Bacterial Community Profiling of Tropical Freshwaters in Bangladesh.
ABSTRACT: Seasonal and spatial variations in the bacterial communities of two tropical freshwater sources in Bangladesh, Lake Dhanmondi in central Dhaka, and a pond in the outskirts of Dhaka, were assessed and compared using PCR-DGGE and deep sequencing of 16S rRNA genes, as well as heterotrophic enrichments using water samples collected at nine different time points during 1 year. Temporal and spatial variations of common aquatic bacterial genera were observed, but no clear seasonal variations could be depicted. The major bacterial genera identified from these two sites were members of the Proteobacteria, Cyanobacteria, Actinobacteria, Bacteroidetes, Chlorobi, Chloroflexi, Verrucomicrobia, and Firmicutes. Among the proteobacterial groups, members of the ? -, ? -, and ? - Proteobacteria predominated. ? - Proteobacteria belonging to the Escherichia coli/Shigella group even the diarrheagenic pathotypes of E. coli e.g., EPEC and ETEC were detected in most samples throughout the year, with no apparent correlations with other microbial groups. The other pathotypes, EHEC, EAEC, and EIEC/Shigella spp. were also detected occasionally. This study represents the first thorough analysis of the microbial diversity of tropical freshwater systems in Bangladesh.
Project description:Vibrio cholerae is an estuarine bacterium associated with a single peak of cholera (March-May) in coastal villages of Bangladesh. For an unknown reason, however, cholera occurs in a unique dual peak (March-May and September-November) pattern in the city of Dhaka that is bordered by a heavily polluted freshwater river system and flood embankment. In August 2007, extreme flooding was accompanied by an unusually severe diarrhea outbreak in Dhaka that resulted in a record high illness. This study was aimed to understand the unusual outbreak and if it was related to the circulation of a new V. cholerae clone. Nineteen V. cholerae isolated during the peak of the 2007 outbreak were subjected to extensive phenotypic and molecular analyses, including multi-locus genetic screening by polymerase chain reaction (PCR), sequence-typing of the ctxB gene, and pulsed-field gel electrophoresis (PFGE). Factors associated with the unusual incidence of cholera were determined and analysis of the disease severity was done. Overall, microbiological and molecular data confirmed that the hypervirulent V. cholerae was O1 biotype El Tor (ET) that possessed cholera toxin (CT) of the classical biotype. The PFGE (NotI) and dendrogram clustering confirmed that the strains were clonal and related to the pre-2007 variant ET from Dhaka and Matlab and resembled one of two distinct clones of the variant ET confirmed to be present in the estuarine ecosystem of Bangladesh. Results of the analyses of both diarrheal case data for three consecutive years (2006-2008) and regional hydroclimatology over three decades (1980-2009) clearly indicate that the pattern of cholera occurring in Dhaka, and not seen at other endemic sites, was associated with flood waters transmitting the infectious clone circulating via the fecal-oral route during and between the dual seasonal cholera peaks in Dhaka. Circular river systems and flood embankment likely facilitate transmission of infectious V. cholerae throughout the year that leads to both sudden and off-season outbreaks in the densely populated urban ecosystem of Dhaka. Clonal recycling of hybrid El Tor with increasing virulence in a changing climate and in a region with a growing urban population represents a serious public health concern for Bangladesh.
Project description:Aquatic microbial diversity, composition, and dynamics play vital roles in sustaining water ecosystem functionality. Yet, there is still limited knowledge on bacterial seasonal dynamics in lotic environments. This study explores a temporal pattern of bacterial community structures in lotic freshwater over a 2-year period. The aquatic bacterial communities were assessed using Illumina MiSeq sequencing of 16S rRNA genes. Overall, the communities were dominated by ?-, ?-, and ?-Proteobacteria, Bacteroidetes, Flavobacteriia, and Sphingobacteriia. The bacterial compositions varied substantially in response to seasonal changes (cold vs. warm), but they were rather stable within the same season. Furthermore, higher diversity was observed in cold seasons compared to warm periods. The combined seasonal-environmental impact of different physico-chemical parameters was assessed statistically, and temperature, suspended solids, and nitrogen were determined to be the primary abiotic factors shaping the temporal bacterial assemblages. This study enriches particular knowledge on the seasonal succession of the lotic freshwater bacteria.
