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

Anaplasmataceae presence in Amblyomma calcaratum associated with anteaters (Tamandua tetradactyla) in the rainforest ecoregion, Argentina

Bacteria of the sister genera Ehrlichia and Anaplasma (Anaplasmataceae) are obligate intracellular Alphaproteobacteria that are transmitted mostly through arthropod vectors. These agents can infect different vertebrate cells, depending on the species involved, and can cause diseases in animals and humans. In this study, we evaluated the presence of Anaplasmataceae bacteria in Amblyomma calcaratum ticks collected from a road-killed Tamandua tetradactyla in the Rainforest ecoregion in Argentina. All samples were screened for Anaplasmataceae DNA using a real-time PCR assay targeting the 16S rRNA gene. Evidence of Anaplasmataceae DNA was detected in three out of thirty-nine Am. calcaratum ticks. Phylogenetic analysis of a portion of 16S rRNA gene positioned one sample (Ehrlichia sp. strain Ac124) with Ehrlichia sequences and the other two samples with Anaplasma sequences; Anaplasma sp. strain Ac145 close to Anaplasma odocoilei and Anaplasma sp. strain Ac152 in an ancestral position to most Anaplasma species. The groEL sequence obtained showed that Ehrlichia sp. strain Ac124 was phylogenetically related to Ehrlichia sp. strain Iberá reported infecting Amblyomma tigrinum from Iberá wetlands in Argentina. Phylogenetic analysis using the rpoB sequence positioned Anaplasma sp. strain Ac145 close to the canine pathogen Anaplasma platys, while Anaplasma sp. strain Ac152 was positioned close to the bovine pathogen Anaplasma marginale. In this study, three Anaplasmataceae agents were detected in adults of Am. calcaratum associated with a T. tetradactyla. These results suggest that the number of Anaplasmataceae species, as well as their distribution, is largely unknown.

Perception of Ticks and Tick-Borne Diseases Worldwide

In this comprehensive review study, we addressed the challenge posed by ticks and tick-borne diseases (TBDs) with growing incidence affecting human and animal health worldwide. Data and perspectives were collected from different countries and regions worldwide, including America, Europe, Africa, Asia, and Oceania. The results updated the current situation with ticks and TBD and how it is perceived by society with information bias and gaps. The study reinforces the importance of multidisciplinary and international collaborations to advance in the surveillance, communication and proposed future directions to address these challenges.

Capybara density and climatic factors as modulators of Ehrlichia prevalence in questing ticks in the Iberá wetlands, Argentina

We evaluated the presence of Ehrlichia spp. in unfed capybara ticks, Amblyomma dubitatum, and explored its association with capybaras density, ticks density and environmental variables. We observed that in the Iberá wetlands ecoregion A. dubitatum is infected by "Candidatus Ehrlichia hydrochoerus" and in a lesser extent with an Ehrlichia species closely related to Ehrlichia chaffeensis. The frequency of "Ca. Ehrlichia hydrochoerus" presence in A. dubitatum was not associated with vector abundance, but the probability of finding "Ca. Ehrlichia hydrochoerus"-infected ticks increased when the density of capybaras was low two months before. We hypothesize that when the density of capybaras decreases, A. dubitatum immature stages may seek out alternative hosts one of which could exhibit high realized reservoir competence for "Ca. Ehrlichia hydrochoerus", leading to an increased prevalence of this ehrlichiae in questing A. dubitatum. High minimum temperatures and high cumulative rainfall in the time period previous to tick collection (15 to 60 days) were positively correlated with the prevalence of "Ca. Ehrlichia hydrochoerus" infection in A. dubitatum. Our results suggest that a combination of factors (both biological and abiotic) could raise the risk of human exposure to tick-borne Ehrlichia in the Iberá wetlands ecoregion.

