Use of amplified fragment length polymorphisms for typing Corynebacterium diphtheriae

Multilocus sequence typing identifies evidence for recombination and two distinct lineages of Corynebacterium diphtheriae

We describe the development of a multilocus sequence typing (MLST) scheme for Corynebacterium diphtheriae, the causative agent of the potentially fatal upper respiratory disease diphtheria. Global changes in diphtheria epidemiology are highlighted by the recent epidemic in the former Soviet Union (FSU) and also by the emergence of nontoxigenic strains causing atypical disease. Although numerous techniques have been developed to characterize C. diphtheriae, their use is hindered by limited portability and, in some instances, poor reproducibility. One hundred fifty isolates from 18 countries and encompassing a period of 50 years were analyzed by multilocus sequence typing (MLST). Strain discrimination was in accordance with previous ribotyping data, and clonal complexes associated with disease outbreaks were clearly identified by MLST. The data produced are portable, reproducible, and unambiguous. The MLST scheme described provides a valuable tool for monitoring and characterizing endemic and epidemic C. diphtheriae strains. Furthermore, multilocus sequence analysis of the nucleotide data reveals two distinct lineages within the population of C. diphtheriae examined, one of which is composed exclusively of biotype belfanti isolates and the other of multiple biotypes.

Comparison of four molecular typing methods for characterization of Corynebacterium diphtheriae and determination of transcontinental spread of C. diphtheriae based on BstEII rRNA gene profiles

The diphtheria epidemic in the Russian Federation in the 1990s made diphtheria a focus of global concern once again. The development of rapid and reproducible typing methods for the molecular characterization of Corynebacterium diphtheriae has become a priority in order to be able to monitor the spread of this important pathogen on a global scale. We report on a comparison of four molecular typing methods (ribotyping, pulsed-field gel electrophoresis [PFGE], random amplification of polymorphic DNA [RAPD], and amplified fragment length polymorphism [AFLP]) for the characterization of C. diphtheriae strains. Initially, 755 isolates originating from 26 countries were analyzed by ribotyping. One strain of each ribotype was then randomly chosen and characterized by PFGE, RAPD, and AFLP. In order to ascertain whether the Eastern European epidemic ribotype could be further discriminated, 10 strains of ribotype D1 (the epidemic ribotype) from different geographical regions were randomly chosen and subjected to analysis by PFGE, RAPD, and AFLP. The results revealed that ribotyping is highly discriminatory and reproducible and is currently the method of choice for typing C. diphtheriae. PFGE and AFLP were less discriminatory than ribotyping and RAPD. An assessment of the transcontinental spread of the organism showed that several genotypes of C. diphtheriae circulated on different continents of the world and that each outbreak was caused by a distinct clone. The ribotypes seen in Europe appeared to be distinct from those seen elsewhere, and certain ribotypes appeared to be unique to particular countries.

Efficient discrimination within a Corynebacterium diphtheriae epidemic clonal group by a novel macroarray-based method

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. Cerdeno-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.

Management of long-term catheter-related Brevibacterium bacteraemia

Brevibacterium has been reported as a rare cause of implanted-device infection. In two cases of recurrent Brevibacterium casei bacteraemia associated with infection of surgically implanted intravascular devices, relapse occurred 2 and 5 months, respectively, after completion of therapy with vancomycin via the infected catheter. A second intravenous antibiotic therapy course by the antibiotic-lock technique led to bacteriological cure in one patient. Molecular typing results demonstrated that the recurrent bacteraemia was caused by the same strain. Implanted-device removal may be necessary, in addition to appropriate antibiotics, for successful management of such infections.

Fluorescent amplified fragment length polymorphism probabilistic database for identification of bacterial isolates from urinary tract infections

The ability of the fluorescent amplified fragment length polymorphism (FAFLP) technique to identify bacterial isolates from urinary tract infections (UTIs) was investigated. FAFLP was carried out using the single primer combination MseI plus CT and EcoRI plus 0, and information-rich FAFLP profiles were generated from all 69 UTI isolates studied, which comprised both gram-negative and gram-positive bacteria encompassing eight genera. The genetic relatedness of these 69 bacteria was determined by cluster analysis, and this revealed eight main groups corresponding to the eight bacterial genera. Finer discrimination on the same dendrogram showed species and subspecies differentiations, thus demonstrating the potential of FAFLP for describing a wide diversity range within microbial populations. The interpretation of FAFLP profiles is often complicated because it relies upon the investigator interpreting dendrograms; this process may be subjective if the tree is complicated, particularly if it includes polytomies (unresolved nodes). Therefore, we have developed a method based on Bayes' theorem for the identification of bacteria against an FAFLP probabilistic identification matrix. Thus, FAFLP is suitable for the objective identification of causal agents of UTI, and the procedure offers great potential in the clinical laboratory.