References

1. World Health Organization. Estimating the Burden of Foodborne Diseases. Available online: (accessed on 20 April 2021).
2. Caniça, M.; Manageiro, V.; Abriouel, H.; Moran-Gilad, J.; Franz, C.M.A.P. Antibiotic resistance in foodborne bacteria. Trends Food Sci. Technol. 2019, 84, 41–44.
3. EFSA (European Food Safety Authority); ECDC (European Centre for Disease Prevention and Control). The European Union Summary Report on Antimicrobial Resistance in zoonotic and indicator bacteria from humans, animals and food in 2018/2019. EFSA J. 2021, 19, 6490.
4. Capita, R.; Alonso-Calleja, C. Antibiotic-Resistant Bacteria: A Challenge for the Food Industry. Crit. Rev. Food Sci. Nutr. 2013, 53, 11–48.
5. Doyle, M.P.; Busta, F.; Cords, B.R.; Davidson, P.M.; Hawke, J.; Hurd, H.S.; Isaacson, R.E.; Matthews, K.; Maurer, J.; Meng, J.; et al. Antimicrobial resistance: Implications for the food system. Compr. Rev. Food Sci. Food Saf. 2006, 5, 71–137.
6. Begley, M.; Hill, C. Stress adaptation in foodborne pathogens. Annu. Rev. Food Sci. Technol. 2015, 6, 191–210.
7. Liao, X.; Ma, Y.; Daliri, E.B.M.; Koseki, S.; Wei, S.; Liu, D.; Ye, X.; Chen, S.; Ding, T. Interplay of antibiotic resistance and food-associated stress tolerance in foodborne pathogens. Trends Food Sci. Technol. 2020, 95, 97–106.
8. Kleiner, D.K.; Katz, S.E.; Ward, P.M.L. Development of in vitro antimicrobial resistance in bacteria exposed to residue level exposures of antimicrobial drugs, pesticides and veterinary drugs. Chemotherapy 2007, 53, 132–136.
9. Bordas, A.C.; Brady, M.S.; Siewierski, M.; Katz, S.E. In vitro enhancement of antibiotic resistance development—Interaction of residue levels of pesticides and antibiotics. J. Food Prot. 1997, 60, 531–536.
10. Pöppe, J.; Bote, K.; Merle, R.; Makarova, O.; Roesler, U. Minimum inhibitory concentration of glyphosate and a glyphosate-containing herbicide in Salmonella enterica isolates originating from different time periods, hosts, and serovars. Eur. J. Microbiol. Immunol. 2019, 9, 35–41.
11. Pöppe, J.; Bote, K.; Ramesh, A.; Murugaiyan, J.; Kuropka, B.; Kühl, M.; Johnston, P.; Roesler, U.; Makarova, O. Selection for resistance to a glyphosate-containing herbicide in Salmonella enterica does not result in a sustained activation of the tolerance response or increased cross-tolerance and cross-resistance to clinically important antibiotics. Appl. Environ. Microbiol. 2020, 86, e01204-20.
12. Fernandes, A.R.; Mortimer, D.; Rose, M.; Smith, F.; Steel, Z.; Panton, S. Recently listed Stockholm convention POPs: Analytical methodology, occurrence in food and dietary exposure. Sci. Total Environ. 2019, 678, 793–800.
13. Zhou, Q.; Wu, W.; Lin, C.; Liang, H.; Long, C.; Lv, F.; Pan, J.; Liu, Z.; Wang, B.; Yang, X.; et al. Occurrence and dietary exposure assessment of pentachlorophenol in livestock, poultry, and aquatic foods marketed in Guangdong Province, China: Based on food monitoring data from 2015 to 2018. J. Food Sci. 2021, 86, 1132–1143.
14. Muller, J.F.; Stevens, A.M.; Craig, J.; Love, N.G. Transcriptome analysis reveals that multidrug efflux genes are upregulated to protect Pseudomonas aeruginosa from pentachlorophenol stress. Appl. Environ. Microbiol. 2007, 73, 4550–4558.
