Restriction endonuclease analysis (REA) and pulsed-field gel electrophoresis (PFGE) for differentiating strains of enterococci: An assessment using clinical epidemiologie data

Rapid assessment of clonality is felt to be important in managing institutional outbreaks of nosocomial infection. The optimal molecular technique for determining clonality is not obvious from reviewing the literature. We compared two common typing methods and examined clinical data to assess likelihood of inter-patient spread for vancomycin-resistant E. faecium (VRE). Chromosomal DNA extracted from 45 isolates was cleaved with HindIII and HaeIII and subjected to agarose gel electrophoresis (REA). The ability of REA to distinguish strains at the subspecies level was compared with results previously determined by PFGE. Chart reviews were performed to provide clinical correlation. REA using HindIII provided 20 distinct patterns (subtypes) that were categorized into 9 Types while HaeIII provided 21 distinct patterns that were categorized into 19 Types. With PFGE, 27 distinct subtypes were found belonging to 21 Types. A likely clinical association was found for 32 patients as part of 2 outbreaks. REA with HindIII and HaeIII found all 20 isolates to the same Type in the first outbreak, with PFGE calling 18 strains the same Type, and 2 isolates each a distinct Type. In the second outbreak, HindIII found 8 the same Type with 2 strains a separate Type, and 2 more strains unique Types. Here HaeIII found 6 the same Type, and PFGE found 5 the same. In the 7 discrepant isolates, HindIII found 4 Types, HaeIII 5 Types, and PFGE 7 Types. In these 7, 2 appeared clonal by both REA enzymes and clinical association, but were not related by PFGE. In summary, there is no ideal method that can be used without clinical assessment, but either of these techniques is useful when reproducibly done and applied to assess possible nosocomial outbreaks of infection in a timely manner.