ribotype

Ribotype refers to a pattern derived from ribosomal RNA gene analysis that is used to distinguish bacterial strains. The term can denote either the observed pattern itself or a strain classified by that pattern. Ribotyping is a foundational approach in molecular typing, leveraging variation in ribosomal RNA gene regions to differentiate closely related organisms.

Two common methods are ribosomal RNA gene restriction fragment length polymorphism (RFLP) analysis and PCR-based ribotyping. In RFLP ribotyping, DNA containing ribosomal RNA operons is digested with restriction enzymes and the resulting fragments are separated by gel electrophoresis to produce a characteristic banding pattern. In PCR ribotyping, the intergenic spacer region between the 16S and 23S rRNA genes is amplified and the lengths of the fragments are analyzed. The resulting patterns are compared to reference databases to assign a ribotype code, such as ribotype 027 in Clostridioides difficile.

Applications of ribotyping include epidemiologic typing, outbreak investigation, and surveillance of bacterial populations. It has been used for pathogens such as Clostridioides difficile, Campylobacter, Listeria, Escherichia coli, and Salmonella. Ribotyping is valued for being relatively cost-effective and scalable, particularly in settings without access to high-resolution whole-genome sequencing.

Advantages and limitations: Ribotyping can provide reproducible patterns and enable inter-laboratory comparisons when standardized methods and reference databases are used. Limitations include variable discriminatory power across species, potential effects of experimental conditions on patterns, and challenges in cross-lab standardization. In many contexts, whole-genome sequencing offers higher resolution, but ribotyping remains a practical tool for routine typing and historical analyses.