Complete Genomic DNA Sequence of the East Asian Spotted Fever Disease Agent Rickettsia japonica

Matsutani, Minenosuke; Ogawa, Motohiko; Takaoka, Naohisa; Hanaoka, Nozomu; Toh, Y.; Yamashita, Atsushi; Oshima, Koichiro; Hirakawa, Hideki; Kuhara, Satoru; Suzuki, Harumi; Hattori, Masahira; Kishimoto, Tadamitsu; Ando, Shuji; Azuma, Yoshinao; Shirai, Mutsunori

doi:10.1371/journal.pone.0071861

Cited by 11 publications

(5 citation statements)

References 48 publications

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“…Consistently with results from previous reports (Dong et al. 2012; Matsutani et al. 2013), the R. japonica genomes contained one set of rRNA genes (not forming an operon), 33 tRNA genes, and three non-coding RNA genes.…”

Section: Resultsmentioning

confidence: 99%

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Extremely low genomic diversity of Rickettsia japonica distributed in Japan

et al. 2017

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Rickettsiae are obligate intracellular bacteria that have small genomes as a result of reductive evolution. Many Rickettsia species of the spotted fever group (SFG) cause tick-borne diseases known as “spotted fevers”. The life cycle of SFG rickettsiae is closely associated with that of the tick, which is generally thought to act as a bacterial vector and reservoir that maintains the bacterium through transstadial and transovarial transmission. Each SFG member is thought to have adapted to a specific tick species, thus restricting the bacterial distribution to a relatively limited geographic region. These unique features of SFG rickettsiae allow investigation of how the genomes of such biologically and ecologically specialized bacteria evolve after genome reduction and the types of population structures that are generated. Here, we performed a nationwide, high-resolution phylogenetic analysis of Rickettsia japonica, an etiological agent of Japanese spotted fever that is distributed in Japan and Korea. The comparison of complete or nearly complete sequences obtained from 31 R. japonica strains isolated from various sources in Japan over the past 30 years demonstrated an extremely low level of genomic diversity. In particular, only 34 single nucleotide polymorphisms were identified among the 27 strains of the major lineage containing all clinical isolates and tick isolates from the three tick species. Our data provide novel insights into the biology and genome evolution of R. japonica, including the possibilities of recent clonal expansion and a long generation time in nature due to the long dormant phase associated with tick life cycles.

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Section: Resultsmentioning

confidence: 99%

“…Although this strain was previously sequenced (Dong et al. 2012; Matsutani et al. 2013), we re-sequenced it to obtain a highly accurate genome sequence that was comparable to those of the other 30 strains analyzed in this study (referred to here as YH_M to distinguish this sequence from the published genome).…”

Section: Methodsmentioning

confidence: 99%

Extremely low genomic diversity of Rickettsia japonica distributed in Japan

et al. 2017

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“…RPEs are short (∼100–150 nt), selfish elements that insert in intergenic regions and functional RNAs, as well as CDS, wherein ORFs are not disrupted ( Ogata et al 2000 ). Under a dozen classes of RPEs have been identified in Rickettsia genomes ( Ogata et al 2002 ; Matsutani et al 2013 ). In the R .…”

Section: Resultsmentioning

confidence: 99%

Genomic Diversification in Strains of Rickettsia felis Isolated from Different Arthropods

Gillespie

Driscoll

Verhoeve

et al. 2014

Genome Biology and Evolution

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Rickettsia felis (Alphaproteobacteria: Rickettsiales) is the causative agent of an emerging flea-borne rickettsiosis with worldwide occurrence. Originally described from the cat flea, Ctenocephalides felis, recent reports have identified R. felis from other flea species, as well as other insects and ticks. This diverse host range for R. felis may indicate an underlying genetic variability associated with host-specific strains. Accordingly, to determine a potential genetic basis for host specialization, we sequenced the genome of R. felis str. LSU-Lb, which is an obligate mutualist of the parthenogenic booklouse Liposcelis bostrychophila (Insecta: Psocoptera). We also sequenced the genome of R. felis str. LSU, the second genome sequence for cat flea-associated strains (cf. R. felis str. URRWXCal2), which are presumably facultative parasites of fleas. Phylogenomics analysis revealed R. felis str. LSU-Lb diverged from the flea-associated strains. Unexpectedly, R. felis str. LSU was found to be divergent from R. felis str. URRWXCal2, despite sharing similar hosts. Although all three R. felis genomes contain the pRF plasmid, R. felis str. LSU-Lb carries an additional unique plasmid, pLbaR (plasmid of L. bostrychophila associated Rickettsia), nearly half of which encodes a unique 23-gene integrative conjugative element. Remarkably, pLbaR also encodes a repeats-in-toxin-like type I secretion system and associated toxin, heretofore unknown from other Rickettsiales genomes, which likely originated from lateral gene transfer with another obligate intracellular parasite of arthropods, Cardinium (Bacteroidetes). Collectively, our study reveals unexpected genomic diversity across three R. felis strains and identifies several diversifying factors that differentiate facultative parasites of fleas from obligate mutualists of booklice.

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“…Previous reports have shown that bacteria very similar to R. felis, R. australis, and R. akari were detected in L. scutellare mites in China and Korea. 5,6 Furthermore, additional reports have shown that other human pathogens, Rickettsia japonica, 27 Rickettsia conorii, 28 and Rickettsia typhi, 29 were detected in mites. Importantly, in all these previous reports, the authors detected bacteria from engorged mites, but not unfed mites.…”

Section: Discussionmentioning

confidence: 98%

Obligate intracellular bacteria diversity in unfed Leptotrombidium scutellare larvae highlights novel bacterial endosymbionts of mites

Ogawa

Takahashi

Matsutani

et al. 2019

Microbiology and Immunology

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It is well known that the mite Leptotrombidium scutellare carries the pathogen of scrub typhus, Orientia tsutsugamushi. However, our understanding of other bacterial endosymbionts of mites is limited. This study investigated the diversity of the obligate intracellular bacteria carried by L. scutellare using 16S rRNA gene amplicon analysis with next-generation sequencing. The results showed that the detected bacteria were classified into the genera Rickettsia, Wolbachia, and Rickettsiella and an unknown genus of the order Rickettsiales. For further classification of the detected bacteria, a representative read that was most closely related to the assigned taxonomic classification was subjected to homology search and phylogenic analysis. The results showed that some bacteria of the genus Rickettsia were identical or very close to the human pathogens Rickettsia akari, Rickettsia aeschlimannii, Rickettsia felis, and Rickettsia australis. The genetic distance between the genus Wolbachia bacteria in the present study and in previous reports is highly indicative that the bacteria in the present study can be classified as a new taxon of Wolbachia. This study detected obligate intracellular bacteria from unfed mites; thus, the mites did not acquire bacteria from infected animals or any other infectious sources. Finally, the present study demonstrated that various and novel bacterial endosymbionts of mites, in addition to O. tsutsugamushi, might uniquely evolve with the host mites throughout overlapping generations of the mite life cycle. The roles of the bacteria in mites and their pathogenicity should be further examined in studies based on bacterial isolation.

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Complete Genomic DNA Sequence of the East Asian Spotted Fever Disease Agent Rickettsia japonica

Cited by 11 publications

References 48 publications

Extremely low genomic diversity of Rickettsia japonica distributed in Japan

Extremely low genomic diversity of Rickettsia japonica distributed in Japan

Genomic Diversification in Strains of Rickettsia felis Isolated from Different Arthropods

Obligate intracellular bacteria diversity in unfed Leptotrombidium scutellare larvae highlights novel bacterial endosymbionts of mites

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