Spatial Variability of Escherichia coli in Rivers of Northern Coastal Ecuador.
Ontology highlight
ABSTRACT:
SUBMITTER: Rao G
PROVIDER: S-EPMC4435963 | biostudies-literature | 2015 Feb
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Microbiological safety of water is commonly measured using indicator organisms, but the spatiotemporal variability of these indicators can make interpretation of data difficult. Here, we systematically explore the variability in Escherichia coil concentrations in surface source and household drinking water in a rural Ecuadorian village over one year. We observed more variability in water quality on an hourly basis (up to 2.4 log difference) than on a daily (2.2 log difference) or weekly basis (up to 1.8 log difference). E. coli counts were higher in the wet season than in the dry season for source (0.42 log difference, p < 0.0001) and household (0.11 log difference, p = 0.077) samples. In the wet season, a 1 cm increase in weekly rainfall was associated with a 3% decrease (p = 0.006) in E. coli counts in source samples and a 6% decrease (p = 0.012) in household samples. Each additional person in the river when source samples were collected was associated with a 4% increase (p = 0.026) in E. coil counts in the wet season. Factors affecting household water quality included rainfall, water source, and covering the container. The variability can be understood as a combination of environmental (e.g., seasonal and soil processes) and other drivers (e.g., human river use, water practices, and sanitation), each working at different time scales.
| S-EPMC3419269 | biostudies-literature
Project description:Dengue virus (DENV) reemerged in the Americas in the 1980s and 1990s, whereas chikungunya virus (CHIKV) emerged in 2014. Although CHIKV produced large epidemics from 2014 to 2017, dengue fever has been the prominent arboviral disease identified through passive surveillance, bringing to question the degree to which cases are misdiagnosed. To address this concern, we conducted an active household-based surveillance of arboviral-like illnesses in six rural and remote communities in northern coastal Ecuador from May 2019 to February 2020. Although passive surveillance conducted by the Ecuadorian Ministry of Health reported only DENV cases in the region, more than 70% of the arbovirus-like illnesses detected by active surveillance in our study were positive for CHIKV. These findings underline the need for active surveillance of arboviral infections with laboratory confirmation, especially in rural communities where arboviral illnesses are more likely to be underreported.
| S-EPMC9768284 | biostudies-literature
Project description:BackgroundUnderstanding local anopheline vector species and their bionomic traits, as well as related human factors, can help combat gaps in protection.MethodsIn San José de Chamanga, Esmeraldas, at the Ecuadorian Pacific coast, anopheline mosquitoes were sampled by both human landing collections (HLCs) and indoor-resting aspirations (IAs) and identified using both morphological and molecular methods. Human behaviour observations (HBOs) (including temporal location and bed net use) were documented during HLCs as well as through community surveys to determine exposure to mosquito bites. A cross-sectional evaluation of Plasmodium falciparum and Plasmodium vivax infections was conducted alongside a malaria questionnaire.ResultsAmong 222 anopheline specimens captured, based on molecular analysis, 218 were Nyssorhynchus albimanus, 3 Anopheles calderoni (n = 3), and one remains unidentified. Anopheline mean human-biting rate (HBR) outdoors was (13.69), and indoors (3.38) (p = 0.006). No anophelines were documented resting on walls during IAs. HBO-adjusted human landing rates suggested that the highest risk of being bitten was outdoors between 18.00 and 20.00 h. Human behaviour-adjusted biting rates suggest that overall, long-lasting insecticidal bed nets (LLINs) only protected against 13.2% of exposure to bites, with 86.8% of exposure during the night spent outside of bed net protection. The malaria survey found 2/398 individuals positive for asymptomatic P. falciparum infections. The questionnaire reported high (73.4%) bed net use, with low knowledge of malaria.ConclusionThe exophagic feeding of anopheline vectors in San Jose de Chamanga, when analysed in conjunction with human behaviour, indicates a clear gap in protection even with high LLIN coverage. The lack of indoor-resting anophelines suggests that indoor residual spraying (IRS) may have limited effect. The presence of asymptomatic infections implies the presence of a human reservoir that may maintain transmission.