Project description:<i>Shigella</i> is a leading cause of moderate-to-severe diarrhea globally and the causative agent of shigellosis and bacillary dysentery. Associated with 80 to 165 million cases of diarrhea and >13% of diarrheal deaths, in many regions, <i>Shigella</i> exposure is ubiquitous while infection is heterogenous. To characterize host-genetic susceptibility to <i>Shigella</i>-associated diarrhea, we performed two independent genome-wide association studies (GWAS) including Bangladeshi infants from the PROVIDE and CBC birth cohorts in Dhaka, Bangladesh. Cases were infants with <i>Shigella</i>-associated diarrhea (<i>n</i> = 143) and controls were infants with no <i>Shigella</i>-associated diarrhea in the first 13 months of life (<i>n</i> = 446). <i>Shigella</i>-associated diarrhea was identified via quantitative PCR (qPCR) threshold cycle (<i>C<sub>T</sub></i> ) distributions for the <i>ipaH</i> gene, carried by all four <i>Shigella</i> species and enteroinvasive <i>Escherichia coli</i> Host GWAS were performed under an additive genetic model. A joint analysis identified protective loci on chromosomes 11 (rs582240, within the <i>KRT18P59</i> pseudogene; <i>P</i> = 6.40 × 10<sup>-8</sup>; odds ratio [OR], 0.43) and 8 (rs12550437, within the lincRNA <i>RP11-115J16.1</i>; <i>P</i> = 1.49 × 10<sup>-7</sup>; OR, 0.48). Conditional analyses identified two previously suggestive loci, a protective locus on chromosome 7 (rs10266841, within the 3' untranslated region [UTR] of <i>CYTH3</i>; <i>P</i> <sub>conditional</sub> = 1.48 × 10<sup>-7</sup>; OR, 0.44) and a risk-associated locus on chromosome 10 (rs2801847, an intronic variant within <i>MPP7</i>; <i>P</i> <sub>conditional</sub> = 8.37 × 10<sup>-8</sup>; OR, 5.51). These loci have all been indirectly linked to bacterial type 3 secretion system (T3SS) activity, its components, and bacterial effectors delivered into host cells. Host genetic factors that may affect bacterial T3SS activity and are associated with the host response to <i>Shigella</i>-associated diarrhea may provide insight into vaccine and drug development efforts for <i>Shigella</i>-associated diarrheal disease.
Project description:BACKGROUND:Undernutrition, an important indicator for monitoring progress of development goals, is a matter of concern in many developing countries, including Bangladesh. Despite regional differences in chronic undernutrition in Bangladesh, regional determinants among children under the age of five were not extensively explored. DATA AND METHODS:Using combined repeated cross-sectional nationwide Bangladesh Demographic and Health Surveys (BDHS 2011 and 2014) and employing bivariate and logistic regression analyses, we estimated prevalence, changes and variations in regional determinants of stunting among children aged 6-59 months over two time periods 2011 and 2014. RESULTS:Our benchmark results suggested that the children from Rajshahi, Khulna, Rangpur, Chittagong and Dhaka tend to be significantly less stunted by 51% (p = 0.000; CI = [0.38, 0.63]), 44% (p = 0.000; CI = [0.44, 0.71]), 26% (p = 0.012; CI = [0.58, 0.93]), 23% (p = 0.012; CI = [0.62, 0.95]) and 22% (p = 0.033; [0.63, 0.97]) respectively, against Sylhet in 2011. With the exception of Dhaka, no region showed significant differences in the odds of stunting over two time periods 2011 and 2014, i.e. only Dhaka revealed significant difference by 30% reductions in the odds of stunting in 2014. Also, rural children were less likely to be stunted (by 19%) of the urban counterparts. Regional covariates of stunting differ. However, children's age, household wealth, mother's height, and parental education were important determinants of stunting in Bangladesh. CONCLUSION:Dhaka made an impressive improvement in child nutrition, thus contributed largely to the reduction of stunting levels in Bangladesh for 2014 over 2011. Sylhet and Barisal require strong push to improve nutritional status of children. Further decline is possible through region-specific multipronged interventions that can address area-specific covariates to break the cycle of undernutrition like strengthening economic and educational status, emphasizing the role of father to augment their knowledge in varying aspects like family planning, reduction of fertility and by improving mother's health.
