Systems-Level Identification of Resistance-Associated Metabolites in Foodborne Pathogens

Year 2025, Volume: 29 Issue: 6, 699 - 716, 23.12.2025

Fatma Gizem Avcı

https://doi.org/10.16984/saufenbilder.1710007

Abstract

Foodborne pathogens remain a pressing global health concern and account for serious infections and even deaths. Among the leading bacterial pathogens contributing to these infections are Campylobacter jejuni, Listeria monocytogenes, and Salmonella enterica, all of which are associated with serious health complications and pose significant challenges for public health systems and food safety. The improper uses of antimicrobials in both human and veterinary settings compound this issue, as the growing threat of antimicrobial resistance is exacerbated by these practices. In the current study, the stress responses in foodborne pathogens C. jejuni subsp. jejuni 81-176, L. monocytogenes EGD-e (serotype 1/2a), and S. enterica serovar Typhimurium were investigated through reporter metabolite analysis. By integrating systems-level insights, it is aimed to discover novel targets and pathways involved in survival and resistance under several stress conditions. The findings will provide a basis for more effective treatment strategies to combat foodborne infections and mitigate the spread of antimicrobial resistance.

Keywords

Foodborne pathogens , Antimicrobial resistance , Reporter metabolites , Stress response , Drug target

References

• World Health Organization. (2022). WHO global strategy for food safety 2022–2030: towards stronger food safety systems and global cooperation: executive summary [Online]. Available: https://iris.who.int/handle/10665/364638
• D. G. White, S. Zhao, S. Simjee, D. D. Wagner, P. F. McDermott, “Antimicrobial resistance of foodborne pathogens,” Microbes and Infection, vol. 4, no. 4, pp. 405–412, 2002.
• A. H. Havelaar, M. D. Kirk, P. R. Torgerson, H. J. Gibb, T. Hald, R. J. Lake, et al., “World health organization global estimates and regional comparisons of the burden of foodborne disease in 2010,” PLoS Medicine, vol. 12, no. 12, e1001923, 2015.
• Z. Bukari, T. Emmanuel, J. Woodward, R. Ferguson, M. Ezughara, N. Darga, et al, “The global challenge of Campylobacter: antimicrobial resistance and emerging intervention strategies,” Tropical Medicine and Infectious Disease, vol. 10, no. 1, p. 25, 2025.
• Y. El Dessouky, S. W. Elsayed, N. A. Abdelsalam, N. A. Saif, A. Álvarez-Ordóñez, M. Elhadidy, “Genomic insights into zoonotic transmission and antimicrobial resistance in Campylobacter jejuni from farm to fork: A one health perspective,” Gut Pathogens, vol. 14, p. 44, 2022.
• J. Lu, D. Linz, I. Struewing, S. P. Keely, M. Jahne, T. M. Gruber, E. N. Villegas, “Virulence and infectious assessment of a Campylobacter jejuni strain isolated from California gull,” Microbiology Spectrum, vol. 13, no. 5, p. e01705-24, 2025.
• H. Jamali, M. Paydar, S. Ismail, C. Y. Looi, W. F. Wong, B. Radmehr, et al., “Prevalence, antimicrobial susceptibility and virulotyping of Listeria species and Listeria monocytogenes isolated from open-air fish markets,” BMC Microbiology, vol. 15, p. 144, 2015.
• K. Linke, I. Rückerl, K. Brugger, R. Karpiskova, J. Walland, S. Muri-Klinger, et al., “Reservoirs of Listeria species in three environmental ecosystems,” Applied and Environmental Microbiology, vol. 80, no. 18, pp. 5583–5592, 2014.
• L. Hafner, M. Pichon, C. Burucoa, S. H. A. Nusser, A. Moura, M. Garcia-Garcera, et al., “Listeria monocytogenes faecal carriage is common and depends on the gut microbiota,” Nature Communications, vol. 12, p. 6826, 2021.