15. Xing, Y.; Wu, S.; Men, Y. Exposure to environmental levels of pesticides stimulates and diversifies evolution in Escherichia coli toward higher antibiotic resistance. Environ. Sci. Technol. 2020, 54, 8770–8778.
16. Nasr, A.M.; Mostafa, M.S.; Arnaout, H.H.; Elshimy, A.A.A. The effect of exposure to sub-inhibitory concentrations of hypochlorite and quaternary ammonium compounds on antimicrobial susceptibility of Pseudomonas aeruginosa. Am. J. Infect. Control 2018, 46, e57–e63.
17. Paul, D.; Chakraborty, R.; Mandal, S.M. Biocides and health-care agents are more than just antibiotics: Inducing cross to co-resistance in microbes. Ecotoxicol. Environ. Saf. 2019, 174, 601–610.
18. Davin-Regli, A.; Pages, J.M. Cross-resistance between biocides and antimicrobials: An emerging question. OIE Rev. Sci. Tech. 2012, 31, 89–104.
19. Yu, T.; Jiang, X.; Zhang, Y.; Ji, S.; Gao, W.; Shi, L. Effect of benzalkonium chloride adaptation on sensitivity to antimicrobial agents and tolerance to environmental stresses in Listeria monocytogenes. Front. Microbiol. 2018, 9, 2906.
20. Mc Cay, P.H.; Ocampo-Sosa, A.A.; Fleming, G.T.A. Effect of subinhibitory concentrations of benzalkonium chloride on the competitiveness of Pseudomonas aeruginosa grown in continuous culture. Microbiology 2010, 156, 30–38.
21. Fraud, S.; Campigotto, A.J.; Chen, Z.; Poole, K. MexCD-OprJ multidrug efflux system of Pseudomonas aeruginosa: Involvement in chlorhexidine resistance and induction by membrane-damaging agents dependent upon the AlgU stress response sigma factor. Antimicrob. Agents Chemother. 2008, 52, 4478–4482.
22. Dodd, M.C. Potential impacts of disinfection processes on elimination and deactivation of antibiotic resistance genes during water and wastewater treatment. J. Environ. Monit. 2012, 14, 1754–1771.
23. Obe, T.; Nannapaneni, R.; Sharma, C.S.; Kiess, A. Homologous stress adaptation, antibiotic resistance, and biofilm forming ability of Salmonella enterica serovar Heidelberg ATCC8326 on different food-contact surfaces following exposure to sublethal chlorine concentrations. Poult. Sci. 2018, 97, 951–961.
24. Wang, H.; Wang, J.; Li, S.; Ding, G.; Wang, K.; Zhuang, T.; Huang, X.; Wang, X. Synergistic effect of UV/chlorine in bacterial inactivation, resistance gene removal, and gene conjugative transfer blocking. Water Res. 2020, 185, 116290.
25. Potenski, C.J.; Gandhi, M.; Matthews, K.R. Exposure of Salmonella Enteritidis to chlorine or food preservatives increases susceptibility to antibiotics. FEMS Microbiol. Lett. 2003, 220, 181–186.
26. Venieri, D.; Gounaki, I.; Bikouvaraki, M.; Binas, V.; Zachopoulos, A.; Kiriakidis, G.; Mantzavinos, D. Solar photocatalysis as disinfection technique: Inactivation of Klebsiella pneumoniae in sewage and investigation of changes in antibiotic resistance profile. J. Environ. Manag. 2017, 195, 140–147.
27. Jutkina, J.; Marathe, N.P.; Flach, C.F.; Larsson, D.G.J. Antibiotics and common antibacterial biocides stimulate horizontal transfer of resistance at low concentrations. Sci. Total Environ. 2018, 616–617, 172–178.
