Phylogenetic analysis of spotted fever group Rickettsiae isolated from ticks in Japan

Utility of ultra-rapid real-time PCR for detection and prevalence of Rickettsia spp. in ticks

Background

Rickettsia spp. are important tick-borne pathogens that cause various human and animal diseases worldwide. A tool for rapid and accurate detection of the pathogens from its vectors is necessary for prevention of Rickettsioses propagation in humans and animals, which are infested by ticks. Therefore, this study was conducted to evaluate a molecular tool, ultra-rapid real-time PCR (UR-qPCR), for rapid and accurate detection of Rickettsia spp. from 5644 ticks in 408 pools collected from livestock and their surrounding environments in Gangwon and Jeju province in South Korea.

Results

The UR-qPCR of Rickettsia DNA showed a limit of detection of 2.72 × 10¹ copies of Rickettsia DNA and no cross reaction with other tick-borne pathogens, namely Anaplasma phagocytophilum, Ehrlichia chaffeensis, E. canis, Toxoplasma gondii, and Borrelia burgdorferi. In addition, the PCR assay also showed possibility of various Rickettsia species detection including R. monacensis, “Candidatus R. longicornii”, R. japonica, R. roultii, and R. tamurae. The collected ticks were identified with major species belonged to Haemaphysalis longicornis (81.62%), followed by H. flava (15.19%), and Ixodes nipponensis (3.19%). Rickettsia detection from tick samples using the UR-qPCR showed that the minimum infection rate (MIR) of Rickettsia in collected ticks was 1.24‰ and that all positive pools contained H. longicornis, equal to the MIR of 1.39‰ of this species. Additionally, MIR of Rickettsia spp. detected in ticks collected in Gangwon and Jeju was 1.53‰ and 0.84‰, respectively. Furthermore, the sequencing results of the 17 kDa protein antigen gene and ompA gene showed that Rickettsia spp. sequences from all pools were related to “Candidatus R. longicornii” and “Candidatus R. jingxinensis”.

Conclusions

The UR-qPCR system was demonstrated to be useful tool for accurate and rapid detection of Rickettsia from its vector, ixodid ticks, within 20 min. The data on Rickettsia spp. in ticks detected in this study provide useful information on the distribution of Rickettsia in previously unstudied Korean provinces, which are important for the prevention and control of the spread of rickettsioses in both animals and humans in the country.

Serological and molecular survey of tick-borne zoonotic pathogens including severe fever with thrombocytopenia syndrome virus in wild boars in Miyazaki Prefecture, Japan

Background

Miyazaki Prefecture is one of the hotspots of severe fever with thrombocytopenia syndrome (SFTS) cases and related deaths in Japan since 2013 and other pathogens of tick‐borne diseases (TBDs). Japanese spotted fever and scrub typhus are also endemic in this region.

Objectives

A total of 105 wild boars, hunted in 2009, were serologically examined as sentinels for TBDs to indirectly demonstrate the potential hazard of ticks transmitting pathogens to humans in the studied area.

Methods

The collected blood and spleens of the wild boars underwent serological and molecular tests for SFTSV, Rickettsia japonica (Rj) [antibody to spotted fever group rickettsiae (SFGR) were tested by using species‐common antigen], and Orientia tsutsugamushi (Ot).

Results

Seroprevalences of SFTSV, SFGR, and Ot were 41.9%, 29.5%, and 33.3%, respectively. SFTS viral RNA was identified in 7.6% of the sera, whereas DNA of Rj or Ot was not detected in any sample. In total, 43.8% of the boars possessed an infection history with SFTSV (viral gene and/or antibody). Of these, 23.8% had multiple‐infection history with SFGR and/or Ot.

Conclusions

The high prevalence of SFTSV in wild boars might reflect the high risk of exposure to the virus in the studied areas. In addition, SFTSV infection was significantly correlated with Ot infection, and so were SFGR infection and Ot infection, indicating that these pathogens have common factors for infection or transmission. These data caution of the higher risk of SFTSV infection in areas with reported cases of other TBDs.

