Genome Sequencing of an Escherichia coli Sequence Type 617 Strain Isolated from Beach Ghost Shrimp (Callichirus major) from a Heavily Polluted Ecosystem Reveals a Wider Resistome against Heavy Metals and Antibiotics.
Ontology highlight
ABSTRACT:
SUBMITTER: Monte DF
PROVIDER: S-EPMC6346163 | biostudies-literature | 2019 Jan
REPOSITORIES: biostudies-literature
Publications
Genome Sequencing of an Escherichia coli Sequence Type 617 Strain Isolated from Beach Ghost Shrimp (Callichirus major) from a Heavily Polluted Ecosystem Reveals a Wider Resistome against Heavy Metals and Antibiotics.
Monte Daniel F DF Sellera Fábio P FP Fernandes Miriam R MR Moura Quézia Q Landgraf Mariza M Lincopan Nilton N
Microbiology resource announcements 20190117 3
Here, we present the draft genome sequence of a multidrug-resistant (MDR) Escherichia coli strain belonging to sequence type 617 (ST617), isolated from beach ghost shrimp from polluted coastal waters in Brazil. These data provide valuable information for comparative genomic analysis, related to the dissemination of MDR E. coli in marine ecosystems. ...[more]
Similar Datasets
Project description:River ecosystems are among the most affected habitats globally by human activities, such as the release of chemical pollutants. However, it remains largely unknown how and to what extent many communities such as zooplankton are affected by these environmental stressors in river ecosystems. Here, we aim to determine major factors responsible for shaping community structure of zooplankton in heavily polluted river ecosystems. Specially, we use rotifers in the Haihe River Basin (HRB) in North China as a case study to test the hypothesis that species sorting (i.e. species are "filtered" by environmental factors and occur at environmental suitable sites) plays a key role in determining community structure at the basin level. Based on an analysis of 94 sites across the plain region of HRB, we found evidence that both local and regional factors could affect rotifer community structure. Interestingly, further analyses indicated that local factors played a more important role in determining community structure. Thus, our results support the species sorting hypothesis in highly polluted rivers, suggesting that local environmental constraints, such as environmental pollution caused by human activities, can be stronger than dispersal limitation caused by regional factors to shape local community structure of zooplankton at the basin level.
| S-EPMC4766567 | biostudies-literature
Project description:The antibiotic and heavy metal resistome of a chronically polluted soil (3S) obtained from an automobile workshop in Ilorin, Kwara State, Nigeria was deciphered via functional annotation of putative ORFs (open reading frames). Functional annotation of antibiotic and heavy metal resistance genes in 3S metagenome was conducted using the Comprehensive Antibiotic Resistance Database (CARD), Antibiotic Resistance Gene-annotation (ARG-ANNOT) and Antibacterial Biocide and Metal Resistance Gene Database (BacMet). Annotation revealed detection of resistance genes for 15 antibiotic classes with the preponderance of beta lactamases, mobilized colistin resistance determinant (mcr), glycopepetide and tetracycline resistance genes, the OqxBgb and OqxA RND-type multidrug efflux pumps, among others. The dominance of resistance genes for antibiotics effective against members of the Enterobacteriaceae indicate possible contamination with faecal materials. Annotation of heavy metal resistance genes revealed diverse resistance genes responsible for the uptake, transport, detoxification, efflux and regulation of copper, zinc, cadmium, nickel, chromium, cobalt, mercury, arsenic, iron, molybdenum and several others. Majority of the antibiotic and heavy metal resistance genes detected in this study are borne on mobile genetic elements, which facilitate their spread and dissemination in the polluted soil. The presence of the heavy metal resistance genes is strongly believed to play a major role in the proliferation of antibiotic resistance genes. This study has established that soil is a huge repertoire of antibiotic and heavy metal resistome and due to the intricate link between human, animals and the soil environment, it may be a major contributor to the proliferation of multidrug-resistant clinical pathogens.