Project description:Virioplankton are an important and abundant biological component of marine and freshwater ecosystems. Often overlooked, aquatic viruses play an important role in biogeochemical cycles on a global scale, infecting both autotrophic and heterotrophic microbes. Viral diversity, abundance, and viral interactions at different trophic levels in aqueous environments are not well understood. Tropical ecosystems are less frequently studied than temperate ecosystems, but could provide new insights into how physical and chemical variability can shape or force microbial community changes. In this study, we found high viral abundance values in Guanabara Bay relative to other estuaries around the world. Viral abundance was positively correlated with bacterioplankton abundance and chlorophyll a concentrations. Moreover, prokaryotic and viral abundance were positively correlated with eutrophication, especially in surface waters. These results provide novel baseline data on the quantitative distribution of aquatic viruses in tropical estuaries. They also provide new information on a complex and dynamic relationship in which environmental factors influence the abundance of bacterial hosts and consequently their viruses. Guanabara Bay is characterized by spatial and seasonal variations, and the eutrophication process is the most important factor explaining the structuring of virioplankton abundance and distribution in this tropical urbanized bay.
Project description:The Yellow Sea features unique characteristics due to strong tides and nutrient-enriched freshwater outflows from China and Korea. The coupling of archaeal and bacterial assemblages associated with environmental factors at two bay areas in the Yellow Sea was investigated. Temporal variations of the archaeal and bacterial assemblages were shown to be greater than the spatial variations based on an analysis of the 16S rRNA gene sequences. Distinct temporal dynamics of both planktonic archaeal and bacterial assemblages was associated with temperature, NO2-, and chlorophyll a ([chl-a]) concentrations in the bays of the Yellow Sea. The [chl-a] was the prime predictor of bacterial abundance, and some taxa were clearly correlated with [chl-a]. Bacteroidetes and Alpha-proteobacteria dominated at high [chl-a] stations while Gamma-proteobacteria (esp. SAR86 clade) and Actinobacteria (Candidatus Actinomarina clade) were abundant at low [chl-a] stations. The archaeal abundance was comparable with the bacterial abundance in most of the October samples. Co-dominance of Marine Group II (MGII) and Candidatus Nitrosopumilus suggests that the assimilation of organic nitrogen by MGII could be coupled with nitrification by ammonia-oxidizing archaea. The distinct temporal dynamics of the archaeal and bacterial assemblages might be attributable to the strong tides and the inflow of nutrient-rich freshwater.
Project description:Although much focus is placed on cholera epidemics, the greatest burden occurs in settings in which cholera is endemic, including areas of South Asia, Africa and now Haiti1,2. Dhaka, Bangladesh is a megacity that is hyper-endemic for cholera, and experiences two regular seasonal outbreaks of cholera each year3. Despite this, a detailed understanding of the diversity of Vibrio cholerae strains circulating in this setting, and their relationships to annual outbreaks, has not yet been obtained. Here we performed whole-genome sequencing of V. cholerae across several levels of focus and scale, at the maximum possible resolution. We analyzed bacterial isolates to define cholera dynamics at multiple levels, ranging from infection within individuals, to disease dynamics at the household level, to regional and intercontinental cholera transmission. Our analyses provide a genomic framework for understanding cholera diversity and transmission in an endemic setting.
Project description:Dengue has been regularly reported in Dhaka, Bangladesh, since a large outbreak in 2000. However, to date, we have limited information on the seasonal distribution of dengue disease and how case distribution correlates with climate. Here, we analyzed dengue cases detected at a private diagnostic facility in Dhaka during 2010-2014. We calculated Pearson cross-correlation coefficients to examine the relationship between the timing of cases and both rainfall and temperature. There were 2,334 cases diagnosed during the study period with 76% over the age of 15 years. Cases were reported in every month of the study; however, 90% of cases occurred between June and November. Increases in rainfall were correlated with increases in cases 2 months later (correlation of 0.7). The large proportion of adult cases is consistent with substantial population susceptibility and suggests Dhaka remains at risk for outbreaks. Although cases occurred year-round, public health preparedness should be focused during peak months.
