Extremely Low Genomic Diversity of Rickettsia japonica Distributed in Japan

Phylogenetic Analysis of Spotted Fever Group Rickettsia Gene from Ticks and Human Patients in Tottori Prefecture, Japan

Background

Japanese spotted fever (JSF) is a tick-borne bacterial febrile disease caused by Rickettsia japonica characterized by fever, rash, and occasional death. The number of patients in Japan and the Tottori Prefecture has been increasing over the past 20 years. Most cases were found in Eastern Tottori; however, the distribution of patients has expanded to the Central and Western regions. Ticks carried by wild animals may be the cause, but the prevalence of R. japonica in ticks has not yet been analyzed.

Methods

Ticks were collected by flagging-dragging from 16 sites in Tottori, Japan. The ticks were morphologically classified and DNA was extracted. The 17-kDa antigen gene was amplified using nested PCR. PCR amplicons from ticks and JSF patients were sequenced and phylogenetically compared.

Results

In total, 177 ticks were collected and identified as Haemahysalis, Ixodes, Amblyomma, and Dermcentor. The Spotted Fever Group Rickettsia (SFGR) was detected in Haemahysalis and Amblyomma spp. using PCR, with positivity rates of 36.8% and 33.3%, respectively. DNA sequencing and phylogenetic analysis revealed that positive ticks harbored R. japonica, P. raoultii, and other Rickettsiae species; however, the patient's samples were restricted to R. japonica. Similar to the incidence of JSF, the rate of R. japonica-positive ticks was higher in the Eastern region; however, R. japonica-positive ticks were also detected in the Western region.

Conclusion

R. japonica sequences had been found in ticks collected in Tottori Prefecture. Ticks harboring R. japonica were found in the Eastern and Western parts of Tottori Prefecture and the sequences were identical to the human cases. Only the R. japonica sequence has been detected in patients with spotted fever symptoms, even though ticks were harboring various SFGRs.

Molecular Survey of Vector-Borne Pathogens in Ticks, Sheep Keds, and Domestic Animals from Ngawa, Southwest China

Vector-borne pathogens are mainly transmitted by blood-feeding arthropods such as ticks, mosquitoes, fleas, lice, mites, etc. They pose a significant threat to animal and human health due to their worldwide distribution. Although much work has been performed on these pathogens, some neglected areas and undiscovered pathogens are still to be further researched. In this study, ticks (Haemaphysalis qinghaiensis), sheep keds (Melophagus ovinus), and blood samples from yaks and goats were collected in Ngawa Tibetan and Qiang Autonomous Prefecture located on the eastern edge of the Qinghai–Tibet Plateau, Southwest China. Several vector-borne bacterial pathogens were screened and studied. Anaplasma bovis strains representing novel genotypes were detected in ticks (8.83%, 37/419), yak blood samples (45.71%, 64/140), and goat blood samples (58.93%, 33/56). Two spotted fever group (SFG) Rickettsiae, Candidatus Rickettsia jingxinensis, and a novel Rickettsia species named Candidatus Rickettsia hongyuanensis were identified in ticks. Another Rickettsia species closely related to the Rickettsia endosymbiont of Polydesmus complanatus was also detected in ticks. Furthermore, a Coxiella species was detected in ticks (3.34%, 14/419), keds (1.89%, 2/106), and yak blood (0.71%, 1/140). Interestingly, another Coxiella species and a Coxiella-like bacterium were detected in a tick and a goat blood sample, respectively. These results indicate the remarkable diversity of vector-borne pathogens circulating in this area. Further investigations on their pathogenicity to humans and domestic animals are still needed.

Genomic evolution and adaptation of arthropod-associated Rickettsia

Rickettsia species are endosymbionts hosted by arthropods and are known to cause mild to fatal diseases in humans. Here, we analyse the evolution and diversity of 34 Rickettsia species using a pangenomic meta-analysis (80 genomes/41 plasmids). Phylogenomic trees showed that Rickettsia spp. diverged into two Spotted Fever groups, a Typhus group, a Canadensis group and a Bellii group, and may have inherited their plasmids from an ancestral plasmid that persisted in some strains or may have been lost by others. The results suggested that the ancestors of Rickettsia spp. might have infected Acari and/or Insecta and probably diverged by persisting inside and/or switching hosts. Pangenomic analysis revealed that the Rickettsia genus evolved through a strong interplay between genome degradation/reduction and/or expansion leading to possible distinct adaptive trajectories. The genus mainly shared evolutionary relationships with α-proteobacteria, and also with γ/β/δ-proteobacteria, cytophagia, actinobacteria, cyanobacteria, chlamydiia and viruses, suggesting lateral exchanges of several critical genes. These evolutionary processes have probably been orchestrated by an abundance of mobile genetic elements, especially in the Spotted Fever and Bellii groups. In this study, we provided a global evolutionary genomic view of the intracellular Rickettsia that may help our understanding of their diversity, adaptation and fitness.

