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Project_ Accession Organisms Bacteria/Virus/Archaea Date Sanger SOLiD 454_PE 454_SG PGM Illumina Status Number number P01 Bacteria Rickettsia conorii str.Malish 7 2001 Sanger AE006914 Published P02 Bacteria Tropheryma whipplei str.Twist 2003 Sanger AE014184 Published P03 Bacteria Rickettsia felis URRWXCal2 2005 Sanger CP000053 Published P04 Bacteria Rickettsia bellii RML369-C 2006 Sanger CP000087 Published P05 Bacteria Coxiella burnetii CB109 2007 Sanger SOLiD 454_PE AKYP00000000 Published P06 Bacteria Minibacterium massiliensis 2007 Sanger CP000269 Published P07 Bacteria Rickettsia massiliae MTU5 2007 Sanger CP000683 Published P08 Bacteria BaBL=Bête à Bernard Lascola 2007 Illumina In progress P09 Bacteria Acinetobacter baumannii AYE 2006 Sanger CU459141 Published P10 Bacteria Acinetobacter baumannii SDF 2006 Sanger CU468230 Published P11 Bacteria Borrelia duttonii Ly 2008 Sanger CP000976 Published P12 Bacteria Borrelia recurrentis A1 2008 Sanger CP000993 Published P13 Bacteria Francisella tularensis URFT1 2008 454_PE ABAZ00000000Published P14 Bacteria Borrelia crocidurae str. Achema 2009 454_PE PRJNA162335 Published P15 Bacteria Citrobacter koseri 2009 SOLiD 454_PE 454_SG In progress P16 Bacteria Diplorickettsia massiliensis 20B 2009 454_PE PRJNA86907 Published P17 Bacteria Enterobacter aerogenes EA1509E 2009 Sanger FO203355 Published P18 Bacteria Actinomyces grossensis 2012 SOLiD 454_PE 454_SG CAGY00000000Published P19 Bacteria Bacillus massiliosenegalensis 2012 SOLiD 454_PE 454_SG CAHJ00000000 Published P20 Bacteria Brevibacterium senegalensis (Brevibacterium sp 2012 SOLiD 454_PE 454_SG CAHK00000000Published P21 Bacteria Enorma massiliensis (Coriobacteriaceae bacteriu2012 SOLiD 454_PE 454_SG CAGZ00000000Published P22 Bacteria Legionella drancourtii LLAP12 2009 454_PE PRJNA39279 Published P23 Bacteria Odysella thessalonicensis 2009 SOLiD 454_PE PRJNA72365 Published P24 Bacteria Parachlamydia acanthamoebae str. Hall's coccus 2009 454_PE PRJNA42977 Published P25 Bacteria Rickettsia africae ESF-5 2009 Sanger PRJNA58799 Published P26 Bacteria Rickettsia helvetica C9P9 2009 454_PE PRJNA173054 Published P27 Bacteria Rickettsia prowazekii Rp22 2009 Sanger CP001584.1 Published P28 Bacteria Rickettsia raoultii 2009 454_PE In progress P29 Bacteria Staphylococcus aureus subsp.aureus str. CF-Mar 2009 454_PE PRJEA28687 Published P30 Bacteria Rickettsia slovaca 13-B 2006 Sanger CP002428.1 Published P31 Bacteria Rickettsia australis Phillips 2010 SOLiD 454_PE AKVZ01000059 Published P32 Bacteria Rickettsia heilongjansis 2010 454_PE In progress P33 Bacteria Acinetobacter baumannii_ABIsac coliR 2011 SOLiD 454_PE 454_SG CAKA01000001Published P34 Bacteria Acinetobacter baumannii_ABIsac coliS 2011 SOLiD 454_PE 454_SG CAKB01000001Published P35 Bacteria Attilina massiliensis (Holosporaceae bacterium S 2011 SOLiD 454_PE 454_SG PRJEB114 In progress P36 Bacteria Azospirillum massiliensis (Candidatus Azospirillu2011 SOLiD 454_PE 454_SG PRJEB112 In progress P37 Bacteria Bartonella birtlesii E7 2011 454_PE ALVF00000000 Published P38 Bacteria Bartonella birtlesii E11 2011 454_PE ALVG00000000Published P39 Bacteria Bartonella birtlesii E4 2011 454_PE ALVH00000000Published P40 Bacteria Bartonella birtlesii H12 2011 454_PE ALWY00000000Published P41 Bacteria Bartonella birtlesii_WT 2011 454_PE PRJNA86617 Published P42 Bacteria Chryseobacterium massiliensis (Candidatus Chry 2011 SOLiD 454_PE 454_SG PRJEB113 In progress P43 Bacteria Clostridium sp. CLO 2011 SOLiD 454_PE In progress P44 Bacteria Eubacterium sp. EBS 2011 SOLiD 454_PE In progress