Comparison of fingerprinting methods for typing methicillin-resistant Staphylococcus aureus sequence type 398

Abstract

This study evaluates the multiple-locus variable-number tandem-repeat assay (MLVA) and pulsed-field gel electrophoresis (PFGE) when using restriction enzymes BstZI, SacII, and ApaI to fingerprint a diverse collection of methicillin (meticillin)-resistant Staphylococcus aureus (MRSA) sequence type 398 (ST398) isolates. These isolates had been characterized previously by multilocus sequence typing, spa typing, and staphylococcal cassette chromosome mec (SCCmec) typing. Typeability and discriminatory power were analyzed, and the concordance between the various methods was determined. All MRSA ST398 isolates were typeable by the MLVA and PFGE using BstZI, SacII, and ApaI. With each method, the MRSA ST398 isolates formed a separate group from the two non-ST398 MRSA strains. PFGE, performed with any of the three restriction enzymes, had the most discriminatory power, followed by MLVA, spa typing, and SCCmec typing. The MLVA showed the highest concordance with PFGE using ApaI and spa typing. As further expressed by the Wallace coefficient, the MLVA type was poorly predicted by spa typing, whereas the spa type was well predicted by MLVA. PFGE, using a combination of all three restriction enzymes, had the highest concordance with the MLVA but had a low probability of being predicted by MLVA. PFGE, using a combination of all three restriction enzymes, was able to predict SCCmec type and MLVA type completely and had a high probability of predicting spa type. Both the MLVA and PFGE could be used to discriminate among the MRSA ST398 isolates. Although the MLVA is a faster technique, PFGE had more discriminatory power than the MLVA, especially when a combination of restriction enzymes was used.

FIG. 1.

Dendrogram and fingerprints for the MLVA with 32 MRSA ST398 isolates and two reference MRSA strains. The similarities between the fingerprints were calculated using the Dice coefficient (optimization, 1%; position tolerance, 0.1% to 1%), and the fingerprints were grouped according to their similarities by use of the UPGMA algorithm.

FIG. 2.

Dendrogram and fingerprints for PFGE using restriction enzyme BstZI with 32 MRSA ST398 isolates and two reference MRSA strains. The similarities among the fingerprints were calculated using the Dice coefficient (optimization, 1%; position tolerance, 0.5% to 1%), and the fingerprints were grouped according to their similarities by use of the UPGMA algorithm. The vertical gray line shows the delineation level of 97%.

FIG. 3.

Dendrogram and fingerprints for PFGE using restriction enzyme SacII with 32 MRSA ST398 isolates and two reference MRSA strains. The similarities among the fingerprints were calculated using the Dice coefficient (optimization, 1%; position tolerance, 0.5% to 1%), and the fingerprints were grouped according to their similarities by use of the UPGMA algorithm. The vertical gray line shows the delineation level of 97%.

FIG. 4.

Dendrogram and fingerprints for PFGE using restriction enzyme ApaI with 32 MRSA ST398 isolates and two reference MRSA strains. The similarities among the fingerprints were calculated using the Dice coefficient (optimization, 1%; position tolerance, 0.5% to 1%), and the fingerprints were grouped according to their similarities by use of the UPGMA algorithm. The vertical gray line shows the delineation level of 97%.