Epigenetic Regulation and Metabolic Adaptation in the Emergence of Multidrug Resistance Among Clinically Significant Gram-Negative Pathogen

Abstract

The swift development of multidrug-resistant (MDR) Gram-negative microbes has emerged as a key health problem in the world, greatly reducing the efficacy of the available antimicrobial treatments. Among the most designable effective pathogens that cause severe healthcare-associated and community-acquired infections, Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Acinetobacter baumannii can be named. Historically, genetic processes, such as horizontal gene transfer, chromosomal mutation, enzymatic inactivation of antibiotics, and overexpression of efflux pumps, have been recognized as the major causes of antibiotic resistance in these organisms. Nevertheless, there is increasingly strong evidence of a significant role of non-genetic regulatory mechanisms in controlling adaptation and survival of bacteria to antimicrobial pressure.

In the recent past, research on epigenetic regulation and metabolic adaptation has been noted as critical factors in the development and maintenance of MDR in Gram-negative pathogens. Flexible gene expression in bacteria is made possible through epigenetic processes, such as DNA methylation, phase variation, and nucleoid-associated protein activity, but does not change the genome sequence. These processes bring about simple and reversible phenotypic alterations in bacteria, which enables the populations to produce phenotypic diversity and increase their ability to endure the environmental exposure as a consequence of antibiotic exposure.

Simultaneously, metabolic adjustment has also been much more highly appreciated as a pivotal determinant in bacterial tolerance and resistance towards antibiotics. When exposed to antimicrobial agents, significant changes are commonly induced on the central metabolic pathways, such as carbon metabolism, energy production, and oxidative stress responses. Such metabolic changes may affect the growth rate of bacteria, the cellular dynamics, and the membrane dynamics, which have an eventual impact on antibiotic susceptibility. Moreover, the metabolic reprogramming can also enhance the development of persister cells, subpopulations with a transient antibiotic tolerance, which can lead to the long-term expansion of stable resistance in the form of long-term mechanisms.

Critically, metabolic processes and epigenetic regulation are thought to be very linked. The expressions of genes in metabolic pathways can be regulated by epigenetic modifications and intracellular metabolic states may affect epigenetic regulation systems via the provision of important metabolites. This bidirectional interaction creates a complicated regulatory network that increases the adaptability of bacteria to the antibiotic pressure and is favorable to the emergence of multidrug resistance.

The purpose of the review is to obtain a complete picture of the present-day knowledge on epigenetic regulation and metabolic adaptation of clinically significant Gram-negative bacteria and their contributions to the development of multidrug resistance. Besides, the therapeutic implications that have been discussed in the review with regard to targeting these regulatory systems and emerging strategies that could play a role in the development of novel antimicrobial interventions are discussed. Better insight into these processes can possibly be used to discover new methods to address MDR infection and enhance the efficacy of future antimicrobial treatment.

Keywords:

Multiple myeloma, Extramedullary disease, Paraspinal mass, Retrovertebral tumor, MRI, Plasmacytoma, Neurosurgery

References

Kollef MH, Bassetti M, Francois B, et al. The intensive care medicine research agenda on multidrug-resistant bacteria, antibiotics, and stewardship. Intensive Care Med. 2017; 43:1187–1197.

Jasovský D, Littmann J, Zorzet A, et al. Antimicrobial resistance-a threat to the world’s sustainable development. Ups J Med Sci. 2016; 121:159–164.

Magiorakos AP, Srinivasan A, Carey RB, et al. Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance. Clin Microbiol Infect. 2012; 18:268–281.

Bassetti M, Poulakou G, Timsit JF. Focus on antimicrobial use in the era of increasing antimicrobial resistance in ICU. Intensive Care Med. 2016; 42:955–958.

Blair JM, WebberMA,BaylayAJ,etal. Molecular mechanisms of antibiotic resistance. Nat Rev Microbiol. 2015; 13:42–51.

Khamees, H. H., Mohammed, A. A., Hussein, S. A. M., Ahmed, M. A., & Raoof, A. S. M. (2024). In-Silico Study OF Destabilizing Alzheimer's Aβ42 Protofibrils with Curcumin. International Journal of Medical Science and Dental Health, 10(05), 76-84.

