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Akter A, Ooka T, Gotoh Y, Yamamoto S, Fujita H, Terasoma F, Kida K, Taira M, Nakadouzono F, Gokuden M, Hirano M, Miyashiro M, Inari K, Shimazu Y, Tabara K, Toyoda A, Yoshimura D, Itoh T, Kitano T, Sato MP, Katsura K, Mondal SI, Ogura Y, Ando S, Hayashi T. Extremely Low Genomic Diversity of Rickettsia japonica Distributed in Japan. Genome Biol Evol 2017; 9:124-133. [PMID: 28057731 PMCID: PMC5381555 DOI: 10.1093/gbe/evw304] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/27/2016] [Indexed: 12/25/2022] Open
Abstract
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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Affiliation(s)
- Arzuba Akter
- Division of Microbiology, Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Tadasuke Ooka
- Department of Microbiology, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Seigo Yamamoto
- Frontier Science Research Center, University of Miyazaki, Miyazaki, Japan
| | - Hiromi Fujita
- Mahara Institute of Medical Acarology, Tokushima, Japan
| | - Fumio Terasoma
- Wakayama Prefectural Research Center of Environment and Public Health, Wakayama, Japan
| | - Kouji Kida
- Okayama Prefectural Institute for Environmental Science and Public Health, Okayama, Japan
| | | | - Fumiko Nakadouzono
- Kagoshima Prefectural Institute for Environmental Research and Public Health, Kagoshima, Japan
| | - Mutsuyo Gokuden
- Kagoshima Prefectural Institute for Environmental Research and Public Health, Kagoshima, Japan
| | - Manabu Hirano
- Seihi Public Health Center of Nagasaki Prefecture, Nagasaki, Japan
| | - Mamoru Miyashiro
- Fukuoka City Institute for Health and Environment, Fukuoka, Japan
| | - Kouichi Inari
- Mahara Institute of Medical Acarology, Tokushima, Japan
| | - Yukie Shimazu
- Hiroshima Prefectural Technology Research Institute, Public Health and Environment Center, Hiroshima, Japan
| | - Kenji Tabara
- Department of Health and Welfare, Shimane Prefectural Government, Shimane, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Shizuoka, Japan
| | - Dai Yoshimura
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Takehiko Itoh
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Tomokazu Kitano
- Division of Microbiology, Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Mitsuhiko P Sato
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Keisuke Katsura
- Frontier Science Research Center, University of Miyazaki, Miyazaki, Japan
| | - Shakhinur Islam Mondal
- Division of Microbiology, Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Yoshitoshi Ogura
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Shuji Ando
- Department of Virology-1, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
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Parola P, Paddock CD, Socolovschi C, Labruna MB, Mediannikov O, Kernif T, Abdad MY, Stenos J, Bitam I, Fournier PE, Raoult D. Update on tick-borne rickettsioses around the world: a geographic approach. Clin Microbiol Rev 2013; 26:657-702. [PMID: 24092850 PMCID: PMC3811236 DOI: 10.1128/cmr.00032-13] [Citation(s) in RCA: 910] [Impact Index Per Article: 82.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Tick-borne rickettsioses are caused by obligate intracellular bacteria belonging to the spotted fever group of the genus Rickettsia. These zoonoses are among the oldest known vector-borne diseases. However, in the past 25 years, the scope and importance of the recognized tick-associated rickettsial pathogens have increased dramatically, making this complex of diseases an ideal paradigm for the understanding of emerging and reemerging infections. Several species of tick-borne rickettsiae that were considered nonpathogenic for decades are now associated with human infections, and novel Rickettsia species of undetermined pathogenicity continue to be detected in or isolated from ticks around the world. This remarkable expansion of information has been driven largely by the use of molecular techniques that have facilitated the identification of novel and previously recognized rickettsiae in ticks. New approaches, such as swabbing of eschars to obtain material to be tested by PCR, have emerged in recent years and have played a role in describing emerging tick-borne rickettsioses. Here, we present the current knowledge on tick-borne rickettsiae and rickettsioses using a geographic approach toward the epidemiology of these diseases.
