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Microorganisms
Special Issues
Combating Antimicrobial Resistance: Innovations and Strategies
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Combating Antimicrobial Resistance: Innovations and Strategies

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Antimicrobial Agents and Resistance".

Deadline for manuscript submissions: closed (31 March 2025) | Viewed by 11367

Special Issue Editor

Dr. Vasiliki Koumaki

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Guest Editor
Department of Medical Microbiology, Medical School of Athens, National and Kapodistrian University of Athens, 75 Mikras Asias Street, Goudi, 115 27 Athens, Greece
Interests: antimicrobial resistance; multidrug resistant gram-negatives; resistance mechanisms; PK/PD studies
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Antimicrobial resistance (AMR) is an escalating global health crisis that threatens the efficacy of antimicrobial agents, including antibiotics, antivirals, antifungals, and antiprotozoals. The misuse and overuse of these drugs in healthcare, agriculture, and animal husbandry have accelerated the development of resistant strains of pathogens.

The battle against AMR requires a multifaceted and coordinated global response. Continued research into understanding resistance mechanisms, the development of new antimicrobial agents, and the implementation of effective stewardship programs are essential to mitigate the growing threat of drug-resistant infections.

In this Special Issue, we encourage research and innovation in diagnostics, vaccines, and new antimicrobial agents to stay ahead of evolving resistance.

Dr. Vasiliki Koumaki
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • antimicrobial agents
  • antimicrobial resistance
  • antimicrobial stewardship

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Published Papers (7 papers)

