scholarly journals Heterogeneity of uidA gene in environmental Escherichia coli populations

2005 ◽  
Vol 3 (3) ◽  
pp. 297-304 ◽  
Author(s):  
Clarivel Lasalde ◽  
Roberto Rodriguez ◽  
Gary A. Toranzos ◽  
Henry H. Smith

Previous studies have shown that Escherichia coli can be isolated from non-polluted rivers and from bromeliad axilae in pristine areas of tropical rain forests. Finding E. coli in pristine environments is unusual because this bacterium is thought to only survive in the gut of warm-blooded animals and thus its presence should indicate recent fecal contamination. The aims of this study were 1) to determine if E. coli is part of the native soil microbiota in tropical rain forests and 2) to determine if genetic heterogeneity exists among E. coli populations. High concentrations of total coliforms (104–105 cells per 10 g of soil dry weight) and low concentrations of thermotolerant coliforms (101–102 cells per 10 g dry soil, the majority of these were found to be E. coli) were detected. PCR using uidA-specific primers was done on DNA purified from E. coli isolates and the resulting amplicons analysed by denaturing-gradient gel electrophoresis (DGGE). Out of several hundred isolates, mixtures of nine different amplicons were consistently observed. The different patterns of DGGE observed indicate that the E. coli populations in these pristine soils are genetically heterogeneous. Fecal and environmental E. coli isolates were also analysed by pulsed-field gel electrophoresis (PFGE) which showed high DNA sequence variation among the E. coli isolates. Because of these differences in the genomes, PFGE did not allow grouping of environmental versus human isolates of E. coli when compared side to side. The apparent genetic polymorphisms, as a result of genetic heterogeneity, observed in isolates from the same pristine site indicate that source tracking may be difficult to carry out using E. coli as the target organism.

2007 ◽  
Vol 53 (10) ◽  
pp. 1174-1184 ◽  
Author(s):  
Thomas V. D’Elia ◽  
Chester R. Cooper ◽  
Carl G. Johnston

This research validates a novel approach for source tracking based on denaturing gradient gel electrophoresis (DGGE) analysis of DNA extracted from Escherichia coli isolates. Escherichia coli from different animal sources and from river samples upstream from, at, and downstream of a combined sewer overflow were subjected to DGGE to determine sequence variations within the 16S–23S intergenic spacer region (ISR) of the rrnB ribosomal operon. The ISR was analyzed to determine if E. coli isolates from various animal sources could be differentiated from each other. DNA isolated from the E. coli animal sources was PCR amplified to isolate the rrnB operon. To prevent amplification of all 7 E. coli ribosomal operons by PCR amplification using universal primers, sequence-specific primers were utilized for the rrnB operon. Another primer set was then used to prepare samples of the 16S–23S ISR for DGGE. Comparison of PCR–DGGE results between human and animal sources revealed differences in the distribution and frequency of the DGGE bands produced. Human and Canada Goose isolates had the most unique distribution patterns and the highest percent of unique isolates and were grouped separately from all other animal sources. Method validation suggests that there are enough host specificity and genetic differences for use in the field. Field results at and around a combined sewer overflow indicate that this method can be used for microbial source tracking.


2014 ◽  
Vol 94 (8) ◽  
pp. 1639-1649 ◽  
Author(s):  
Jin-Long Yang ◽  
Xuan Zhou ◽  
Yi-Feng Li ◽  
Xing-Pan Guo ◽  
Xiao Liang ◽  
...  

Surface properties affect the attachment of micro- and macroscopic marine organisms. The current study examined the settlement response of the musselMytilus coruscusplantigrades to natural biofilms formed on surfaces of different wettability. The percentages of plantigrade settlement were not influenced by the biofilms formed on variously wettable surfaces in the short term, but after 10 days, the plantigrade settlement rates decreased on biofilms formed on lower wettability surfaces. In general, lower wettability of the surfaces resulted in the decrease of the dry weight, bacterial and diatom density and the thickness of natural biofilms when compared to high wettability surfaces. In contrast, chlorophyll-aconcentration in biofilms was independent of the initial wettability of the surfaces. Comparative cluster analysis of bacterial denaturing gradient gel electrophoresis patterns revealed that high variability existed between the bacterial community on high wettability surfaces and that on low wettability surfaces. Thus, surface wettability affects the formation of natural biofilms, and this variation in biofilms developed on different wettability surfaces may explain the discrepancy in their corresponding inducing activities onM. coruscusplantigrade settlement. This finding provides new insight into interactions between mussel settlement, biofilm characteristics and surface properties.


