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Microorganisms
Special Issues
Combating Antimicrobial Resistance: Innovations and Strategies, Second Edition
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Combating Antimicrobial Resistance: Innovations and Strategies, Second Edition

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

Deadline for manuscript submissions: 30 September 2026 | Viewed by 2462

Special Issue Editor

Dr. Vasiliki Koumaki

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

Special Issue Information

Dear Colleagues,

This Special Issue is a continuation of our previous Special Issue, “Combating Antimicrobial Resistance: Innovations and Strategies”.

Antimicrobial resistance (AMR) is an escalating global health crisis that threatens the efficacy of antimicrobial agents such as 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 is essential to mitigate the growing threat of drug-resistant infections.

In this Special Issue, we will publish research and innovations in diagnostics, vaccines, and new antimicrobial agents that will help us stay ahead of these pathogens’ 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 250 words) can be sent to the Editorial Office for assessment.

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 (3 papers)

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Research

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13 pages, 382 KB  
Article
Molecular Epidemiology of Toxigenic Clostridioides difficile Isolated from Bulgarian Patients and the Prevalence of Hypervirulent ST1 Clone
by Rumyana Markovska, Georgi Dimitrov, Denis Niyazi, Temenuga Stoeva, Kalina Mihova and Lyudmila Boyanova
Microorganisms 2026, 14(3), 532; https://doi.org/10.3390/microorganisms14030532 - 25 Feb 2026
Viewed by 454
Abstract
The aim of the study was to investigate the MLST types and genes encoding Clostridioides difficile toxins from fecal clinical samples of patients from two large Bulgarian cities. Overall, 100 toxigenic isolates were obtained during a 10-year period from five hospitals in Sofia [...] Read more.
The aim of the study was to investigate the MLST types and genes encoding Clostridioides difficile toxins from fecal clinical samples of patients from two large Bulgarian cities. Overall, 100 toxigenic isolates were obtained during a 10-year period from five hospitals in Sofia and Varna, Bulgaria. Toxin gene patterns of the isolates were determined with conventional polymerase chain reaction, and multilocus sequence typing (MLST) types were determined according to Griffith’s scheme. The evolutionary relatedness of ST types was analyzed through PHYLOViZ. Binary toxin-positive isolates accounted for 35% (35/100), and the most prevalent sequence type (ST) type was ST1 (clade2) with 34%. One binary toxin-positive isolate belonged to ST11 (clade5). The cdt-negative isolates were of two clades: clade 4 (ST37), with 1 tcdA-tcdB+ isolate, and clade 1, with 64 isolates. All the cdt-positive isolates showed 18 bp deletions of tcdC, except a ST11 isolate exhibiting a 39 bp deletion. Importantly, there was more than a 6-fold increase in ST1 isolates in the 2020–2023 period versus 2014–2019. The main cdt-negative isolates were ST3 (14%), ST2 (6%), ST42 (5%), and ST92 (5%). They were tcdA+tcdB+. Four main clonal complexes (with one allele difference) were found. The first one encompassed 19 isolates and included ST3 and ST42; the second included ST8, ST16, ST52, ST92 and ST36 (11 isolates); the third consisted of 13 isolates (ST2, ST49, ST13 and ST110 clones); and the fourth included ST10 and ST44 (5 isolates). The significance of our work is the detection of a high frequency of hypervirulent isolates during the COVID-19 pandemic period, which we attribute to the national consumption of systemic antibiotics, which increased during the second period, unlike the trend in other European countries. The results highlight the need for enhanced infection control measures and strict compliance with antibiotic stewardship programs. Full article
(This article belongs to the Special Issue Combating Antimicrobial Resistance: Innovations and Strategies, Second Edition)
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12 pages, 257 KB  
Article
Epidemiological and Microbiological Characterization of Carbapenemase-Producing Klebsiella pneumoniae Isolates in a Regional Greek Hospital: A Retrospective Study
by Pandora Tsolakidou and Maria Chatzidimitriou
Microorganisms 2025, 13(9), 2132; https://doi.org/10.3390/microorganisms13092132 - 12 Sep 2025
Cited by 2 | Viewed by 1257
Abstract
Carbapenemase-producing Klebsiella pneumoniae (CRKP) is a critical public health threat, particularly in Greece, where high prevalence limits therapeutic options. This retrospective study analyzed 26 CRKP isolates recovered at the General Hospital of Volos between July 2024 and January 2025, aiming to correlate carbapenemase [...] Read more.
Carbapenemase-producing Klebsiella pneumoniae (CRKP) is a critical public health threat, particularly in Greece, where high prevalence limits therapeutic options. This retrospective study analyzed 26 CRKP isolates recovered at the General Hospital of Volos between July 2024 and January 2025, aiming to correlate carbapenemase phenotypes with clinical and epidemiological parameters. Demographic, clinical, and microbiological data were extracted from patient records, and isolates underwent phenotypic carbapenemase detection, antimicrobial susceptibility testing, and molecular characterization using real-time PCR; four isolates were further analyzed using whole-genome sequencing. CRKP was detected across multiple hospital departments, notably in the Emergency Department (n = 5) and Intensive Care Unit (n = 6). KPC producers predominated (n = 9), followed by NDM (n = 6), VIM (n = 1), and OXA-48 (n = 6). All VIM- or NDM + VIM-positive cases were associated with mortality. High-risk clones, including ST15, ST11, and ST307, were identified, with one ST15 isolate harboring blaNDM-1, blaVIM-1, and chromosomal colistin resistance; this is the first such report in Greece. Colistin and gentamicin were the most active agents in vitro; three isolates were pan-drug-resistant. The findings highlight significant CRKP circulation outside ICUs, the role of horizontal gene transfer in resistance dissemination, and the need to expand screening and rapid diagnostics to non-ICU settings. Enhanced molecular surveillance targeted at infection control and strengthened antimicrobial stewardship programs are essential for limiting the spread of CRKP. Full article
(This article belongs to the Special Issue Combating Antimicrobial Resistance: Innovations and Strategies, Second Edition)

