Since the development of the necessary molecular biological tools, analysis of nucleic acid biomarkers for the detection and identification of bacteria has become widespread. rRNA has often been the target of choice for such studies, and consequently there is an enormous amount of sequence data available for rRNA molecules. In addition to providing species-specific markers, rRNA sequence comparisons have been used to reassess phylogenetic relationships (Olsen et aZ., 1994). However, rRNA molecules, even the variable regions, are often indistinguishable when closely related species or strains of the same species are compared. This means that rRNA sequence analysis is of limited use when estimation of genetic variation amongst closely related bacterial populations is required, for studies of population genetics, for epidemiological analysis, or for the development of strain-specific detection methods.

Proteins located on the surface of a bacterial cell show a much greater rate of divergence in amino acid sequence than those located internally (Whittam, 1995). The genes encoding such proteins are therefore ideal candidates as potential biomarkers to assess intraspecies genetic variation. Increasingly, flagellin genes are being targeted for such approaches. This review aims to summarize the nature of flagellin gene and protein variation, and the exploitation of such variability for detection, population genetics and epidemiological analysis.