Dynamic Subspecies Population Structure of Vibrio Cholerae in Dhaka, Bangladesh

Abstract

Cholera has been endemic to the Ganges delta for centuries. Although the causative agent, Vibrio cholerae, is autochthonous to coastal and brackish water, cholera occurs continually in Dhaka, the inland capital city of Bangladesh which is surrounded by fresh water. Despite the persistence of this problem, little is known about the environmental abundance and distribution of lineages of V. cholerae, the most important being the pandemic generating lineage (PG) consisting mostly of serogroup O1 strains. To understand spatial and temporal dynamics of PG and other lineages belonging to the V. cholerae species in surface water in and around Dhaka city, we used qPCR and high throughput amplicon sequencing. Seven different freshwater sites across Dhaka were investigated for six consecutive months and physiochemical parameters were measured in situ. Total abundance of V. cholerae was found to be relatively stable throughout the six months sampling period, with 2×105 to 4×105 genome copies/L at six sites and around 5 ×105 genome copies/L at the site located in the most densely populated part of Dhaka city. PG O1 V. cholerae was present in high abundance during the entire sampling period and composed between 24-92% of the total V. cholerae population, only showing occasional but sudden reductions in abundance. In instances where PG O1 lost its dominance, other lineages underwent a rapid expansion while the size of the total V. cholerae population remained almost unchanged. Intraspecies richness of V. cholerae was positively correlated to salinity, conductivity and total dissolved solids (TDS), while it was negatively correlated to dissolved oxygen (DO) concentration in water. Interestingly, negative correlation was observed specifically between PG O1 and salinity, even though the changes in this variable were minor (0-0.8 ppt). Observations in this study suggest that at the subspecies level, population composition of naturally occurring V. cholerae can be influenced by fluctuations in environmental factors, which can lead to altered competition dynamics among the lineages.

Population Analysis of Vibrio cholerae in Aquatic Reservoirs Reveals a Novel Sister Species ( Vibrio paracholerae sp. nov.) with a History of Association with Humans

“…nov. has been found to exist abundantly in local water reservoirs. In one particular site, the number even surpassed that of PG V. cholerae , which was otherwise the most predominant lineage found in Dhaka ( 11 ). That site (Kamrangirchar) happened to be the most densely populated area among those sampled, indicating a possible link between human population and the prevalence of V. paracholerae sp.…”

“…Similarity percentage (SIMPER) analysis based on Bray-Curtis dissimilarity suggests that the allele most responsible for the overall dissimilarities between Dhaka and Oyster Pond is indeed viuB -73. This allele was predominant throughout the 9-month sampling period in Dhaka ( 11 ), constituting around 60% of the total V. cholerae population on average, whereas its presence was stochastic in Oyster Pond, constituting around 5% of the total population ( 9 ).…”

“…S2). From an ecological perspective, lineages within the LB clade have shown distinct and cohesive abundance patterns in natural ecosystems of Dhaka, Bangladesh ( 11 ). Abundance and distribution of viuB alleles corresponding to the clade were found to be tightly correlated with each other, whereas they were negatively correlated with the abundance of the viu B allele corresponding to the dominant PG V. cholerae lineage ( 11 ).…”

“…Overall, ecological analysis of the population in Dhaka suggests that the environmental abundance and distribution of the lineages corresponding to V. paracholerae sp. nov. strains are correlated with human population density ( 11 ). Although data from other locations are required to confirm this correlation, this observation raises the possibility of adaptation to the human gut as an alternate niche and an important factor in the ecology of this novel species.…”

“…This method was used to study a cholera-free region on the east coast of the United States, the Oyster Pond ecosystem (Falmouth, MA), where differences in abundance of individual alleles in particular locations/habitats indicated potential adaptation to ecological conditions at the subspecies level ( 9 , 10 ). A similar study was performed in V. cholerae populations in an inland location (Dhaka) in Bangladesh where cholera is endemic ( 9 , 11 ).…”