title: Gene sequence-based criteria for identification of new rickettsia isolates and description of Rickettsia heilongjiangensis sp. nov.
abstract: We propose genetic guidelines for the classification of rickettsial isolates at the genus, group, and species levels by using sequences of the 16S rRNA (rrs) gene and four protein-coding genes, the gltA, ompA, and ompB genes and gene D. To be classified as a member of the genus Rickettsia, an isolate should exhibit degrees of rrs and gltA homology with any of the 20 Rickettsia species studied of >/=98.1 and >/=86.5%, respectively. A member of the typhus group should fulfill at least two of the following four criteria: pairwise nucleotide sequence homologies with rrs, gltA, ompB, and gene D of either Rickettsia typhi or Rickettsia prowazekii of >/=99.4, >/=96.6, >/=92.4, and >/=91.6%, respectively. A member of the spotted fever group should either possess the ompA gene or fulfill at least two of the following four criteria: pairwise nucleotide sequence homologies with rrs, gltA, ompB, and gene D of any member of this group of >/=98.8, >/=92.7, >/=85.8, and >/=82.2%, respectively. The existence of a distinct "ancestral" group should be questioned. To be classified as a new Rickettsia species, an isolate should not exhibit more than one of the following degrees of nucleotide similarity with the most homologous validated species: >/=99.8 and >/=99.9% for the rrs and gltA genes, respectively, and, when amplifiable, >/=98.8, >/=99.2, and >/=99.3% for the ompA and ompB genes and gene D, respectively. By use of our classification scheme, "Rickettsia heilongjiangii" belongs to a new species for which we officially propose the name Rickettsia heilongjiangensis sp. nov.
authors.affiliation: Unité des Rickettsies, IFR 48, CNRS UMR 6020, Faculté de Médecine, Université de la Méditerranée, 13385 Marseille cedex 05, France.
authors.forename: Pierre-Edouard
authors.initials: PE
authors.lastname: Fournier
authors.forename: J Stephen
authors.initials: JS
authors.lastname: Dumler
authors.forename: Gilbert
authors.initials: G
authors.lastname: Greub
authors.forename: Jianzhi
authors.initials: J
authors.lastname: Zhang
authors.forename: Yimin
authors.initials: Y
authors.lastname: Wu
authors.forename: Didier
authors.initials: D
authors.lastname: Raoult
mesh_terms: D004275:DNA, Ribosomal / Q000235:genetics; D005798:Genes, Bacterial / Q000235:genetics*; D005838:Genotype; D006801:Humans; D010802:Phylogeny; D016133:Polymerase Chain Reaction / Q000379:methods; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012281:Rickettsia / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D012282:Rickettsia Infections / Q000145:classification / Q000175:diagnosis / Q000382:microbiology; D012373:Rocky Mountain Spotted Fever / Q000382:microbiology
chemical_list: D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S