Quantitative strain-specific detection of Lactobacillus rhamnosus GG in human faecal samples by real-time PCR

To develop a strain-specific rapid assay for identification and quantification of Lactobacillus rhamnosus GG in human faecal samples. A unique random amplified polymorphic DNA (RAPD) band of the L. rhamnosus GG strain was isolated and sequenced. Strain-specific polymerase chain reaction (PCR) primers and probes were designed based on the sequence. Quantification was performed by the real-time PCR using a fluorescent resonance energy transfer (FRET) system. The specificity of the assay was tested with DNA isolated from a set of known strains and human faecal samples. The analytical sensitivity of the method for L. rhamnosus GG was about 10 CFU per assay, which corresponds to 10(5) CFU g(-1) of wet faeces. Quantitative real-time PCR is a suitable method for strain-specific identification of L. rhamnosus GG in human faecal samples. Lactobacillus rhamnosus GG is one of the most studied probiotic strains in clinical trials but still lacks a DNA-based identification method. This study describes a real-time PCR method for strain-specific identification and quantification of L. rhamnosus GG in human faecal samples.