Comparison of genomic methods for differentiating strains of Enterococcus faecium: assessment using clinical epidemiologic data

Abstract

Genomic DNA extracted from 45 vancomycin-resistant Enterococcus faecium (VRE) isolates was cleaved with HindIII and HaeIII and subjected to agarose gel electrophoresis. The ability of this method (restriction endonuclease analysis [REA]) to distinguish strains at the subspecies level was compared with results previously determined by pulsed-field gel electrophoresis (PFGE). Chart reviews were performed to provide a clinical correlation of possible epidemiologic relatedness. A likely clinical association was found for 29 patients as part of two outbreaks. REA found 21 of 21 isolates were the same type in the first outbreak, with PFGE calling 19 strains the same type. In the second outbreak with eight patient isolates, HindIII found six were the same type and two were unique types. HaeIII found three strains were the same type, two strains were a separate type, and three more strains were unique types, while PFGE found three were the same type and five were unique types. No single "ideal" method can be used without clinical epidemiologic investigation, but any of these techniques is helpful in providing focus to infection control practitioners assessing possible outbreaks of nosocomial infection.

Figures

FIG. 1

Representative isolates of each type analyzed by the REA technique (HindIII [A] and HaeIII [B]). The lanes, from left to right, represent a 1-kb DNA molecular weight ladder; strains EF18 (HindIII type B2, HaeIII type B2), EF20 (HindIII type C1, HaeIII type D0), EF23 (HindIII type B5, HaeIII type E0), EF27 (HindIII type B6, HaeIII type G0), EF32 (HindIII type B3), EF33 (HindIII type E0, HaeIII type H0), EF36 (HindIII type B4, HaeIII type B4), EF39 (HindIII type D0, HaeIII type J0), EF3 (HindIII type B0, HaeIII type B1), and EF45 (HindIII type C1, HaeIII type D0); and another 1-kb DNA molecular weight ladder standard.

FIG. 2

Representative isolates of each type analyzed by PFGE. The lanes, from left to right, represent a 48.5-kb lambda DNA molecular weight ladder; a Staphylococcus aureus control digested with SmaI; strains EF18 (type B5), EF20 (type D), EF23 (type E), EF27 (type G), EF32 (type I), EF33 (type J), EF36 (type M), EF39 (type O), EF3 (type B1), and EF45 (type U); another lambda molecular weight ladder; and another S. aureus control.