| S-EPMC7205953 | biostudies-literature
Project description:BackgroundAlthough ambient fine particulate matter (PM(2.5); particulate matter ? 2.5 µm in aerodynamic diameter) has been linked to adverse human health effects, the chemical constituents that cause harm are unknown. To our knowledge, the health effects of PM(2.5) constituents have not been reported for a developing country.ObjectivesWe examined the short-term association between PM(2.5) constituents and daily mortality in Xi'an, a heavily polluted Chinese city.MethodsWe obtained daily mortality data and daily concentrations of PM(2.5), organic carbon (OC), elemental carbon (EC), and 10 water-soluble ions for 1 January 2004 through 31 December 2008. We also measured concentrations of fifteen elements 1 January 2006 through 31 December 2008. We analyzed the data using overdispersed generalized linear Poisson models.ResultsDuring the study period, the mean daily average concentration of PM(2.5) in Xi'an was 182.2 µg/m³. Major contributors to PM(2.5) mass included OC, EC, sulfate, nitrate, and ammonium. After adjustment for PM(2.5) mass, we found significant positive associations of total, cardiovascular, or respiratory mortality with OC, EC, ammonium, nitrate, chlorine ion, chlorine, and nickel for at least one lag period. Nitrate demonstrated stronger associations with total and cardiovascular mortality than PM(2.5) mass. For a 1-day lag, interquartile range increases in PM(2.5) mass and nitrate (114.9 and 15.4 µg/m³, respectively) were associated with 1.8% [95% confidence interval (CI): 0.8%, 2.8%] and 3.8% (95% CI: 1.7%, 5.9%) increases in total mortality.ConclusionsOur findings suggest that PM(2.5) constituents from the combustion of fossil fuel may have an appreciable influence on the health effects attributable to PM(2.5) in Xi'an.
| S-EPMC3295342 | biostudies-literature
Project description:Urban rivers represent a unique ecosystem in which pollution occurs regularly, altering the biogeochemical characteristics of waterbodies and sediments. However, little is presently known about the spatiotemporal patterns of planktonic and sediment bacterial community diversities and compositions in urban rivers. Herein, Illumina MiSeq high-throughput sequencing was performed to reveal the spatiotemporal dynamics of bacterial populations in Liangtan River, a heavily polluted urban river in Chongqing City (China). The results showed the richness and diversity of sediment bacteria were significantly higher than those of planktonic bacteria, whereas a strong overlap (46.7%) in OTUs was identified between water and sediment samples. Bacterial community composition remarkably differed in waters and sediments. Planktonic bacterial communities were dominated by Proteobacteria, Bacteroidetes, Cyanobacteria and Actinobacteria, while sediment bacterial communities mainly included Proteobacteria, Actinobacteria, Chloroflexi and Bacteroidetes. Additionally, several taxonomic groups of potential bacterial pathogens showed an increasing trend in water and sediment samples from residential and industrial areas (RI). Variation partition analysis (VPA) indicated that temperature and nutrient were identified as the main drivers determining the planktonic and sediment bacterial assemblages. These results highlight that bacterial communities in the polluted urban river exhibit spatiotemporal variation due to the combined influence of environmental factors associated with sewage discharge and hydropower dams.
| S-EPMC7912603 | biostudies-literature
Project description:Fire is a key driver in savannah systems and widely used as a land management tool. Intensifying human land uses are leading to rapid changes in the fire regimes, with consequences for ecosystem functioning and composition. We undertake a novel analysis describing spatial patterns in the fire regime of the Serengeti-Mara ecosystem, document multidecadal temporal changes and investigate the factors underlying these patterns. We used MODIS active fire and burned area products from 2001 to 2014 to identify individual fires; summarizing four characteristics for each detected fire: size, ignition date, time since last fire and radiative power. Using satellite imagery, we estimated the rate of change in the density of livestock bomas as a proxy for livestock density. We used these metrics to model drivers of variation in the four fire characteristics, as well as total number of fires and total area burned. Fires in the Serengeti-Mara show high spatial variability-with number of fires and ignition date mirroring mean annual precipitation. The short-term effect of rainfall decreases fire size and intensity but cumulative rainfall over several years leads to increased standing grass biomass and fuel loads, and, therefore, in larger and hotter fires. Our study reveals dramatic changes over time, with a reduction in total number of fires and total area burned, to the point where some areas now experience virtually no fire. We suggest that increasing livestock numbers are driving this decline, presumably by inhibiting fire spread. These temporal patterns are part of a global decline in total area burned, especially in savannahs, and we caution that ecosystem functioning may have been compromised. Land managers and policy formulators need to factor in rapid fire regime modifications to achieve management objectives and maintain the ecological function of savannah ecosystems.
