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Multi-Drug Resistant Gram-Negative Infections: Molecular Epidemiology, Microbiological Diagnosis, and Antimicrobial...
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Multi-Drug Resistant Gram-Negative Infections: Molecular Epidemiology, Microbiological Diagnosis, and Antimicrobial Treatment, 2nd Edition

A special issue of Antibiotics (ISSN 2079-6382). This special issue belongs to the section "Antibiotics Use and Antimicrobial Stewardship".

Deadline for manuscript submissions: 31 August 2026 | Viewed by 2426

Special Issue Editor

Dr. Paolo Gaibani

E-Mail Website
Guest Editor
Department of Diagnostics and Public Health, Section of Microbiology, University of Verona, Verona, Italy
Interests: antimicrobial resistance; genomic analysis; molecular epidemiology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Multi-drug resistant (MDR) Gram-negative bacilli (BNG) represent a serious threat among antimicrobials resistances. MDR-GNB are resistant to multiple antimicrobial molecules, thus reducing the antimicrobial options available for treating infections sustained by these microorganisms. Among them, extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae, carbapenem-resistant Enterobacteriales (CRE), carbapenem-resistant Acinetobacter baumannii (CRAB), and MDR Pseudomonas aeruginos represent the most urgent threat for which there is an imminent need for novel antimicrobial treatment strategies. To counteract the paucity of the antimicrobial molecules for the treatment of infections due to MDR-GNB, multidisciplinary approaches are required. In this context, innovative strategies for diagnosis, infection control and antimicrobial stewardship are the key factors. In this Special Issue, we invite authors to send in their manuscripts on the following areas of interest:

  • Novel in vitro diagnostic tools for MDR-GNB detection and antimicrobial susceptibility testing;
  • The molecular epidemiology of Gram-negative pathogens and resistance mechanisms;
  • The evaluation of antimicrobial treatment regimens for MDR-GNB;
  • New drugs against MDR-GNB: clinical use, in vitro susceptibility testing and emerging resistance.
  • Pharmacodynamics/pharmacokinetics (PK/PD) parameter to optimise antimicrobial treatments for MDR-GNB

Dr. Paolo Gaibani
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. Antibiotics 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 2900 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

  • pharmacodynamics/pharmacokinetics (PK/PD)
  • enterobacterales
  • carbapenemase
  • novel molecules
  • antimicrobial resistance

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Related Special Issue

Published Papers (3 papers)