P45 Bacteria Legionella tunisiensis_LT 2011 SOLiD 454_PE CALJ01000001- Published P46 Bacteria Peptoniphilus sp. PEP 2011 454_PE In progress P47 Bacteria Aeromicrobium massiliense_AM 2011 SOLiD 454_PE 454_SG CAEF00000000 Published P48 Bacteria Alistipes senegalensis_JC50 2011 SOLiD 454_PE 454_SG CAHI00000000 Published P49 Bacteria Alistipes timonensis_JC136 2011 SOLiD 454_PE 454_SG CAEG00000000Published P50 Bacteria Anaerococcus obesiensis (Anaerococcus sp. Ph9 2011 SOLiD 454_PE 454_SG CAGV00000000Published P51 Bacteria Anaerococcus senegalensis (Anaerococcus sp. JC2011 SOLiD 454_PE 454_SG CAEK00000000 Published P52 Bacteria Bacillus cayorensis_BBI 2011 SOLiD 454_PE In progress P53 Bacteria Bacillus senegalensis_BMS 2011 SOLiD 454_PE In progress P54 Bacteria Bacillus timonensis_BT 2011 SOLiD 454_PE CAET00000000 Published P55 Bacteria Brevibacillus massiliensis (Brevibacillus sp. phR) 2011 SOLiD 454_PE 454_SG Published P56 Bacteria Cellulomonas massiliensis_CM 2011 SOLiD 454_PE 454_SG CAHD00000000Published P57 Bacteria Clostridium dakarense_CBI 2011 SOLiD 454_PE 454_SG In progress P58 Bacteria Clostridium senegalense (Clostridium sp. JC122) 2011 SOLiD 454_PE 454_SG CAEV00000000Published P59 Bacteria Dielma anaerobia > Dielma fastidiosa (Clostridia2011 SOLiD 454_PE 454_SG CAEN00000000Published P60 Bacteria Enterobacter massiliensis_ENT 2011 SOLiD 454_PE 454_SG CAEO00000000Published P61 Bacteria Peptoniphilus obesi >>Grassa massiliensis 2011 SOLiD 454_PE CAHA00000000Published P62 Bacteria Alistipes obesi >> Grosso massiliensis 2011 SOLiD 454_PE 454_SG CAHB00000000Published P63 Bacteria Herbaspirillum massiliense (massiliensis) 2011 SOLiD 454_PE 454_SG CAHF00000000Published P64 Bacteria Kallipyga massiliensis 2011 SOLiD 454_PE CAHC00000000Published P65 Bacteria Kurthia massiliensis 2011 SOLiD 454_PE CAEU00000000Published P66 Bacteria Kurthia senegalensis 2011 SOLiD 454_PE CAEW00000000Published P67 Bacteria Kurthia timonensis 2011 SOLiD 454_PE CAEP00000000 Published P68 Bacteria Microvirga massiliensis 2011 SOLiD 454_PE PGM In progress P69 Bacteria Obesia massiliensis 2011 SOLiD 454_PE In progress P70 Bacteria Oceanobacillus massiliensis 2011 SOLiD 454_PE CAER00000000 In progress P71 Bacteria Paenibacillus senegalensis 2011 SOLiD 454_PE CAES00000000 Published P72 Bacteria Peptoniphilus grossensis 2011 SOLiD 454_PE CAGX00000000Published P73 Bacteria Peptoniphilus senegalensis 2011 SOLiD 454_PE CAEL00000000 Published P74 Bacteria Peptoniphilus Timonensis 2011 SOLiD 454_PE CAHE00000000In progress P75 Bacteria Ruminococcus massiliensis 2011 SOLiD 454_PE In progress P76 Bacteria Timonella senegalensis (Sanguibacter massiliens 2011 SOLiD 454_PE CAHH00000000Published P77 Bacteria Senegalemassilia fastidiosa 2011 SOLiD 454_PE CAEM00000000Published P78 Bacteria Staphylococcus senegalensis 2011 SOLiD 454_PE In progress P79 Virus MarseilleVirus 2008 454_PE NC_013756 Published P80 Virus OcculloVirus (mimi150) 2011 454_PE In progress P81 Virus Mamavirus 2007 SOLiD 454_PE JF801956 Published P82 Virus Moumouvirus 2008 SOLiD 454_PE JX962719.1 Published P83 Virus Sputnik1 2007 454_PE NC_011132 Published P84 Virus Sputnik2 2010 454_PE JN603369 Published P85 Virus Sputnik3 2011 454_PE JN603370 Published P86 Virus Courdo 11 2009 SOLiD 454_PE In progress P87 Virus Terra 2 2009 SOLiD 454_PE In progress P88 Virus Terre 1 2009 SOLiD 454_PE In progress P89 Virus Cannes 9 2010 454_PE In progress P90 Virus Lentille (Gros Virus de l'œil) 2010 SOLiD 454_PE In progress P91 Virus Pointe Rouge 1 2010 SOLiD 454_PE In progress P92 Virus Pointe Rouge 2 2010 SOLiD 454_PE In progress P93 Virus Monve 