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Journal of Clinical Microbiology, December 2004, p. 5757-5766, Vol. 42, No. 12
0095-1137/04/$08.00+0     DOI: 10.1128/JCM.42.12.5757-5766.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.

Use of Highly Variable Intergenic Spacer Sequences for Multispacer Typing of Rickettsia conorii Strains

Pierre-Edouard Fournier,1,{dagger} Yong Zhu,1,{dagger} Hiroyuki Ogata,2 and Didier Raoult1*

Unité des Rickettsies, IFR 48, CNRS UMR 6020, Faculté de Médecine, Université de la Méditerranée,1 Information Génomique et Structurale, CNRS UPR2589, Marseille, France2

Received 13 April 2004/ Returned for modification 28 June 2004/ Accepted 9 August 2004

By use of the nearly perfectly colinear genomes of Rickettsia conorii and Rickettsia prowazekii, we compared the usefulness of three types of sequences for typing of R. conorii isolates: (i) 5 variable coding genes comprising the 16S ribosomal DNA, gltA, ompB, and sca4 (gene D) genes, which are present in both genomes, and the ompA gene, which is degraded in R. prowazekii; (ii) 28 genes degraded in R. conorii but intact in R. prowazekii, including 23 split and 5 remnant genes; and (iii) 27 conserved and 25 variable intergenic spacers. The 4 conserved and 23 split genes as well as the 27 conserved intergenic spacers each had identical sequences in 34 human and 5 tick isolates of R. conorii. Analysis of the ompA sequences identified three genotypes of R. conorii. The variable intergenic spacers were significantly more variable than conserved genes, split genes, remnant genes, and conserved spacers (P < 10–2 in all cases). Four of the variable intergenic spacers (dksA-xerC, mppA-purC, rpmE-tRNAfMet, and tRNAGly-tRNATyr) had highly variable sequences; when they were combined for typing, multispacer typing (MST) identified 27 different genotypes in the 39 R. conorii isolates. Two batches from the same R. conorii strain, Malish (Seven), with different culture passage histories were found to exhibit the same MST type. MST was more discriminatory for strain genotyping than multiple gene sequencing (P < 10–2). Phylogenetic analysis based on MST sequences was concordant with the geographic origins of R. conorii isolates. Our study supports the usefulness of MST for strain genotyping. This tool may be useful for tracing a strain and identifying its source during outbreaks, including those resulting from bioterrorism.

* Corresponding author. Mailing address: Unit é des Rickettsies, IFR 48, CNRS UMR 6020, Facult é de Médecine, Universit é de la Mediterranée, 27 Blvd. Jean Moulin, 13385 Marseille Cedex 5, France. Phone: 33 491 38 55 17. Fax: 33 491 38 77 72. E-mail: didier.raoult{at}medecine.univ-mrs.fr.

{dagger} P.-E.F. and Y.Z. contributed equally to this work.

Journal of Clinical Microbiology, December 2004, p. 5757-5766, Vol. 42, No. 12
0095-1137/04/$08.00+0     DOI: 10.1128/JCM.42.12.5757-5766.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.



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