Neonatal pigs were inoculated with porcine enterotoxigenic Escherichia coli 431, which carries genes for K99 fimbriae and STaP enterotoxin. Colonies of strain 431 were recovered from feces of pigs for up to 17 days after inoculation and tested for hybridization with gene probes for K9 and STaP. Variants of strain 431 that did not hybridize with the probes were considered to have lost the genes. Variants were recovered from 10 of 13 suckling pigs that survived the infection. Only 0.4% of the isolates recovered during the first 2 days after inoculation were variants. Of the isolates recovered 3 to 5 days after inoculation, 20 to 36% were variants. Variant colonies were detected more frequently among pigs in some litters than in others. The litter with the highest number of variant-shedding pigs had the dam with the highest titer of K9 antibody in her colostrum. Variants also occurred in colostrum-deprived, artificially reared pigs. However, the number of variants detected was lower and they occurred later in the course of the infection in colostrum-deprived pigs than in suckling pigs. More variants were detected and they were detected earlier in colostrum-deprived pigs fed anti-K99 monoclonal antibody than in controls fed anti-K88 monoclonal antibody. Loss of STaP appeared to be secondary to loss of K99 in that some variants lacked only K99 (K99-STaP+) and some lacked both genes (K99-STaP-), but none was of the K99+ STaP-type. Our results confirmed reports of gene loss from enterotoxigenic E. coli during infection. They are consistent with the hypothesis that variants emerge under in vivo selection pressure of K99 antibody and with the speculation that gene loss may be an important component of protection in vaccinated populations. However, the emergence of variants did not appear to play a major role in the recovery of individual pigs from clinical disease. Fimbriae (pili) and enterotoxins are virulence factors of enterotoxigenic Escherichia coli (ETEC) (1,15). Fimbriae mediate adherence of E. coli to host intestinal epithelium, and enterotoxins stimulate intestinal secretion of water and electrolytes, resulting in diarrhea. Some ETEC strains of the K88 (F4) and K99 (F5) fimbrial antigen types lose these antigens (and, apparently, the plasmids carrying the genes encoding them) during experimental infections in mice (5). Loss of K88 antigen also occurs during infections in pigs, which are natural hosts for K88+ ETEC (17,18). A human ETEC strain (6) and an enteropathogenic E. coli strain (7) have been shown to lose genes encoding heat-labile enterotoxin and an adherence factor, respectively, during infection in humans.Loss of K88 in pigs is thought to be caused by antibody, because it was detected in immunized pigs but not in control pigs (18) and because it can be induced in vitro by growth in immune colostrum (8,17,18). It has been suggested that the antibodies involved in loss of K88 are not K88 specific but rather are directed against a novel antigen(s) and act by a novel mechanism which also impedes the spread ...