| S-EPMC6852266 | biostudies-literature
Project description:More than a century of dam construction and water development in the western United States has led to extensive ecological alteration of rivers. Growing interest in improving river function is compelling practitioners to consider ecological restoration when managing dams and water extraction. We developed an Ecological Response Model (ERM) for the Cache la Poudre River, northern Colorado, USA, to illuminate effects of current and possible future water management and climate change. We used empirical data and modeled interactions among multiple ecosystem components to capture system-wide insights not possible with the unintegrated models commonly used in environmental assessments. The ERM results showed additional flow regime modification would further alter the structure and function of Poudre River aquatic and riparian ecosystems due to multiple and interacting stressors. Model predictions illustrated that specific peak flow magnitudes in spring and early summer are critical for substrate mobilization, dynamic channel morphology, and overbank flows, with strong subsequent effects on instream and riparian biota that varied seasonally and spatially, allowing exploration of nuanced management scenarios. Instream biological indicators benefitted from higher and more stable base flows and high peak flows, but stable base flows with low peak flows were only half as effective to increase indicators. Improving base flows while reducing peak flows, as currently proposed for the Cache la Poudre River, would further reduce ecosystem function. Modeling showed that even presently depleted annual flow volumes can achieve substantially different ecological outcomes in designed flow scenarios, while still supporting social demands. Model predictions demonstrated that implementing designed flows in a natural pattern, with attention to base and peak flows, may be needed to preserve or improve ecosystem function of the Poudre River. Improved regulatory policies would include preservation of ecosystem-level, flow-related processes and adaptive management when water development projects are considered.
| S-EPMC9285520 | biostudies-literature
Project description:Anthropogenic disturbances intertwined with climatic changes can have a large impact on the upper trophic levels of marine ecosystems, which may cascade down the food web. So far it has been difficult to demonstrate multi-level trophic cascades in pelagic marine environments. Using field data collected during a 33-year period, we show for the first time a four-level community-wide trophic cascade in the open Baltic Sea. The dramatic reduction of the cod (Gadus morhua) population directly affected its main prey, the zooplanktivorous sprat (Sprattus sprattus), and indirectly the summer biomass of zooplankton and phytoplankton (top-down processes). Bottom-up processes and climate-hydrological forces had a weaker influence on sprat and zooplankton, whereas phytoplankton variation was explained solely by top-down mechanisms. Our results suggest that in order to dampen the occasionally harmful algal blooms of the Baltic, effort should be addressed not only to control anthropogenic nutrient inputs but also to preserve structure and functioning of higher trophic levels.
| S-EPMC2587786 | biostudies-literature
Project description:Soil contamination with heavy metals is a widespread problem, especially prominent on grounds lying in the vicinity of mines, smelters, and other industrial facilities. Many such areas are located in Southern Poland; they are polluted mainly with Pb, Zn, Cd, or Cu, and locally also with Cr. As for now, little is known about most bacterial species thriving in such soils and even less about a core bacterial community--a set of taxa common to polluted soils. Therefore, we wanted to answer the question if such a set could be found in samples differing physicochemically and phytosociologically. To answer the question, we analyzed bacterial communities in three soil samples contaminated with Pb and Zn and two contaminated with Cr and lower levels of Pb and Zn. The communities were assessed with 16S rRNA gene fragments pyrosequencing. It was found that the samples differed significantly and Zn decreased both diversity and species richness at species and family levels, while plant species richness did not correlate with bacterial diversity. In spite of the differences between the samples, they shared many operational taxonomic units (OTUs) and it was possible to delineate the core microbiome of our sample set. The core set of OTUs comprised members of such taxa as Sphingomonas, Candidatus Solibacter, or Flexibacter showing that particular genera might be shared among sites ~40 km distant.
