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Volume 26
Issue 15
10.3390/ijms26157255
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Review

Proteomic Insights into Bacterial Responses to Antibiotics: A Narrative Review

by
Sara Elsa Aita
1,
Maria Vittoria Ristori
2,3,*,
Antonio Cristiano
2,4,
Tiziana Marfoli
2,
Marina De Cesaris
2,
Vincenzo La Vaccara
1,
Roberto Cammarata
1,
Damiano Caputo
1,5,
Silvia Spoto
6 and
Silvia Angeletti
2,3
1
Operative Research Unit of General Surgery, Fondazione Policlinico Universitario Campus Bio-Medico, 00128 Rome, Italy
2
Operative Research Unit of Laboratory, Fondazione Policlinico Universitario Campus Bio-Medico, 00128 Rome, Italy
3
Research Unit of Clinical Laboratory Science, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21, 00128 Rome, Italy
4
Department of Biomedicine and Prevention, PhD Program in Immunology, Molecular Medicine and Applied Biotechnologies, Tor Vergata University, 00133 Rome, Italy
5
Research Unit of General Surgery, Università Campus Bio-Medico di Roma, 00128 Rome, Italy
6
Diagnostic and Therapeutic Medicine Department, Fondazione Policlinico Universitario Campus Bio-Medico, 00128 Rome, Italy
*
Author to whom correspondence should be addressed.
Int. J. Mol. Sci. 2025, 26(15), 7255; https://doi.org/10.3390/ijms26157255 (registering DOI)
Submission received: 13 June 2025 / Revised: 22 July 2025 / Accepted: 23 July 2025 / Published: 27 July 2025
(This article belongs to the Special Issue Proteomics: An Invaluable Tool to Gain Information on Biological Systems and Their Disease Alterations)
Versions Notes

Abstract

Antimicrobial resistance is an escalating global threat that undermines the efficacy of modern antibiotics and places a substantial economic burden on healthcare systems—costing Europe alone over EUR 11.7 billion each year due to rising medical expenses and productivity losses. While genomics and transcriptomics have significantly advanced our understanding of the genetic foundations of resistance, they often fail to capture the dynamic, real-time adaptations that enable bacterial survival. Proteomics, particularly mass spectrometry-based strategies, bridges this gap by uncovering the functional protein-level changes that drive resistance, persistence, and tolerance under antibiotic pressure. In this review, we examine how proteomic approaches provide new insights into resistance mechanisms across various antibiotic classes, with a particular focus on β-lactams, aminoglycosides, and fluoroquinolones, highlighting clinically relevant pathogens, especially members of the ESKAPE group. Finally, we examine future directions, including the integration of proteomics with other omic technologies and the growing role of artificial intelligence in resistance prediction, paving the way for more predictive, personalized, and effective solutions to combat antimicrobial resistance.
Keywords: antimicrobial resistance; multi-drug-resistance; proteomics; mass spectrometry; ESKAPE pathogens antimicrobial resistance; multi-drug-resistance; proteomics; mass spectrometry; ESKAPE pathogens

Share and Cite

MDPI and ACS Style

Aita, S.E.; Ristori, M.V.; Cristiano, A.; Marfoli, T.; De Cesaris, M.; La Vaccara, V.; Cammarata, R.; Caputo, D.; Spoto, S.; Angeletti, S. Proteomic Insights into Bacterial Responses to Antibiotics: A Narrative Review. Int. J. Mol. Sci. 2025, 26, 7255. https://doi.org/10.3390/ijms26157255

AMA Style

Aita SE, Ristori MV, Cristiano A, Marfoli T, De Cesaris M, La Vaccara V, Cammarata R, Caputo D, Spoto S, Angeletti S. Proteomic Insights into Bacterial Responses to Antibiotics: A Narrative Review. International Journal of Molecular Sciences. 2025; 26(15):7255. https://doi.org/10.3390/ijms26157255

Chicago/Turabian Style

Aita, Sara Elsa, Maria Vittoria Ristori, Antonio Cristiano, Tiziana Marfoli, Marina De Cesaris, Vincenzo La Vaccara, Roberto Cammarata, Damiano Caputo, Silvia Spoto, and Silvia Angeletti. 2025. "Proteomic Insights into Bacterial Responses to Antibiotics: A Narrative Review" International Journal of Molecular Sciences 26, no. 15: 7255. https://doi.org/10.3390/ijms26157255

APA Style

Aita, S. E., Ristori, M. V., Cristiano, A., Marfoli, T., De Cesaris, M., La Vaccara, V., Cammarata, R., Caputo, D., Spoto, S., & Angeletti, S. (2025). Proteomic Insights into Bacterial Responses to Antibiotics: A Narrative Review. International Journal of Molecular Sciences, 26(15), 7255. https://doi.org/10.3390/ijms26157255

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