2008 SOLiD 454_PE JN885994 Published P94 Virus Fauteuil dentaire 2010 SOLiD 454_PE In progress P95 Virus Bus (RTM2) 2010 SOLiD 454_PE In progress P96 Virus Fontaine Palais Longchamp 2010 SOLiD 454_PE In progress P97 Virus Cannes 8A 2010 SOLiD 454_PE In progress P98 Virus Courdo 5 2010 SOLiD 454_PE In progress P99 Virus Courdo 7 2010 SOLiD 454_PE JN885990 Published P100 Virus Montpellier 3 2011 SOLiD 454_PE In progress P101 Virus SaintCharles 2011 SOLiD 454_PE In progress P102 Virus SenegalVirus 2011 SOLiD 454_PE In progress P103 Virus Univirus 2011 SOLiD 454_PE In progress P104 Virus Lactours 2011 SOLiD 454_PE In progress P105 Virus Maraivirus 2011 454_PE In progress P106 Virus Ochanvirus 2011 SOLiD 454_PE In progress P107 Bacteria Acinetobacter baumannii_ColiS (Spain) 2011 SOLiD 454_PE In progress P108 Bacteria Acinetobacter baumannii_ColiR (Spain) 2011 SOLiD 454_PE In progress P109 Virus Goulette 2012 SOLiD 454_PE In progress P110 Virus Avenue 9 2012 SOLiD 454_PE In progress P111 Virus Fontaine 2 2011 SOLiD 454_PE In progress P112 Virus Pathomime BAL156 2012 SOLiD 454_PE In progress P113 Virus Megavirus lba isolate LBA111 2012 SOLiD 454_PE JX885207 Published P114 Bacteria Microbacterium massiliensis>M.timonensis> M.2012 SOLiD CAJF01000001-Published P115 Virus Mycobacterium bolletii phage 2011 454_PE In progress P116 Bacteria Paenibacillus provencensis 2012 SOLiD In progress P117 Bacteria Paenibacillus massiliensis 2012 SOLiD In progress P118 Bacteria Paenibacillus sanguinis 2012 SOLiD In progress P119 Bacteria Paenibacillus urinalis 2012 SOLiD In progress P120 Bacteria Paenibacillus timonensis 2012 SOLiD Published P121 Bacteria Brevibacterium massiliensis 2012 SOLiD 454_PE 454_SG CAJD01000001-Published P122 Bacteria Streptococcus massiliensis 2012 SOLiD 454_PE 454_SG PRJEB449 Published P123 Bacteria Actinomyces massiliensis 2012 SOLiD 454_PE 454_SG AKIO01000000 Published P124 Bacteria Kingella kingae 11220434 2012 SOLiD 454_PE 454_SG ALIJ01000000 Published P125 Bacteria Rhodopirellula callelongua>Rhodopirellula mass 2013 SOLiD 454_PE 454_SG PRJEB97 Published P126 Bacteria Anorexica massiliensis 2012 SOLiD 454_PE In progress P127 Bacteria Dorea massiliensis 2012 SOLiD 454_PE In progress P128 Bacteria Holdemania massiliensis 2012 SOLiD 454_PE CALK01000001 Published P129 Bacteria Bacteroides timonensis 2012 SOLiD 454_PE PRJEB186 In progress P130 Bacteria Anaerococcus
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  • Diversity of Spotted Fever Group Rickettsiae and Their Association

    Diversity of Spotted Fever Group Rickettsiae and Their Association

    www.nature.com/scientificreports OPEN Diversity of spotted fever group rickettsiae and their association with host ticks in Japan Received: 31 July 2018 May June Thu1,2, Yongjin Qiu3, Keita Matsuno 4,5, Masahiro Kajihara6, Akina Mori-Kajihara6, Accepted: 14 December 2018 Ryosuke Omori7,8, Naota Monma9, Kazuki Chiba10, Junji Seto11, Mutsuyo Gokuden12, Published: xx xx xxxx Masako Andoh13, Hideo Oosako14, Ken Katakura2, Ayato Takada5,6, Chihiro Sugimoto5,15, Norikazu Isoda1,5 & Ryo Nakao2 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 amplifcation of the citrate synthase gene (gltA). Conventional PCR and sequencing analyses of gltA indicated the presence of 15 diferent genotypes of SFG rickettsiae. Based on the analysis of fve additional genes, we characterised fve Rickettsia species; R. asiatica, R. helvetica, R. monacensis (formerly reported as Rickettsia sp. In56 in Japan), R. tamurae, and Candidatus R. tarasevichiae and several unclassifed 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.