The objective of this study was to correlate the relative transcription of Listeria monocytogenes (strains C-5, 6179) stress- (gad2, sigB) and virulence- (prfA) associated genes following habituation at twenty-five pH (4.8, 5.0, 5.2, 5.5, 6.4) and NaCl (2, 4, 6, 8, 10% w/ v) combinations at 7 degrees C, with the survival against subsequent exposure to severe acid stress (pH 2.0 at 37 degrees C). Our findings pointed out the inter-strain variation governing growth inhibiting conditions (pH <= 5.0 and NaCl >= 6%), where C-5 was less affected (a reduction of 2.0-3.0 log CFU/mL) than 6179 which was reduced by 4.0-6.0 log CFU/mL at the end of storage. Nevertheless, the higher the habituation at the growth permitting (pH >= 5.5; NaCl <= 4% w/ v) or growth inhibiting conditions, the higher the acquired acid resistance or sensitization, respectively. At day 2, gad2 increased relative transcriptional levels are more related to elevated acid resistance, while at day 6 both gad2 transcriptional levels and upregulation of sigB were correlated to low log reductions and high D-pH: 2.0-values against severe acid stress. Regarding virulence, the increased transcriptional levels of prfA at day 2 were correlated to adverse pH and NaCl combinations, while prolonged stay in suboptimal conditions as well as exposure to severe acid stress resulted in general activation of the virulence regulator. Such data could definitely contribute in designing safe intervention strategies and additionally integrate eomics aspects in quantitative microbial risk assessment. (C) 2014 Elsevier Ltd. All rights reserved.