| S-EPMC7532652 | biostudies-literature
Project description:We investigated the seasonal and annual variability of surface sulphur plumes in the northern Benguela upwelling system off Namibia because of their significant impacts on the marine ecosystem, fishing industry, aquaculture farming and tourism due to their toxic properties. We identified the sulphur plumes in ocean colour satellite data of the medium resolution imaging spectrometer (MERIS) for the 2002-2012 time period using the differences in the spectral properties of Namibian Benguela optical water types. The sulphur events have a strong seasonal cycle with pronounced main and off-seasons forced by local and remote-driven processes. The main peak season is in late austral summer and early austral autumn at the beginning of the annual upwelling cycle caused by increasing equatorwards alongshore winds. The sulphur plume activity is high between February and April during the seasonal oxygen minimum associated with the seasonal reduction of cross-shore ventilation of the bottom waters, the seasonal southernmost position of the Angola Benguela Frontal Zone, the seasonal maximum of water mass fractions of South Atlantic and Angola Gyre Central Waters as well as the seasonal arrival of the downwelling coastal trapped waves. The off-season is in austral spring and early austral summer during increased upwelling intensity and enhanced oxygen supply. The annual variability of sulphur events is characterized by very high activities in years 2004, 2005 and 2010 interrupted by periods of lower activity in years 2002 to 2003, 2006 to 2009 and 2011 to 2012. This result can be explained by the relative contributions or adding effects of local and remote-driven forces (from the equatorial area). The probability for the occurrence of sulphur plumes is enhanced in years with a lower annual mean of upwelling intensity, decreased oxygen supply associated with decreased lateral ventilation of bottom waters, more southern position of the Angola Benguela Frontal Zone, increased mass fraction of South Atlantic Central Water and stronger downwelling coastal trapped waves. Understanding of the variability and forcing processes of the toxic sulphur events will help in the future to monitor and forecast them as well as to manage their social and economic consequences in the northern Benguela upwelling system off Namibia.
| S-EPMC5805238 | biostudies-other
Project description:Antimicrobial resistance (AR) is a worldwide concern. Up to a 160% increase in antibiotic usage in food animals is expected in Latin American countries. The poultry industry is an increasingly important segment of food production and contributor to AR. The objective of this study was to evaluate the prevalence, AR patterns and the characterization of relevant resistance genes in Extended Spectrum ?-lactamases (ESBL) and AmpC-producing E. coli from large poultry farms in Ecuador. Sampling was performed from June 2013 to July 2014 in 6 slaughterhouses that slaughter broilers from 115 farms totaling 384 flocks. Each sample of collected caeca was streaked onto TBX agar supplemented with cefotaxime (3 mg/l). In total, 176 isolates were analyzed for AR patterns by the disk diffusion method and for blaCTX-M, blaTEM, blaCMY, blaSHV, blaKPC, and mcr-1 by PCR and sequencing. ESBL and AmpC E. coli were found in 362 flocks (94.3%) from 112 farms (97.4%). We found that 98.3% of the cefotaxime-resistant isolates were multi-resistant to antibiotics. Low resistance was observed for ertapenem and nitrofurantoin. The most prevalent ESBL genes were the ones belonging to the blaCTX-M group (90.9%), specifically the blaCTX-M-65, blaCTX-M-55 and blaCTX-M-3 alleles. Most of the AmpC strains presented the blaCMY-2 gene. Three isolates showed the mcr-1 gene. Poultry production systems represent a hotspot for AR in Ecuador, possibly mediated by the extensive use of antibiotics. Monitoring this sector in national and regional plans of AR surveillance should therefore be considered.
| S-EPMC6450624 | biostudies-literature
Project description:Diarrheal diseases are a leading cause of mortality and morbidity in low- and middle-income countries. Diarrhea is associated with a wide array of etiological agents including bacterial, viral, and parasitic enteropathogens. Previous studies have captured between- but not within-country heterogeneities in enteropathogen prevalence and severity. We conducted a case-control study of diarrhea to understand how rates and outcomes of infection with diarrheagenic pathotypes of Escherichia coli vary across an urban-rural gradient in four sites in Ecuador. We found variability by site in enteropathogen prevalence and infection outcomes. Any pathogenic E. coli infection, coinfections, diffuse adherent E. coli (DAEC), enteroinvasive E. coli (EIEC), and rotavirus were significantly associated with acute diarrhea. DAEC was the most common pathotype overall and was more frequently associated with disease in urban areas. Enteropathogenic E. coli (EPEC) and enterotoxigenic E. coli (ETEC) were more common in rural areas. ETEC was only associated with diarrhea in one site. Phylogenetic analysis revealed that associations with disease were not driven by any single clonal complex. Higher levels of antibiotic resistance were detected in rural areas. Enteropathogen prevalence, virulence, and antibiotic resistance patterns vary substantially by site within Ecuador. The variations in E. coli pathotype prevalence and virulence in this study have important implications for control strategies by context and demonstrate the importance of capturing within-country differences in enteropathogen disease dynamics.
| S-EPMC10484266 | biostudies-literature
Project description:Dengue is recognized as a major health issue in large urban tropical cities but is also observed in rural areas. In these environments, physical characteristics of the landscape and sociodemographic factors may influence vector populations at small geographic scales, while prior immunity to the four dengue virus serotypes affects incidence. In 2019, a rural northwestern Ecuadorian community, only accessible by river, experienced a dengue outbreak. The village is 2-3 hours by boat away from the nearest population center and comprises both Afro-Ecuadorian and Indigenous Chachi households. We used multiple data streams to examine spatial risk factors associated with this outbreak, combining maps collected with an unmanned aerial vehicle (UAV), an entomological survey, a community census, and active surveillance of febrile cases. We mapped visible water containers seen in UAV images and calculated both the green-red vegetation index (GRVI) and household proximity to public spaces like schools and meeting areas. To identify risk factors for symptomatic dengue infection, we used mixed-effect logistic regression models to account for the clustering of symptomatic cases within households. We identified 55 dengue cases (9.5% of the population) from 37 households. Cases peaked in June and continued through October. Rural spatial organization helped to explain disease risk. Afro-Ecuadorian (versus Indigenous) households experience more symptomatic dengue (OR = 3.0, 95%CI: 1.3, 6.9). This association was explained by differences in vegetation (measured by GRVI) near the household (OR: 11.3 95% 0.38, 38.0) and proximity to the football field (OR: 13.9, 95% 4.0, 48.4). The integration of UAV mapping with other data streams adds to our understanding of these dynamics.
