RESEARCH Table 2. Number of isolates tested and distinct sequence types, by year No. 1992 1993 1994 Isolates examined 9 9 12 Novel sequence types Novel sequence types per isolate examined 3 0.33 6 0.66 6 0.5 1995 10 7 0.7 1996 13 8 0.62 1997 11 6 0.55 1998 12 7 0.58 1999 12 4 0.33 2000 8 7 0.88 Total 96 51 0.53 novel alleles identified in a previous study (18), 11 of the 13 would be considered to have resulted from LGT, since the number of nucleotide differences to the ancestral allele varied from 4 to 19. Thus, for V. cholerae, like Neisseria, Streptococcus, and other bacterial species (11–14), conspe- cific recombination of homologous genes appears to be common and responsible for most of the alleles with mul- tiple nucleotide differences and the majority of the nucleotide differences. The genetic variability at the nine loci alters our understanding of evolution in bacteria, showing that recombination in V. cholerae occurs fre- quently and most nucleotide changes occur by means of a recombination that can alter any gene. The proportion of recombinants from conspecific recombination, 3.5% (28/785) is greater than that from transgeneric recombination (0.01% from the acquisition of E. coli gmd by one isolate). One potential implication of a greater rate of conspecific recombination may be that, over time, it will maintain the species identity of each individ- ual bacterium, despite the constant bombardment of homologous genes from other genera. Although at first glance the frequency of the novel sequence types appears to conflict between our study and an earlier study (18), the observations may be reconciled on the basis of both the observed frequencies and the timing of the observations. Both studies identified a common ancestral allele in from 77% to 99% of isolates in our study and a series of rare alleles with 1–19 variant alleles for each locus. These stud- ies reported 10% novel sequence types in 29 isolates that were collected from “the first epidemic period,” from 1992 to 1993 (18). Our data from 1992 showed 33% novel sequence types from a sample of nine. These data are not statistically different (chi-square test=2.4, p=0.12). However, the researchers’ estimate of frequency (18) is more likely to be correct because of the larger sample size. The dates of collection may also be important because our collection of isolates from 1993 began in March, when the number of O139 cases at the Infectious Diseases Hospital rose from <10 to >80 per month, corresponding to a rapid population expansion or flush. Thus, we can predict that we would see substantial variation in our sample. The genetic diversity was greater in the V. cholerae O139 isolates than in other clinically associated clones. In V. parahaemolyticus O3:K6, a pandemic strain, 94% of strains were identical at four loci (N. Chowdhury et al., unpub. data). In E. coli O157, all 77 isolates were identical at seven loci in spite of variation between isolates on PFGE (17). Although V. parahaemolyticus and E. coli are widespread pathogens, they differ from V. cholerae O139 because their population size has expanded much more slowly. Among O139 isolates, the substantial genetic diversity found in the first year of the epidemic may reflect a “founder flush” phenomenon. During times of population expansion, i.e., a flush, any novel genotype with similar or even slightly deleterious fitness compared to the founder genotype will produce sufficient offspring to become established in the population (27). A founder flush appears to have occurred in the establishment of Helicobacter pylori in a single person (28). Although other previous descriptions of this phenomenon have been limited to insects, specifically butterflies (29) and drosophilids (30), we believe that the founder flush phenomenon may become the paradigm for epidemic bacterial expansion in individual patients and populations. This founder flush phenomenon, in turn, has implications for our interpreta- tion of “clonality” among epidemic isolates and for our Figure 2. Five groups of related sequence types of Vibrio cholerae O139. Emerging Infectious Diseases • Vol. 9, No. 7, July 2003 813