Cohen NR, Lobritz MA, Collins JJ. Microbial persistence and the road to drug resistance. Cell Host Microbe. 2013; 13:632–642.

Kauffman SA. The epigenetic landscape and clinical implications. J Crit Care. 2011;26: e15.

Casadesús J, Low DA. Programmed heterogeneity: epigenetic mechanisms in bacteria. J Biol Chem. 2013; 288:13929–13935.

Day T. Interpreting phenotypic antibiotic tolerance and persister cells as evolution via epigenetic inheritance. Mol Ecol. 2016; 25:1869–1882.

Fernández L, Breidenstein EB, Hancock RE. Creeping baselines and adaptive resistance to antibiotics. Drug Resist Updat. 2011; 14:1–21.

Netea MG, Joosten LA, Latz E, et al. Trained immunity: a program of innate immune memory in health and disease. Science. 2016;352:aaf1098.

Crimi E, Cirri S, Benincasa G, et al. Epigenetics mechanisms in multiorgan dysfunction syndrome. Anesth Analg. 2019; 129:1422–1432. doi:10.1213/ANE. 0000000000004331

van der Wijst MG, Venkiteswaran M, Chen H, et al. Local chromatin microenvironment determines DNMT activity: from DNA methyltransferase to DNA demethylase or DNA dehydroxymethylase. Epigenetics. 2015; 10:671–676.

Greenberg MVC, Bourc’his D. The diverse roles of DNA methylation in mammalian development and disease. Nat Rev Mol Cell Biol.2019; 20:590–607.

Aherkar, V. V., Mohammed, A. A., Al-Shimary, A. A., Kshirsagar, V., Shendage, R., Ubale, P. A., ... & Ovhal, R. M. (2025). Photocatalytic dye degradation efficacy and antimicrobial potency of zinc oxide nanoparticles synthesized via sol-gel method. Next Materials, 9, 100972.

Jones PA. Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet. 2012;13 (7):484–492.

Fritz KS. Chemical acetylation and deacetylation. Methods Mol Biol. 2013; 1077:191–201.

Taniguchi Y. BET Bromodomain as a target of epigenetic therapy. 2016; 64:540–547. Chem Pharm Bull (Tokyo).

Seto E, Yoshida M. Erasers of histone acetylation: the histone deacetylase enzymes. Cold Spring Harb Perspect Biol. 2014;6: a018713.

Greer EL, Shi Y. Histone methylation: a dynamic mark in health, disease and inheritance. Nat Rev Genet. 2012; 13:343–357.

Holoch D, Moazed D. RNA-mediated epigenetic regulation of gene expression. Nat Rev Genet. 2015; 16:71–84.

Chan AO, Lam SK, Wong BC, et al. Promoter methylation of E-cadherin gene in gastric mucosa associated with Helicobacter pylori infection and in gastric cancer. Gut. 2003; 52:502–506.

Bussiere FI, Michel V, Memet S, et al. H. pylori-induced promoter hypermethylation downregulates USF1 and USF2 transcription factor gene expression. Cell Microbiol. 2010; 12:1124–1133.

Yan J, Zhang M, Zhang J, et al. Helicobacter pylori infection promotes methylation of WWOX gene in human gastric cancer. Biochem Biophys Res Commun. 2011; 408:99–102.

Mohammed, A. A., Barale, S. S., Dhotare, P. S., & Sonawane, K. D. (2025). Polymyxin-B as a novel inhibitor of amyloid beta aggregation: Computational insights and experimental validation. Journal of Molecular Structure, 143738.

Ando T, Yoshida T, Enomoto S, et al. DNA methylation of microRNA genes in gastric mucosae of gastric cancer patients: its possible involvement in the formation of epigenetic field defect. Int J Cancer. 2009;124:2367–2374.

Tolg C, Sabha N, Cortese R, et al. Uropathogenic E. coli infection provokes epigenetic downregulation of CDKN2A (p16INK4A) in uroepithelial cells. Lab Invest. 2011; 91:825–836.

Pacis A, Tailleux L, Morin AM, et al. Bacterial infection remodels the DNA methylation landscape of human dendritic cells. Genome Res. 2015; 25:1801–1811.