Unravelling the Diversity of Microorganisms in Ticks from Australian Wildlife

Ticks and tick-borne pathogens pose a significant threat to the health and welfare of humans and animals. Our knowledge about pathogens carried by ticks of Australian wildlife is limited. This study aimed to characterise ticks and tick-borne microorganisms from a range of wildlife species across six sites in Victoria, Australia. Following morphological and molecular characterisation (targeting 16S rRNA and cytochrome c oxidase I), tick DNA extracts (n = 140) were subjected to microfluidic real-time PCR-based screening for the detection of microorganisms and Rickettsia-specific real-time qPCRs. Five species of ixodid ticks were identified, including Aponomma auruginans, Ixodes (I.) antechini, I. kohlsi, I. tasmani and I. trichosuri. Phylogenetic analyses of 16S rRNA sequences of I. tasmani revealed two subclades, indicating a potential cryptic species. The microfluidic real-time PCR detected seven different microorganisms as a single (in 13/45 ticks) or multiple infections (27/45). The most common microorganisms detected were Apicomplexa (84.4%, 38/45) followed by Rickettsia sp. (55.6%, 25/45), Theileria sp. (22.2% 10/45), Bartonella sp. (17.8%, 8/45), Coxiella-like sp. (6.7%, 3/45), Hepatozoon sp. (2.2%, 1/45), and Ehrlichia sp. (2.2%, 1/45). Phylogenetic analyses of four Rickettsia loci showed that the Rickettsia isolates detected herein potentially belonged to a novel species of Rickettsia. This study demonstrated that ticks of Australian wildlife carry a diverse array of microorganisms. Given the direct and indirect human-wildlife-livestock interactions, there is a need to adopt a One Health approach for continuous surveillance of tick-associated pathogens/microorganisms to minimise the associated threats to animal and human health.

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

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

Current debates and advances in tick microbiome research

The main importance of ticks resides in their ability to harbor pathogens that can be transmitted to terrestrial vertebrates including humans. Recently, studies have focused on the taxonomic and functional composition of the tick microbiome, its microbial diversity and variation under different factors including tick species, sex, and environment among others. Of special interest are the interactions between the tick, the microbiome and pathogens since tick microbiome can influence pathogen colonization within the tick vector, and potentially, transmission to the vertebrate host. In this review, we tackled a synthesis on the growing field of tick microbiomes. We focus on the current state of tick microbiome research, addressing controversial and hotly debated topics and advances in the precise manipulation of tick microbiome. Furthermore, we discuss the innovative anti-tick microbiota vaccines as a possible tool for microbiome modulation and thus, control of tick-borne diseases. Deciphering tick-microbiome pathogen interactions can spur new strategies to control tick-borne diseases via modulation of tick microbiome.

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Whether the diversity observed in tick microbiomes concerns the biology or the methodology remains an open question.

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Tick immunity must play a major role in selecting ‘who stays and who leaves’ the microbiome.

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Anti-tick microbiota vaccines can target specific bacteria and subsequently modulate tick microbiome.

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.

Diversity unearthed by the estimated molecular phylogeny and ecologically quantitative characteristics of uncultured Ehrlichia bacteria in Haemaphysalis ticks, Japan

Ehrlichia species are obligatory intracellular bacteria transmitted by arthropods, and some of these species cause febrile diseases in humans and livestock. Genome sequencing has only been performed with cultured Ehrlichia species, and the taxonomic status of such ehrlichiae has been estimated by core genome-based phylogenetic analysis. However, many uncultured ehrlichiae exist in nature throughout the world, including Japan. This study aimed to conduct a molecular-based taxonomic and ecological characterization of uncultured Ehrlichia species or genotypes from ticks in Japan. We first surveyed 616 Haemaphysalis ticks by p28-PCR screening and analyzed five additional housekeeping genes (16S rRNA, groEL, gltA, ftsZ, and rpoB) from 11 p28-PCR-positive ticks. Phylogenetic analyses of the respective genes showed similar trees but with some differences. Furthermore, we found that V1 in the V1-V9 regions of Ehrlichia 16S rRNA exhibited the greatest variability. From an ecological viewpoint, the amounts of ehrlichiae in a single tick were found to equal approx. 6.3E+3 to 2.0E+6. Subsequently, core-partial-RGGFR-based phylogenetic analysis based on the concatenated sequences of the five housekeeping loci revealed six Ehrlichia genotypes, which included potentially new Ehrlichia species. Thus, our approach contributes to the taxonomic profiling and ecological quantitative analysis of uncultured or unidentified Ehrlichia species or genotypes worldwide.

