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Microorganisms
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Antibiotic Resistance in Pathogenic Bacteria
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Antibiotic Resistance in Pathogenic Bacteria

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 January 2026) | Viewed by 3303

Special Issue Editors

Dr. Sara Domingues

E-Mail Website
Guest Editor
Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal
Interests: natural transformation; antimicrobial resistance; mobile genetic elements; Gram-negative bacteria; One Health
Special Issues, Collections and Topics in MDPI journals
Dr. Gabriela Jorge Da Silva

E-Mail Website
Guest Editor
Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal
Interests: molecular epidemiology; antimicrobial resistance; horizontal gene transfer; Gram-negative bacteria; One Health
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Antibiotic resistance is a global health threat impacting Gram-negative and Gram-positive bacteria. An increasing number of strains are now virtually resistant to all available antibiotics, making infectious diseases difficult or impossible to treat. The World Health Organization has identified species that urgently require new antimicrobials. At the same time, the Centers for Disease Control and Prevention has highlighted the species posing the most significant health threats due to antibiotic resistance. Several species appear on both lists.

Understanding the mechanisms of antimicrobial resistance, their acquisition, and the events associated with the dissemination of resistance determinants is essential to developing strategies to overcome resistance. This Special Issue thus welcomes original research or review manuscripts focused on the molecular mechanisms of resistance and dissemination, bacterial strategies to evade antimicrobial action, specific resistant bacterial strains, antimicrobial stewardship, novel strategic therapeutics to fight resistant infections, and broader scientific concepts related to this critical global health challenge in the most impactful human pathogens.

Dr. Sara Domingues
Dr. Gabriela Jorge Da Silva
Guest Editors

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

  • antibiotic resistance genes
  • antibiotic resistance mechanisms
  • multidrug-resistant bacteria
  • mobile genetic elements
  • horizontal gene transfer
  • antibiotic stewardship

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Published Papers (3 papers)