• V. Yadav, A. K. Poonia, D. Pal, “Salmonella Typhimurium biofilm,” in: Salmonella Biofilms, Infection, and Therapeutic Management, A. Kumar, A. Upadhyay, Academic Press, 2025, pp. 63–74.
• C. Vinueza-Burgos, J. Medina-Santana, M. Ishida, B. Sauders, G. Deiulio, A. Dickey, et al., “Salmonella isolated from street foods and environment of an urban park: A whole genome sequencing approach,” PLoS One, vol. 20, no. 4, p. e0320735, 2025.
• Y. Xiang, K. Zhu, K. Min, Y. Zhang, J. Liu, K. Liu, et al., “Characterization of a Salmonella enterica serovar Typhimurium lineage with rough colony morphology and multidrug resistance,” Nature Communications, vol. 15, p. 6123, 2024.
• M. Farrukh, A. Munawar, Z. Nawaz, N. Hussain, A. Bin Hafeez, P. Szweda, “Antibiotic resistance and preventive strategies in foodborne pathogenic bacteria: A comprehensive review,” Food Science and Biotechnology, vol. 34, pp. 2101–2129, 2025.
• K. Avican, J. Aldahdooh, M. Togninalli, A. K. M. F. Mahmud, J. Tang, K. M. Borgwardt, et al., “RNA atlas of human bacterial pathogens uncovers stress dynamics linked to infection,” Nature Communications, vol. 12, p. 3282, 2021.
• H. Wang, S. Marcišauskas, B. J. Sánchez, I. Domenzain, D. Hermansson, R. Agren, et al., “RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor,” PLoS Computational Biology, vol. 14, p. e1006541, 2018.
• M. Kanehisa, S. Goto, “KEGG: Kyoto Encyclopedia of Genes and Genomes,” Nucleic Acids Research, vol. 28, pp. 27–30, 2000.
• M. Kanehisa, S. Goto, M. Hattori, K. F. Aoki-Kinoshita, M. Itoh, S. Kawashima, et al., “From genomics to chemical genomics: New developments in KEGG,” Nucleic Acids Research, vol. 34, pp. D354–D357. 2006.
• A. P. Oliveira, K. R. Patil, J. Nielsen, “Architecture of transcriptional regulatory circuits is knitted over the topology of bio-molecular interaction networks,” BMC Systems Biology, vol. 2, p. 17, 2008.
• K. R. Patil, J. Nielsen, “Uncovering transcriptional regulation of metabolism by using metabolic network topology,” Proceedings of the National Academy of Sciences of the United States of America, vol. 102, no. 8, pp. 2685–2689, 2005.
• F. G. Avci, “Unraveling bacterial stress responses: Implications for next-generation antimicrobial solutions,” World Journal of Microbiology and Biotechnology, vol. 40, p. 285, 2024.
• J. Lopez-Ibanez, F. Pazos, M. Chagoyen, “MBROLE3: improved functional enrichment of chemical compounds for metabolomics data analysis,” Nucleic Acids Research, vol. 51, pp. W305–W309, 2023.
• G. Cox, A. Sieron, A. M. King, G. De Pascale, A. C. Pawlowski, K. Koteva, et al., “A Common platform for antibiotic dereplication and adjuvant discovery,” Cell Chemical Biology, vol. 24, no. 1, pp. 98–109, 2017.
• G. Kiskó, B. Bajramović, F. Elzhraa, P. Erdei-Tombor, V. Dobó, C. Mohácsi-Farkas, et al., “The invisible threat of antibiotic resistance in food,” Antibiotics, vol. 14, p. 250, 2025.
• S. Dühring, S. Germerodt, C. Skerka, P. F. Zipfel, T. Dandekar, S. Schuster, “Host-pathogen interactions between the human innate immune system and Candida albicans-understanding and modeling defense and evasion strategies,” Frontiers in Microbiology, vol. 6, p. 144328, 2015.