Spotted fever group rickettsiae (SFGR) detection in ticks following reported human case of Japanese spotted fever in Niigata Prefecture, Japan

Japanese spotted fever, a tick-borne disease caused by Rickettsia japonica, was firstly described in southwestern Japan. There was a suspicion of Rickettsia japonica infected ticks reaching the non-endemic Niigata Prefecture after a confirmed case of Japanese spotted fever in July 2014. Therefore, from 2015 to 2017, 38 sites were surveyed and rickettsial pathogens were investigated in ticks from north to south of Niigata Prefecture including Sado island. A total of 3336 ticks were collected and identified revealing ticks of three genera and ten species: Dermacentor taiwanensis, Haemaphysalis flava, Haemaphysalis hystricis, Haemaphysalis longicornis, Haemaphysalis megaspinosa, Ixodes columnae, Ixodes monospinosus, Ixodes nipponensis, Ixodes ovatus, and Ixodes persulcatus. Investigation of rickettsial DNA showed no ticks infected by R. japonica. However, three species of spotted fever group rickettsiae (SFGR) were found in ticks, R. asiatica, R. helvetica, and R. monacensis, confirming Niigata Prefecture as a new endemic area to SFGR. These results highlight the need for public awareness of the occurrence of this tick-borne disease, which necessitates the establishment of public health initiatives to mitigate its spread.

Japanese Spotted Fever in Eastern China, 2013

We isolated Rickettsia japonica from a febrile patient in Lu'an City, China, in 2013. Subsequently, we found an R. japonica seroprevalence of 54.8% (494/902) in the rural population of Anhui Province and an R. japonica prevalence in Haemaphysalis longicornis ticks of 0.5% (5/935). R. japonica and its tick vector exist in China.

Tick-borne pathogens and the vector potential of ticks in China

Ticks, as obligate blood-sucking ectoparasites, attack a broad range of vertebrates and transmit a great diversity of pathogenic microorganisms. They are considered second only to mosquitoes as vectors of human disease, and the most important vector of pathogens of domestic and wild animals. Of the 117 described species in the Chinese tick fauna, 60 are known to transmit one or more diseases: 36 species isolated within China and 24 species isolated outside China. Moreover, 38 of these species carry multiple pathogens, indicating the potentially vast role of these vectors in transmitting pathogens. Spotted fever is the most common tick-borne disease, and is carried by at least 27 tick species, with Lyme disease and human granulocytic anaplasmosis ranked as the second and third most widespread tick-borne diseases, carried by 13 and 10 species, respectively. Such knowledge provides us with clues for the identification of tick-associated pathogens and suggests ideas for the control of tick-borne diseases in China. However, the numbers of tick-associated pathogens and tick-borne diseases in China are probably underestimated because of the complex distribution and great diversity of tick species in this country.

A systems biology approach to the characterization of stress response in Dermacentor reticulatus tick unfed larvae

Background

Dermacentor reticulatus (Fabricius, 1794) is distributed in Europe and Asia where it infests and transmits disease-causing pathogens to humans, pets and other domestic and wild animals. However, despite its role as a vector of emerging or re-emerging diseases, very little information is available on the genome, transcriptome and proteome of D. reticulatus. Tick larvae are the first developmental stage to infest hosts, acquire infection and transmit pathogens that are transovarially transmitted and are exposed to extremely stressing conditions. In this study, we used a systems biology approach to get an insight into the mechanisms active in D. reticulatus unfed larvae, with special emphasis on stress response.

Principal Findings

The results support the use of paired end RNA sequencing and proteomics informed by transcriptomics (PIT) for the analysis of transcriptomics and proteomics data, particularly for organisms such as D. reticulatus with little sequence information available. The results showed that metabolic and cellular processes involved in protein synthesis were the most active in D. reticulatus unfed larvae, suggesting that ticks are very active during this life stage. The stress response was activated in D. reticulatus unfed larvae and a Rickettsia sp. similar to R. raoultii was identified in these ticks.

Significance

The activation of stress responses in D. reticulatus unfed larvae likely counteracts the negative effect of temperature and other stress conditions such as Rickettsia infection and favors tick adaptation to environmental conditions to increase tick survival. These results show mechanisms that have evolved in D. reticulatus ticks to survive under stress conditions and suggest that these mechanisms are conserved across hard tick species. Targeting some of these proteins by vaccination may increase tick susceptibility to natural stress conditions, which in turn reduce tick survival and reproduction, thus reducing tick populations and vector capacity for tick-borne pathogens.