Project description:<h4>Background</h4>Mortality exhibits seasonal variations, which to a certain extent can be considered as mid-to long-term influences of meteorological conditions. In addition to atmospheric effects, the seasonal pattern of mortality is shaped by non-atmospheric determinants such as environmental conditions or socioeconomic status. Understanding the influence of season and other factors is essential when seeking to implement effective public health measures. The pressures of climate change make an understanding of the interdependencies between season, climate and health especially important.<h4>Methods</h4>This study investigated daily death counts collected within the Sample Vital Registration System (VSRS) established by the Bangladesh Bureau of Statistics (BBS). The sample was stratified by location (urban vs. rural), gender and socioeconomic status. Furthermore, seasonality was analyzed for all-cause mortality, and several cause-specific mortalities. Daily deviation from average mortality was calculated and seasonal fluctuations were elaborated using non parametric spline smoothing. A seasonality index for each year of life was calculated in order to assess the age-dependency of seasonal effects.<h4>Results</h4>We found distinctive seasonal variations of mortality with generally higher levels during the cold season. To some extent, a rudimentary secondary summer maximum could be observed. The degree and shape of seasonality changed with the cause of death as well as with location, gender, and SES and was strongly age-dependent. Urban areas were seen to be facing an increased summer mortality peak, particularly in terms of cardiovascular mortality. Generally, children and the elderly faced stronger seasonal effects than youths and young adults.<h4>Conclusion</h4>This study clearly demonstrated the complex and dynamic nature of seasonal impacts on mortality. The modifying effect of spatial and population characteristics were highlighted. While tropical regions have been, and still are, associated with a marked excess of mortality in summer, only a weakly pronounced secondary summer peak could be observed for Bangladesh, possibly due to the reduced incidence of diarrhoea-related fatalities. These findings suggest that Bangladesh is undergoing an epidemiological transition from summer to winter excess mortality, as a consequence of changes in socioeconomic conditions and health care provision.
Project description:While the effect of weather and seasons on physical activity (PA) is well documented for leisure-time physical activities in western countries, scant information is available for developing countries where lifestyle PA is the major source of energy expenditure (EE). In Bangladesh, the traditional calendar divides the year to six seasons that last two months each: summer, rainy, autumn, late autumn, winter, and spring. We developed the Past Year Physical Activity Questionnaire to record culturally relevant physical activities and to help assess the seasonal variation in total and domain-specific PA in Bangladesh. We have applied this tool to 162 men and women aged 18-60 years residing in Dhaka city and in the northern rural district of Thakurgaon. Repeated measures analysis of variance (RMANOVA) was used to test for evidence of variation in PA between place and seasons. The age- and gender-adjusted model revealed significantly lower levels of EE in urban residents compared to rural residents across all seasons and domains. We also found evidence of seasonal variations in moderate-to-vigorous physical activity (MVPA) MET-min/weekamong rural participants only; for total PA (ranging from 3192 in autumn to 4124 in winter; <i>p</i> = 0.0001) and for two domains: the occupation domain (ranging from 935 in autumn to 1645 in winter; <i>p</i> = 0.0001) and the leisure time domain(ranging from 229 in late autumn to 272 in rainy season; <i>p</i> = 0.005). Seasonality in gardening was also noted (ranging from 2.46 in late autumn to 29.28 in rainy season; <i>p</i> = 0.0001). There were no seasonal differences of total and domain-specific MVPA in urban except household-related PA. Among rural participants, PA was higher in the summer, rainy, and winter seasons and lower in autumn and late autumn. The most common leisure-time physical activities were walking, bicycling, and swimming with higher participation in the rural area. Leisure-time physical activity needs to be promoted to urban residents all year long but more focused on autumn, late autumn, and spring in rural areas.