If the acquisition of virulence genes (VGs) for pathogenicity were not solely acquired through horizontal gene transfers of pathogenicity islands, transposons, and phages, then clonal clusters of enterotoxigenic Escherichia coli (ETEC) would contain few or even none of the VGs found in strains responsible for extraintestinal infections. To evaluate this possibility, 47 postweaning diarrhea (PWD) ETEC strains from different geographical origins and 158 commensal E. coli isolates from the gastrointestinal tracts of eight group-housed healthy pigs were screened for 36 extraintestinal and 18 enteric VGs using multiplex PCR assays. Of 36 extraintestinal VGs, only 8 were detected (fimH, traT, fyuA, hlyA, kpsMtII, k5, iha, and ompT) in the ETEC collection. Among these, hlyA (␣-hemolysin) and iha (nonhemagglutinating adhesin) occurred significantly more frequently among the ETEC isolates than in the commensal isolates. Clustering analysis based on the VG profiles separated commensal and ETEC isolates and even differentiated serogroup O141 from O149. On the other hand, pulsed-field gel electrophoresis (PFGE) successfully clustered ETEC isolates according to both serotype and geographical origin. In contrast, the commensal isolates were heterogeneous with respect to both serotype and DNA fingerprint. This study has validated the use of VG profiling to examine pathogenic relationships between porcine ETEC isolates. The clonal relationships of these isolates can be further clarified by PFGE fingerprinting. The presence of extraintestinal VGs in porcine ETEC confirmed the hypothesis that individual virulence gene acquisitions can occur concurrently against a background of horizontal gene transfers of pathogenicity islands. Over time, this could enable specific clonotypes to respond to host selection pressure and to evolve into new strains with increased virulence.Enterotoxigenic Escherichia coli (ETEC) is the major cause of postweaning diarrhea (PWD) in weaned pigs. ETEC strains colonize the small intestine with the aid of adhesion factors (e.g., F4 or F18 fimbriae). Once attached, the release of either heat-labile or heat-stable (STa or STb) enterotoxins induces diarrhea by affecting the electrolyte balance of the small intestine. The presence of virulence genes (VGs) encoding these determinants is a key requirement for pathogenicity in ETEC and is generally used to distinguish these pathogens from the nonpathogenic or commensal E. coli normally carried in the intestine (37).Characterization of isolates from outbreaks of PWD has shown that ETEC strains lacking recognized fimbriae, such as F4 and F18, are becoming more common (19,26,44). This may be related to the widespread use of vaccines incorporating fimbriated strains, providing selection pressure for the acquisition and carriage of novel, unrecognized VGs. For example, Noamani et al. (37) found that most of the PWD isolates recovered in the period 1998 to 2001 in Ontario, Canada, were associated with a new type of O149 ETEC, which possessed VGs for STa and an enteroag...