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Research

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16 pages, 1559 KiB  
Article
Etiology and Oral Antibiotic Susceptibility Patterns of the First Urinary Tract Infection Episode in Infants Under 6 Months of Age: A 17-Year, Retrospective, Single-Center Study in Italy
by Francesca Bagnasco, Francesca Lorenzini Ceradelli, Alessio Mesini, Carolina Saffioti, Erica Ricci, Chiara Russo, Marcello Mariani, Elisabetta Ugolotti, Emanuela Caci, Debora Contu, Elisa Tavella, Alessia Cafaro, Giorgio Piaggio, Enrico Verrina, Roberto Bandettini and Elio Castagnola
Microorganisms 2025, 13(3), 607; https://doi.org/10.3390/microorganisms13030607 - 6 Mar 2025
Viewed by 473
Abstract
Background: Urinary tract infections (UTIs) are among the most common bacterial infections in children, and the antibiotic susceptibility in the youngest patients remains poorly understood. This study aimed to describe the distribution of uropathogens and their antibiotic susceptibility, focusing on oral formulations. Methods: [...] Read more.
Background: Urinary tract infections (UTIs) are among the most common bacterial infections in children, and the antibiotic susceptibility in the youngest patients remains poorly understood. This study aimed to describe the distribution of uropathogens and their antibiotic susceptibility, focusing on oral formulations. Methods: Data from the first microbiological isolation, between January 2007 and December 2023, at Istituto Gaslini, in young infants (aged <6 months), were analyzed. Results: We isolated 2473 infants’ first pathogen, with a median age in the sample of 2.8 months and 62.6% male. A total of 2498 bacterial isolates were identified, of which 88.8% were Gram-negative and 11.2% were Gram-positive. Escherichia coli (53%) was the most frequent isolate, followed by Klebsiella pneumoniae (12.3%) and Enterococcus spp. (9.6%). No significant differences were observed between males and females, but infants younger than 3 months exhibited a significantly different pathogen distribution compared to older infants. The pathogen distribution showed significant changes before and after 2015, with a marked increase in Klebsiella pneumoniae isolates post-2015. Escherichia coli showed increases in resistance to amoxicillin-clavulanate and ciprofloxacin after 2015. Conclusions: Escherichia coli remains the most common uropathogen; however, Klebsiella pneumoniae has not only shown a high prevalence but also significant resistance, particularly in recent years. Full article
(This article belongs to the Special Issue Combating Antimicrobial Resistance: Innovations and Strategies)
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13 pages, 784 KiB  
Article
Bacteriophage Resistance, Adhesin’s and Toxin’s Genes Profile of Staphylococcus aureus Causing Infections in Children and Adolescents
by Nikolaos Giormezis, Assimina Rechenioti, Konstantinos Doumanas, Christos Sotiropoulos, Fotini Paliogianni and Fevronia Kolonitsiou
Microorganisms 2025, 13(3), 484; https://doi.org/10.3390/microorganisms13030484 - 21 Feb 2025
Viewed by 464
Abstract
Staphylococcus aureus is a common pathogen, often recovered from children’s infections. Βiofilm formation, antimicrobial resistance and production of adhesins and toxins contribute to its virulence. As resistance to antimicrobials rises worldwide, alternative therapies like bacteriophages (among them the well-studied Bacteriophage K) can be [...] Read more.
Staphylococcus aureus is a common pathogen, often recovered from children’s infections. Βiofilm formation, antimicrobial resistance and production of adhesins and toxins contribute to its virulence. As resistance to antimicrobials rises worldwide, alternative therapies like bacteriophages (among them the well-studied Bacteriophage K) can be helpful. The aim of this study was to determine the bacteriophage and antimicrobial susceptibility and the presence of virulence genes among S. aureus from infections in children and adolescents. Eighty S. aureus isolates were tested for biofilm formation and antimicrobial susceptibility. The presence of two genes of the ica operon (icaA, icaD), adhesin’s (fnbA, fnbB, sasG) and toxin’s genes (PVL, tst, eta, etb) was tested by PCRs. Susceptibility to Bacteriophage K was determined using a spot assay. Thirteen isolates were methicillin-resistant (MRSA) and 41 were multi-resistant. Twenty-five S. aureus (31.3%) were resistant to Bacteriophage K, mostly from ocular and ear infections. Twelve S. aureus (15%) were PVL-positive, seven (8.8%) positive for tst, 18 (22.5%) were eta-positive and 46 were (57.5%) etb-positive. A total of 66 (82.5%) isolates carried fnbA, 16 (20%) fnbB and 26 (32.5%) sasG. PVL, tst and sasG carriage were more frequent in MRSA. Bacteriophage-susceptible isolates carried more frequently eta (32.7%) and etb (69.1%) compared to phage-resistant S. aureus (0% and 32%, respectively). Although mainly methicillin-sensitive, S. aureus from pediatric infections exhibited high antimicrobial resistance and carriage of virulence genes (especially for exfoliative toxins and fnbA). MRSA was associated with PVL, tst and sasG carriage, whereas Bacteriophage susceptibility was associated with eta and etb. The high level of Bacteriophage K susceptibility highlights its potential use against staphylococcal infections. Full article
(This article belongs to the Special Issue Combating Antimicrobial Resistance: Innovations and Strategies)
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25 pages, 1853 KiB  
Article
Cross-Sectional Assessment on Carbapenem-Resistant Gram-Negative Bacteria Isolated from Patients in Moldova
