Korean J Infect Dis.  1999 Dec;31(6):474-480.

Comparison of Pulsed-field Gel Electrophoresis, Amplified Fragment Length Polymorphism, and Infrequent Restriction Site-Polymerase Chain Reaction for Molecular Typing of Escherichia coli and Staphylococcus aureus Strains

• Kim SI
• Yoo JH
• Cho YK
• Lee DG
• Wie SH
• Choi JH
• Kim YR
• Shin WS
• Kang MW

Abstract

BACKGROUND: Pulsed-field gel electrophoresis (PFGE) has been regarded a standard method for genotyping in epidemiologic studies. However, it is tedious and time-consuming to perform. Two alternative genotyping methods have recently been developed using the polymerase chain reaction (PCR):amplified fragment length polymorphism (AFLP) and infrequent restriction site-polymerase chain reaction (IRS-PCR). These methods have not yet been applied yet to common pathogens such as Staphylococcus aureus. The purpose of this study was to determine the applicability of AFLP and IRS-PCR for the genotyping of E. coli and S. aureus isolates.
METHODS
We performed PFGE, AFLP, and IRS-PCR on clinical isolates of E. coli (n=27) and S. aureus (n=30). We assessed each method in terms of discriminatory power, quality, and efficiency.
RESULTS
In E. coli, the discriminatory powers of IRS-PCR and AFLP were comparable to that of PFGE. PFGE discerned 24 (88.8%) out of 27 strains, IRS-PCR discerned 22 (81.5%) out of 27, and AFLP discerned 25 (92.6%) out of 27. In the case of S. aureus, PFGE discerned 27 (90%) out of 30 strains, while both IRA-PCR and AFLP discerned 12 (40%) out of 30. The test-ing took four days to complete with PFGE, two days with AFLP, and was completed within one day with IRS-PCR. IRS-PCR showed better resolution than both PFGE and AFLP.
CONCLUSION
In cases of E. coli, AFLP and IRS-PCR could be good alternatives for epidemiologic typing, as they offer better efficiency and comparable discriminatory power to PFGE. On the other hand, IRS-PCR and AFLP do not seem to be suitable for the strain-to-strain differentiation of S. aureus.

Keyword

Escherichia coli; Staphylococcus aureus; Pulsed-field gel electrophoresis; Amplified fragment length polymorphism; Infrequent restriction site-polymerase chain reaction

MeSH Terms

Electrophoresis, Gel, Pulsed-Field*
Escherichia coli*
Escherichia*
Hand
Molecular Typing*
Polymerase Chain Reaction
Staphylococcus aureus*
Staphylococcus*