Although Vibrio cholerae is an important human pathogen, little is known about its populations in regions where the organism is endemic but where cholera disease is rare. A total of 31 independent isolates confirmed as V. cholerae were collected from water, sediment, and oysters in 2008 and 2009 from the Great Bay Estuary (GBE) in New Hampshire, a location where the organism has never been detected. Environmental analyses suggested that abundance correlates most strongly with rainfall events, as determined from data averaged over several days prior to collection. Phenotyping, genotyping, and multilocus sequence analysis (MLSA) revealed a highly diverse endemic population, with clones recurring in both years. Certain isolates were closely related to toxigenic O1 strains, yet no virulence genes were detected. Multiple statistical tests revealed evidence of recombination among strains that contributed to allelic diversity equally as mutation. This relatively isolated population discovered on the northern limit of detection for V. cholerae can serve as a model of natural population dynamics that augments predictive models for disease emergence.Vibrio cholerae is a ubiquitous waterborne bacterium found commonly in estuarine environments (37). Although V. cholerae is comprised of over 200 serotypes, only serotypes O1 and O139 are currently responsible for epidemic and pandemic cholera outbreaks (1,9,14,15,37,49,57,60). Closely related clones of types O1 and O139 are found rarely in the environment and only in warm waters (16,54). Whereas these pandemic serotypes and their associated populations have been the subjects of intense study, investigations of the remaining ecotypes are less common (29, 31-33, 36, 53). Yet other serotypes could be reservoirs of new pathogenic lineages that emerge by horizontal transfer and recombination. Recombination has been observed in several V. cholerae collections (31, 61) and is thought to have driven the emergence of new infective variants (16).Only 40 domestically acquired toxigenic V. cholerae cases have been reported in the United States since 1995 (66), but epidemics are ongoing in warm, subtropical climates, the most recent occurring in Haiti, which had been cholera-free for decades (6). Variation in disease incidence is caused in part by transmission between patients by feces-contaminated drinking water and by endemic populations of toxigenic cholera organisms in warm subtropical environments (11,12,37). Endemic cholera has not posed a public health threat in temperate regions in modern times (38, 60). Toxigenic O1 and O139 serotypes of V. cholerae are not regularly isolated from temperate waters in the United States, but some environmental non-O1/non-O139 populations, a few of which are associated with disease, have been described (11,31,43,58). Even so, the pathogenic potential and ecology of most endemic populations are not well understood.Here we describe the genotypic and phenotypic characteristics of a newly identified and highly diverse population of non-O1 V. cholerae is...