Sharma G, Sowpati DT, Singh P, et al. Genome-wide non-CpG methylation of the host genome during M. tuberculosis infection. Sci Rep. 2016; 6:25006.

Napoli C, Benincasa G. Loscalzo J epigenetic inheritance underlying pulmonary arterial hypertension. Arterioscler Thromb Vasc Biol. 2019; 39:653–664. doi:10.1213/ANE.0000000000004331

Napoli C, Benincasa G, Schiano C, et al. Differential epigenetic factors in the prediction of cardiovascular risk in diabetic patients. Eur Heart J Cardiovasc Pharmacother. 2019. DOI:10.1093/ehjcvp/pvz062

de Nigris F, Cacciatore F, Mancini FP, et al. Epigenetic hallmarks of fetal early atherosclerotic lesions in humans. JAMA Cardiol. 2018;3:1184–1191. doi:10.1001/jama cardio.2018.3546

Napoli C, Crudele V, Soricelli A, et al. Primary prevention of atherosclerosis: a clinical challenge for the reversal of epigenetic mechanisms? Circulation. 2012; 125:2363–2373. doi:10.1161/CIRCULATIONAHA. 111.085787

Bobetsis YA, Barros SP, Lin DM, et al. Bacterial infection promotes DNA hypermethylation. J Dent Res. 2007; 86:169–174.

Sharba, M. M., Mohammed, A. A., & Mohammed, S. F. (2022). Isolation and Characterization of tannase from isolated Bacillus subtilis.

Bierne H, Hamon M, Cossart P. Epigenetics and bacterial infections. Cold Spring Harb Perspect Med. 2012;2: a010272.

Schmeck B, Beermann W, van Laak V, et al. Intracellular bacteria differentially regulated endothelial cytokine release by MAPK-dependent histone modification. J Immunol. 2005; 175:2843–2850.

Bandyopadhaya A, Tsurumi A, Maura D, et al. A quorum-sensing signal promotes host tolerance training through HDAC1-mediated epigenetic reprogramming. Nat Microbiol. 2016; 1:16174.

Descamps HC, Herrmann B, Wiredu D, et al. The path toward using microbial metabolites as therapies. EBioMedicine. 2019; 44:747–754.

Saeed S, Quintin J, Kerstens HH, et al. Epigenetic programming of monocyte-to-macrophage differentiation and trained innate immunity. Science. 2014; 345:1251086.

Rolando M, Sanulli S, Rusniok C, et al. Legionella pneumophila effector RomA uniquely modifies host chromatin to repress gene expression and promote intracellular bacterial replication. Cell Host Microbe. 2013; 13:395–405.

Qi Y, Cui L, Ge Y, et al. Altered serum microRNAs as biomarkers for the early diagnosis of pulmonary tuberculosis infection. BMC Infect Dis. 2012; 12:384.

Cui JY, Liang HW, Pan XL, et al. Characterization of a novel panel of plasma microRNAs that discriminates between mycobacterium tuberculosis infection and healthy individuals. PLoS One. 2017;12: e0184113.

Alipoor SD, Tabarsi P, Varahram M, et al. Serum exosomal miRNAs are associated with active pulmonary tuberculosis. Dis Markers. 2019; 2019:1907426.

Al-Karawi, A. S., Kadhim, A. S., Mohammed, A. A., Alajeeli, F., & Lippi, G. (2024). The Impact of Spirulina Supplementation on Iraqi Obese Females: A Cohort Study. Al-Mustansiriyah Journal of Science, 35(4), 24-30.

Yan H, Xu R, Zhang X, et al. Identifying differentially expressed long non-coding RNAs in PBMCs in response to the infection of multidrug-resistant tuberculosis. Infect Drug Resist. 2018; 11:945–959.

Parmeciano Di Noto G, Molina MC, Quiroga C. Insights into non-coding RNAs as novel antimicrobial drugs. Front Genet. 2019; 10:57.

Li W, Sun Z. Mechanism of action for HDAC inhibitors-insights from omics approaches. Int J Mol Sci. 2019; 20:1616.

