Molecular Characterization of Gram-Negative Bacteria: Antimicrobial Resistance, Virulence and Epidemiology, 2nd Edition

A special issue of Antibiotics (ISSN 2079-6382). This special issue belongs to the section "Mechanism and Evolution of Antibiotic Resistance".

Deadline for manuscript submissions: 31 March 2027 | Viewed by 4932

Editors


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Guest Editor
Department of Clinical Microbiology, University Hospital Kerry, V92 NX94 Tralee, Ireland
Interests: multidrug-resistant gram-negative bacteria; molecular epidemiology; antimicrobial resistance; infection control measures
Special Issues, Collections and Topics in MDPI journals

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Guest Editor
Department of Clinical Microbiology, University Hospital Kerry, V92 NX94 Tralee, Ireland
Interests: multidrug-resistant Gram-negative bacteria; molecular epidemiology; virology; hemorrhagic fever viruses

Special Issue Information

Dear Colleagues,

The success of the Special Issue “Molecular Characterization of Gram-Negative Bacteria: Antimicrobial Resistance, Virulence and Epidemiology” has encouraged us to launch a second volume on the same topic. As a continuation of the Special Issue published in 2024, this second volume will focus on antimicrobial resistance in Gram-negative bacteria and their molecular epidemiology.

Despite growing global attention, multidrug-resistant (MDR), extensively drug-resistant (XDR), and pan-drug-resistant (PDR) Gram-negative pathogens—such as Klebsiella pneumoniae, Pseudomonas aeruginosa, and Acinetobacter baumannii—continue to pose a critical threat to public health.

These pathogens not only have a negative impact on the patients’ outcomes but also significantly increase the burden on healthcare systems due to prolonged hospital stays and heightened treatment costs. Although efforts have been made to control their spread, challenges remain. The irrational use and overuse of antimicrobials, combined with insufficient infection control practices, are key contributors to the persistence and evolution of resistance in clinical settings.

The second volume of this Special Issue will continue to explore these pressing issues, with a particular emphasis on advances in understanding resistance mechanisms, the development and role of virulence factors, and the molecular epidemiology underlying the dissemination of resistant strains. We are especially interested in studies that investigate novel therapeutic strategies, surveillance data, genomic insights, and emerging resistance patterns globally. Articles on all MDR Gram-negative bacteria will also be considered. Review articles are also welcome.

We are looking forward to your contributions!

Dr. Theodoros Karampatakis
Dr. Katerina Tsergouli
Guest Editors

Manuscript Submission Information

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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-anonymized 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.

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Keywords

  • Gram-negative bacteria
  • virulence factors
  • antimicrobial resistance
  • molecular epidemiology
  • Klebsiella pneumoniae
  • Pseudomonas aeruginosa
  • Acinetobacter baumannii

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Related Special Issue

Published Papers (3 papers)