Other

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11 pages, 591 KB  
Case Report
Clinical Case Report on the Use of Rezafungin in Pneumocystis jirovecii Pneumonia in a Critically Ill Patient
by Rosario Fernández-Fernández, Roberto García-Martínez, Waldo Sánchez-Yebra Fernández, Natalia Chueca-Porcuna and Manuel Colmenero-Ruiz
Microorganisms 2026, 14(3), 683; https://doi.org/10.3390/microorganisms14030683 - 18 Mar 2026
Viewed by 356
Abstract
Pneumocystis jirovecii pneumonia (PJP) is a life-threatening opportunistic infection predominantly affecting immunocompromised patients. Trimethoprim–sulfamethoxazole (TMP–SMX) remains the standard therapy but is often limited by severe toxicity. Rezafungin, a next-generation echinocandin with a long half-life, has shown preclinical activity against Pneumocystis spp., but its [...] Read more.
Pneumocystis jirovecii pneumonia (PJP) is a life-threatening opportunistic infection predominantly affecting immunocompromised patients. Trimethoprim–sulfamethoxazole (TMP–SMX) remains the standard therapy but is often limited by severe toxicity. Rezafungin, a next-generation echinocandin with a long half-life, has shown preclinical activity against Pneumocystis spp., but its use in humans remains largely unexplored. We report the case of a 67-year-old man with inflammatory bowel disease who developed severe PJP complicated by acute respiratory failure, septic shock, and multiorgan dysfunction following corticosteroid and biologic therapy. Standard TMP–SMX therapy was contraindicated due to renal impairment and pancytopenia. The patient received rezafungin via a compassionate-use programme, with serial monitoring of serum and bronchoalveolar β-D-glucan levels. Despite a partial biomarker response, the patient ultimately progressed to refractory acute respiratory distress syndrome and multiorgan failure. This case provides preliminary human data suggesting that rezafungin may offer a potential therapeutic option for PJP when standard treatment is contraindicated or poorly tolerated. Close clinical and biomarker monitoring is essential. Further clinical and experimental studies are warranted to determine its efficacy, optimal dosing, and safety in critically ill immunocompromised patients. Full article
(This article belongs to the Special Issue Combating Antimicrobial Resistance: Innovations and Strategies, Second Edition)
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