Gene sequence-based criteria for identification of new rickettsia isolates and description of Rickettsia heilongjiangensis sp. nov.
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.
Fournier
Pierre-Edouard
PE
Unité des Rickettsies, IFR 48, CNRS UMR 6020, Faculté de Médecine, Université de la Méditerranée, 13385 Marseille cedex 05, France.
Dumler
J Stephen
JS
Greub
Gilbert
G
Zhang
Jianzhi
J
Wu
Yimin
Y
Raoult
Didier
D
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
D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S