Factors Influencing Diarrheal Pathogen Presence in Tubewells of Bangladesh

Diarrheal disease pathogens remain a major concern in developing countries as rotavirus is the leading cause of hospitalization of young children worldwide. A recent study has shown shallow groundwater in rural Bangladesh to be contaminated with bacterial and viral pathogens, but found no correlation between rotavirus and any fecal indicator or environmental parameter during the monsoon season of July, 2009. The objectives of this thesis were to examine the non-relationship between pathogens and fecal indicators, as well as to improve the understanding of the seasonal transport of viral pathogens, especially rotavirus, in shallow, sandy aquifers of Bangladesh. This was achieved by comparing the previously published July 2009 data to new measurements of samples collected from the same tubewells in March 2009 and January 2011, as well as surface water data collected during the same months. Quantitative PCR (qPCR) was used to measure the concentrations of several pathogens and fecal indicators, including E. coli, Shigella, Bacteroides, rotavirus, and adenovirus in a total of 25 surface water and 145 well water samples. Norovirus was also measured, but only in March 2009 well water samples. These measurements were used to compare pathogen presence to molecular and environmental fecal indicators, including pH, seasonality, and Cl/Br ratios. The viral community was also characterized using metagenomic sequence analysis. In both surface and ground water samples, the viral pathogen (primarily rotavirus) frequency of occurrence and mean log concentration exceeded those of the bacterial pathogens, with mean log concentrations being at least ten-fold higher in most cases. Rotavirus G12 showed no statistically significant differences between the months sampled and was not predicted by the presence of culturable E. coli, total coliform, or molecular E. coli. Rotavirus concentration in groundwater was also not correlated to temperature, dissolved oxygen (DO), or oxidation reduction potential (ORP), which were the only other environmental parameters found to have significant differences between the months sampled. This study indicates that E. coli, temperature, DO and ORP are not useful indicators of rotavirus presence or concentration in the shallow aquifers of rural Bangladesh