Transport of escherichia coli through soil to groundwater traced by randomly amplified polymorphic DNA (RAPD)

1997 ◽  
Vol 35 (11-12) ◽  
pp. 351-357 ◽  
Author(s):  
R. Rothmaier ◽  
A. Weidenmann ◽  
K. Botzenhart
Keyword(s):  
Negative Impact ◽  
Random Amplified Polymorphic Dna ◽  
Coli Strain ◽  
Soil Samples ◽  
Test Field ◽  
Liquid Manure ◽  
E Coli ◽  
Rapd Pattern ◽  
Geological Situation ◽  
Different Strains

Isolates (50) of E. coli obtained from liquid manure (20 bovine, 20 porcine) were genotyped using random amplified polymorphic DNA (RAPD). Typing revealed 9 and 14 different strains in bovine and porcine liquid manure respectively with no strains in common. One porcine strain, showing a simple RAPD pattern, was subcultured and spread on a test field (1.5l/m2 at 1010 cfu/l) in a drinking water protection zone with loamy to sandy sediments in the Donauried area, Baden-Wurttemberg. Soil samples and groundwaters were collected at monthly intervals October 1994 – June 1995 during which 114 E. coli isolates were recovered. The first occurrence and maximum concentration of E. coli in soil samples taken from more than 20cm depth was in January 1995, declining rapidly with depth and time. All isolates from soil and only one from groundwater showed the RAPD pattern of the spread E. coli strain. The results could not demonstrate a severe negative impact of the spreading of liquid manure on the bacteriological quality of the groundwater in the given geological situation. The distinct strain patterns found in different kinds of liquid manure suggest that genotyping of E. coli by RAPD may be an adequate tool for tracing sources of faecal contamination.

scholarly journals Molecular Characterization of Commensal Escherichia coli Adapted to Different Compartments of the Porcine Gastrointestinal Tract

2012 ◽  
Vol 78 (19) ◽  
pp. 6799-6803 ◽  
Author(s):  
Sam Abraham ◽  
David M. Gordon ◽  
James Chin ◽  
Huub J. M. Brouwers ◽  
Peter Njuguna ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Gastrointestinal Tract ◽  
Random Amplified Polymorphic Dna ◽  
Content Type ◽  
E Coli ◽  
Plasmid Replicon ◽  
Different Strains ◽  
Different Characteristics

ABSTRACTThe role ofEscherichia colias a pathogen has been the focus of considerable study, while much less is known about it as a commensal and how it adapts to and colonizes different environmental niches within the mammalian gut. In this study, we characterizeEscherichia coliorganisms (n= 146) isolated from different regions of the intestinal tracts of eight pigs (dueodenum, ileum, colon, and feces). The isolates were typed using the method of random amplified polymorphic DNA (RAPD) and screened for the presence of bacteriocin genes and plasmid replicon types. Molecular analysis of variance using the RAPD data showed thatE. coliisolates are nonrandomly distributed among different gut regions, and that gut region accounted for 25% (P< 0.001) of the observed variation among strains. Bacteriocin screening revealed that a bacteriocin gene was detected in 45% of the isolates, with 43% carrying colicin genes and 3% carrying microcin genes. Of the bacteriocins observed (H47, E3, E1, E2, E7, Ia/Ib, and B/M), the frequency with which they were detected varied with respect to gut region for the colicins E2, E7, Ia/Ib, and B/M. The plasmid replicon typing gave rise to 25 profiles from the 13 Inc types detected. Inc F types were detected most frequently, followed by Inc HI1 and N types. Of the Inc types detected, 7 were nonrandomly distributed among isolates from the different regions of the gut. The results of this study indicate that not only may the different regions of the gastrointestinal tract harbor different strains ofE. colibut also that strains from different regions have different characteristics.

Molecular typing of the Legionella pneumophila population isolated from several locations in a contaminated water network

2004 ◽  
Vol 50 (1) ◽  
pp. 281-285 ◽  
Author(s):  
A.-S. Lepeuple ◽  
M. Jovic ◽  
M.-R. de Roubin
Keyword(s):  
Legionella Pneumophila ◽  
Molecular Typing ◽  
Random Amplified Polymorphic Dna ◽  
Hot Water ◽  
Water Network ◽  
Rapd Pattern ◽  
Different Populations ◽  
Definition Of ◽  
Different Strains ◽  
Key Steps

The RAPD (random amplified polymorphic DNA) technique has been developed for the molecular typing of Legionella in order to characterise the populations of hot water systems. During this study, 22 primers were tested and the four most informative ones were selected. The optimisation of the PCR conditions allowed the setting up of a powerful discriminative genotyping method. Moreover, the definition of a quality management method allowed definition of the key steps and the number of replicates to ensure reproducibility of the RAPD pattern. The RAPD was used to study the hot water network of a building. Legionella colonies (91) were isolated from seven locations and genotyped. The diversity of the population in one sample could vary from one to seven different strains. The study of the traceability showed that, in most of the cases, different populations could be present at different locations of the same network.