| S-EPMC3962847 | biostudies-literature
Project description:Studies in systematic palaeontology are greatly aided when numerous, well-preserved specimens are available so that quantitative methods can be used to substantiate qualitative observations. This is often not the case for fossil decapod crustaceans due to their relatively low preservation potential. Here, we examined primarily two large collections of the well-preserved ghost shrimp Glypturus from the Holo-Pleistocene of Panama and the late Miocene of Florida. Using descriptive, bivariate, multivariate and geometric morphometric methods, two new species are described based on appendage material: Glypturus panamacanalensis sp. nov. and G. sikesi sp. nov. New characters are identified, and size-related and intraspecific variation are assessed for these taxa and modern G. acanthochirus. Taxonomic placement of single specimens from other localities was confirmed by multivariate methods. Furthermore, Glypturus is revised, especially with regard to Western Atlantic species that inhabited both carbonate and siliciclastic environments. Callianassa anguillensis, C. latidigata, and Neocallichirus? quisquellanus are referred to as Glypturus sp. until more material is available to determine the validity of these species. Diversity within Glypturus may thus be underestimated, thereby also impacting the assessment of phylogenetic relationships. Minor propodi appear under-represented relative to major propodi, suggesting a taphonomic bias. Single specimens of interest include a specimen of G. panamacanalensis sp. nov. exhibiting a peculiar swelling in the fixed finger and another showing damage on the propodal upper margin, suggesting failed predation or antagonistic behaviour. Glypturus is first found in the Oligocene in the Western Atlantic and may have expanded its palaeobiogeographical range since the Miocene. The genus was still present on the Pacific side of the Isthmus of Panama in the Holo-Pleistocene, but is only known from the Western Atlantic today, suggesting a relatively recent extinction on the Pacific side.
| S-EPMC4724948 | biostudies-literature
Project description:ObjectiveInvestigators have extensively explored the short-term safety and efficacy data on 177Lu-PSMA-617 radioligand therapy (RLT) in mCRPC patients. However, scarce literature is reported on the long-term outcome of these patients. The current goal of this study is focused on the long-term outcome of mCRPC patients treated with 177Lu-PSMA-617 RLT.MethodsAmong 135 patients, 121 mCRPC patients fulfilled the eligibility criteria and were included in the final analysis. Patients received a median of 3 cycles of 177Lu-PSMA-617 RLT at 6 to 12-week intervals. Primary endpoint included overall survival (OS) and secondary endpoints involved progression-free survival (PFS), predictive factors of OS and PFS, PSA response rate, molecular response, clinical response, and toxicity assessment.ResultsThe median administered cumulative activity was 20 GBq (3.7-37 GBq). The median follow-up duration was 36 months (6-72 months). The estimated median PFS and OS were 12 months (mo) (95% CI: 10.3-13 mo) and 16 mo (95% CI: 13-17 mo), respectively. Any PSA decline and PSA decline >50% was achieved in 73% and 61% of the patients, respectively. Multivariate analysis revealed only failure to achieve >50% PSA decline as a significant factor associated with a poor PFS. Prognostic factors associated with reduced OS included, failure to experience >50% PSA decline, heavily pre-treated patient cohort who received >2 lines of prior treatment options, and patient sub-group treated with ≥2 lines of chemotherapy. Patients re-treated with additional treatment options after attaining 177Lu-PSMA refractory disease showed a remarkably prolonged OS. A significant clinical benefit was achieved post 177Lu-PSMA-617 RLT. The most common toxicities observed were fatigue (34.7%), followed by nausea (33%), and dry mouth (24.7%).ConclusionThe current study supports the short-term safety and efficacy results of high response rates, prolonged PFS and OS, improved quality of life, and low treatment-related toxicities in patients treated with 177Lu-PSMA-617 radioligand therapy.
| S-EPMC8109776 | biostudies-literature