• G. Jorge, D. Silva, J. Dawan, J. Ahn, “Bacterial Stress Responses as Potential Targets in Overcoming Antibiotic Resistance,” Microorganisms, vol. 10, no. 7, p. 1385, 2022.
• R. Pei, L. Zhang, C. Duan, M. Gao, R. Feng, Q. Jia, et al., “Investigation of stress response genes in antimicrobial resistant pathogens sampled from five countries,” Processes, vol. 9, no. 6, p. 927, 2021.
• K. J. Boor, “Bacterial stress responses: What doesn’t kill them can make them stronger,” PLOS Biology, vol. 4, no. 1, p. e23, 2006.
• T. M. Amorim Franco, J. S. Blanchard, “Bacterial branched-chain amino acid biosynthesis: Structures, mechanisms, and drugability,” Biochemistry, vol. 56, pp. 5849–5865, 2017.
• A. Wróbel, K. Arciszewska, D. Maliszewski, D. Drozdowska, “Trimethoprim and other nonclassical antifolates an excellent template for searching modifications of dihydrofolate reductase enzyme inhibitors,” The Journal of Antibiotics, vol. 73, pp. 5–27, 2019.
• M. Tong, E. D. Brown, “Food for thought: Opportunities to target carbon metabolism in antibacterial drug discovery,” Annals of the New York Academy of Sciences, vol. 1524, no. 1, pp. 51–64, 2023.
• F. M. Mobegi, S. A. F. T. van Hijum, P. Burghout, H. J. Bootsma, S. P. W. de Vries, C. E. van der Gaast-de Jongh, E. Simonetti, J. D. Langereis, P. W. M. Hermans, M. I. de Jonge, A. Zomer, “From microbial gene essentiality to novel antimicrobial drug targets,” BMC Genomics, vol. 15, p. 958, 2014.
• N. O. Kaakoush, N. Castaño-Rodríguez, H. M. Mitchell, S. M. Man, “Global epidemiology of Campylobacter infection,” Clinical Microbiology Reviews, vol. 28, no. 3, pp. 687–720, 2015.
• D. A. Rossi, C. F. Dumont, A. C. de S. Santos, M. E. de Lourdes Vaz, R. R. Prado, G. P. Monteiro, et al., “Antibiotic Resistance in the Alternative Lifestyles of Campylobacter jejuni,” Frontiers in Cellular and Infection Microbiology, vol. 11, p. 535757, 2021.
• M. M. A. K. Shawan, H. Al Mahmud, P. S. Gope, N. M. Salauddin, H. Rahman, M. A. Ahmed, et al., “Campylobacter jejuni ATCC 700819: An in silico approach to identify and categorize probable drug targets by subtractive genome analysis,” Journal of Pure and Applied Microbiology, vol. 10, no. 1, pp. 229–241, 2016.
• K. Mehla, J. Ramana, “Novel Drug Targets for food-borne pathogen Campylobacter jejuni: An integrated subtractive genomics and comparative metabolic pathway study,” OMICS: A Journal of Integrative Biology, vol. 19, no. 7, pp. 369–434, 2015.
• D. A. Smith, T. Parish, N. G. Stoker, G. J. Bancroft, “Characterization of auxotrophic mutants of Mycobacterium tuberculosis and their potential as vaccine candidates,” Infection and Immunity, vol. 69, no. 2, pp. 1142–1150, 2001.
• L. Jelsbak, H. Hartman, C. Schroll, J. T. Rosenkrantz, S. Lemire, I. Wallrodt, et al., “Identification of Metabolic pathways essential for fitness of Salmonella typhimurium In Vivo,” PLoS One, vol. 9, no. 7, p. e101869, 2014.
• S. Consalvi, C. Scarpecci, M. Biava, G. Poce, “Mycobacterial tryptophan biosynthesis: A promising target for tuberculosis drug development?” Bioorganic and Medicinal Chemistry Letters, vol. 29, no. 23, p. 126731, 2019.