28. Nguyen, C.C.; Hugie, C.N.; Kile, M.L.; Navab-Daneshmand, T. Association between heavy metals and antibiotic-resistant human pathogens in environmental reservoirs: A review. Front. Environ. Sci. Eng. 2019, 13, 46.
29. Al-Nabulsi, A.A.; Osaili, T.M.; Elabedeen, N.A.Z.; Jaradat, Z.W.; Shaker, R.R.; Kheirallah, K.A.; Tarazi, Y.H.; Holley, R.A. Impact of environmental stress desiccation, acidity, alkalinity, heat or cold on antibiotic susceptibility of Cronobacter sakazakii. Int. J. Food Microbiol. 2011, 146, 137–143.
30. McMahon, M.A.S.; Xu, J.; Moore, J.E.; Blair, I.S.; McDowell, D.A. Environmental stress and antibiotic resistance in food-related pathogens. Appl. Environ. Microbiol. 2007, 73, 211–217.
31. Komora, N.; Bruschi, C.; Magalhães, R.; Ferreira, V.; Teixeira, P. Survival of Listeria monocytogenes with different antibiotic resistance patterns to food-associated stresses. Int. J. Food Microbiol. 2017, 245, 79–87.
32. EFSA Panel on Food Contact Materials; Enzymes and Processing Aids (CEP); Silano, V.; Baviera, B.; Manuel, J.; Bolognesi, C.; Brüschweiler, B.J.; Chesson, A.; Cocconcelli, P.S.; Crebelli, R.; et al. Evaluation of the safety and efficacy of the organic acids lactic and acetic acids to reduce microbiological surface contamination on pork carcasses and pork cuts. EFSA J. 2018, 16, 5482.
33. Skandamis, P.N.; Stopforth, J.D.; Kendall, P.A.; Belk, K.E.; Scanga, J.A.; Smith, G.C.; Sofos, J.N. Modeling the effect of inoculum size and acid adaptation on growth/no growth interface of Escherichia coli O157:H7. Int. J. Food Microbiol. 2007, 120, 237–249.
34. Samelis, J.; Sofos, J.N.; Kendall, P.A.; Smith, G.C. Effect of acid adaptation on survival of Escherichia coli O157:H7 in meat decontamination washing fluids and potential effects of organic acid interventions on the microbial ecology of the meat plant environment. J. Food Prot. 2002, 65, 33–40.
35. Mani-López, E.; García, H.S.; López-Malo, A. Organic acids as antimicrobials to control Salmonella in meat and poultry products. Food Res. Int. 2012, 45, 713–721.
36. Alonso-Calleja, C.; Guerrero-Ramos, E.; Alonso-Hernando, A.; Capita, R. Adaptation and cross-adaptation of Escherichia coli ATCC 12806 to several food-grade biocides. Food Control 2015, 56, 86–94.
37. Gadea, R.; Glibota, N.; Pérez Pulido, R.; Gálvez, A.; Ortega, E. Effects of exposure to biocides on susceptibility to essential oils and chemical preservatives in bacteria from organic foods. Food Control 2017, 80, 176–182.
38. McMahon, M.A.S.; Blair, I.S.; Moore, J.E.; Mc Dowell, D.A. The rate of horizontal transmission of antibiotic resistance plasmids is increased in food preservation-stressed bacteria. J. Appl. Microbiol. 2007, 103, 1883–1888.
39. Combarros-Fuertes, P.; Fresno, J.M.; Estevinho, M.M.; Sousa-Pimenta, M.; Tornadijo, M.E.; Estevinho, L.M. Honey: Another alternative in the fight against antibiotic-resistant bacteria? Antibiotics 2020, 9, 774.
40. Levinger, O.; Bikels-Goshen, T.; Landau, E.; Fichman, M.; Shapira, R. Epigallocatechin gallate induces upregulation of the two-component VraSR system by evoking a cell wall stress response in Staphylococcus aureus. Appl. Environ. Microbiol. 2012, 78, 7954–7959.