Comparison of different media for preservation and transport of viable rickettsiae

Rickettsiae tend to have a rapid decrease of viability outside living cells. Therefore, the transport of samples containing viable rickettsiae for culturing in cell culture for diagnostic purposes is challenging. The viability of rickettsiae in different transport media (commercially available transport medium COPAN "UTM-RT transport medium for viruses, chlamydia, mycoplasma, and ureaplasma," minimal essential medium (MEM) with and without 10% foetal calf serum) at various time points at 4 °C and at ambient temperature (22 °C) was compared. Rickettsia honei was used as model organism. After 2 weeks of storage at room temperature, no viable rickettsiae were detectable any more while storage at 4 °C kept rickettsiae viable for up to 4 weeks. The commercially available COPAN medium showed similarly good or slightly better stabilizing effects on rickettsiae compared with MEM + 10% foetal calf serum, pure MEM demonstrated the poorest results. It is important to transport and store media with potentially rickettsiae-containing samples at 4 °C to prevent inactivation. MEM + 10% foetal calf serum can be used if no commercial medium is available with similarly good results.

Inactivation of rickettsiae

A reliable and complete inactivation is an indispensable premise for any concentration of rickettsiae or for the development of diagnostic strategies based on their antigens. This study deals with the testing of methods to inactivate rickettsiae. Rickettsia honei was used as a model organism. The inactivating potency of formalin, Qiagen® antiviral lysozyme (AVL) buffer, heating to 56 °C, and β-propiolactone was analyzed in cell culture. The inactivation limits for rickettsiae were 0.1% formalin about 10 min, Qiagen AVL buffer about 5 min, 56 °C about 5 min, 0.125% β-propiolactone about 1 h, and 0.0125% β-propiolactone overnight. The interpretation was limited by cytotoxic effects of the inactivation procedures and by the culturally achievable rickettsial density in the cell culture supernatants that were used for the inactivation experiments. Reliable modes of inactivation were identified, allowing for the secure handling of rickettsial antigens for diagnostic purposes.

Phylogenetic Analysis of Spotted Fever Group Rickettsiae Based on gltA, 17-kDa, and rOmpA Genes Amplified by Nested PCR from Ticks in Japan

In order to understand the natural situation of rickettsiae in the ticks in Japan, the rickettsial genes, gltA gene, rOmpA gene, and 17-kDa gene, were amplified from the ticks by nested PCR. The prevalences of rickettsial gltA genes among Haemaphysalis formosensis, H. longicornis, H. megaspinosa, Ixodes ovatus, H. flava, H. kitaokai, and I. persulcatus were 62, 57, 24, 24, 19, 13, and 10%, respectively; 26% (186/722) being the average. The gltA genes amplified from the ticks were classified into 9 genotypes (I to IX) by the difference in nucleotide sequences. Genotype I was detected from 7 species of ticks. Genotype II mainly was detected from H. longicornis and H. formosensis. Genotypes III and VII mainly were detected from H. flava and I. ovatus. The polarization in the distribution of genotypes among regions where the ticks were collected was not clear. Based on the phylogenetic analysis of the three genes presented here, genotypes I, III, and IV (detected from H. formosensis, H. hystricia, and I. ovatus ) are genetically close with each other, but rickettsiae of the same property still have not been isolated from ticks anywhere in the world. These genotypes should be considered as new species among SFG rickettsiae. Genotype II was identical with strain FUJ-98, genetically close to R. japonica which has been isolated from ticks in China. Genotype V was identical with R. felis and strain California 2 isolated from the cat flea. This is the first report on the detection of R. felis from ticks. Genotype VI detected from Ixodes sp. did not seem to belong to genus Rickettsia. Based on the previous antigenic data and the phylogenetic analysis presented here, Genotype VII should be considered a variant of R. helvetica and genotype VIII detected from I. ovatus and I. persulcatus were identical with R. helvetica. Genotype IX detected from I. nipponensis was genetically close to the strains IRS3, IRS4, and IrR/Munich isolated from I. ricinus in Slovakia and German.

