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The epidemic re-emergence of diphtheria in Russia and the Newly Independent States (NIS) of the former Soviet Union in the 1990s demonstrated the continued threat of this thought to be rare disease. The bacteriophage encoded toxin is a main virulence factor of Corynebacterium diphtheriae, however, an analysis of the first complete genome sequence of C. diphtheriae revealed a recent acquisition of other pathogenicity factors including iron-uptake systems, adhesins and fimbrial proteins as indeed this extracellular pathogen has more possibilities for lateral gene transfer than, e.g., its close relative, mainly intracellular Mycobacterium tuberculosis. C. diphtheriae appears to have a phylogeographical structure mainly represented by area-specific variants whose circulation is under strong influence of human host factors, including health control measures, first of all, vaccination, and social economic conditions. This framework core population structure may be challenged by importation of the endemic and eventually toxigenic strains from new areas thus leading to localized or large epidemics caused directly by imported strains or by bacteriophage-lysogenized indigenous strains converted into toxin production. A feature of C. diphtheriae co-existence with humans is its periodicity: following large epidemic in the 1990s, the present period is marked by increasing heterogeneity of the circulating populations whereas re-emergence of new toxigenic variants along with persistent circulation of invasive non-toxigenic strains appear alarming. To identify and rapidly monitor subtle changes in the genome structure at an infraclonal level during and between epidemics, portable and discriminatory typing methods of C. diphtheriae are still needed. In this view, CRISPRs and minisatellites are promising genomic markers for development of high-resolution typing schemes and databasing of C. diphtheriae.

International audience; Screening for viruses in samples taken from acidic hot springs of Kamchatka (Russia) revealed a collection of morphotypes, including linear, spherical and complex fusiform shapes, which show partial similarity to those found in acidic geothermal environments in other geographical locations. One of the viruses, Acidianus filamentous virus 9, AFV9, was isolated and its structure and genome were studied in detail.

The development of tuberculosis (TB) infection in humans depends on the mycobacterial strain and the human host, and is multigenically controlled in both. ATP ligation of P2X7receptors expressed on human macrophages infected with mycobacteria induces cell death and subsequent loss of intracellular bacterial viability. This study analysed the allelic distribution of two single-nucleotide polymorphisms (SNPs) in theP2RX7gene in the Slavic population of the St Petersburg area of Russia. Analysis of the −762 C/TP2RX7promoter SNP revealed no significant association between pulmonary TB patients and control subjects (3×2χ2=3.2, 1 d.f.,P=0.2). The −762C allele was highly and almost equally represented in both groups in this study (68.2 % in patients and 69.3 % in controls). This result differs strikingly from a Gambian study where this allele was found in only 7 and 12 % of pulmonary TB patients and controls, respectively [Li, C. M., Campbell, S. J., Kumararatne, D. S., Bellamy, R., Ruwende, C., McAdam, K. P. W. J., Hill, A. V. S. & Lammas, D. A. (2002).J Infect Dis186, 1458–1462]. In contrast, the frequency of the C allele at position 1513 in exon 13, resulting in a loss of P2X7function, was significantly higher among pulmonary TB patients in this study (P=0.02). Thus, analysis of the P2X7receptor gene in the Russian Slavic population showed that the 1513C allele, acting dominantly, is a possible risk factor for clinical TB, whereas the −762P2RX7polymorphism did not appear to be associated with human susceptibility to TB.

International audience; A large diphtheria epidemic in the 1990s in Russia and neighboring countries underlined the importance of permanent surveillance of the circulating and emerging clones of Corynebacterium diphtheriae, and hence there is a need for highly discriminatory, simple and portable typing methods. In the complete genome sequence of C. diphtheriae strain NCTC13129, we previously identified in silico two clustered, regularly interspaced short palindromic repeat (CRISPR) loci, and developed a macroarray-based method to study polymorphism in the larger DRB locus. We named this method spoligotyping (spacer oligonucleotide typing), analogously to a similar method of Mycobacterium tuberculosis genotyping. Here, we included in the analysis novel spacers of the other CRISPR locus in C. diphtheriae (DRA); both loci were simultaneously co-amplified and co-hybridized against the membrane with 27 different immobilized spacer-probes. The use of additional DRA spacers improved strain differentiation and discriminated within large DRB clusters. The 156 Russian strains of the epidemic clone were subdivided into 45 combined spoligotypes compared to 35 DRB-spoligotypes and only two ribotypes ('Sankt-Peterburg' and 'Rossija'). The spoligotyping method allows digital presentation of profiles and therefore it is perfectly suitable for interlaboratory comparison and database management; it may become a powerful tool for epidemiological monitoring and phylogenetic analysis of C. diphtheriae.

A large diphtheria epidemic in the 1990s in Russia and neighboring countries was caused by a clonal group of closely related Corynebacterium diphtheriae strains (ribotypes Sankt-Peterburg and Rossija). In the recently published complete genome sequence of C. diphtheriae strain NCTC13129, representative of the epidemic clone (A. M. Cerdeño-Tarraga et al., Nucleic Acids Res. 31:6516-6523, 2003), we identified in silico two direct repeat (DR) loci 39 kb downstream and 180 kb upstream of the oriC region, consisting of minisatellite (27- to 36-bp) alternating DRs and variable spacers. We designated these loci DRA and DRB, respectively. A reverse-hybridization macroarray-based method has been developed to study polymorphism (the presence or absence of 21 different spacers) in the larger DRB locus. We name it spoligotyping (spacer oligonucleotide typing), analogously to a similar method of Mycobacterium tuberculosis genotyping. The method was evaluated with 154 clinical strains of the C. diphtheriae epidemic clone from the St. Petersburg area in Russia from 1997 to 2002. By comparison with the international ribotype database (Institut Pasteur, Paris, France), these strains were previously identified as belonging to ribotypes Sankt-Peterburg ( n = 79) and Rossija ( n = 75). The 154 strains were subdivided into 34 spoligotypes: 14 unique strains and 20 types shared by 2 to 46 strains; the Hunter Gaston discriminatory index (HGDI) was 0.85. DRB locus-based spoligotyping allows fast and efficient discrimination within the C. diphtheriae epidemic clonal group and is applicable to both epidemiological investigations and phylogenetic reconstruction. The results are easy to interpret and can be presented and stored in a user-friendly digital database (Excel file), allowing rapid type determination of new strains.