scholarly journals Anti-Tick Microbiota Vaccine Impacts Ixodes ricinus Performance during Feeding

Vaccines ◽  
2020 ◽  
Vol 8 (4) ◽  
pp. 702 ◽  
Author(s):  
Lourdes Mateos-Hernández ◽  
Dasiel Obregón ◽  
Jennifer Maye ◽  
Jeremie Borneres ◽  
Nicolas Versille ◽  
...  
Keyword(s):  
Wide Distribution ◽  
Experimental Manipulation ◽  
Coli Strain ◽  
E Coli ◽  
Promising Tool ◽  
The Family ◽  
Strain Bl21 ◽  
The Stability ◽  
Different Strains ◽  
In Silico Analyses

The tick microbiota is a highly complex ensemble of interacting microorganisms. Keystone taxa, with a central role in the microbial networks, support the stability and fitness of the microbial communities. The keystoneness of taxa in the tick microbiota can be inferred from microbial co-occurrence networks. Microbes with high centrality indexes are highly connected with other taxa of the microbiota and are expected to provide important resources to the microbial community and/or the tick. We reasoned that disturbance of vector microbiota by removal of ubiquitous and abundant keystone bacteria may disrupt the tick-microbiota homeostasis causing harm to the tick host. These observations and reasoning prompted us to test the hypothesis that antibodies targeting keystone bacteria may harm the ticks during feeding on immunized hosts. To this aim, in silico analyses were conducted to identify keystone bacteria in the microbiota of Ixodes nymphs. The family Enterobacteriaceae was among the top keystone taxa identified in Ixodes microbiota. Immunization of α-1,3-galactosyltransferase-deficient-C57BL/6 (α1,3GT KO) mice with a live vaccine containing the Enterobacteriaceae bacterium Escherichia coli strain BL21 revealed that the production of anti-E. coli and anti-α-Gal IgM and IgG was associated with high mortality of I. ricinus nymphs during feeding. However, this effect was absent in two different strains of wild type mice, BALB/c and C57BL/6. This result concurred with a wide distribution of α-1,3-galactosyltransferase genes, and possibly α-Gal, in Enterobacteriaceae and other bacteria of tick microbiota. Interestingly, the weight of I. ricinus nymphs that fed on E. coli-immunized C57BL/6 was significantly higher than the weight of ticks that fed on C57BL/6 immunized with a mock vaccine. Our results suggest that anti-tick microbiota vaccines are a promising tool for the experimental manipulation of vector microbiota, and potentially the control of ticks and tick-borne pathogens.

scholarly journals Temporal Appraisal and Molecular Characterization of Escherichia coli from Oyun River, Kwara State, Nigeria

2020 ◽  
pp. 56-63
Author(s):  
Olatunji Matthew Kolawole ◽  
Oluwasanmi Anuoluwapo Adeyemi
Keyword(s):  
Escherichia Coli ◽  
Molecular Characterization ◽  
Bacterial Load ◽  
Disease Outbreaks ◽  
Coli Strain ◽  
Microbial Count ◽  
Mean Values ◽  
E Coli ◽  
Risk Variants ◽  
Different Strains

Introduction: Escherichia coli, an indicator of feacal contamination has been proven to be the cause of several disease outbreaks in countries and continents around the world. Aim: To determine the genotypic variants of Escherichia coli present in Oyun River and provide information regarding the high-risk variants of E. coli in Oyun River. Study Design: The study cuts across the two seasons of Nigeria’s tropical climate weather, being the peak of the Harmattan season and the onset of the Rainy season. Three sampling sites (Jimba Oja; Unilorin Dam and Oyun in Ilorin, Kwara State) along the River course were examined for three months (February – April). Methodology: Heterotrophic counts, coli form counts and molecular characterization via PCR   using 16 sRNA primers, of water samples were done using standard microbiological and molecular methods. Results: Bacteriological results showed monthly mean values of microbial counts, ranged from 23.5 x 106 – 45.17 x 106 cfu/mL and total coli form count ranged from 53 cfu/100 mL to 256 cfu/100 mLs, both of which exceed the WHO standards of 100 cfu/mL for total microbial count and <1 cfu/100 mLs for total coliforms. A total of forty-eight coliforms were isolated, thirty two of which were Escherichia coli. Sequencing and BLAST analysis of eleven of the isolates using NCBI’s online database revealed five different strains. They include: Escherichia coli FAP1 genome (9.1%); Escherichia coli strain ST2747 (54.5%); Escherichia coli strain EADK4 (9.1%); Escherichia coli strain ST540 (18.2%) and Escherichia coli strain NCM3722 (9.1%). Correlation of results with previous studies showed that most of the strains identified were pathogenic. The E. coli strains isolated, coupled with the bacterial load, coliform count and some physicochemical parameters of Oyun River makes it unsafe for public consumption if not treated. Efforts therefore should be made to treat the water before use, while making frantic efforts to prevent further contamination of Oyun River.

scholarly journals Transduction, restriction and recombination patterns in Escherichia coli.