Fischer N, Sechet E, Friedman R, et al. Histone deacetylase inhibition enhances antimicrobial peptide but not inflammatory cytokine expression upon bacterial challenge. Proc Natl Acad Sci U S A. 2016;113:2993–3001.

Ariffin JK, Das Gupta K, Kapetanovic R, et al. Histone deacetylase inhibitors promote mitochondrial reactive oxygen species production and bacterial clearance by human macrophages. Antimicrob Agents Chemother. 2015; 60:1521–1529.

Zhang T, Yu J, Zhang Y, et al. Salmonella enterica serovar enteritidis modulates intestinal epithelial miR-128 levels to decrease macrophage recruitment via macrophage colony-stimulating factor. J Infect Dis. 2014; 209:2000–2011.

Vincent JL, Rello J, Marshall J, et al. International study of the prevalence and outcomes of infection in intensive care units. JAMA. 2009; 302:2323–2329.

Zilahi G, Artigas A, Martin-Loeches I. What’s new in multidrug-resistant pathogens in the ICU? Ann Intensive Care.2016; 6:96.

Eichenberger EM, Thaden JT. Epidemiology and mechanisms of resistance of extensively drug resistant gram-negative bacteria. Antibiotics (Basel). 2019;8. DOI:10.3390/antibiotics8020037

Nadaf, N. H., Mohammed, A. A., & Nadaf, S. H. (2025). Inspiration from Natural Biomass Utilization System for a Sustainable Lignocellulosic Refinery. In Recent Trends in Lignocellulosic Biofuels and Bioenergy: Advancements and Sustainability Assessment (pp. 123-141). Singapore: Springer Nature Singapore.

Liao J, Tsai C, Patel S, et al. Acetylome of Acinetobacter baumanni SK17 reveals a highly-conserved modification of histone-like protein HU. Front Mol Biosci. 2017; 4:77.

LenO, Garzoni C,LumbrerasC,etal. Recommendations for screening of donor and recipient prior to solid organ transplantation and to minimize transmission of donor-derived infections. Clin Microbiol Infect. 2014; 20:10–18.

Westphal GA, Garcia VD, Souza RL, et al. Guidelines for the assessment and acceptance of potential brain-dead organ donors. Rev Bras Ter Intensiva. 2016; 28:220–255.

Grossi PA. Donor-derived infections, lessons learnt from the past, and what is the future going to bring us. Curr Opin Organ Transplant. 2018; 23:417–422.

Fishman JA. Infection in organ transplantation. Am J Transplant. 2017; 17:856.

Franci G, Folliero V, Cammarota M, et al. Epigenetic modulator UVI5008 inhibits MRSA by interfering with bacterial gyrase. Sci Rep. 2018; 8:13117.

Choi SW, Braun T, Chang L, et al. Vorinostat plus tacrolimus and mycophenolate to prevent graft-versushost disease after related-donor reduced-intensity conditioning allogeneic haemopoietic stem-cell transplantation: a phase 1/2 trial. Lancet Oncol. 2014; 15:87–95.

Cole J, Morris P, Dickman MJ, et al. The therapeutic potential of epigenetic manipulation during infectious diseases. Pharmacol Ther. 2016; 167:85–99.

Ostuni R, Piccolo V, Barozzi I, et al. Latent enhancers activated by stimulation in differentiated cells. Cell. 2013; 152:157–171.

MOHAMMED, A. A., AL-SHIMARY, A. A., MAHMOUD, H. Q., ABDULLAH, T. H., & JASIM, B. H. (2025). Comparative Molecular Insights into the Interaction of Dobutamine, Quercetin, and Fisetin with Amyloid Beta Monomer and Protofibril. Chinese Journal of Analytical Chemistry, 100674.

Glant TT, Besenyei T, Kádár A, et al. Differentially expressed epigenome modifiers, including aurora kinases A and B, in immune cells in rheumatoid arthritis in humans and mouse models. Arthritis Rheum. 2013; 65:1725–1735.

Brasacchio D, Okabe J, Tikellis C, et al. Hyperglycemia induces a dynamic cooperativity of histone methylase and demethylase enzymes associated with gene-activating epigenetic marks that coexist on the lysine tail. Diabetes. 2009; 58:1229–1236.