41. Liu, X.; Shen, B.; Du, P.; Wang, N.; Wang, J.; Li, J.; Sun, A. Transcriptomic analysis of the response of Pseudomonas fluorescens to epigallocatechin gallate by RNA-seq. PLoS ONE 2017, 12, e0177938.
42. Hammer, K.A.; Carson, C.F.; Rileya, T.V. Effects of Melaleuca alternifolia (tea tree) essential oil and the major monoterpene component terpinen-4-ol on the development of single- and multistep antibiotic resistance and antimicrobial susceptibility. Antimicrob. Agents Chemother. 2012, 56, 909–915.
43. Hammer, K.A.; Carson, C.F.; Riley, T.V.; Nielsen, J.B. A review of the toxicity of Melaleuca alternifolia (tea tree) oil. Food Chem. Toxicol. 2006, 44, 616–625.
44. McMahon, M.A.S.; Tunney, M.M.; Moore, J.E.; Blair, I.S.; Gilpin, D.F.; McDowell, D.A. Changes in antibiotic susceptibility in staphylococci habituated to sub-lethal concentrations of tea tree oil (Melaleuca alternifolia). Lett. Appl. Microbiol. 2008, 47, 263–268.
45. Fadli, M.; Chevalier, J.; Hassani, L.; Mezrioui, N.E.; Pagès, J.M. Natural extracts stimulate membrane-associated mechanisms of resistance in Gram-negative bacteria. Lett. Appl. Microbiol. 2014, 58, 472–477.
46. Becerril, R.; Nerín, C.; Gómez-Lus, R. Evaluation of bacterial resistance to essential oils and antibiotics after exposure to oregano and cinnamon essential oils. Foodborne Pathog. Dis. 2012, 9, 699–705.
47. Johny, A.K.; Frye, J.G.; Donoghue, A.; Donoghue, D.J.; Porwollik, S.; McClelland, M.; Venkitanarayanan, K. Gene expression response of Salmonella enterica Serotype Enteritidis phage type 8 to subinhibitory concentrations of the plant-derived compounds trans-cinnamaldehyde and eugenol. Front. Microbiol. 2017, 8, 1828.
48. Brul, S.; Coote, P. Preservative agents in foods: Mode of action and microbial resistance mechanisms. Int. J. Food Microbiol. 1999, 50, 1–17.
49. Ibarra-Sánchez, L.A.; El-Haddad, N.; Mahmoud, D.; Miller, M.J.; Karam, L. Advances in nisin use for preservation of dairy products. J. Dairy Sci. 2020, 103, 2041–2052.
50. U.S. Food & Drug Administration. Microorganisms & Microbial-Derived Ingredients Used in Food (Partial List). Available online: (accessed on 10 April 2021).
51. Kumar, S.; Devi, S.; Sood, S.K.; Kapila, S.; Narayan, K.S.; Shandilya, S. Antibiotic resistance and virulence genes in nisin-resistant Enterococcus faecalis isolated from raw buffalo milk modulate the innate functions of rat macrophages. J. Appl. Microbiol. 2019, 127, 897–910.
52. Dubois-Brissonnet, F.; Naïtali, M.; Mafu, A.A.; Briandet, R. Induction of fatty acid composition modifications and tolerance to biocides in Salmonella enterica serovar Typhimurium by plant-derived terpenes. Appl. Environ. Microbiol. 2011, 77, 906–910.
53. Apolónio, J.; Faleiro, M.L.; Miguel, M.G.; Neto, L. No induction of antimicrobial resistance in Staphylococcus aureus and Listeria monocytogenes during continuous exposure to eugenol and citral. FEMS Microbiol. Lett. 2014, 354, 92–101.