by Vadim Nirca, Frieder Fuchs, Tessa Burgwinkel, Rocío Arazo del Pino, Ecaterina Zaharcenco, Ralf Matthias Hagen, Sven Poppert, Hagen Frickmann and Paul G. Higgins
Microorganisms 2025, 13(2), 421; https://doi.org/10.3390/microorganisms13020421 - 14 Feb 2025
Viewed by 572
Abstract
Information on the molecular epidemiology and carbapenem resistance mechanisms in Gram-negative bacterial isolates in Moldova is scarce. To close this knowledge gap, carbapenem-resistant Gram-negative bacteria were collected over an 11-month period in a routine diagnostic laboratory in Moldova. Antimicrobial susceptibility was phenotypically and [...] Read more.
Information on the molecular epidemiology and carbapenem resistance mechanisms in Gram-negative bacterial isolates in Moldova is scarce. To close this knowledge gap, carbapenem-resistant Gram-negative bacteria were collected over an 11-month period in a routine diagnostic laboratory in Moldova. Antimicrobial susceptibility was phenotypically and genotypically assessed. Phylogenetic relationships were investigated and multi-locus sequence types were provided. The assessment indicated several clusters of phylogenetically closely related carbapenem-resistant Klebsiella pneumoniae (sequence types ST101, ST395 and ST377), Acinetobacter baumannii (ST2, ST19 and ST78) and Pseudomonas aeruginosa (ST357 and ST654) isolates next to a number of less frequently observed species and sequence types. A phylogenetic relationship to characterized isolates from neighboring Ukraine could be confirmed. Identified carbapenemase genes comprised blaOXA-23, blaOXA-72 and blaGES-11 in A. baumannii, blaKPC-3, blaNDM-1 and blaOXA-48 in K. pneumoniae, as well as blaVIM-2 in Pseudomonas aeruginosa. In conclusion, the assessment suggested the spread of carbapenem-resistant Gram-negative bacteria in Moldova which were partly pre-described from neighboring Ukraine, as well as likely spill-over events, facilitating the regional spread of carbapenem-resistant clones. Several isolates with very high genomic similarity further support the hypothesis of likely regional transmission events driven by several evolutionary successful clonal lineages. Full article
(This article belongs to the Special Issue Combating Antimicrobial Resistance: Innovations and Strategies)
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13 pages, 1230 KiB  
Article
Detection and Characterisation of Colistin-Resistant Escherichia coli in Broiler Meats
by Abu Zubayer Tanzin, Chandan Nath, Md. Raihan Khan Nayem, Md Abu Sayeed, Shahneaz Ali Khan, Ricardo Soares Magalhaes, John I. Alawneh and Mohammad Mahmudul Hassan
Microorganisms 2024, 12(12), 2535; https://doi.org/10.3390/microorganisms12122535 - 9 Dec 2024
Viewed by 1281
Abstract
The irrational use of antimicrobials has led to the emergence of resistance, impacting not only pathogenic bacteria but also commensal bacteria. Resistance against colistin, a last-resort antibiotic, mediated by globally disseminated plasmid-borne mobile colistin resistance (mcr) genes, has raised significant global [...] Read more.
The irrational use of antimicrobials has led to the emergence of resistance, impacting not only pathogenic bacteria but also commensal bacteria. Resistance against colistin, a last-resort antibiotic, mediated by globally disseminated plasmid-borne mobile colistin resistance (mcr) genes, has raised significant global concerns. This cross-sectional study aimed to investigate the antimicrobial resistance patterns of colistin-resistant Escherichia coli (E. coli) and mobilised colistin resistance (mcr 1–5) genes from broiler meat. A total of 570 broiler samples (285 liver and 285 muscle) were collected from 7 supermarkets and 11 live bird markets (LBMs) in Chattogram metropolitan areas of Bangladesh. The isolation and identification of E. coli were carried out using standard bacteriological and molecular techniques. Antimicrobial susceptibility testing (AST) was performed using the Kirby–Bauer disc diffusion method, and colistin’s minimum inhibitory concentration (MIC) was determined by the broth microdilution (BMD) method. Colistin-resistant isolates were further tested for the presence of mcr (1–5) genes using polymerase chain reaction (PCR). Out of the 570 samples, 311 (54.56%; 95% confidence interval: 50.46–58.60) were positive for E. coli. AST results showed the highest resistance to sulphamethoxazole–trimethoprim (89.39%), while the highest susceptibility was observed for cefalexin (62.70%). A total of 296 isolates (95.18%) were found to be multidrug-resistant (MDR), with the multiple antibiotic resistance (MAR) index ranging from 0.38 to 1. Additionally, 41 isolates (13.18%) exhibited resistance to five antimicrobial classes, with resistance patterns of CIP + SXT + AMP + DO + TE + CT. A total of 233 isolates (74.92%) were resistant to colistin (MIC > 2 mg/L). A strong correlation between colistin resistance and the presence of the mcr-1 gene was observed (r = 1). All phenotypic colistin-resistant E. coli isolates carried the mcr-1 gene, while no isolates were positive for mcr (2–5). The detection of mcr genes in E. coli strains from poultry sources poses a significant risk, as these resistance genes can be transferred to humans through the food chain. The prevalence of multidrug-resistant Escherichia coli and the mcr-1 gene in poultry products in Bangladesh presents a significant public health and food safety concern. Full article
(This article belongs to the Special Issue Combating Antimicrobial Resistance: Innovations and Strategies)
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Review