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Research

13 pages, 1725 KB  
Article
Detection of ARGs from Gram-Negative Bacteria in Positive Blood Cultures Using a Microarray-Based System: Towards a Molecular Antibiotic Susceptibility Assay
by Cataldo Maria Mannavola, Giordana Cafaro, Barbara Fiori, Roberto Rosato, Francesca Romana Monzo, Tiziana D’Inzeo, Brunella Posteraro, Maurizio Sanguinetti and Flavio De Maio
Antibiotics 2025, 14(12), 1221; https://doi.org/10.3390/antibiotics14121221 - 4 Dec 2025
Viewed by 346
Abstract
Background/Objectives: Antimicrobial resistance (AMR) represents a major global health challenge, driving the need for rapid and accurate diagnostic tools. Novel molecular assays, including multiplex PCR and DNA microarray-based systems, have emerged to detect antimicrobial resistance genes (ARGs) alongside bacterial identification. Methods: [...] Read more.
Background/Objectives: Antimicrobial resistance (AMR) represents a major global health challenge, driving the need for rapid and accurate diagnostic tools. Novel molecular assays, including multiplex PCR and DNA microarray-based systems, have emerged to detect antimicrobial resistance genes (ARGs) alongside bacterial identification. Methods: In this study, we evaluated the performance of the HybriSpot12 PCR AUTO (HS12a) system and the MDR Direct Flow Chip (MDR-FC) Kit—an automatic microarray assay based on reverse hybridization—for the detection of ARGs directly from positive blood culture (PBC) samples. A total of 111 Gram-negative bacterial isolates (92 Enterobacterales, 14 Acinetobacter baumannii, and 6 Pseudomonas spp.), previously characterized by whole-genome sequencing (WGS), were each used to generate a PBC, which was then analyzed with the HS12a/MDR-FC assay. Results: We demonstrated perfect agreement for the detection of macrolide resistance genes across all bacterial species and high agreement for genes conferring resistance to sulfonamides and β-lactams. In contrast, aminoglycoside resistance genes showed only moderate agreement, with minor discrepancies observed in Klebsiella pneumoniae and Escherichia coli, largely attributable to specific SNP variations. Conclusions: The HS12a/MDR-FC assay includes 51 ARGs, though not all were represented in our isolate set, and some false negatives were observed. Despite these limitations, its broad coverage and rapid turnaround remain advantageous compared to other rapid assays with fewer targets. Future refinements should aim at broader gene coverage, inclusion of key mutations, and detection of emerging variants, making this approach a promising tool for rapid AMR surveillance and antimicrobial stewardship. Full article
(This article belongs to the Special Issue Multi-Drug Resistant Gram-Negative Infections: Molecular Epidemiology, Microbiological Diagnosis, and Antimicrobial Treatment, 2nd Edition)
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14 pages, 821 KB  
Article
Correlation Between Antimicrobial Consumption and Resistance in Klebsiella pneumoniae During the COVID-19 Pandemic Using Dynamic Regression Models: A Quasi-Experimental Epidemiological Time-Series Study
by Paul Laffont-Lozes, Florian Salipante, Paul Loubet, Catherine Dunyach-Remy, Jean-Philippe Lavigne, Albert Sotto and Romaric Larcher
Antibiotics 2025, 14(10), 1020; https://doi.org/10.3390/antibiotics14101020 - 14 Oct 2025
Viewed by 656
Abstract
Background/Objectives: The COVID-19 pandemic has been reported to impact antimicrobial consumption (AMC) and antimicrobial resistance (AMR) worldwide. We aimed to assess this correlation in Klebsiella pneumoniae before and during the COVID-19 pandemic and to estimate the burden of each antibiotic. Methods: [...] Read more.
Background/Objectives: The COVID-19 pandemic has been reported to impact antimicrobial consumption (AMC) and antimicrobial resistance (AMR) worldwide. We aimed to assess this correlation in Klebsiella pneumoniae before and during the COVID-19 pandemic and to estimate the burden of each antibiotic. Methods: We collected data on AMC of penicillins and beta-lactamase inhibitors (PBIs), anti-pseudomonal activity penicillins and beta-lactamase inhibitors (AAPBIs), cephalosporins, carbapenems, fluoroquinolones, aminoglycosides, and AMR in K. pneumoniae strains. The correlation between AMC and AMR was studied using dynamic regression models. Results: Overall, AMC of AAPBIs and fourth-generation cephalosporin increased, while fluoroquinolone consumption and AMR in the 2862 K. pneumoniae strains analyzed decreased. However, during the first year of the pandemic, we reported an increase in AMC and AMR. We found that 46% to 48% of the increase in cephalosporin, AAPBI, and fluoroquinolone resistance was explained by increased cephalosporin and fluoroquinolone consumption, 55% of the increase in PBI resistance was explained by increased PBI, cephalosporin, and fluoroquinolone consumption, and 58% of the increase in aminoglycoside resistance was explained by increased aminoglycoside consumption. Conclusions: During the COVID-19 pandemic, the increase in AMR in K. pneumoniae was correlated with the increase in AMC of several antibiotics, mainly cephalosporins and especially fluoroquinolones. Full article
(This article belongs to the Special Issue Multi-Drug Resistant Gram-Negative Infections: Molecular Epidemiology, Microbiological Diagnosis, and Antimicrobial Treatment, 2nd Edition)
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14 pages, 1389 KB  
Article
Lack of Association Between qacE and qacE∆1 Gene Variants and Sodium Hypochlorite Resistance in Clinical Isolates of ESBL- and Carbapenemase-Producing Klebsiella spp. and Enterobacter spp., from Gaborone, Botswana
by Pearl Ntshonga, Tlhalefo Dudu Ntereke, Tshiamo Zankere, Daniel Paul Morse, Garesego Koto, Irene Gobe and Giacomo Maria Paganotti
Antibiotics 2025, 14(7), 662; https://doi.org/10.3390/antibiotics14070662 - 30 Jun 2025
Viewed by 1002
Abstract
Background: The qacE gene and its variant, qacE∆1, have been associated with resistance to antimicrobials and biocides. This poses a threat to infection prevention, control and treatment. Several studies investigated this relationship with conflicting results. The aim of this research was [...] Read more.
Background: The qacE gene and its variant, qacE∆1, have been associated with resistance to antimicrobials and biocides. This poses a threat to infection prevention, control and treatment. Several studies investigated this relationship with conflicting results. The aim of this research was to determine the prevalence of qacE and qacE∆1 in clinical extended spectrum β-lactamase- (ESBL) and carbapenemase-producing Klebsiella spp. and Enterobacter spp. and elucidate the association of these genes with resistance to sodium hypochlorite. Methods: This study included 216 isolates of ESBL- and carbapenemase-producing multidrug-resistant (MDR) Klebsiella spp. and Enterobacter spp. These isolates were identified by VITEK-2 analyser. The MIC and MBC of sodium hypochlorite were determined using the microbroth serial-dilution method. PCR was used to detect gene variants. A regression analysis investigated any association between qacE genotypes, MIC and MBC, as well as antimicrobial drug resistance profiles. Results: Overall, there was a high prevalence of qacE and qacE∆1 variants (84.7%; 95% CI, 79.2–89.2). There was a high prevalence of qacE∆1 (80.6%; 95% CI, 74.6–85.6) as compared to qacE (15.3%, 95% CI, 10.8–20.8). The MIC50 and MIC90 of the isolates ranged between 7031 mg/L and 9375 mg/L and 14,060 mg/L and 18,750 mg/L, respectively, while the MBC ranged from 48,750 mg/L to 18,750 mg/L. There was no association between qacE genotypes and high MIC and MBC as well as antimicrobial drug resistance. Conclusions: The MIC and MBC of sodium hypochlorite are higher than what is currently used for disinfection in Botswana. There is a high prevalence of qacE and qacE∆1; however, these genes do not seem to be associated with resistance to sodium hypochlorite. Full article
(This article belongs to the Special Issue Multi-Drug Resistant Gram-Negative Infections: Molecular Epidemiology, Microbiological Diagnosis, and Antimicrobial Treatment, 2nd Edition)
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