Thin agar layer- versus most probable number-PCR to enumerate viable and stressed Escherichia coli O157:H7 and application in a traditional raw milk pasta filata cheese

► SMAC with BCIG underestimated viable/stressed E. coli O157:H7 cells in the matrices. ► MPN-PCR and TAL-PCR results overlapped those obtained by plating on unselective TSAYE. ► MPN-PCR and TAL-PCR were effective in enumerating viable and stressed E. coli O157:H7. ► The more the matrix was complex, the more E. coli O157:H7 was protected. ► Pathogen inactivation (104 cfu/mL inoculum) during cheese-making is not achievable.