrelia burgdorferisensu lato, in Australian ticks, the etiological basis of this disease syndrome remains controversial. To characterize the viruses associated with Australian ticks, particularly those that might be associated with mammalian infection, we performed unbiased RNA sequencing on 146 ticks collected across two locations along the coast of New South Wales, Australia. This revealed 19 novel RNA viruses from a diverse set of families. Notably, three of these viruses clustered with known mammalian viruses, including a novel coltivirus that was related to the human pathogen Colorado tick fever virus.

Understanding the microbiome of ticks in Australia is of considerable interest given the ongoing debate over whether Lyme disease and its causative agent, the bacterium Borrelia burgdorferisensu lato, are present in Australia. The diversity of bacteria infecting Australian ticks has been studied using both culture- and metagenomics-based techniques. However, little is known about the virome of Australian ticks, including whether this includes viruses with the potential to infect mammals. We used a meta-transcriptomics approach to reveal the diversity and evolution of viruses from Australian ticks collected from two locations on the central east coast of Australia, including metropolitan Sydney. From this we identified 19 novel RNA viruses belonging to 12 families, as well as 1 previously described RNA virus. The majority of these viruses were related to arthropod-associated viruses, suggesting that they do not utilize mammalian hosts. However, two novel viruses discovered in ticks feeding on bandicoot marsupials clustered closely within the mammal-associated hepacivirus and pestivirus groups (family Flaviviridae). Another bandicoot tick yielded a novel coltivirus (family Reoviridae), a group of largely tick-associated viruses containing the known human pathogen Colorado tick fever virus and its relative, Eyach virus. Importantly, our transcriptomic data provided no evidence for the presence of B. burgdorferisensu lato in any tick sample, providing further evidence against the presence of Lyme disease in Australia. In sum, this study reveals that Australian ticks harbor a diverse virome, including some viruses that merit additional screening in the context of emerging infectious disease.

IMPORTANCE Each year a growing number of individuals along the east coast of Australia experience debilitating disease following tick bites. As there is no evidence for the presence of the causative agent of Lyme disease, Borrelia burgdorferisensu lato, in Australian ticks, the etiological basis of this disease syndrome remains controversial. To characterize the viruses associated with Australian ticks, particularly those that might be associated with mammalian infection, we performed unbiased RNA sequencing on 146 ticks collected across two locations along the coast of New South Wales, Australia. This revealed 19 novel RNA viruses from a diverse set of families. Notably, three of these viruses clustered with known mammalian viruses, including a novel coltivirus that was related to the human pathogen Colorado tick fever virus.

Microbiome differences between river-dwelling and cave-adapted populations of the fish Astyanax mexicanus (De Filippi, 1853)

Symbiotic relationships between host and microbiome can play a major role in local adaptation. Previous studies with freshwater organisms have shown that microbiome performs numerous important biochemical functions for the host, playing a key role in metabolism, physiology or health. Experimental studies in fish groups have found an effect of enzymatic activity of gut microbiota on a variety of metabolic processes. The goal of this study was to compare stomach microbiome from cave and surface Astyanax mexicanus, in order to evaluate the potential response of microbiota to contrasting environmental conditions and physiological adaptations of the host. Stomach microbiota was obtained from three different populations: Pachón cave, and two surface rivers (Rascón and Micos rivers). The stomach microbiome was analyzed using the Ion 16S Metagenomic kit considering seven variable regions: V2, V3, V4, V6-7, V8 and V9. A high diversity was observed across samples, including 16 phyla, 120 families and 178 genera. Gammaproteobacteria, Firmicutes, Bacteroidetes and Betaproteobacteria were the most abundant phyla across the samples. Although the relative abundance of the core OTUs at genus level were highly contrasting among populations, we did not recover differences in stomach microbiome between contrasting habitats (cave vs. surface rivers). Rather, we observed a consistent association between β-diversity and dissolved oxygen concentration in water. Therefore, and unexpectedly, the microbiota of A. mexicanus is not linked with the contrasting conditions of the habitat considered here but is related to water parameters.

The microbiota of hematophagous ectoparasites collected from migratory birds

Arthropod vectors are responsible for the transmission of human pathogens worldwide. Several arthropod species are bird ectoparasites, however, no study to date has characterized their microbiota as a whole. We sampled hematophagous ectoparasites that feed on migratory birds and performed 16S rRNA gene metabarcoding to characterize their microbial community. A total of 194 ectoparasites were collected from 115 avian hosts and classified into three groups: a) Hippoboscidae diptera; b) ticks; c) other arthropods. Metabarcoding showed that endosymbionts were the most abundant genera of the microbial community, including Wolbachia for Hippoboscidae diptera, Candidatus Midichloria for ticks, Wolbachia and Arsenophonus for the other arthropod group. Genera including pathogenic species were: Rickettsia, Borrelia, Coxiella, Francisella, Bartonella, Anaplasma. Co-infection with Borrelia-Rickettsia and Anaplasma-Rickettsia was also observed. A global overview of the microbiota of ectoparasites sampled from migratory birds was obtained with the use of 16S rRNA gene metabarcoding. A novel finding is the first identification of Rickettsia in the common swift louse fly, Crataerina pallida. Given their possible interaction with pathogenic viruses and bacteria, the presence of endosymbionts in arthropods merits attention. Finally, molecular characterization of genera, including both pathogenic and symbiont species, plays a pivotal role in the design of targeted molecular diagnostics.

Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing

In recent decades, vector-borne diseases have re-emerged and expanded at alarming rates, causing considerable morbidity and mortality worldwide. Effective and widely available vaccines are lacking for a majority of these diseases, necessitating the development of novel disease mitigation strategies. To this end, a promising avenue of disease control involves targeting the vector microbiome, the community of microbes inhabiting the vector. The vector microbiome plays a pivotal role in pathogen dynamics, and manipulations of the microbiome have led to reduced vector abundance or pathogen transmission for a handful of vector-borne diseases. However, translating these findings into disease control applications requires a thorough understanding of vector microbial ecology, historically limited by insufficient technology in this field. The advent of next-generation sequencing approaches has enabled rapid, highly parallel sequencing of diverse microbial communities. Targeting the highly-conserved 16S rRNA gene has facilitated characterizations of microbes present within vectors under varying ecological and experimental conditions. This technique involves amplification of the 16S rRNA gene, sample barcoding via PCR, loading samples onto a flow cell for sequencing, and bioinformatics approaches to match sequence data with phylogenetic information. Species or genus-level identification for a high number of replicates can typically be achieved through this approach, thus circumventing challenges of low detection, resolution, and output from traditional culturing, microscopy, or histological staining techniques. Therefore, this method is well-suited for characterizing vector microbes under diverse conditions but cannot currently provide information on microbial function, location within the vector, or response to antibiotic treatment. Overall, 16S next-generation sequencing is a powerful technique for better understanding the identity and role of vector microbes in disease dynamics.