Genomic profiles of clinical and environmental isolates of Vibrio cholerae O1 in cholera-endemic areas of Bangladesh

Abstract

Diversity, relatedness, and ecological interactions of toxigenic Vibrio cholerae O1 populations in two distinctive habitats, the human intestine and the aquatic environment, were analyzed. Twenty environmental isolates and 42 clinical isolates were selected for study by matching serotype, geographic location of isolation in Bangladesh, and season of isolation. Genetic profiling was done by enterobacterial repetitive intergenic consensus sequence-PCR, optimized for profiling by using the fully sequenced V. cholerae El Tor N16961 genome. Five significant clonal clusters of haplotypes were found from 57 electrophoretic types. Isolates from different areas or habitats intermingled in two of the five significant clusters. Frequencies of haplotypes differed significantly only between the environmental populations (exact test; P < 0.05). Analysis of molecular variance yielded a population genetic structure reflecting the differentiating effects of geographic area, habitat, and sampling time. Although a parameter confounding the latter differences explained 9% of the total molecular variance in the entire population (P < 0.01), the net effect of habitat and time could not be separated because of the small number of environmental isolates included in the study. Five subpopulations from a single area were determined, and from these we were able to estimate a relative differentiating effect of habitat, which was small compared with the effect of temporal change. In conclusion, the resulting population structure supports the hypothesis that spatial and temporal fluctuations in the composition of toxigenic V. cholerae populations in the aquatic environment can cause shifts in the dynamics of the disease.

Fig 1.

Unrooted neighbor-joining tree based on Euclidean distances (d) among ERIC-PCR band patterns of V. cholerae O1 isolates. Isolates from environmental sources are enclosed in rectangles. When a branching point is significant by having bootstrap support value from 0.5 to 0.9, it is marked as a open circle. When a branching point is significant by appearing consistently in the trees by unweighted pair group method with arithmetic averages (UPGMA) or maximum parsimony (MP), it is marked as triangle. When a branching point is significant by both methods, it is marked as a open square. When a branching point is significant both by bootstrap support >0.9 and by consensus occurrence, it is marked as a solid square. Labeling of the strains follows that of Tables 2 and 3, except for GONGI, a V. cholerae O1 El Tor Inaba strain isolated from coastal water off Chittagong, Bangladesh (22.1°N 91.8°E).