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Pulsed-field gel electrophoresis as a molecular tool for characterizing genomes of certain food-borne bacterial isolates - a review

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Pal P.

International Letters of Natural Sciences

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2015

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tom 02

The evolutionary transition from phenotypic to molecular analysis of infectious disease in bacterial epidemiology led to the search for suitable approaches to ascertain genomic relatedness or heterogeneity between bacterial clinical isolates. Pulsed-field gel electrophoresis (PFGE) technique was developed for separating and analyzing long DNA fragments of several megabases in alternating electric field. Comparison of electrophoresis profiles of restriction enzyme-digested genomic DNA from bacterial isolates has proved to be a useful epidemiological tool for genetic discrimination of bacterial strains, detection of genetic relatedness, to locate the source of outbreak and to monitor the spread of the microorganisms in endemic zones. PFGE is considered as a gold standard method for typing of bacterial isolates because of the remarkable endurance of this technique as a typing method for the last 20 years in molecular epidemiology. In this current review the pros and cons of PFGE use in current molecular microbiological research are explored in the context of determination of genome organization of certain food-borne bacterial isolates causing infectious diseases in human beings.

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Rep-PCR fingerprinting as a tool for the analysis of genomic diversity of Escherichia coli strains isolated from a water environment

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Niedbach J., Blady-Chudzik K., Stosik M.

Cellular and Molecular Biology Letters

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2002

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tom 07

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nr Suppl.

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

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Baldy-Chudzik K., Stosik M.

Polish Journal of Environmental Studies

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2005

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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.

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Rep-PCR fingerprinting as a tool for the analysis of genomic diversity in Escherichia coli strains isolated from an aqueous-freshwater environment

100%

Baldy-Chudzik K., Niedbach J., Stosik M.

Cellular and Molecular Biology Letters

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2003

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tom 08

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nr 3

The rep-PCR fingerprinting method, with the support of ERIC and REP primers, was used to analyse the genomic diversity of 93 E. coli strains isolated from lake water samples drawn at two different depths. The applied UPGMA for DNA analysis did not reveale any genomic similarities between the 48 E. coli strains derived from the subsurface-zone water and the 43 of the bottom-zone water. The considerable genomic diversity of the E. coli of the surface zone was expressed as a dendrogram in the form of 8 similarity groups comprising strains isolated from samples drawn over one month. The bottom-zone strains, which display a lesser degree of genomic diversity (5 similarity groups), showed distinct common features in their DNA fingerprints. In the similarity dendrogram for the bottom-zone, strains derived in different months of sampling were segregated into the same similarity groups. Applying REP primers in rep-PCR generates more complex fingerprints increasing the discriminatory power of the analysis, whereas the ERIC primer generates less complex fingerprint patterns, and is thus clearer to interpret.

Ograniczanie wyników

2 Cellular and Molecular Biology Letters

1 International Letters of Natural Sciences

1 Polish Journal of Environmental Studies

3 Stosik M.

2 Baldy-Chudzik K.

2 Niedbach J.

1 Blady-Chudzik K.

1 Pal P.

1 2015

1 2005

1 2003

1 2002

Pulsed-field gel electrophoresis as a molecular tool for characterizing genomes of certain food-borne bacterial isolates - a review

Rep-PCR fingerprinting as a tool for the analysis of genomic diversity of Escherichia coli strains isolated from a water environment

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

Rep-PCR fingerprinting as a tool for the analysis of genomic diversity in Escherichia coli strains isolated from an aqueous-freshwater environment