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Affiliation(s)
- Philippe Parola
- Aix Marseille Université, Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63, CNRS 7278, IRD 198, Inserm 1095, WHO Collaborative Center for Rickettsioses and Other Arthropod-Borne Bacterial Diseases, Faculté de Médecine, Marseille, France
| | | | - Cristina Socolovschi
- Aix Marseille Université, Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63, CNRS 7278, IRD 198, Inserm 1095, WHO Collaborative Center for Rickettsioses and Other Arthropod-Borne Bacterial Diseases, Faculté de Médecine, Marseille, France
| | - Marcelo B. Labruna
- Departamento de Medicina Veterinária Preventiva e Saúde Animal, Faculdade de Medicina Veterinária e Zootecnia Universidade de São Paulo, Cidade Universitária, São Paulo, SP, Brazil
| | - Oleg Mediannikov
- Aix Marseille Université, Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63, CNRS 7278, IRD 198, Inserm 1095, WHO Collaborative Center for Rickettsioses and Other Arthropod-Borne Bacterial Diseases, Faculté de Médecine, Marseille, France
| | - Tahar Kernif
- Service d'Ecologie des Systèmes Vectoriels, Institut Pasteur d'Algérie, Algiers, Algeria
| | - Mohammad Yazid Abdad
- Division of Veterinary and Biomedical Science, Murdoch University, Australian Rickettsial Reference Laboratory, Barwon Health, Geelong, Victoria, Australia
| | - John Stenos
- Division of Veterinary and Biomedical Science, Murdoch University, Australian Rickettsial Reference Laboratory, Barwon Health, Geelong, Victoria, Australia
| | - Idir Bitam
- University of Boumerdes, Boumerdes, Algeria
| | - Pierre-Edouard Fournier
- Aix Marseille Université, Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63, CNRS 7278, IRD 198, Inserm 1095, WHO Collaborative Center for Rickettsioses and Other Arthropod-Borne Bacterial Diseases, Faculté de Médecine, Marseille, France
| | - Didier Raoult
- Aix Marseille Université, Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63, CNRS 7278, IRD 198, Inserm 1095, WHO Collaborative Center for Rickettsioses and Other Arthropod-Borne Bacterial Diseases, Faculté de Médecine, Marseille, France
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5
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Complete genomic DNA sequence of the East Asian spotted fever disease agent Rickettsia japonica. PLoS One 2013; 8:e71861. [PMID: 24039725 PMCID: PMC3767692 DOI: 10.1371/journal.pone.0071861] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2013] [Accepted: 07/05/2013] [Indexed: 12/04/2022] Open
Abstract
Rickettsia japonica is an obligate intracellular alphaproteobacteria that causes tick-borne Japanese spotted fever, which has spread throughout East Asia. We determined the complete genomic DNA sequence of R. japonica type strain YH (VR-1363), which consists of 1,283,087 base pairs (bp) and 971 protein-coding genes. Comparison of the genomic DNA sequence of R. japonica with other rickettsiae in the public databases showed that 2 regions (4,323 and 216 bp) were conserved in a very narrow range of Rickettsia species, and the shorter one was inserted in, and disrupted, a preexisting open reading frame (ORF). While it is unknown how the DNA sequences were acquired in R. japonica genomes, it may be a useful signature for the diagnosis of Rickettsia species. Instead of the species-specific inserted DNA sequences, rickettsial genomes contain Rickettsia-specific palindromic elements (RPEs), which are also capable of locating in preexisting ORFs. Precise alignments of protein and DNA sequences involving RPEs showed that when a gene contains an inserted DNA sequence, each rickettsial ortholog carried an inserted DNA sequence at the same locus. The sequence, ATGAC, was shown to be highly frequent and thus characteristic in certain RPEs (RPE-4, RPE-6, and RPE-7). This finding implies that RPE-4, RPE-6, and RPE-7 were derived from a common inserted DNA sequence.
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