• S. F. Chiu, K. W. Teng, P. C. Wang, H. Y. Chung, C. J. Wang, H. C. Cheng, et al., “Helicobacter pylori GmhB enzyme involved in ADP-heptose biosynthesis pathway is essential for lipopolysaccharide biosynthesis and bacterial virulence,” Virulence, vol. 12, no. 1, pp. 1610–1628, 2021.
• S. H. Joo, “Lipid a as a drug target and therapeutic molecule,” Biomolecules and Therapeutics (Seoul), vol. 23, no. 6, pp. 510–516, 2015.
• A. Samantha, A. Vrielink, “Lipid a phosphoethanolamine transferase: Regulation, structure and immune response,” Journal of Molecular Biology, vol. 432, no. 18, pp. 5184–5196, 2020.
• V. C. Thai, K. A. Stubbs, M. Sarkar-Tyson, C. M. Kahler, “Phosphoethanolamine transferases as drug discovery targets for therapeutic treatment of multi-drug resistant pathogenic gram-negative bacteria,” Antibiotics, vol. 12, no. 9, p. 1382, 2023.
• M. Kumaraswamy, C. Do, G. Sakoulas, P. Nonejuie, G. W. Tseng, H. King, et al., “Listeria monocytogenes endocarditis: Case report, review of the literature, and laboratory evaluation of potential novel antibiotic synergies,” International Journal of Antimicrobial Agents, vol. 51, no. 3, pp. 468–478, 2018.
• H. Zhang, J. Wang, Z. Chang, X. Liu, W. Chen, Y. Yu, et al., “Listeria monocytogenes contamination characteristics in two ready-to-eat meat plants from 2019 to 2020 in Shanghai,” Frontiers in Microbiology, vol. 12, p. 729114, 2021.
• N. Chandra, T. Qidwai, S. Singh, “Drug Target Identification for Listeria monocytogenes by Subtractive Genomics Approach,” Journal of Pure and Applied Microbiology, vol. 17, no. 3, pp. 1893–1906, 2023.
• B. Zhang, H. Ren, X. Wang, C. Han, Y. Jin, X. Hu, et al., “Comparative genomics analysis to explore the biodiversity and mining novel target genes of Listeria monocytogenes strains from different regions,” Frontiers in Microbiology, vol. 15, p. 1424868, 2024.
• G. A. Prosser, L. P. S. De Carvalho, “Kinetic mechanism and inhibition of Mycobacterium tuberculosis D-alanine: D-alanine ligase by the antibiotic D-cycloserine,” FEBS Journal, vol. 280, no. 4, pp. 1150–1166, 2013.
• V. Škedelj, E. Arsovska, T. Tomašić, A. Kroflič, V. Hodnik, M. Hrast, et al., “6-Arylpyrido[2,3-d]pyrimidines as Novel ATP-Competitive Inhibitors of Bacterial D-Alanine:D-Alanine Ligase,” PLoS One, vol. 7, no. 8, p. e39922, 2012.
• R. Murakami, Y. Muramatsu, E. Minami, K. Masuda, Y. Sakaida, S. Endo, et al., “A novel assay of bacterial peptidoglycan synthesis for natural product screening,” Journal of Antibiotics, vol. 62, pp. 153–158, 2009.
• M. Hrast, B. Vehar, S. Turk, J. Konc, S. Gobec, D. Janežič, “Function of the D-alanine: D-alanine ligase lid loop: A molecular modeling and bioactivity study,” Journal of Medicinal Chemistry, vol. 55, no. 15, pp. 6849–6856, 2012.
• Y. Nakatani, H. K. Opel-Reading, M. Merker, D. Machado, S. Andres, S. S. Kumar, et al., “Role of alanine racemase mutations in Mycobacterium tuberculosis D-cycloserine resistance,” Antimicrobial Agents and Chemotherapy, vol. 61, no. 12, p. e01575-17, 2017.