| S-EPMC8475985 | biostudies-literature
Project description:Despite the recognized potential of long-term survival or even growth of fecal indicators bacteria (FIB) in marine sediments, this compartment is largely ignored by health protection authorities. We conducted a large-scale study over approximately 50 km of the Marche coasts (Adriatic Sea) at depths ranging from 2 to 5 m. Total and fecal coliforms (FC) were counted by culture-based methods. Escherichia coli was also quantified using fluorescence in situ hybridization targeting specific 16S rRNA sequences, which yielded significantly higher abundances than culture-based methods, suggesting the potential importance of viable but nonculturable E. coli cells. Fecal coliforms displayed high abundances at most sites and showed a prevalence of E. coli. FC isolates (n = 113) were identified by API 20E, additional biochemical tests, and internal transcribed spacer-PCR. E. coli strains, representing 96% of isolates, were then characterized for genomic relatedness and phylogenetic group (A, B1, B2, and D) of origin by randomly amplified polymorphic DNA and multiplex-PCR. The results indicated that E. coli displayed a wide genotypic diversity, also among isolates from the same station, and that 44 of the 109 E. coli isolates belonged to groups B2 and D. Further characterization of B2 and D isolates for the presence of 11 virulence factor genes (pap, sfa/foc, afa, eaeA, ibeA, traT, hlyA, stx(1), stx(2), aer, and fyuA) showed that 90% of B2 and 65% of D isolates were positive for at least one of these. Most of the variance of both E. coli abundance and assemblage composition (>62%) was explained by a combination of physical-chemical and trophic variables. These findings indicate that coastal sediments could represent a potential reservoir for commensal and pathogenic E. coli and that E. coli distribution in marine coastal sediments largely depends upon the physical and trophic status of the sediment. We conclude that future sampling designs aimed at monitoring the microbiological quality of marine coastal areas should not further neglect the analysis of the sediment and that monitoring of these environments can be improved by including molecular methods as a complement of culture-based techniques.
| S-EPMC2935034 | biostudies-literature
Project description:BackgroundIn bacterial genomes, the compactly encoded genes and operons are well organized, with genes in the same biological pathway or operons in the same regulon close to each other on the genome sequence. In addition, the linearly close genes have a higher probability of co-expression and their protein products tend to form protein-protein interactions. However, the organization features of bacterial genomes in a three-dimensional space remain elusive. The DNA interaction data of Escherichia coli, measured by the genome conformation capture (GCC) technique, have recently become available, which allowed us to investigate the spatial features of bacterial genome organization.ResultsBy renormalizing the GCC data, we compared the interaction frequency of operon pairs in the same regulon with that of random operon pairs. The results showed that arrangements of operons in the E. coli genome tend to minimize the spatial distance between operons in the same regulon. A similar global organization feature exists for genes in biological pathways of E. coli. In addition, the genes close to each other spatially (even if they are far from each other on the genome sequence) tend to be co-expressed and form protein-protein interactions. These results provided new insights into the organization principles of bacterial genomes and support the notion of transcription factory.ConclusionsThis study revealed the organization features of Escherichia coli genomic functional units in the 3D space and furthered our understanding of the link between the three-dimensional structure of chromosomes and biological function.
| S-EPMC4326437 | biostudies-literature
Project description:Microzooplankton are considered the primary consumers of phytoplankton in marine environments. Microzooplankton grazing rates on phytoplankton have been studied across the globe, but there are still large regions of the ocean that are understudied, such as sub-tropical coastal oceans. One of these regions is the coastal area around south Florida, USA. We measured microzooplankton grazing rates in two distinct environments around south Florida; the oligotrophic Florida Keys and the mesotrophic outflow from the Everglades. For 2-years from January 2018 to January 2020, we set up 55 dilution and light-dark bottle experiments at five stations to estimate the microzooplankton community grazing rate, instantaneous phytoplankton growth rate, and primary production. Our results suggest that microzooplankton are consuming a higher proportion of the primary production near the Everglades outflow compared to the Florida Keys. We also found that changes in phytoplankton growth rates are disconnected from changes in the microzooplankton grazing rates in the Florida Keys. Overall, the data from the Everglades outflow is what would be expected based on global patterns, but factors other than microzooplankton grazing are more important in controlling phytoplankton biomass in the Florida Keys.
| S-EPMC9048640 | biostudies-literature