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.

Molecular characterization of novel Ehrlichia genotypes in Ixodes auritulus from Uruguay

Ehrlichia are small intracellular Gram-negative bacteria transmitted by ticks. These microorganisms cause ehrlichiosis, a complex of life-threatening emerging zoonoses and diseases of global veterinary relevance. The aim of this study was to investigate the presence of Ehrlichia in free-living Ixodes auritulus collected in Uruguay. Ticks were collected from vegetation in five localities from the southeast and northeast of the country between 2014 and 2017. Detection of Ehrlichia DNA was performed in pools of adults or nymphs grouped according to the collection site and date. A total of 1,548 I. auritulus ticks were collected in four of the five locations sampled. Fragments of three loci (16S rRNA, dsb and groEL) were obtained by PCR, and phylogenies inferred using Bayesian inference analysis for each gene independently. DNA of Ehrlichia spp. was found in 15 out of 42 tick pools. Based on the topology of the phylogenetic trees, our sequences represent two novel genotypes for the genus named as Ehrlichia sp. Serrana and Ehrlichia sp. Laguna Negra. Both genotypes were closely related to Ehrlichia sp. Magellanica, a species detected in Ixodes uriae and Magellanic penguins. Considering that all stages of I. auritulus and I. uriae are parasites of birds, their phylogenetic relationships, and common eco–epidemiological profiles, it is reasonable to state that these genotypes of Ehrlichia spp. may represent a natural group likely associated with birds. Our results constitute the first characterization of Ehrlichia spp. in Uruguay. Future studies on birds reported as hosts for I. auritulus are needed to further understand the epidemiological cycles of both Ehrlichia genotypes in the country. Finally, I. auritulus does not feed on humans, so the two Ehrlichia species reported herein might have no implications in human health.

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First molecular characterization of Ehrlichia in Uruguay.

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Two novel genotypes of Ehrlichia were detected in Ixodes auritulus.

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Evidence of a natural lineage of Ehrlichia associated with birds is reinforced.

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.

A putative novel strain of Ehrlichia infecting Amblyomma tigrinum associated with Pampas fox (Lycalopex gymnocercus) in Esteros del Iberá ecoregion, Argentina

The current work evaluated road-killed Pampas foxes (Lycalopex gymnocercus) and their ticks for the presence of vector-borne agents in the ecoregion Esteros del Iberá in northeastern Argentina. Spleen, lung and blood samples and Amblyomma tigrinum adult ticks collected from the foxes were tested by polymerase chain reaction (PCR) assays targeting bacteria of the genera Ehrlichia, Anaplasma, and Rickettsia. All foxes tested were negative for the three genera, but evidence of Ehrlichia and Rickettsia infection was detected in the ticks. One A. tigrinum (out of 12 tested) was infected by an ehrlichial agent, here named Ehrlichia sp. strain Iberá, related to ehrlichial agents recently detected in platypuses in Tasmania (Ornithorhynchus anatinus) and in voles (Myodes rutilus and Myodes rufocanus) and shrews (Sorex araneus) in the Russian Far East. Regarding Rickettsia, all A. tigrinum ticks (100%) were infected by ´Candidatus Rickettsia andeanae´, a member of the spotted fever group rickettsia of unknown pathogenicity. Further research is necessary to unveil the ecology of Ehrlichia sp. strain Iberá as well as its zoonotic relevance. The species of the genus Ehrlichia are known to be pathogenic to mammals, including humans and domestic animals, thus the presence of this ehrlichial agent in A. tigrinum is a potential risk for veterinary and public health, as the adults of A. tigrinum are common parasites of dogs in rural and peri-urban environments, and humans are also frequently bitten by this tick species.