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Research

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18 pages, 3912 KB  
Article
Reduced Susceptibility to Cefiderocol Among Clinical MCR-1-Producing Escherichia coli Isolates from Tunisia
by Nadia Jaidane, Thierry Naas, Souad Fayad, Pierre Châtre, Wejdene Mansour, Aymen Bouaziz, Pauline François, Laetitia Du Fraysseix, Bogdan I. Iorga, Nahed A. Al Laham, Lamia Tilouche, Farouk Barguellil and Marisa Haenni
Antibiotics 2026, 15(8), 802; https://doi.org/10.3390/antibiotics15080802 - 18 Aug 2026
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Abstract
Background/Objectives: The emergence of plasmid-mediated mcr genes has enabled horizontal dissemination of resistance to colistin, a last-resort antibiotic against multidrug-resistant Enterobacterales. In Tunisia, genomic data on mcr-positive Escherichia coli are still limited. This study reports the genomic characterization of human clinical [...] Read more.
Background/Objectives: The emergence of plasmid-mediated mcr genes has enabled horizontal dissemination of resistance to colistin, a last-resort antibiotic against multidrug-resistant Enterobacterales. In Tunisia, genomic data on mcr-positive Escherichia coli are still limited. This study reports the genomic characterization of human clinical mcr-positive E. coli isolates from the Military Hospital of Tunis. Methods: Between August 2023 and March 2025, seven E. coli isolates with low-level colistin-resistance (MIC = 4–8 µg/mL) were collected from six patients. They were characterized by antibiotic susceptibility testing and WGS to determine resistome, MLST, genetic relatedness, and plasmid content. Results: The E. coli isolates belonged to diverse sequence types (STs), except for two isolates collected from the same patient 2.5 months apart, which were highly related. Overall, this pattern is consistent with a polyclonal spread. The mcr-1.1 gene was located on IncI2 (n = 5) or IncX4 (n = 2) plasmids, which exhibited high similarity both among themselves and in comparison with plasmids previously reported in human and livestock isolates. Most isolates were multidrug-resistant, harboring acquired resistance genes to multiple antibiotic classes, and chromosomal mutations conferring fluoroquinolone resistance. Three isolates additionally carried chromosomal insertions of the blaCTX-M-55 gene. Resistance to cefiderocol was observed in one isolate and was associated with CirA and Fiu truncation. Conclusions: These findings highlight ongoing dissemination of mcr-1.1-positive E. coli isolates in Tunisia, primarily driven by plasmid transfer. Continuous genomic surveillance and One Health-oriented antibiotic stewardship are essential to limit the spread of colistin-resistance and the emergence of resistance to newer agents such as cefiderocol. Full article
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16 pages, 1659 KB  
Article
Short-Term Within-Host Genomic Diversity and Clone Turnover of Carbapenem-Resistant Klebsiella pneumoniae in an Intensive Care Unit Patient
by Yulia Mikhaylova, Anna Slavokhotova, Oksana Ni, Denis Protsenko, Sergey Bruskin, Andrey Shelenkov and Vasiliy Akimkin
Antibiotics 2026, 15(6), 605; https://doi.org/10.3390/antibiotics15060605 - 14 Jun 2026
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Abstract
Background: Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a critical public health threat because infections caused by this pathogen are associated with high morbidity, mortality, and limited effective therapeutic options. Whilst the majority of studies have concentrated on inter-patient bacterial transmission, within-host genomic analysis [...] Read more.
Background: Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a critical public health threat because infections caused by this pathogen are associated with high morbidity, mortality, and limited effective therapeutic options. Whilst the majority of studies have concentrated on inter-patient bacterial transmission, within-host genomic analysis offers unprecedented resolution for tracking dynamic clone predominance, plasmid rearrangements, and microevolution under clinical selection pressures. Methods and Results: Whole-genome sequencing (WGS) of nine isolates recovered from oral and rectal swabs revealed an exceptional case of CRKP clonal turnover in an intensive care unit (ICU) patient. Three distinct high-risk clones were identified during the 18 days of surveillance: an initial ST101 (Clonal Group (CG) 101) strain (days 1–7) followed by concurrent colonization with ST395 (carrying blaNDM-5) and ST512 lineages (both CG258, days 11–18). Conclusions: This study describes a rare instance of within-host heterogeneity of CRKP, involving three distinct STs spanning two CGs. Whole-genome analysis revealed potential structural rearrangements of resistance- and virulence-associated plasmids between coexisting lineages. These genomic shifts likely reflect rapid adaptation under the intense selective pressure of broad-spectrum antibiotic therapy, culminating in the persistence of a less virulent yet multidrug-resistant ST512 clone and a favorable clinical outcome with patient recovery. Full article
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Review

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40 pages, 1018 KB  
Review
Carbapenem-Resistant Serratia marcescens: Genomic Plasticity, Virulence Architecture, and the Expanding Threat of Multidrug Resistance
by Theodoros Karampatakis, Katerina Tsergouli and Payam Behzadi
Antibiotics 2026, 15(4), 359; https://doi.org/10.3390/antibiotics15040359 - 1 Apr 2026
Cited by 2 | Viewed by 2910
Abstract
Serratia marcescens is a highly adaptable Gammaproteobacterium with broad ecological distribution and growing clinical importance. Advances in whole-genome sequencing (WGS) and pangenome analysis reveal extensive genomic plasticity, driven by mobile genetic elements (MGEs) such as plasmids, transposons, integrons, prophages, and extracellular vesicles, which [...] Read more.
Serratia marcescens is a highly adaptable Gammaproteobacterium with broad ecological distribution and growing clinical importance. Advances in whole-genome sequencing (WGS) and pangenome analysis reveal extensive genomic plasticity, driven by mobile genetic elements (MGEs) such as plasmids, transposons, integrons, prophages, and extracellular vesicles, which collectively accelerate virulence and antimicrobial resistance (AMR) evolution. S. marcescens displays a dynamic accessory genome enriched in resistance and virulence determinants, supporting persistence in diverse environments, including hospital water systems. Clinically, S. marcescens is an emerging opportunistic pathogen associated with severe healthcare-associated infections, ICU outbreaks, and multidrug-resistant “superbug” phenotypes. Its resistome includes intrinsic AmpC β-lactamase, broad efflux systems, and chromosomal determinants conferring resistance to β-lactams, polymyxins, and multiple additional drug classes, while acquired ESBLs and carbapenemases urther limit therapeutic options. Integrating genomic, evolutionary, and clinical insights underscores the urgent need for improved surveillance, mechanistic understanding, and targeted interventions against carbapenem-resistant S. marcescens (CRSM). Full article
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