Evaluation of PCR-based typing methods for the identification of probiotic Enterococcus faecium strains from animal feeds

Probiotic enterococci are frequently encountered as additives in animal nutrition, but no fast standardized methods for their unambiguous identification at strain level exist. Six polymerase chain reaction (PCR)-based methods previously described for similar tasks but other genera were evaluated concerning their suitability for the rapid, stringent and reliable identification of Enterococcus at strain level. The most appropriate method should facilitate the instant identification of isolates from animal feeds and should be applicable in routine quality control. Amplified ribosomal DNA analysis (ARDRA), internally transcribed spacer region (ITS)-PCR, randomly amplified polymorphic DNA (RAPD)-PCR, repetitive element sequence based (rep)-PCR, tRNA intergenic spacer PCR and 16S rRNA gene typing were investigated with 74 Enterococcus, mainly E. faecium, strains representing 11 species. RAPD-PCR proved superior by discriminating at the strain level. Depending on the enzyme, ARDRA yielded fingerprints specific for a species or even single strains. The remaining methods successfully identified enterococci at the genus level.