Novel Ehrlichia sp. detected in Magellanic penguins (Sphenicus magellanicus) and in the seabird tick Ixodes uriae from Magdalena Island, southern Chile

Ehrlichia spp. are obligatory intracellular microorganisms that infect hematopoietic, endothelial or blood cells of mammals. Ticks are the only vectors of these agents in nature. To date, the role of birds and their associated ticks as reservoirs of ehrlichiae remains almost unexplored. In this study, we performed a molecular screening for bacteria of Anaplasmataceae family in samples of spleen (n = 72) and lung (n = 17), recovered from 72 carcasses of Magellanic penguins (Spheniscus magellanicus) in Brazil and Chile. One apparently unengorged tick (Ixodes uriae) was also collected while wandering upon one of the carcasses and submitted to molecular analyses as well. Through conventional and nested PCR protocols three genes (16S rRNA, dsb and groEL) of a new Ehrlichia sp. were partially characterized upon organs of three penguins and in the tick coming from Magdalena Island (Chile). First matches after BLASTn comparisons showed that our sequences share 99.4% (16S rRNA), 94.6% (groEL) and 79.3% (dsb) of identity with "Candidatus Ehrlichia ornithorhynchi", Ehrlichia sp. NS101 and Ehrlichia canis CCZ, respectively. Matrixes of genetic distance including other representatives of the Ehrlichia genus point a 99.4%, 94.0%, and 80.0% of identity with 16S rRNA, groEL and dsb genes from Ehrlichia sp. It25, Ehrlichia sp. NS101, and Ehrlichia chaffeensis San Louis, respectively. A Bayesian phylogenetic analysis of Anaplasmataceae 16S rRNA gene places the detected Ehrlichia sp. into a group with Ehrlichia sp. BAT and Ehrlichia sp. Natal. Although depicting different topologies, Bayesian unrooted phylogenetic trees constructed for groEL and dsb genes position this Ehrlichia sp. into well-supported branches, which reinforces the finding of a new taxon. For the moment, any pathogenic effect of this new Ehrlichia sp. on penguins is still unknown. However, this fact becomes important to assess from a conservation point of view since populations of Magellanic penguins are currently threatened and in an ongoing decrease.

Using Core Genome Alignments To Assign Bacterial Species

With the exponential increase in the number of bacterial taxa with genome sequence data, a new standardized method to assign species designations is needed that is consistent with classically obtained taxonomic analyses. This is particularly acute for unculturable, obligate intracellular bacteria with which classically defined methods, like DNA-DNA hybridization, cannot be used, such as those in the Rickettsiales. In this study, we generated nucleotide-based core genome alignments for a wide range of genera with classically defined species, as well as those within the Rickettsiales. We created a workflow that uses the length, sequence identity, and phylogenetic relationships inferred from core genome alignments to assign genus and species designations that recapitulate classically obtained results. Using this method, most classically defined bacterial genera have a core genome alignment that is ≥10% of the average input genome length. Both Anaplasma and Neorickettsia fail to meet this criterion, indicating that the taxonomy of these genera should be reexamined. Consistently, genomes from organisms with the same species epithet have ≥96.8% identity of their core genome alignments. Additionally, these core genome alignments can be used to generate phylogenomic trees to identify monophyletic clades that define species and neighbor-network trees to assess recombination across different taxa. By these criteria, Wolbachia organisms are delineated into species different from the currently used supergroup designations, while Rickettsia organisms are delineated into 9 distinct species, compared to the current 27 species. By using core genome alignments to assign taxonomic designations, we aim to provide a high-resolution, robust method to guide bacterial nomenclature that is aligned with classically obtained results. IMPORTANCE With the increasing availability of genome sequences, we sought to develop and apply a robust, portable, and high-resolution method for the assignment of genera and species designations that can recapitulate classically defined taxonomic designations. Using cutoffs derived from the lengths and sequence identities of core genome alignments along with phylogenetic analyses, we sought to evaluate or reevaluate genus- and species-level designations for diverse taxa, with an emphasis on the order Rickettsiales, where species designations have been applied inconsistently. Our results indicate that the Rickettsia genus has an overabundance of species designations, that the current Anaplasma and Neorickettsia genus designations are both too broad and need to be divided, and that there are clear demarcations of Wolbachia species that do not align precisely with the existing supergroup designations.