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

• Autorzy: Baldy-Chudzik K , Niedbach J. , Stosik M.
• Języki publikacji: EN

Abstrakty

EN

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.

Słowa kluczowe

EN

tool; analysis; fingerprinting; genomic diversity; Escherichia coli; aquatic environment

• Wydawca: -
• Czasopismo: Cellular and Molecular Biology Letters
• Rocznik: 2003
• Tom: 08
• Numer: 3
• Opis fizyczny: p.793-798,fig.

Twórcy

autor

Baldy-Chudzik K

• University of Zielona Gora, Monte Cassino 21b, 65-561 Zielona Gora, Poland

autor

Niedbach J.

autor

Stosik M.

Bibliografia

• 1.Lecrerc, H., Mossel, D.A.A., Egberg, S.C. and Struijk, C.B. Advances in the bacteriology of the coliform group: Their suitability as markers of microbial water safety. Annu. Rev. Microbiol. 55 (2001) 201-234.
• 2.Versalovic, J., Schneider, M., de Bruijn, F.J. and Lupski, J.R. Genomic fingerprinting of bacteria using repetitive sequence-based polymerase chain reaction. Methods Mol. Cell. Biol. 5 (1994) 25-40.
• 3.Gilson, E., Clement, J.M., Brutlag, D. and Hofnung, M. A family of dispersed repetitive extragenic palindromic DNA sequences in E. coli. EMBO J. 3 (1984) 1417-1421.
• 4.Hulton, C.S.J., Higgins, C.F. and Sharp, P.M. ERIC sequences: a novel family of repetitive elements in the genomes of Escherichia coli, Salmonella typhimurium and other enterobacteria. Mol. Microbiol. 5 (1991) 825-834.
• 5.Lipman, L.J.A., de Nijs, A., Lam, T.J.G.M. and Gaastra, W. Identification of Escherichia coli strains from cows with clinical mastitis by serotyping and DNA polymorphism patterns with REP and ERIC primers. Vet. Microbiol. 43 ( 1995) 13-19.
• 6.Dombek, P.E., Johnson, L.K., Zimmerley, S.T. and Sadowsky, M.J. Use of repetitive DNA sequences and the PCR to differentiate Escherichia coli isolates from human and animal sources. Appl. Envir. Microbiol. 66 (2000) 2572-2577.
• 7.Baldy-Chudzik, K., Niedbach, J. and Stosik M. Application of rep-PCR fingerprinting for genotyping of Escherichia coli strains in Wojnowskie Wschodnie and Wojnowskie Zachodnie lake. Acta Microbiol. Polon. 50 (2001) 233-242.
• 8.Rademaker, J.L.W. and de Bruijn, F.J. Characterization and classification of microbes by rep-PCR genomic fingerprinting and computer assisted pattern analysis. In: DNA markers: protocols, applications and overviews, (Caetano-Anollés, G., Gresshoff, P.M. Eds), Willey-Liss, Inc., New York, 1997, 151-171.
• 9.Turner, S.J., Lewis, G.D. and Bellamy, A.R. A genomic polymorphism located downstream of the gcvP gene of Escherichia coli that correlates with ecological niche. Mol. Ecol. 6 (1997) 1019-1032.