Variation in Bordetella bronchiseptica flaA does not correlate with typing by macro-restriction analysis by pulsed-field gel electrophoresis

A genotyping method based on PCR-RFLP analysis of the flagellin gene ( flaA ) was applied to 30 mainly feline isolates of Bordetella bronchiseptica . These isolates were separated into three PCR-RFLP groups with the restriction endonucleases Hae III, Msp I, Mbo I and Rsa I. flaA nucleotide sequences representing each of the three groups differed from each other by 11–13%. One of the groups exhibited far greater flaA sequence identity with the cryptic flagellin gene sequence of B. pertussis (>97%) than with flaA sequences from representatives of the other B. bronchiseptica PCR-RFLP groups. Amongst the 30 isolates were at least 10 representing each of the two major genotypes (A and B) identified in a previous study by macro-restriction analysis and pulsed-field gel electrophoresis (PFGE), as well as representatives of other less common genotypes. Each of the major PFGE genotypes contained strains representing more than one flagellin genotype. Indeed, there was no correlation between the two molecular typing methods. PFGE analysis may identify differences due to genomic re-arrangements rather than genuine variations in gene content. If so, relationships inferred on the basis of PFGE or other molecular methods for whole genome comparison should be treated with caution.