Novel PCR-based identification of Weissella confusa using an AFLP-derived marker

► A species-specific PCR for Weissella (W.) confusa was succesfully developed. ► Fluorescent AFLP of 30 LAB allowed indivituating W. confusa species-specific markers. ► A purified fragment of 303 bp showed a high identity to the lepA gene of several LAB. ► This marker was successfully used to develop a species-specific PCR. ► Our PCR assay resulted in 100% specificity with a detection limit of 16 pg.