Ann Lab Med.  2012 Jan;32(1):50-56. 10.3343/alm.2012.32.1.50.

Comparison of Modified Multiple-locus Variable-number Tandem-repeat Fingerprinting with Pulsed-field Gel Electrophoresis for Typing Clinical Isolates of Staphylococcus aureus

  • 1Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea.
  • 2Department of Laboratory Medicine, Pusan National University Yangsan Hospital, Yangsan, Korea.
  • 3Department of Laboratory Medicine, Pusan National University School of Medicine, Busan, Korea.
  • 4Department of Laboratory Medicine, National Medical Center, Seoul, Korea.


Multiple-locus variable-number tandem-repeat fingerprinting (MLVF) is based on multiplex PCR, utilizing variable number tandem repeat. Our goal was to compare the performance of MLVF in distinguishing clinical Staphylococcus aureus isolates with that of pulsed-field gel electrophoresis (PFGE), which has traditionally been the gold standard.
Sixty-three clinically significant S. aureus isolates were tested using both PFGE and MLVF. Multiplex PCR for MLVF was performed using PCR primers for clfA, clfB, sdrCDE, sspA, and spa. PFGE was performed with genomic DNA fragments generated by SmaI endonuclease digestion. Banding patterns of MLVF or PFGE were analyzed using InfoQuestFP software.
The hands-on time of our modified method was about 3 h, on average, for each of 18 isolates. PFGE (80% cutoff) or MLVF (75% cutoff) separated all of the 63 isolates into 13 and 12 types, respectively. Three types generated by PFGE were identical to those generated by MLVF. PFGE and MLVF yielded similar Simpson's diversity indices, indicating similar discriminatory power. The overall concordance between PFGE and MLVF was low, as represented by adjusted Rand indices (0.266-0.278). PFGE predicted MLVF type better than MLVF predicted PFGE type, as reflected by Wallace coefficients (PFGE cutoff 80% vs. MLVF cutoff 75%, 0.389 vs. 0.233). Analysis of the relationship between a pair of isolates showed 91.0% concordance between the PFGE (80% cutoff) and MLVF (75% cutoff).
Our simple, low-cost, modified MLVF protocol can effectively discriminate between S. aureus clinical isolates. MLVF can replace PFGE for the hospital infection control of S. aureus.


Staphylococcus aureus; Pulsed-field gel electrophoresis; Multiple-locus variable-number tandem-repeat fingerprinting

MeSH Terms

Bacterial Typing Techniques/*methods
*DNA Fingerprinting
DNA, Bacterial/analysis
*Electrophoresis, Gel, Pulsed-Field
Methicillin-Resistant Staphylococcus aureus/classification/genetics/isolation & purification
Multiplex Polymerase Chain Reaction
Staphylococcal Infections/*microbiology
Staphylococcus aureus/*classification/*genetics/isolation & purification


  • Fig. 1 Pulsed-field gel electrophoresis (PFGE) types of the study isolates generated by the unweighted pair-group method with arithmetic mean (UPGMA) algorithm, using 80% and 75% similarity cutoff values. The isolates that were not included in the above types were considered to be unique patterns. Isolate numbers presented in boldface were not included in any types generated by the 80% cutoff.

  • Fig. 2 Multiple-locus variable-number tandem-repeat fingerprinting (MLVF) types of the study isolates generated by the unweighted pairgroup method with arithmetic mean (UPGMA) algorithm using 75% and 70% similarity cutoff values. The isolates that were not included in the above types were considered to be unique patterns. Isolate numbers presented in boldface were not included in any types generated by the 75% cutoff.


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