2014 ◽  
Vol 12 (4) ◽  
pp. 846-857 ◽  
Author(s):  
M. A. Esseili ◽  
I. I. Kassem ◽  
J. Lis ◽  
V. Sigler

We investigated the effectiveness of Escherichia coli community fingerprinting for identifying fecal pollution sources impacting a recreational beach. E. coli in water collected from the beach, nearby creek and storm sewer outfall were enumerated using membrane filtration, while E. coli communities were characterized following polymerase chain reaction analysis and denaturing gradient gel electrophoresis (DGGE) fingerprinting. Analysis of E. coli densities to determine the contributions of the creek and storm sewer during dry weather was inconclusive. However, DGGE fingerprinting indicated that the creek E. coli communities had a greater impact on the beach community composition (80–95% similarity), than on storm sewer communities (41–64%). Following rainfall events, E. coli communities in the creek were at least 93% similar to those at the beach, while the similarity of the outfall and beach communities varied from 72 to 96%. Furthermore, E. coli communities at the beach were more similar to creek communities than to storm sewer communities after the first 2 h and 48 h following the onset of rainfall, and of comparable similarity following 24 h of rainfall, suggesting transient contributions from the storm sewer. DGGE analysis of E. coli communities provided evidence that the creek was a consistent source of E. coli to the beach, while the storm sewer was a transient source.


2008 ◽  
Vol 74 (16) ◽  
pp. 5241-5243 ◽  
Author(s):  
Michael E. Hume ◽  
Charles M. Scanlan ◽  
Roger B. Harvey ◽  
Kathleen Andrews ◽  
James D. Snodgrass ◽  
...  

ABSTRACT A continuous-flow porcine cecal bacterial culture has been used experimentally as treatment against enterotoxigenic Escherichia coli in weanling pigs. Periodically, the cultures must be started from frozen stock. Our results indicate that denaturing gradient gel electrophoresis can be applied as an indirect indication of culture similarity for each new batch generated from frozen stock.


2013 ◽  
Vol 11 (4) ◽  
pp. 600-612 ◽  
Author(s):  
Aneta Luczkiewicz ◽  
Ewa Felis ◽  
Aleksandra Ziembinska ◽  
Anna Gnida ◽  
Ewa Kotlarska ◽  
...  

In this study, the susceptibility to erythromycin (E) and to trimethoprim/sulfamethoxazole (SXT) among isolates of Enterococcus spp. and Escherichia coli was tested, respectively. Both fecal indicators were detected and isolated from raw (RW) and treated wastewater (TW) as well as from samples of activated sludge (AS) collected in a local wastewater treatment plant (WWTP). Biodiversity of bacterial community in AS was also monitored using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). Additionally, distribution of sul1–3 genes conferring sulfonamide resistance was tested among SXT-resistant E. coli. Simultaneously, basic physicochemical parameters and concentrations of eight antimicrobial compounds (belonging to folate pathway inhibitors and macrolides class) were analyzed in RW and TW samples. Six of the selected antimicrobial agents, namely: erythromycin, clarithromycin, trimethoprim, roxithromycin, sulfamethoxazole, and N-acetyl-sulfamethoxazole were detected in the wastewater samples. Bacterial biodiversity of AS samples were comparable with no relevant differences. Among tested Enterococcus spp., E-resistant isolates constituted 41%. SXT resistance was less prevalent in E. coli with 11% of isolates. The genes conferring resistance to sulfonamides (sul1–3) were detected in SXT-resistant E. coli of wastewater origin with similar frequencies as in other environmental compartments, including clinical ones.


2020 ◽  
Vol 51 (2) ◽  
pp. 125-146
Author(s):  
Nasiruddin Nasiruddin ◽  
Yu Zhangxin ◽  
Ting Zhao Chen Guangying ◽  
Minghui Ji

We grew cucumber in pots in greenhouse for 9-successive cropping cycles and analyzed the rhizosphere Pseudomonas spp. community structure and abundance by PCR-denaturing gradient gel electrophoresis and quantitative PCR. Results showed that continuous monocropping changed the cucumber rhizosphere Pseudomonas spp. community. The number of DGGE bands, Shannon-Wiener index and Evenness index decreased during the 3rd cropping and thereafter, increased up to the 7th cropping, however, however, afterwards they decreased again. The abundance of Pseudomonas spp. increased up to the 5th successive cropping and then decreased gradually. These findings indicated that the structure and abundance of Pseudomonas spp. community changed with long-term cucumber monocropping, which might be linked to soil sickness caused by its continuous monocropping.


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