The diphtheria epidemic in Russia and neighboring countries in the 1990s (140,000 cases, 4,000 deaths in 1991 to 1996 [39]) stimulated research activities on Corynebacterium diphtheriae, a causative agent of the disease. A number of the typing methods available at that time (multilocus enzyme electrophoresis [MLE], pulsed-field gel electrophoresis [PFGE], ribotyping, and randomly amplified polymorphic DNA [RAPD] analysis) and newer methods (amplified fragment length polymorphism analysis) were applied for interstrain differentiation of the pathogen (6,7,8,20,22,23,28,29,33,36,40). These methods allowed the identification of a clonal group of closely related strains responsible for the epidemic in Russia and all other countries of the former Soviet Union and to trace strains exported into other countries (6,22,23,32,33). These strains were indistinguishable by PFGE, RAPD analysis, and amplified fragment length polymorphism analysis and very similar by ribotyping (there were two principal profiles, "Rossija" and "Sankt-Peterburg," which differed by one band [6, 14, 33]). Minor rare variants were identified by RAPD and ribotyping techniques (22), and a total of 27 types similar by Ͼ80% were identified by MLE typing of all strains of this clonal group studied to date (32, 33). However, MLE, PFGE, and ribotyping are time-consuming and rather cumbersome methods, while RAPD analysis lacks interlaboratory reproducibility and hence exchangeability of results. To identify and rapidly monitor subtle changes in the genome structure at an infraclonal level during and between epidemics, fast, simple, portable, and discriminatory molecular typing methods of C. diphtheriae are still needed.Repetitive genome sequences present important sources of intraspecies variation. A new family of such loci (clustered, regularly interspaced, short palindromic repeats [CRISPR]) has recently been identified by in silico analysis of many bacterial species (19). This family is characterized by direct repeats (DR) varying in size from 21 to 37 bp, interspaced by similarly sized nonrepetitive sequences (variable spacers). DR and adjacent variable spacers form direct variant repeats (DVR) (20). The DNA reverse-hybridization method was developed to study variation in the Mycobacterium tuberculosis DR locus (the presence or absence of 43 different spacers) by using the macroarray format; this method was named "spoligotyping" (spacer oligonucleotide typing [20]) and has been widely used for epidemiological and phylogenetic purposes (12,20,35).In 2003, a complete genome sequence of the C. diphtheriae epidemic strain of biotype gravis ribotype Sankt-Peterburg was published (4). This publication made possible a more thorough, precise, and comprehensive search of candidate polymorphic loci for the development of new typing methods for this pathogen. In the present study, we identified in silico a large DR region in the genome of C. diphtheriae and developed a reverse-hybridization macroarray-based method to study its polymorphism. Using this method, we e...