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28 pages, 2904 KiB  
Review
Developing a Versatile Arsenal: Novel Antimicrobials as Offensive Tools Against Pathogenic Bacteria
by Junze Ma and Zheng Lu
Microorganisms 2025, 13(1), 172; https://doi.org/10.3390/microorganisms13010172 - 15 Jan 2025
Viewed by 1154
Abstract
The pervasive and often indiscriminate use of antibiotics has accelerated the emergence of drug-resistant bacterial strains, thus presenting an acute threat to global public health. Despite a growing acknowledgment of the severity of this crisis, the current suite of strategies to mitigate antimicrobial [...] Read more.
The pervasive and often indiscriminate use of antibiotics has accelerated the emergence of drug-resistant bacterial strains, thus presenting an acute threat to global public health. Despite a growing acknowledgment of the severity of this crisis, the current suite of strategies to mitigate antimicrobial resistance remains markedly inadequate. This paper asserts the paramount need for the swift development of groundbreaking antimicrobial strategies and provides a comprehensive review of an array of innovative techniques currently under scrutiny. Among these, nano-antimicrobials, antimicrobials derived from ribosomal proteins, CRISPR/Cas-based systems, agents that undermine bacterial bioenergetics, and antimicrobial polysaccharides hold particular promise. This analysis gives special attention to CRISPR/Cas-based antimicrobials, scrutinizing their underlying mechanisms, exploring their potential applications, delineating their distinct advantages, and noting their likely limitations. Furthermore, we extend our exploration by proposing theoretical advancements in antimicrobial technology and evaluating feasible methods for the effective delivery of these agents. This includes leveraging these advances for broader biomedical applications, potentially revolutionizing how we confront bacterial pathogens in the future, and laying a foundation for extended research in multimodal therapeutic strategies. Full article
(This article belongs to the Special Issue Combating Antimicrobial Resistance: Innovations and Strategies)
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23 pages, 1725 KiB  
Review
Food Webs and Feedbacks: The Untold Ecological Relevance of Antimicrobial Resistance as Seen in Harmful Algal Blooms
by Aabir Banerji, Nichole E. Brinkman, Benjamin Davis, Alison Franklin, Michael Jahne and Scott P. Keely
Microorganisms 2024, 12(11), 2121; https://doi.org/10.3390/microorganisms12112121 - 23 Oct 2024
Viewed by 2492
Abstract
Antimicrobial resistance (AMR) has long been framed as an epidemiological and public health concern. Its impacts on the environment are unclear. Yet, the basis for AMR is altered cell physiology. Just as this affects how microbes interact with antimicrobials, it can also affect [...] Read more.
Antimicrobial resistance (AMR) has long been framed as an epidemiological and public health concern. Its impacts on the environment are unclear. Yet, the basis for AMR is altered cell physiology. Just as this affects how microbes interact with antimicrobials, it can also affect how they interact with their own species, other species, and their non-living environment. Moreover, if the microbes are globally notorious for causing landscape-level environmental issues, then these effects could alter biodiversity and ecosystem function on a grand scale. To investigate these possibilities, we compiled peer-reviewed literature from the past 20 years regarding AMR in toxic freshwater cyanobacterial harmful algal blooms (HABs). We examined it for evidence of AMR affecting HAB frequency, severity, or persistence. Although no study within our scope was explicitly designed to address the question, multiple studies reported AMR-associated changes in HAB-forming cyanobacteria (and co-occurring microbes) that pertained directly to HAB timing, toxicity, and phase, as well as to the dynamics of HAB-afflicted aquatic food webs. These findings highlight the potential for AMR to have far-reaching environmental impacts (including the loss of biodiversity and ecosystem function) and bring into focus the importance of confronting complex interrelated issues such as AMR and HABs in concert, with interdisciplinary tools and perspectives. Full article
(This article belongs to the Special Issue Combating Antimicrobial Resistance: Innovations and Strategies)
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26 pages, 669 KiB  
Review
Antibiotic Resistance in the Elderly: Mechanisms, Risk Factors, and Solutions
by Nikolaos Theodorakis, Georgios Feretzakis, Christos Hitas, Magdalini Kreouzi, Sofia Kalantzi, Aikaterini Spyridaki, Iris Zoe Boufeas, Aikaterini Sakagianni, Evgenia Paxinou, Vassilios S. Verykios and Maria Nikolaou
Microorganisms 2024, 12(10), 1978; https://doi.org/10.3390/microorganisms12101978 - 30 Sep 2024
Cited by 11 | Viewed by 3776
Abstract
Antibiotic resistance presents a critical challenge in healthcare, particularly among the elderly, where multidrug-resistant organisms (MDROs) contribute to increased morbidity, mortality, and healthcare costs. This review focuses on the mechanisms underlying resistance in key bacterial pathogens and highlights how aging-related factors like immunosenescence, [...] Read more.
Antibiotic resistance presents a critical challenge in healthcare, particularly among the elderly, where multidrug-resistant organisms (MDROs) contribute to increased morbidity, mortality, and healthcare costs. This review focuses on the mechanisms underlying resistance in key bacterial pathogens and highlights how aging-related factors like immunosenescence, frailty, and multimorbidity increase the burden of infections from MDROs in this population. Novel strategies to mitigate resistance include the development of next-generation antibiotics like teixobactin and cefiderocol, innovative therapies such as bacteriophage therapy and antivirulence treatments, and the implementation of antimicrobial stewardship programs to optimize antibiotic use. Furthermore, advanced molecular diagnostic techniques, including nucleic acid amplification tests and next-generation sequencing, allow for faster and more precise identification of resistant pathogens. Vaccine development, particularly through innovative approaches like multi-epitope vaccines and nanoparticle-based platforms, holds promise in preventing MDRO infections among the elderly. The role of machine learning (ML) in predicting resistance patterns and aiding in vaccine and antibiotic development is also explored, offering promising solutions for personalized treatment and prevention strategies in the elderly. By integrating cutting-edge diagnostics, therapeutic innovations, and ML-based approaches, this review underscores the importance of multidisciplinary efforts to address the global challenge of antibiotic resistance in aging populations. Full article
(This article belongs to the Special Issue Combating Antimicrobial Resistance: Innovations and Strategies)
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