• S. Rahman, A. Bhattacharya, P. Jana, M. Ganguly, A. K. Das, D. Hazra, et al., “Subtractive proteomics unravel the potency of D-alanine-D-alanine ligase as the drug target for Burkholderia pseudomallei,” International Journal of Biological Macromolecules, vol. 314, p. 144106, 2025.
• M. A. Mraheil, R. Frantz, L. Teubner, H. Wendt, U. Linne, J. Wingerath, et al., “Requirement of the RNA-binding protein SmpB during intracellular growth of Listeria monocytogenes,” International Journal of Medical Microbiology, vol. 307, no. 3, pp. 166–173, 2017.
• J. K. Lithgow, E. J. Hayhurst, G. Cohen, Y. Aharonowitz, S. J. Foster, “Role of a Cysteine Synthase in Staphylococcus aureus,” Journal of Bacteriology, vol. 186, no. 6, pp. 1579–1590, 2004.
• P. Joshi, A. Gupta, V. Gupta, “Insights into multifaceted activities of CysK for therapeutic interventions,” 3 Biotech, vol. 9, p. 44, 2019.
• K. Nishino, E. Nikaido, A. Yamaguchi, “Regulation and physiological function of multidrug efflux pumps in Escherichia coli and Salmonella, Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, vol. 1794, vol. 5, pp. 834–843, 2009.
• World Health Organization. (2024). WHO bacterial priority pathogens list, 2024: Bacterial pathogens of public health importance to guide research, development and strategies to prevent and control antimicrobial resistance, 2024 [Online]. Available: https://www.who.int/publications/i/item/9789240093461
• Y. Gu, X. Kuang, A. Sajid, Y. Wang, Z. Zhang, Z. Xu, et al., “Prevalence and mechanism of antimicrobial resistance and pathogenicity of Salmonella isolated from foodborne animal in China,” LWT Food Science and Technology, vol. 184, p. 114906, 2023.
• Y. Liu, F. Zhang, J. L. Hawkins, J. R. Elder, G. M. Baranzoni, Z. Huang, et al., “Comparative Gene Expression Analysis of Salmonella Typhimurium DT104 in Ground Chicken Extract and Brain Heart Infusion Broth,” Microorganisms, vol. 12, p. 1461, 2024.
• J. S. Matarlo, C. E. Evans, I. Sharma, L. J. Lavaud, S. C. Ngo, R. Shek, et al., “Mechanism of MenE inhibition by acyl-adenylate analogues and discovery of novel antibacterial agents,” Biochemistry, vol. 54, no. 42, pp. 6514–6524, 2015.
• X. Lu, R. Zhou, I. Sharma, X. Li, G. Kumar, S. Swaminathan, et al., “Stable analogues of OSB-AMP: Potent inhibitors of MenE, the o-Succinylbenzoate-CoA synthetase from bacterial menaquinone biosynthesis,” ChemBioChem, vol. 13, no.1, pp. 129–136, 2012.
• C. E. Evans, J. S. Matarlo, P. J. Tonge, D. S. Tan, “Stereoselective synthesis, docking, and biological evaluation of difluoroindanediol-based MenE inhibitors as antibiotics,” Organic Letters, vol. 18, no. 24, pp. 6384–6387, 2016.
• Y. Tian, D. H. Suk, F. Cai, D. Crich, A. D. Mesecar, “Bacillus anthracis o-succinylbenzoyl-CoA synthetase: Reaction kinetics and a novel inhibitor mimicking its reaction intermediate,” Biochemistry, vol. 47, pp. 12434–12447, 2008.
• C. O. Rock, J. E. Cronan, “Escherichia coli as a model for the regulation of dissociable (type II) fatty acid biosynthesis,” Biochimica et Biophysica Acta (BBA) - Lipids and Lipid Metabolism, vol. 1302, no. 1, pp. 1–16, 1996.