[Genome analysis-based studies on bacterial genetic diversity]

There are a huge number of bacterial species on earth, and a huge intra-species genomic diversity are also observed in many bacteria. The high ability of bacteria to acquire foreign DNA and the presence of various mobile genetic elements contribute the generation of such genomic diversity. During the biochemical and genetic analysis of a Pseudomonas aeruginosa toxin, called cytotoxin, and its converting phage, which I first engaged in my research carrier, I became very interested in the genetic diversity of bacteria and mobile genetic elements such as bacteriophages, and realized the usefulness and power of genome analysis. Since then, I have been involved in genome analyses of various pathogenic bacteria such as enterohemorrhagic Escherichia coli (EHEC), commensal bacteria of human and other animals, and bacteria or bacterial communities in natural environments. I was so lucky that I jumped in this research field at the very begging of genome analyses and experienced a very exciting time of surprisingly rapid advance in genome sequencing technologies which revolutionized a wide range of biology. In this article, I first review the main findings which our group obtained from the genome analyses on the P. aeruginosa cytotoxin converting phage and those on the evolution and genomic diversity of EHEC and related bacteria. The results of our analyses of Rickettsiaceae family genomes, which show surprisingly very low genomic diversity, and genome sequence-based analyses of an intrahospital bacterial outbreak and within-host genomic diversity are also summarized.

The evolution of hard tick-borne relapsing fever borreliae is correlated with vector species rather than geographical distance

Background

Relapsing fever (RF) borreliae are arthropod-borne spirochetes and some of them cause human diseases, which are characterized by relapsing or recurring episodes of fever. Recently, it has been classified into two groups: soft tick-borne RF (STRF) borreliae and hard tick-borne RF (HTRF) borreliae. STRF borreliae include classical RF agents and HTRF borreliae, the latter of which include B. miyamotoi, a human pathogen recently identified in Eurasia and North America.

Results

In this study, we determined the genome sequences of 16 HTRF borreliae strains: 15 B. miyamotoi strains (9 from Hokkaido Island, Japan, 3 from Honshu Island, Japan, and 3 from Mongolia) and a Borrelia sp. tHM16w. Chromosomal gene synteny was highly conserved among the HTRF strains sequenced in this study, even though they were isolated from different geographic regions and different tick species. Phylogenetic analysis based on core gene sequences revealed that HTRF and STRF borreliae are clearly distinguishable, with each forming a monophyletic group in the RF borreliae lineage. Moreover, the evolutionary relationships of RF borreliae are consistent with the biological and ecological features of each RF borreliae sublineage and can explain the unique characteristics of Borrelia anserina. In addition, the pairwise genetic distances between HTRF borreliae strains were well correlated with those of vector species rather than with the geographical distances between strain isolation sites. This result suggests that the genetic diversification of HTRF borreliae is attributed to the speciation of vector ticks and that this relationship might be required for efficient transmission of HTRF borreliae within vector ticks.

Conclusions

The results of the present study, together with those from previous investigations, support the hypothesis that the common ancestor of borreliae was transmitted by hard-bodied ticks and that only STRF borreliae switched to using soft-bodied ticks as a vector, which was followed by the emergence of Borrelia recurrentis, lice-borne RF borreliae. Our study clarifies the phylogenetic relationships between RF borreliae, and the data obtained will contribute to a better understanding of the evolutionary history of RF borreliae.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-021-01838-1.