Kleinnijenhuis J, Quintin J, Preijers F, et al. Bacille Calmette-Guerin induces NOD2-dependent nonspecific protection from reinfection via epigenetic reprogramming of monocytes. Proc Natl Acad Sci U S A. 2012; 109:17537–17542.

van Splunter M, van Osch TLJ, Brugman S, et al. Induction of trained innate immunity in human monocytes by bovine milk and milk-derived immunoglobulin G. Nutrients. 2018;10. DOI:10.3390/nu10101378

Benincasa G, Mansueto G, Napoli C. Fluid-based assays and precision medicine of cardiovascular diseases: the ‘hope’ for Pandora’sbox? JClinPathol.2019;72:785–799. doi:10.1136/jclinpath-2019-206178

Sommese L, Zullo A, Mancini FP, et al. Clinical relevance of epigenetics in the onset and management of type 2 diabetes mellitus. Epigenetics. 2017;12:401–415. doi:10.1080/15592294.2016.1278097

Benincasa G, Marfella R, Della Mura N, et al. Strengths and opportunities of network medicine in cardiovascular diseases. Circ J. 2020; 84:144–152. doi:10.1253/circj. CJ-19-0879

Miryala SK, Ramaiah S. Exploring the multi-drug resistance in Escherichia coli O157: h7by gene interaction network: a systems biology approach. Genomics. 2019; 111:958–965.

Lin J, Zhou D, Steitz TA, Polikanov YS, Gagnon MG. 2018. Ribosome-targeting antibiotics: modes of action, mechanisms of resistance, and implications for drug design. Annu Rev Biochem 87:451–478. https://doi.org/ 10.1146/annurev-biochem-062917-011942.

Sat B, Hazan R, Fisher T, Khaner H, Glaser G, Engelberg-Kulka H. 2001. Programmed cell death in Escherichia coli: some antibiotics can trigger mazEF lethality. J Bacteriol 183:2041–2045. https://doi.org/10.1128/JB.183.6.2041-2045.2001.

Schlegel A, Böhm A, Lee SJ, Peist R, Decker K, Boos W. 2002. Network regulation of the Escherichia coli maltose system. J Mol Microbiol Biotechnol 4:301–307.

JochimsenB, LolleS,McSorleyFR,NabiM,StougaardJ,ZechelDL,HoveJensen B. 2011. Five phosphonate operon gene products as components of a multi-subunit complex of the carbon-phosphorus lyase pathway. Proc Natl Acad Sci U S A108:11393–11398.https://doi.org/10.1073/pnas.1104922108.

Choi U, Lee CR. 2019. Distinct roles of outer membrane porins in antibiotic resistance and membrane integrity in Escherichia coli. Front Microbiol 10:953. https://doi.org/10.3389/fmicb.2019.00953.

Jacoby GA. 2009. AmpC beta-lactamases. Clin Microbiol Rev 22: 161–182, Table of Contents. https://doi.org/10.1128/CMR.00036-08.

Kouidmi I, Levesque RC, Paradis-Bleau C. 2014. The biology of Mur ligases as an antibacterial target. Mol Microbiol 94:242–253. https://doi.org/10 .1111/mmi.12758.

Marceau AH. 2012. Functions of single-strand DNA-binding proteins in DNA replication, recombination, and repair. Methods Mol Biol 922:1–21. https://doi.org/10.1007/978-1-62703-032-8_1.

Jin J, Wu R, Zhu J, Yang S, Lei Z, Wang N, Singh VK, Zheng J, Jia Z. 2015. Insights into the cellular function of YhdE, a nucleotide pyrophosphatase from Escherichia coli. PLoS One 10: e0117823. https://doi.org/10.1371/ journal. pone.0117823.

Ilic S, Cohen S, Singh M, Tam B, Dayan A, Akabayov B. 2018. DnaG primase-A target for the development of novel antibacterial agents. Antibiotics (Basel) 7:72. https://doi.org/10.3390/antibiotics7030072.

Nanninga N. 1998. Morphogenesis of Escherichia coli. Microbiol Mol Biol Rev 62:110–129. https://doi.org/10.1128/MMBR.62.1.110-129.1998.