Genetics ◽  
1995 ◽  
Vol 139 (1) ◽  
pp. 35-43
Author(s):  
M McKane ◽  
R Milkman
Keyword(s):  
Escherichia Coli ◽  
Coli Strain ◽  
Chromosomal Dna ◽  
Bacteriophage P1 ◽  
E Coli ◽  
Sequence Patterns ◽  
Single Marker ◽  
Different Strains ◽  
Restriction Modification ◽  
Restriction Modification Systems

Abstract Chromosomal DNA from several Escherichia coli reference (ECOR) strains was transduced by bacteriophage P1 into E. coli strain K12 W3110 trpA33. Recombination patterns of the transductants were determined by restriction fragment length polymorphism over a 40-kb region centering on a single marker (trpA+) in the tryptophan operon. These experiments demonstrate that transduction between different strains of E. coli can result in recombinational replacements that are small in comparison to the entrant molecule (replacements average 8-14 kb, whereas P1 packages approximately 100 kb) often in a series of discrete segments. The transduction patterns generated resemble the natural mosaic sequence patterns of the ECOR strains described in previous work. Extensive polymorphisms in the restriction-modification systems of the ECOR strains are a possible explanation for the sequence patterns in nature. To test this possibility two transductants were back-transduced into strain K12 W3110 trpA33. The resulting patterns were strikingly different from the original transductions. The size of the replacements was greater, and no multiple replacements were observed, suggesting a role for restriction-modification systems in the transduction patterns and perhaps for the mosaic sequence patterns in nature.

Molecular Characterization ofStreptococcus PyogenesIsolates to investigate an outbreak of Puerperal Sepsis

2005 ◽  
Vol 26 (5) ◽  
pp. 455-461 ◽  
Author(s):  
Josette Raymond ◽  
Laurent Schlegel ◽  
Fabien Garnier ◽  
Anne Bouvet
Keyword(s):  
Molecular Characterization ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Index Patient ◽  
Restriction Pattern ◽  
Microbiological Characteristics ◽  
Rapd Pattern ◽  
Close Relationship ◽  
Different Strains ◽  
Predominant Strain

AbstractObjective:To describe microbiological characteristics and epidemiologic features of an outbreak of postpartum endometritis.Methods:Various markers were investigated in five patients and three throat carriage isolates ofStreptococcus pyogenesobtained during an outbreak of endometritis occurring in a 13-week period. Molecular characterization included biotyping, T-serotyping,emmgene sequence and restriction, pulsed-field gel electrophoresis (PFGE), and random amplified polymorphic DNA (RAPD) analysis.Results:Biotype, T-serotype, and genotypic data (emmanalysis, PFGE, and RAPD analysis) revealed a close relationship among the isolates from three patients, suggesting that cross-contamination had occurred. These isolates were biotype 1, T type 28, andemmtype 28. The isolates from one patient and one carrier differed from those of the index patient by minor variations of theemmamplicon restriction pattern, PFGE pattern, or RAPD pattern. The remaining isolates were phenotypically and genetically different.Conclusion:Identification of different isolates demonstrated that different strains may circulate simultaneously during a true outbreak and that the predominant strain might persist for several months.

scholarly journals Accessory DNA in the Genomes of Representatives of the Escherichia coli Reference Collection

1999 ◽  
Vol 181 (8) ◽  
pp. 2548-2554 ◽  
Author(s):  
Ana Hurtado ◽  
Francisco Rodríguez-Valera
Keyword(s):  
Escherichia Coli ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
The Other ◽  
Rna Helicases ◽  
Significant Similarity ◽  
E Coli ◽  
Reference Collection ◽  
Different Strains ◽  
K 12

ABSTRACT Different strains of the Escherichia coli reference collection (ECOR) differ widely in chromosomal size. To analyze the nature of the differential gene pool carried by different strains, we have followed an approach in which random amplified polymorphic DNA (RAPD) was used to generate several PCR fragments. Those present in some but not all the strains were screened by hybridization to assess their distribution throughout the ECOR collection. Thirteen fragments with various degrees of occurrence were sequenced. Three of them corresponded to RAPD markers of widespread distribution. Of these, two were housekeeping genes shown by hybridization to be present in all theE. coli strains and in Salmonella enterica LT2; the third fragment contained a paralogous copy of dnaK with widespread, but not global, distribution. The other 10 RAPD markers were found in only a few strains. However, hybridization results demonstrated that four of them were actually present in a large selection of the ECOR collection (between 42 and 97% of the strains); three of these fragments contained open reading frames associated with phages or plasmids known in E. coli K-12. The remaining six fragments were present in only between one and four strains; of these, four fragments showed no similarity to any sequence in the databases, and the other two had low but significant similarity to a protein involved in the Klebsiella capsule synthesis and to RNA helicases of archaeal genomes, respectively. Their percent GC, dinucleotide content, and codon adaptation index suggested an exogenous origin by horizontal transfer. These results can be interpreted as reflecting the presence of a large pool of strain-specific genes, whose origin could be outside the species boundaries.

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