Growth Characteristics of Rickettsia Species LON Strains Closely Related to Rickettsia japonica Isolated from Haemaphysalis longicornis Ticks in Mouse Derived L929 and Human-Derived THP-1 Host Cell Lines

Non-pathogenic Rickettsia species LON strains closely related to an agent of Japanese spotted fever (JSF), R. japonica, were isolated in Japan from Haemaphysalis longicornis ticks in 2001. However, the biological properties of LONs in mammalian host cells are poorly understood. In this study, microscopic analysis showed that LONs in a mouse-derived L929 host cell line were rod shaped with sizes of 0.3-0.5 × 0.5-2.0 μm. Molecular analysis revealed the existence of a LON-specific disrupted open reading frame in R. japonica-related group-specific DNA regions. Growth kinetics of LON-2 and LON-13 strains analyzed by a quantitative real-time PCR showed 100-fold or more increment of LONs cultured in L929 host cells at 30°C and slightly less increment at 33°C, and 25-fold increment in human-derived THP-1 host cells at 35°C on day 7 (168 h) post infection. The generation times of the two LON strains cultured in L929 and THP-1 were estimated to be 9.4-12.9 h and 9.6-10.9 h, respectively. To our knowledge, this is the first report on the biological characteristics of Rickettsia sp. LON strains in mammalian cells, which may provide significant information for the experimental approaches for other rickettsiae.

Genomic Features of Rickettsia heilongjiangensis Revealed by Intraspecies Comparison and Detailed Comparison With Rickettsia japonica

Rickettsia heilongjiangensis is the causative agent of Far-Eastern spotted fever (FESF). In Japan, a human case of FESF was identified in Sendai in Miyagi Prefecture in 2008, and R. heilongjiangensis bacteria were isolated from Haemaphysalis concinna ticks collected in the suspected geographical area of infection. Although the intraspecies genome diversity of Rickettsia has been poorly investigated, our recent analysis revealed extremely low genomic diversity of R. japonica, the agent of Japanese spotted fever, which is a close relative of R. heilongjiangensis. In this study, to investigate the genomic diversity of R. heilongjiangensis and understand the genetic relationship between Japanese and Chinese isolates, we sequenced three isolates from H. concinna ticks collected in Sendai and one isolate from a H. concinna tick collected in Inner Mongolia, China, and performed genomic comparisons between these isolates and strain 054, the type strain isolated from a Dermacentor silvarum tick in Heilongjiang Province, China. Although the three Japanese strains were isolated in 2008, 2009, and 2012, their genome sequences were identical, indicating that H. concinna ticks carrying a single R. heilongjiangensis clone have been distributed in Sendai, Japan. Among the five R. heilongjiangensis isolates, only 81 SNPs and 13 insertion/deletion sites were identified, despite the significant differences in these isolates both geographically and temporally. A significant portion of the 81 SNPs (16/81) were found to be recombinogenic. These results indicate low genomic diversity of R. heilongjiangensis, as observed in R. japonica. We further performed a detailed genomic comparison of R. heilongjiangensis and R. japonica to accurately define conserved and species-specific genes. This analysis revealed that although notable variations were found in the genomic loci encoding RelA/SpoT family proteins and tandem repeats in major surface proteins, there was only a small difference in the gene repertoire between the two species, suggesting that SNPs and small InDels are responsible for the functional or physiological differences between the two species, if present. Through this analysis, several species-specific genomic regions that can serve as ideal PCR targets for distinguishing R. heilongjiangensis and R. japonica were also identified.

Diversity of spotted fever group rickettsiae and their association with host ticks in Japan

Spotted fever group (SFG) rickettsiae are obligate intracellular Gram-negative bacteria mainly associated with ticks. In Japan, several hundred cases of Japanese spotted fever, caused by Rickettsia japonica, are reported annually. Other Rickettsia species are also known to exist in ixodid ticks; however, their phylogenetic position and pathogenic potential are poorly understood. We conducted a nationwide cross-sectional survey on questing ticks to understand the overall diversity of SFG rickettsiae in Japan. Out of 2,189 individuals (19 tick species in 4 genera), 373 (17.0%) samples were positive for Rickettsia spp. as ascertained by real-time PCR amplification of the citrate synthase gene (gltA). Conventional PCR and sequencing analyses of gltA indicated the presence of 15 different genotypes of SFG rickettsiae. Based on the analysis of five additional genes, we characterised five Rickettsia species; R. asiatica, R. helvetica, R. monacensis (formerly reported as Rickettsia sp. In56 in Japan), R. tamurae, and Candidatus R. tarasevichiae and several unclassified SFG rickettsiae. We also found a strong association between rickettsial genotypes and their host tick species, while there was little association between rickettsial genotypes and their geographical origins. These observations suggested that most of the SFG rickettsiae have a limited host range and are maintained in certain tick species in the natural environment.