• S. Smith, A. Witkowski, A.K. Joshi, “Structural and functional organization of the animal fatty acid synthase,” Progress in Lipid Research, vol. 42, no. 4, pp. 289–317, 2003.
• J. W. Campbell, J. Cronan, “Bacterial fatty acid biosynthesis: Targets for antibacterial drug discovery,” Annual Review of Microbiology, vol. 55, pp. 305–332, 2001.
• C. J. Zheng, M. J. Sohn, W. G. Kim, “Vinaxanthone, a new FabI inhibitor from Penicillium sp.,” Journal of Antimicrobial Chemotherapy, vol. 63, no. 5, pp. 949–953, 2009.
• T. Banerjee, S. K. Sharma, N. Surolia, A. Surolia, “Epigallocatechin gallate is a slow-tight binding inhibitor of enoyl-ACP reductase from Plasmodium falciparum,” Biochemical and Biophysical Research Communications, vol. 377, no. 4, pp. 1238–1242, 2008.
• V. Soni, E. H. Rosenn, R. Venkataraman, “Insights into the central role of N-acetyl-glucosamine-1-phosphate uridyltransferase (GlmU) in peptidoglycan metabolism and its potential as a therapeutic target,” Biochemical Journal, vol. 480, no. 15, pp. 1147–1164, 2023.
• J. A. Wyllie, M. V. McKay, A. S. Barrow, T. P. Soares da Costa, “Biosynthesis of uridine diphosphate N-Acetylglucosamine: An underexploited pathway in the search for novel antibiotics?” IUBMB Life, vol. 74, no. 12, pp. 1232–1252, 2022.
• I. Mochalkin, S. Lightle, Y. Zhu, J. F. Ohren, C. Spessard, N. Y. Chirgadze, et al., “Characterization of substrate binding and catalysis in the potential antibacterial target N‐acetylglucosamine‐1‐phosphate uridyltransferase (GlmU),” Protein Science, vol. 16, no. 12, pp. 2657–2666, 2007.
• H. M. Patel, M. Palkar, R. Karpoormath, “Exploring MDR-TB Inhibitory Potential of 4-Aminoquinazolines as Mycobacterium tuberculosis N-Acetylglucosamine-1-Phosphate Uridyltransferase (GlmUMTB) Inhibitors,” Chemistry and Biodiversity, vol. 17, no. 8, p. e2000237, 2020.
• Y. Li, Y. Zhou, Y. Mac, X. Li, “Design and synthesis of novel cell wall inhibitors of Mycobacterium tuberculosis GlmM and GlmU,” Carbohydrate Research, vol. 346, no. 13, pp. 1714–1720, 2011.
• R. Sharma, I. A. Khan, “Mechanism and Potential Inhibitors of GlmU: A Novel Target for Antimicrobial Drug Discovery,” Current Drug Targets, vol. 18, no. 14, pp. 1587–1597, 2017.
• J. Min, D. Lin, Q. Zhang, J. Zhang, Z. Yu, “Structure-based virtual screening of novel inhibitors of the uridyltransferase activity of Xanthomonas oryzae pv. oryzae GlmU,” European Journal of Medicinal Chemistry, vol. 53, pp. 150–158, 2012.
• R. Sharma, C. Rani, R. Mehra, A. Nargotra, R. Chib, V. S. Rajput, et al., “Identification and characterization of novel small molecule inhibitors of the acetyltransferase activity of Escherichia coli N-acetylglucosamine-1-phosphate-uridyltransferase/glucosamine-1-phosphate-acetyltransferase (GlmU),” Applied Microbiology and Biotechnology, vol. 100, no. 7, pp. 3071–3085, 2016.
• E. B. Brazel, A. Tan, S. L. Neville, A. R. Iverson, S. R. Udagedara, B. A. Cunningham, et al., “Dysregulation of Streptococcus pneumoniae zinc homeostasis breaks ampicillin resistance in a pneumonia infection model,” Cell Reports, vol. 38, no. 2, p. 110202, 2022.