Infection with bacterial species belonging to the Burkholderia cepacia complex contribute significantly to morbidity and mortality in persons with cystic fibrosis (CF). The majority of isolates recovered from CF patients belong to B. cepacia genomovar III and several distinct 'epidemic' strains have been described. This study examined the population structure of B. cepacia genomovar III by using multilocus restriction typing, indexing allelic variation at five chromosomal genes by restriction analysis of PCR-amplified genes. A collection of 375 isolates, recovered from CF and non-CF patients and natural environments in North America, Europe and Australia, was examined. Among these isolates 144 different restriction types were found. Overall, the population is at linkage disequilibrium, indicating that it has a clonal structure. The majority (86.7 %) of restriction types grouped into three major clonal complexes, comprising the epidemic ET12, PHDC and Midwest clonal lineages. The analysis indicates that these complexes are geographically widespread and demonstrate varying degrees of genetic recombination. These differences in population structure among major clonal complexes within the same species are likely related to differences in evolutionary history and ecology. The observation that genetic recombination is frequent within some B. cepacia genomovar III populations has important implications for the biotechnological use of B. cepacia complex species.
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