Comparison of dragging and sweeping methods for collecting ticks and determining their seasonal distributions for various habitats, Gyeonggi Province, Republic of Korea

As part of the 65th Medical Brigade tick-borne disease surveillance program to determine the abundance, geographical and seasonal distributions, and tick-borne pathogens present in the Republic of Korea, dragging and sweeping methods were compared to determine their efficiency for collecting ticks in grass and deciduous, conifer, and mixed forest habitats at military training sites and privately owned lands in northern Gyeonggi Province near the demilitarized zone from April-October, 2004-2005. Three species of Ixodid ticks, Haemaphysalis longicornis, Haemaphysalis flava, and Ixodes nipponensis, were collected. Overall, H. longicornis adults and nymphs were most frequently collected from grass and deciduous forest habitats, accounting for 98.2 and 66.2%, respectively, of all ticks collected. H. flava adults and nymphs were most frequently collected from conifer and mixed forests, accounting for 81.6, and 77.8%, respectively, of all ticks collected. I. nipponensis adults and nymphs accounted for 9.3% of all ticks collected from mixed forests, were less commonly collected from deciduous (4.1%) and conifer (4.1%) forests, and infrequently collected from grass habitats (0.9%). Overall, there were no significant differences between dragging and sweeping methods for the three species when the areas sampled were similar (sweeping = 2 x the area over the same transect). Adults and nymphs of H. longicornis were most commonly collected from April-August, while those of H. flava and I. nipponensis were most commonly collected during April-July and again during October. Larvae of all three species were most frequently observed from July-September.

Genomic analysis of Rickettsia japonica strain YHT

Rickettsia japonica strain YH, isolated in 1984 in Japan, is the type strain of R. japonica, the tick-borne agent of Japanese spotted fever. Here, we report the 1.33-Mb genome of this rickettsial species.

Evaluation of Rickettsia japonica pathogenesis and reservoir potential in dogs by experimental inoculation and epidemiologic survey

Rickettsia japonica pathogenesis and reservoir potential in dogs were evaluated by both experimental inoculation and epidemiologic survey. In the experimental inoculation study, dogs 1 and 2 were pretreated with an immunosuppressive dose of cyclosporine 14 days before inoculation and became ill after exposure to R. japonica. Dogs exhibited clinical signs, including fever, anorexia, depression, and decreased water consumption, between 36 and 96 h after inoculation, but these signs disappeared spontaneously by 5 days after inoculation. Dogs 3 and 4 were not pretreated with cyclosporine, and no clinical signs were detected in them throughout the 14-day observation period. The control dog was clinically normal and had a normal rectal temperature throughout the study period. We attempted to detect rickettsial DNA from peripheral blood and aspiration samples from kidney and spleen by nested PCR, but all samples examined were negative. The control dog lacked detectable titers to R. japonica antigen on day 14, while positive antibodies to R. japonica were detected in all four experimentally infected dogs, with titers of 1:160 to 1:80. In the epidemiologic survey, 24 (1.8%) of the 1,363 dogs examined throughout Japan had antibodies against R. japonica, with titers of 1:40 or more. However, we observed neither clinical signs at the time of sample collection nor nested PCR results indicative of rickettsial infection in these dogs. In conclusion, dogs in Japan can be exposed to R. japonica, and infected dogs with immunosuppressive conditions can temporarily develop clinical symptoms, including fever, anorexia, depression, and decreased water consumption.

Evidence for the presence of Francisella and spotted fever group rickettsia DNA in the tick Amblyomma fimbriatum (Acari: Ixodidae), Northern Territory, Australia

Ticks (n = 252) were collected from five wild-caught reptile species during routine trapping in the Djukbinj National Park and Fogg Dam Reserve, Northern Territory, Australia. Pooling of ticks (one to four ticks per pool), according to sex or host animal, resulted in 187 samples used for screening for the presence of Rickettsia species via molecular methods. Rickettsia DNA was detected via the amplification of the gltA, ompA, and ompB genes in 57 (34%) of the 187 tick samples, all of which contained only the tick Amblyomma fimbriatum Koch (Acari: Ixodidae). Further amplification and sequencing of nine of the positive samples (4.8%) for the gltA, ompA, ompB, 17-kDa, and 16S rRNA genes identified a Rickettsia species sharing closest identity to Rickettsia tamurae. In addition, amplification and sequencing of the 16S rRNA gene detected in the same tick samples the presence of a Francisella species closely related to other tick-borne Francisellae identified in ticks from the Northern Hemisphere.