54. Oliveira, A.R.; Domingues, F.C.; Ferreira, S. The influence of resveratrol adaptation on resistance to antibiotics, benzalkonium chloride, heat and acid stresses of Staphylococcus aureus and Listeria monocytogenes. Food Control 2017, 73, 1420–1425.
55. Chen, Y.; Wen, Q.; Chen, S.; Guo, D.; Xu, Y.; Liang, S.; Xia, X.; Yang, B.; Shi, C. Effect of thymoquinone on the resistance of Cronobacter sakazakii to environmental stresses and antibiotics. Food Control 2020, 109, 106944.
56. Monte, D.F.M.; Tavares, A.G.; Albuquerque, A.R.; Sampaio, F.C.; Oliveira, T.C.R.M.; Franco, O.L.; Souza, E.L.; Magnani, M. Tolerance response of multidrug-resistant Salmonella enterica strains to habituation to Origanum vulgare L. essential oil. Front. Microbiol. 2014, 5, 721.
57. Faezi-Ghasemi, M.; Kazemi, S. Effect of sub-lethal environmental stresses on the cell survival and antibacterial susceptibility of Listeria monocytogenes PTCC1297. Zahedan J. Res. Med. Sci. 2014, 17, e1915.
58. Taher, E.M.; Hemmatzadeh, F.; Aly, S.A.; Elesswy, H.A.; Petrovski, K.R. Molecular characterization of antimicrobial resistance genes on farms and in commercial milk with emphasis on the effect of currently practiced heat treatments on viable but nonculturable formation. J. Dairy Sci. 2020, 103, 9936–9945.
59. Guo, M.; Huang, J.; Hu, H.; Liu, W.; Yang, J. UV inactivation and characteristics after photoreactivation of Escherichia coli with plasmid: Health safety concern about UV disinfection. Water Res. 2012, 46, 4031–4036.
60. Delorme, M.M.; Guimarães, J.T.; Coutinho, N.M.; Balthazar, C.F.; Rocha, R.S.; Silva, R.; Margalho, L.P.; Pimentel, T.C.; Silva, M.C.; Freitas, M.Q.; et al. Ultraviolet radiation: An interesting technology to preserve quality and safety of milk and dairy foods. Trends Food Sci. Technol. 2020, 102, 146–154.
61. Zhang, G.; Li, W.; Chen, S.; Zhou, W.; Chen, J. Problems of conventional disinfection and new sterilization methods for antibiotic resistance control. Chemosphere 2020, 254, 126831.
62. Fiorentino, A.; Ferro, G.; Alferez, M.C.; Polo-López, M.I.; Fernández-Ibañez, P.; Rizzo, L. Inactivation and regrowth of multidrug resistant bacteria in urban wastewater after disinfection by solar-driven and chlorination processes. J. Photochem. Photobiol. B Biol. 2015, 148, 43–50.
63. Umar, M.; Roddick, F.; Fan, L. Moving from the traditional paradigm of pathogen inactivation to controlling antibiotic resistance in water—Role of ultraviolet irradiation. Sci. Total Environ. 2019, 662, 923–939.
64. Guo, M.T.; Yuan, Q.-B.; Yang, J. Ultraviolet reduction of erythromycin and tetracycline resistant heterotrophic bacteria and their resistance genes in municipal wastewater. Chemosphere 2013, 93, 2864–2868.
65. Rizzo, L.; Fiorentino, A.; Anselmo, A. Advanced treatment of urban wastewater by UV radiation: Effect on antibiotics and antibiotic-resistant E. coli strains. Chemosphere 2013, 92, 171–176.
66. Arslan-Alaton, I.; Karatas, A.; Pehlivan, Ö.; Ucun, O.K.; Ölmez-Hancı, T. Effect of UV-A-assisted iron-based and UV-C-driven oxidation processes on organic matter and antibiotic resistance removal in tertiary treated urban wastewater. Catal. Today 2021, 361, 152–158.