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Research

18 pages, 2334 KB  
Article
Occurrence and Genomic Characterization of ESBL-, AmpC-, and Carbapenemase-Producing Escherichia coli and Klebsiella pneumoniae Isolated from Surface Water in Southern Italy, 2023–2024
by Gaia Nobili, Annachiara Cocomazzi, Maria Grazia Basanisi, Annita Maria Damato, Rosa Coppola, Maria Grazia Cariglia, Ilenia Franconieri, Antonella Stallone, Michelina Notarangelo, Tommaso Scirocco, Valeria Bortolaia and Giovanna La Salandra
Microorganisms 2026, 14(2), 508; https://doi.org/10.3390/microorganisms14020508 - 22 Feb 2026
Viewed by 826
Abstract
Antimicrobial resistance (AMR) is recognised as a major global public health threat, with the environment increasingly acknowledged as a key reservoir and dissemination pathway for resistant bacteria and resistance genes. In this study, 148 surface water samples were collected between 2023 and 2024 [...] Read more.
Antimicrobial resistance (AMR) is recognised as a major global public health threat, with the environment increasingly acknowledged as a key reservoir and dissemination pathway for resistant bacteria and resistance genes. In this study, 148 surface water samples were collected between 2023 and 2024 from six rivers and three canals discharging wastewater into two lake waters in Southern Italy to assess the occurrence and genomic features of extended-spectrum β-lactamase (ESBL)-, AmpC-, and carbapenemase-producing Escherichia coli and Klebsiella pneumoniae. Relevant isolates were obtained using selective culturing, and tested for antimicrobial susceptibility by broth microdilution. Major β-lactam resistance genes were detected by real-time PCR. Whole-genome sequencing (WGS) was performed on presumptive carbapenemase-producing isolates. ESBL- and/or carbapenemase-producing Enterobacterales were detected in 67.6% of samples, yielding a total of 176 non-duplicate isolates. The most prevalent gene was blaCTX-M, detected in 79.3% of positive isolates (96/121), while carbapenemase genes were detected in 20.6% (25/121) of isolates, mainly blaOXA-48 and blaVIM. WGS analysis of carbapenemase PCR-positive isolates revealed occurrence of clinically relevant high-risk clones, such as K. pneumoniae ST512/ST307 carrying blaKPC-3 and E. coli ST10 harbouring blaOXA-244. These findings highlight a potential risk to public health and underscore the importance of integrating environmental compartments into One Health surveillance frameworks for AMR. Full article
(This article belongs to the Special Issue Antibiotic Resistance in Pathogenic Bacteria)
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11 pages, 763 KB  
Article
Detection of K. pneumoniae Hospital-Acquired Strains That Produce Carbapenemases in Thrace Tertiary Hospital
by Anastasia Vezyridou, Aikaterini Skeva, Ioanna Alexandropoulou, Valeria Iliadi, Georgios Euthymiou, Dimitrios Themelidis, Athina Xanthopoulou, Vasilios Petrakis, Theocharis Konstantinidis and Maria Panopoulou
Microorganisms 2025, 13(11), 2496; https://doi.org/10.3390/microorganisms13112496 - 30 Oct 2025
Viewed by 805
Abstract
In recent decades, the problem of resistant strains, which present resistance to different types of antimicrobials, has increased. Klebsiella pneumoniae is one of the most important species that exhibits an acquired resistance phenotype to at least one agent in three or more classes [...] Read more.
In recent decades, the problem of resistant strains, which present resistance to different types of antimicrobials, has increased. Klebsiella pneumoniae is one of the most important species that exhibits an acquired resistance phenotype to at least one agent in three or more classes of antimicrobials and is thus characterized as a multidrug-resistant bacterium (MDR). 98 nosocomial strains of K. pneumoniae were isolated during the pre-COVID-19 period, and more specifically, from February 2015 to March 2019, were analyzed for the detection of class A, D, and B carbapenemase genes. The existence of KPC, OXA-48 like, IMP, VIM, and NDM carbapenemases has been examined. The immunochromatography showed that NDM carbapenemases are more frequently detected in the samples, reaching a percentage of 30.7%, while correspondingly the percentage for VIM carbapenemases was 7.68% among the strains with resistant phenotypes. No strain with carbapenemase IMP was found. Real-time multiplex polymerase chain reaction (PCR) showed, in contrast to immunochromatography kits, that a high percentage of bacterial isolates (94.26%) carry NDM and VIM carbapenemase genes, while no IMP carbapenemase genes were detected. Regarding the KPC enzymes, the immunochromatography kits showed that KPC positive strains are reaching 53.1%, and OXA-48 positive strains are reaching 3.1% among the strains with resistant phenotypes. Real-time multiplex polymerase chain reaction revealed a much higher percentage of 89.6% KPC positive isolates and a percentage of 14.6% OXA-48 carbapenemase producers. The aforementioned results indicate the dominance of the Multiplex Real-Time PCR as a “gold standard” method. This study could not fully support the usefulness of rapid immunochromatographic tests as a fast and useful diagnostic tool in the laboratory daily routine, as per the results of previous studies. Thus, more studies need to be conducted in this field to introduce these rapid tests safely into the daily laboratory workflow as a screening tool. Additionally, this study underlines the predominance of KPC enzymes from clinical isolates of ICUs and a significant shift over the OXA-48 like enzymes that are not limited to the ICU environment. Full article
(This article belongs to the Special Issue Antibiotic Resistance in Pathogenic Bacteria)
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13 pages, 694 KB  
Article
Risk Factors and Prognosis of Polymyxin- and Carbapenem-Resistant Enterobacteriaceae Infections: A Propensity-Matched Real-World Study
by Jian Xu, Mei Liang, Yanan Luo and Junyan Qu
Microorganisms 2025, 13(6), 1256; https://doi.org/10.3390/microorganisms13061256 - 29 May 2025
Cited by 1 | Viewed by 1053
Abstract
The risk factors and prognosis of polymyxin- and carbapenem-resistant Enterobacteriaceae (PR-CRE) infections were analyzed to reduce their incidence and concurrently improve patient prognosis. This retrospective study analyzed patients with CRE infections admitted to West China Hospital of Sichuan University between 1 September 2019 [...] Read more.
The risk factors and prognosis of polymyxin- and carbapenem-resistant Enterobacteriaceae (PR-CRE) infections were analyzed to reduce their incidence and concurrently improve patient prognosis. This retrospective study analyzed patients with CRE infections admitted to West China Hospital of Sichuan University between 1 September 2019 and 30 September 2023. Based on polymyxin susceptibility, the cases were categorized into PR-CRE and PS-CRE (polymyxin-susceptible CRE) groups, with 1:1 propensity score matching performed between the two cohorts. Comprehensive data, including demographic characteristics, laboratory findings, antibiotic regimens, and clinical outcomes, were collected and analyzed to identify risk factors for PR-CRE infections and evaluate treatment efficacy. This study aims to provide evidence-based references for infection control strategies and antimicrobial stewardship in managing PR-CRE infections. A total of 254 patients were included in this study, with 127 patients in the PR-CRE group. The sensitivity rates of isolates in the PR-CRE group to tigecycline and ceftazidime–avibactam were 94.4% and 88.9%, respectively. Multivariate analysis identified chronic organic disease (OR 2.747, 95% CI 1.303–5.789; p = 0.008) and the use of polymyxin ≥ 3 days (OR 19.203, 95% CI 7.126–51.752; p < 0.001) as independent risk factors for PR-CRE infection. Moreover, ceftazidime–avibactam-based regimens were superior to tigecycline-based regimens for the treatment of PR-CRE infections (71.43% vs. 58.46%), especially in critically ill patients (33.33% vs. 58.82%). Finally, a SOFA score ≥ 5.5 (HR 6.718, 95% CI 2.526–17.866; p < 0.001) was identified as an independent risk factor for 28-day mortality in patients with PR-CRE infection. The presence of chronic organic diseases and the use of polymyxin for ≥3 days were identified as independent risk factors associated with PR-CRE infections in hospitalized patients, highlighting the need to optimize polymyxin use. Furthermore, the efficacy of ceftazidime–avibactam-based regimens may be superior to tigecycline-based regimens for the treatment of PR-CRE infections. Full article
(This article belongs to the Special Issue Antibiotic Resistance in Pathogenic Bacteria)
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