Detection of Rickettsia spp. in Haemaphysalis ticks collected in La Rioja, Spain

In an attempt to know the potential risk of human disease after exposure to ticks in La Rioja (North of Spain), the objective of our study was to investigate the presence of Rickettsia species in Haemaphysalis ticks collected in our area. A total of 177 Haemaphysalis spp. belonging to three species (H. punctata, H. sulcata, and H. inermis) were subjected to DNA extraction and tested by polymerase chain reaction (PCR) targeting three rickettsial genes: gltA, ompB, and ompA. Six (3 H. inermis, 2 H. punctata, and 1 H. sulcata) of the 177 specimens were found to be infected (3.4%). The rickettsiae in H. inermis ticks (n = 3) were identified as Rickettsia aeschlimannii by sequencing of the genes coding for gltA, ompB, and ompA. Nucleotide sequences from H. punctata and H. sulcata samples that yielded PCR products (n = 3), showed >99% similarity with sequences of Rickettsia endosymbiont of H. sulcata and 'Candidatus Rickettsia hoogstraalii' for gltA and ompB genes, respectively. Attempts to amplify ompA from these two H. punctata and one H. sulcata failed. This study suggests that H. inermis could be a vector for tick-borne spotted fever caused by R. aeschlimannii in the north of Spain. Further studies on characterization and culture of rickettsial endosymbionts found in Haemaphysalis spp. should be performed.

Serological survey of Rickettsia japonica infection in dogs and cats in Japan

Antibodies against Rickettsia japonica in 20 of 1,207 dogs and 5 of 584 cats in Japan were detected using immunofluorescence. Some antibody-positive animals were detected in Niigata and Kagawa Prefectures, areas in which Japanese spotted fever in human patients has never been identified. Some animals were positive for antibodies against other new Rickettsia species.

Plasmids and rickettsial evolution: insight from Rickettsia felis

BACKGROUND

The genome sequence of Rickettsia felis revealed a number of rickettsial genetic anomalies that likely contribute not only to a large genome size relative to other rickettsiae, but also to phenotypic oddities that have confounded the categorization of R. felis as either typhus group (TG) or spotted fever group (SFG) rickettsiae. Most intriguing was the first report from rickettsiae of a conjugative plasmid (pRF) that contains 68 putative open reading frames, several of which are predicted to encode proteins with high similarity to conjugative machinery in other plasmid-containing bacteria.

METHODOLOGY/PRINCIPAL FINDINGS

Using phylogeny estimation, we determined the mode of inheritance of pRF genes relative to conserved rickettsial chromosomal genes. Phylogenies of chromosomal genes were in agreement with other published rickettsial trees. However, phylogenies including pRF genes yielded different topologies and suggest a close relationship between pRF and ancestral group (AG) rickettsiae, including the recently completed genome of R. bellii str. RML369-C. This relatedness is further supported by the distribution of pRF genes across other rickettsiae, as 10 pRF genes (or inactive derivatives) also occur in AG (but not SFG) rickettsiae, with five of these genes characteristic of typical plasmids. Detailed characterization of pRF genes resulted in two novel findings: the identification of oriV and replication termination regions, and the likelihood that a second proposed plasmid, pRFdelta, is an artifact of the original genome assembly.

CONCLUSION/SIGNIFICANCE

Altogether, we propose a new rickettsial classification scheme with the addition of a fourth lineage, transitional group (TRG) rickettsiae, that is unique from TG and SFG rickettsiae and harbors genes from possible exchanges with AG rickettsiae via conjugation. We offer insight into the evolution of a plastic plasmid system in rickettsiae, including the role plasmids may have played in the acquirement of virulence traits in pathogenic strains, and the likely origin of plasmids within the rickettsial tree.

