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Background  High-pressure processing (HPP) is a commonly used technique in the food industry to inactivate pathogens, including  L. monocytogenes . It has been shown that  L. monocytogenes  is able to recover from HPP injuries and can start to grow again during long-term cold storage. To date, the gene expression profiling of  L. monocytogenes  during HPP damage recovery at cooling temperature has not been studied. In order identify key genes that play a role in recovery of the damage caused by HPP treatment, we performed RNA-sequencing (RNA-seq) for two  L. monocytogenes  strains (barotolerant RO15 and barosensitive ScottA) at nine selected time points (up to 48 h) after treatment with two pressure levels (200 and 400 MPa).    Results  The results showed that a general stress response was activated by SigB after HPP treatment. In addition, the phosphotransferase system (PTS; mostly fructose-, mannose-, galactitol-, cellobiose-, and ascorbate-specific PTS systems), protein folding, and cobalamin biosynthesis were the most upregulated genes during HPP damage recovery. We observed that cell-division-related genes ( divIC ,  dicIVA ,  ftsE , and  ftsX ) were downregulated. By contrast, peptidoglycan-synthesis genes ( murG ,  murC , and  pbp2A ) were upregulated. This indicates that cell-wall repair occurs as a part of HPP damage recovery. We also observed that prophage genes, including anti-CRISPR genes, were induced by HPP. Interestingly, a large amount of RNA-seq data (up to 85%) was mapped to Rli47, which is a non-coding RNA that is upregulated after HPP. Thus, we predicted that Rli47 plays a role in HPP damage recovery in  L. monocytogenes . Moreover, gene-deletion experiments showed that amongst peptidoglycan biosynthesis genes,  pbp2A  mutants are more sensitive to HPP.    Conclusions  We identified several genes and mechanisms that may play a role in recovery from HPP damage of  L. monocytogenes . Our study contributes to new information on pathogen inactivation by HPP.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12864-021-07407-6.

High-pressure processing-induced transcriptome response during recovery of Listeria monocytogenes