Pathogenic Vibrio cholerae continues to emerge and replace existing pandemic and/or endemic strains. Recent studies have revealed that competition among mobile genetic elements (MGEs) can play an important role in the succession of V. cholerae lineages; however, the origins and transmission trajectories of MGEs in pathogenic and environmental V. cholerae remain unclear. In this project, we aim to identify MGEs in V. cholerae isolates from various ecological niches and to reconstruct their transmission routes among bacterial populations. The findings may enhance our understanding of the role of MGEs in the evolution of pathogenicity in V. cholerae