Prevalence of Tick-Borne Rickettsia and Ehrlichia in Ixodes persulcatus and Ixodes ovatus in Tokachi District, Eastern Hokkaido, Japan

DNA from 111 ticks collected by flagging in Tokachi district, Eastern Hokkaido, Japan were examined for infection with Rickettsia and Ehrlichia, by PCR and sequencing methodology. For Rickettsia, analysis of the partial sequence of the citrate synthase gene was successfully performed on 11 DNA samples from I. persulcatus, and 7 of them showed 99.8% identical with Rickettsia helvetica while the other 4 showed 99.8% identical with ;Candidatus Rickettsia tarasevichiae'. For Ehrlichia, a partial sequence of the 16S rRNA gene detected from I. persulcatus was 100% identical with that from Ehrlichia muris, and another DNA sample from I. ovatus showed 99.8% identical with Ehrlichia species detected from I. ovatus. The results suggest that the pathogens detected here might be distributed in this area.

Infection of Ixodes scapularis ticks with Rickettsia monacensis expressing green fluorescent protein: a model system

Ticks (Acari: Ixodidae) are ubiquitous hosts of rickettsiae (Rickettsiaceae: Rickettsia), obligate intracellular bacteria that occur as a continuum from nonpathogenic arthropod endosymbionts to virulent pathogens of both arthropod vectors and vertebrates. Visualization of rickettsiae in hosts has traditionally been limited to techniques utilizing fixed tissues. We report epifluorescence microscopy observations of unfixed tick tissues infected with a spotted fever group endosymbiont, Rickettsia monacensis, transformed to express green fluorescent protein (GFP). Fluorescent rickettsiae were readily visualized in tick tissues. In adult female, but not male, Ixodes scapularis infected by capillary feeding, R. monacensis disseminated from the gut and infected the salivary glands that are crucial to the role of ticks as vectors. The rickettsiae infected the respiratory tracheal system, a potential dissemination pathway and possible infection reservoir during tick molting. R. monacensis disseminated from the gut of capillary fed I. scapularis nymphs and was transstadially transmitted to adults. Larvae, infected by immersion, transstadially transmitted the rickettsiae to nymphs. Infected female I. scapularis did not transovarially transmit R. monacensis to progeny and the rickettsiae were not horizontally transmitted to a rabbit or hamsters. Survival of infected nymphal and adult I. scapularis did not differ from that of uninfected control ticks. R. monacensis did not disseminate from the gut of capillary fed adult female Amblyomma americanum (L.), or adult Dermacentor variabilis (Say) ticks of either sex. Infection of I. scapularis with R. monacensis expressing GFP provides a model system allowing visualization and study of live rickettsiae in unfixed tissues of an arthropod host.

Detection of Rickettsial DNA in Ixodid Ticks Recovered from Dogs and Cats in Japan

DNA from ticks recovered from 1137 dogs and 133 cats from all over Japan were examined for Rickettsia infection by citrate synthase gene (gltA)-based PCR and partial nucleotide sequencing. A total of 91 dog tick samples and 18 cat tick samples showed a single band of the appropriate size in the nested PCR. Sequence analysis was successfully performed on 102 samples. DNA of Rickettsia japonica or closely related Rickettsia spp. strains were detected from 38 ticks in 16 prefectures mainly in western Japan. The other 33, detected from 13 prefectures including Hokkaido and Okinawa, were found to be Rickettsia helvetica or closely related strains. A total of 29 DNA that showed highest homology with Rickettsia akari or closely related strains were detected in 19 prefectures, widespread throughout Japan. Rickettsia canada-like DNA was detected from Haemaphysalis sp. removed from a dog in Fukuoka, and ;Candidatus Rickettsia tarasevichiae'-like DNA was from Ixodes sp. removed from a dog in Hokkaido.

First serologic evidence of human spotted fever group rickettsiosis in Korea

To investigate the prevalence of spotted fever group rickettsioses in Korea, a serosurvey of Japanese spotted fever rickettsiosis in patients with acute febrile illness was conducted with an indirect immunofluorescence assay. Overall, 19.88% of the patients were found to have polyvalent antibody against Rickettsia japonica. This study is the first documentation of spotted fever group rickettsiosis in Korea.