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The type 1 pilin encoded byfim is present in bothEscherichia coli andSalmonella natural isolates, but several lines of evidence indicate that similarities at thefim locus may be an example of independent acquisition rather than common ancestry. For example, thefim gene cluster is found at different chromosomal locations and with distinct gene orders in these closely related species. In this work we examined thefim gene cluster ofSalmonella , the genes of which show high nucleotide sequence divergence from theirE. coli counterparts, as well as a different G+C content and codon usage. DNA hybridization analysis revealed that, among the salmonellae, thefim gene cluster is present in all isolates ofS. enterica but is absent fromS. bongori . Molecular phylogenetic analyses of thefimA andfimI genes yield an estimate of phylogeny that is in satisfactory congruence with housekeeping and other virulence genes examined in this species. In contrast, phylogenetic analyses of thefimZ ,fimY , andfimW genes indicate that horizontal transfer of this region has occurred more than once. There is also size variation in thefimZ ,fimY , andfimW intergenic regions in the 3′ region, and these genes are absent in isolate S2983 of subspecies IIIa. Interestingly, the G+C contents of thefimZ ,fimY , andfimW genes are less than 46%, which is considerably lower than those of the other six genes of thefim cluster. This study demonstrates that horizontal transmission of all or part of the same gene cluster can occur repeatedly, with the result that different regions of a single gene cluster may have different evolutionary histories.

Analysis of the Type 1 Pilin Gene Cluster fim in Salmonella : Its Distinct Evolutionary Histories in the 5′ and 3′ Regions