Foodborne pathogens pose a major threat to food safety, and they are able to develop stress resistance to many physical treatments (e.g., heating) and chemical agents (e.g., disinfectant) commonly used in food industries, making it easier to cause food poisoning. The development of stress resistance in foodborne pathogens is usually due to the coordinated function of multiple genes, sRNAs, proteins and metabolites, and these genetic elements are generally involved in multiple metabolic pathways. Recent advances in omics technologies have provided solid technical support for the exploration of genetic elements related to bacterial stress resistance and the characterization of their interaction networks, which will eventually contribute to the establishment of resistome databases for foodborne pathogens. In this context, this article provides a systematic overview on the application of genomics, transcriptomics, proteomics, and metabolomics technologies in research on stress resistance mechanisms in foodborne pathogens. Furthermore, future research perspectives are also presented to provide a theoretical basis to curb foodborne diseases caused by stress-resistant pathogens.

The emergence of colistin-resistant gram-negative bacteria poses a serious challenge for healthcare, and the two-component system PmrAB is closely associated with colistin resistance. This study aimed to characterize the colistin-resistant Salmonella isolates collected from 211 retail chicken meat samples between December 2020 and January 2022 in Shanghai, China. Overall, 90 Salmonella isolates (42.7%, 90/211) were identified, which were identified as 13 serotypes. Antimicrobial resistance profiling showed that 15.6% (14/90) of the isolates exhibited resistance to colistin. Among these, five isolates were found to carry the mcr-1 gene, which could be horizontally transferred to other hosts. The mechanism of resistance in the remaining nine mcr-negative colistin-resistant isolates was further studied, and it was found that there were seven amino acid substitutions in PmrAB. Site-directed mutagenesis was used to construct mutants, demonstrating that three novel substitutions (L105P in PmrA, P94L, and L331R in PmrB) contributed to colistin resistance in Salmonella (MIC = 8 or 16 μg/mL). Quantitative PCR and lipid A analysis were then employed to explore the resistance regulatory pathway. It was found that these substitutions resulted in the production of L-Ara4N by upregulating the expression of the genes udg and pmrK, which in turn modified lipid A. Finally, the genes udg and pmrK in the mutants were knocked out to investigate whether these substitutions conferred colistin resistance through these genes. The colistin MIC of the udg or pmrK deletion in mutants was similar to that of the parental strains (MIC = 0.25 μg/mL), indicating that these substitutions might confer colistin resistance through the pmrE and udg pathways. These findings demonstrate that amino acid substitutions in PmrAB contribute to the development of colistin resistance in Salmonella by modifying lipid A through the genes udg and pmrK to produce L-Ara4N, providing insight into the mechanisms of colistin resistance in Salmonella.

Benzalkonium chloride (BAC) is an effective disinfectant against Salmonella and widely used in the food industry. However, there are growing concerns about the risk of inducing Salmonella to produce cross-resistance to antibiotics resulting from the excessive use of BAC. In this study, 50 foodborne Salmonella isolates were exposed to sub-inhibitory concentrations of BAC. It was demonstrated that 7 isolates showed direct resistance to BAC, and 35 isolates showed cross-resistance to at least one of 10 tested antibiotics. Among these 35 isolates, 15 isolates exhibited an increase in minimum inhibitory concentration (MIC) for tetracycline, followed by 11 isolates for kanamycin and 9 isolates for ampicillin. Salmonella Enteritidis (S. Enteritidis) SJTUSM06 with the highest increase in MIC of tetracycline (from 4 μg/mL to 32 μg/mL) was selected for further study. TMT-labeled proteomics was used to determine key proteins involved in development of cross-resistance to tetracycline in BAC-adapted S. Enteritidis. It was identified that there were 146 differentially expressed proteins, including 95 up-regulated and 51 down-regulated proteins, most of which were involved in carbohydrate and lipid metabolism, ribosomes, transporters, virulence, motility, and stress response pathways. The efflux pump AcrB was significantly upregulated by 2.03-fold in BAC-adapted S. Enteritidis. It was also demonstrated that efflux pump inhibitor phenylalanine-arginine β-naphthylamide (PaβN) decreased the MIC of tetracycline in BAC-adapted S. Enteritidis from 32 μg/mL to 8 μg/mL, indicating that active efflux pump played an important role in the development of resistance to tetracycline induced by BAC. Deletion of acrB resulted in a decrease in the resistance to tetracycline in BAC-adapted S. Enteritidis. Compared with the parent strain, MIC for tetracycline in ΔacrB mutant was 16 μg/mL with a 2-fold decrease. These results demonstrated that AcrB played a positive role in the development of cross-resistance to tetracycline after adaptation of S. Enteritidis to BAC.

Cross protection can undermine the effectiveness of control measures on foodborne pathogens, and therefore brings major implications for food safety. In this work, the capacity of Salmonella Enteritidis to mount ethanol tolerance following acid adaptation was characterized by analysis of cell viability and cell membrane property. It was observed that preadaptation to pH 4.5 significantly (P < 0.05) increased the tolerance of log-phase cells to ethanol; in contrast, stationary-phase cells displayed reduced ethanol tolerance after acid adaptation. However, acid adaptation did not cause cell leakage and morphological change in both log-phase and stationary-phase S. Enteritidis. Fatty acid analysis further revealed that the amount of C_14:0, C_{17:0 cyclo} and C_{19:0 cyclo} fatty acids was increased, while that of C and C fatty acids was decreased, respectively, in response to acid adaptation, regardless of bacterial growth phase. Notably, acid adaptation significantly (P < 0.05) increased the proportion of C_16:0 fatty acid in log-phase cells, but this effect did not occur in stationary-phase cells. Moreover, exogenous addition of C_16:0 fatty acid to stationary-phase acid-adapted cultures was able to enhance bacterial ethanol tolerance. Taken together, C_16:0 fatty acid is involved in the growth-phase-dependent protective effect of acid adaptation on ethanol tolerance in S. Enteritidis.