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1

Specific genomic fingerprints of Escherichia coli strains with repetitive sequences and PCR as an effective tool for monitoring freshwater environments

100%
Baldy-Chudzik K., Stosik M.
Polish Journal of Environmental Studies
|
2005
|
tom 14
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nr 5
The Rep-PCR fingerprinting method has been applied to identify genomic diversity of 252 E. coli strains derived in the area of a flowing-water basin. The received results show that applying UPGMA and Nearest Neighbour-Joining clustering methods to statistical analysis of rep-PCR fingerprints has made it possible to discriminate and group the strains, revealing a characteristic structure of E. coli population for particular stands of sample drawing. The proposed procedure of the analysis may be useful for routinely monitoring water quality.
2

Rep-PCR - a variant to RAPD or an independent technique of bacteria genotyping? A comparison of the typing properties of rep-PCR with other recognised methods of genotyping of microorganisms

84%
Baldy-Chudzik K.
Acta Microbiologica Polonica
|
2001
|
tom 50
|
nr 3-4
189-204
3

Evaluation of three methods for DNA fingerprinting of Corynebacterium pseudotuberculosis strains isolated from goats in Poland

84%
Stefanska I., Rzewuska M., Binek M.
Polish Journal of Microbiology
|
2008
|
tom 57
|
nr 2
Phenotypic approaches based on metabolic and biological characteristics of Corynebacterium pseudotuberculosis have been limited due to insufficient discrimination between closely related isolates. In this paper we present performance and convenience of three molecular typing methods: BOX-PCR, random amplification of polymorphic DNA (RAPD) and amplification of DNA fragments surrounding rare restriction site (ADSRRS-fingerprinting) in genome analysis of these bacteria. Among examined 61 strains there were distinguished four, eight and 10 different genotypes by BOX-PCR, RAPD and ADSRRS-fingerprinting, respectively. The value of discrimination index was the lowest for BOX-PCR (D = 0.265), much bigger for RAPD (D = 0.539) and the highest for ADSRRS-fingerprinting (D = 0.604). The good discriminatory ability and reproducibility of RAPD and ADSRRS-fingerprinting indicates that those techniques may be particularly applied for epidemiological studies of C. pseudotuberculosis isolates. We found that ADSRRS-fingerprinting is a rapid method offering good discrimination power, excellent reproducibility and may be applied for epidemiological studies of intraspecific genetic relatedness of C. pseudotuberculosis strains.
4

Application of rep-PCR fingerprinting for genotyping of Escherichia coli strains in Wojnowskie Wschodnie and Wojnowskie Zachodnie Lake

67%
Baldy-Chudzik K., Niedbach J., Stosik M.
Acta Microbiologica Polonica
|
2001
|
tom 50
|
nr 3-4
233-242
5

Repetitive extragenic palindromic PCR [REP-PCR] as an alternative method for detection of bulking in activated sludge

67%
Soltysik D. A., Bednarek I. A., Loch T. M., Galka S. E., Sypniewski D. J., Machnik G. M., Blaszczyk D. K.
Polish Journal of Microbiology
|
2010
|
tom 59
|
nr 1
11-20
Bulking of activated sludge is a world-wide problem which negatively affects wastewater treatment efficiency. The most common reasons of bulking are bacterial community changes, especially excessive growth of filamentous bacteria (filamentous bulking) or excess of biopolymers on the surface of non-filamentous microbes (non-filamentous or Zoogleal bulking). Because of the complex nature of the bulking phenomenon finding a successful bulking control strategy remains a very important issue that awaits new options and advices. The REP-PCR fingerprinting method has been applied to distinguish a bacterial community in non-bulking and bulking activated sludge. The characteristic REP-PCR fingerprinting patterns were compared with each other in terms of the presence or absence of bands and in terms of measured integrated optical density (IOD) of the bands. The obtained fingerprinting patterns, using Ward's clustering method, have been analyzed to determine homology/similarity relations between specific non-bulking and bulking sludge sampling. The received clustering results were in high concordance with activated sludge typing which generally is done based on physicochemical sludge analysis. The proposed REP-PCR method and statistical analysis of fingerprinting patterns seems to be a simple, rapid and effective method revealing differences between populations in non-bulking and bulking activated sludge. It may be useful for routine activated sludge monitoring and may be helpful in the early detection of the bulking process.
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