67. Chu, L.; Chen, D.; Wang, J.; Yang, Z.; Yang, Q.; Shen, Y. Degradation of antibiotics and inactivation of antibiotic resistance genes (ARGs) in Cephalosporin C fermentation residues using ionizing radiation, ozonation and thermal treatment. J. Hazard. Mater. 2020, 382, 121058.
68. Álvarez-Molina, A.; de Toro, M.; Ruiz, L.; López, M.; Prieto, M.; Alvarez-Ordóñez, A. Selection for antimicrobial resistance in foodborne pathogens through exposure to UV light and nonthermal atmospheric plasma decontamination techniques. Appl. Environ. Microbiol. 2020, 86.
69. Guo, L.; Xu, R.; Zhao, Y.; Liu, D.; Liu, Z.; Wang, X.; Chen, H.; Kong, M.G. Gas plasma pre-treatment increases antibiotic sensitivity and persister eradication in methicillin-resistant Staphylococcus aureus. Front. Microbiol. 2018, 9, 537.
70. Zuo, P.; Yu, P.; Alvarez, P.J.J. Beta-lactam-induced outer membrane alteration confers E. coli a fortuitous competitive advantage through cross-resistance to bacteriophages. Environ. Sci. Technol. Lett. 2020, 7, 428–433.
71. Breitbart, M.; Bonnain, C.; Malki, K.; Sawaya, N.A. Phage puppet masters of the marine microbial realm. Nat. Microbiol. 2018, 3, 754–766.
72. Clokie, M.R.J.; Millard, A.D.; Letarov, A.V.; Heaphy, S. Phages in nature. Bacteriophage 2011, 1, 31–45.
73. Lin, D.M.; Koskella, B.; Lin, H.C. Phage therapy: An alternative to antibiotics in the age of multi-drug resistance. World J. Gastrointest. Pharmacol. Ther. 2017, 8, 162–173.
74. Burmeister, A.R.; Fortier, A.; Roush, C.; Lessing, A.J.; Bender, R.G.; Barahman, R.; Grant, R.; Chan, B.K.; Turner, P.E. Pleiotropy complicates a trade-off between phage resistance and antibiotic resistance. Proc. Natl. Acad. Sci. USA 2020, 117, 11207–11216.
75. Chan, B.K.; Sistrom, M.; Wertz, J.E.; Kortright, K.E.; Narayan, D.; Turner, P.E. Phage selection restores antibiotic sensitivity in MDR Pseudomonas aeruginosa. Sci. Rep. 2016, 6, 26717.
76. Kim, M.; Jo, Y.; Hwang, Y.J.; Hong, H.W.; Hong, S.S.; Park, K.; Myung, H. Phage-antibiotic synergy via delayed lysis. Appl. Environ. Microbiol. 2018, 84, e02085-18.
77. Allen, R.C.; Pfrunder-Cardozo, K.R.; Meinel, D.; Egli, A.; Hall, A.R. Associations among antibiotic and phage resistance phenotypes in natural and clinical Escherichia coli isolates. MBio 2017, 8, e01341-17.
78. Gómez-Gómez, C.; Blanco-Picazo, P.; Brown-Jaque, M.; Quirós, P.; Rodríguez-Rubio, L.; Cerdà-Cuellar, M.; Muniesa, M. Infectious phage particles packaging antibiotic resistance genes found in meat products and chicken feces. Sci. Rep. 2019, 9, 13281.
79. Gurney, J.; Pradier, L.; Griffin, J.S.; Gougat-Barbera, C.; Chan, B.K.; Turner, P.E.; Kaltz, O.; Hochberg, M.E. Phage steering of antibiotic-resistance evolution in the bacterial pathogen, Pseudomonas aeruginosa. Evol. Med. Public Health 2020, 2020, 148–157.
80. German, G.J.; Misra, R. The TolC protein of Escherichia coli serves as a cell-surface receptor for the newly characterized TLS bacteriophage. J. Mol. Biol. 2001, 308, 579–585.