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Microorganisms
Special Issues
Antimicrobial Resistance (AMR) Diagnostics and Genomic/Molecular Epidemiology of Multidrug-Resistant Isolates
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Antimicrobial Resistance (AMR) Diagnostics and Genomic/Molecular Epidemiology of Multidrug-Resistant Isolates

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

Deadline for manuscript submissions: 31 December 2025 | Viewed by 1578

Special Issue Editor

Prof. Dr. Anna Baraniak

E-Mail Website
Guest Editor
Department of Pharmaceutical Microbiology and Laboratory Diagnostics, National Medicines Institute, Warsaw, Poland
Interests: SARS-CoV-2; enterobacterales; Antibiotic Resistance; ß-lactamases; carbapenemases
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The treatment and outcomes of healthcare-acquired infections have been severely threatened by the increasing antimicrobial resistance (AMR) worldwide. AMR is determined by a variety of mechanisms, including mainly enzymatic drug hydrolysis or modification, target site structural change by mutation, recombination or enzymatic modification, and drug level decrease by efflux or permeability alteration. Some organisms are naturally resistant to an antibiotic(s) due to the target absence or activity of a chromosomally encoded mechanism occurring in all isolates of a species. Acquired AMR genes are localized in the chromosome or on plasmid(s) and may spread with organisms in which they have emerged (clonal spread) or appear in new isolates of the same or different species by the horizontal DNA transfer, associated with various mobile genetic elements (e.g., transposable elements, plasmids, bacteriophages). AMR affects both first-line drugs, thanks to which specific pathogens have been controlled over years, but also last-line drugs, which until recently guaranteed therapeutic success in the treatment of serious infections. Finally, pathogens have been constantly accumulating different types of AMR mechanisms, including those against different drug classes, resulting in their multidrug resistance (MDR). New terminology was launched to describe extensively drug-resistant (XDR) and pan drug-resistant (PDR) phenotypes, with very limited or no treatment options, and their major Gram-negative representatives are K. pneumoniae (and other Enterobacterales), Acinetobacter baumannii, and Pseudomonas aeruginosa.

Accordingly, this Special Issue focuses on all approaches to characterizing the epidemiology of multidrug-resistant isolates, including antibiotic susceptibility profiles and AMR mechanisms, identification of particularly dangerous clones, and any studies aimed at improving the implementation of infection control measures to reduce the prevalence of these pathogens.

Prof. Dr. Anna Baraniak
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

  • enterobacterales
  • antibiotic resistance
  • ß-lactamases
  • carbapenemases
  • multidrug-resistant isolates
  • epidemiology

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Published Papers (2 papers)

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Research

16 pages, 1043 KiB  
Article
Dissemination of IncQ1 Plasmids Harboring NTEKPC-IId in a Brazilian Hospital
by Camila Maria dos Santos Boralli, Julian Andres Paganini, Rodrigo Silva Meneses, Camila Pacheco Silveira Martins da Mata, Edna Marilea Meireles Leite, Anita C. Schürch, Fernanda L. Paganelli, Rob J. L. Willems and Ilana L. B. C. Camargo
Microorganisms 2025, 13(1), 180; https://doi.org/10.3390/microorganisms13010180 - 16 Jan 2025
Viewed by 522
Abstract
KPC is a clinically significant serine carbapenemase in most countries, and its rapid spread threatens global public health. blaKPC transmission is commonly mediated by Tn4401 transposons. The blaKPC gene has also been found in non-Tn4401 elements (NTEKPC). To [...] Read more.
KPC is a clinically significant serine carbapenemase in most countries, and its rapid spread threatens global public health. blaKPC transmission is commonly mediated by Tn4401 transposons. The blaKPC gene has also been found in non-Tn4401 elements (NTEKPC). To fill the gap in the understanding of the stability and dissemination of NTEKPC-carrying plasmids, we selected and characterized carbapenem-resistant bacteria isolated between 2009 and 2016 from a hospital for a retrospective study of their plasmids conjugation capacity, impact on fitness, and replication in different species. Different clones were selected using PFGE, and their genomes were sequenced using Illumina and Oxford Nanopore methods. Minimum inhibitory concentrations (MICs) were determined by broth microdilution. Plasmid copy numbers (PCNs) were determined using qPCR. Doubling time was used to analyze fitness change. Most isolates (67%, 33/49) carried blaKPC, of which 85% presented blaKPC in a NTEKPC. The 25 isolates selected presented the blaKPC gene in NTEKPC-IId in IncQ1-type plasmids, showing multispecies dissemination. IncQ1 plasmids were mobilizable and PCN seemed to be directly linked to the species, presenting a high-copy number, mainly in K. pneumoniae. No relationship was observed between IncQ1 PCN and carbapenems MIC values. IncQ1 and a conjugative plasmid from K. pneumoniae BHKPC10 were transferred to E. coli J53 without fitness changes, and MIC values were maintained for carbapenems despite the low transconjugant PCN. In addition to IncQ1 with NTEKPC, Enterobacter cloacae BHKPC28 contained the mcr-9 gene in an IncHI2/IncHI2A conjugative plasmid, which may help the mobility of IncQ1 and the dissemination of two resistance determinants to last-resort antibiotics. Understanding the interaction between plasmids and high-risk lineages can help develop new therapies to prevent the dissemination of resistance traits. Full article
(This article belongs to the Special Issue Antimicrobial Resistance (AMR) Diagnostics and Genomic/Molecular Epidemiology of Multidrug-Resistant Isolates)
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15 pages, 582 KiB  
Article
Sequencing Analysis of Invasive Carbapenem-Resistant Klebsiella pneumoniae Isolates Secondary to Gastrointestinal Colonization
by Gaetano Maugeri, Maddalena Calvo, Dafne Bongiorno, Dalida Bivona, Giuseppe Migliorisi, Grete Francesca Privitera, Guido Scalia and Stefania Stefani
Microorganisms 2025, 13(1), 89; https://doi.org/10.3390/microorganisms13010089 - 5 Jan 2025
Viewed by 783
Abstract
Klebsiella pneumoniae represent a common invasive infection etiological agent, whose potential carbapenem-resistance and hypermucoviscosity complicate the patient’s management. Infection development often derives from gastrointestinal colonization; thus, it is fundamental to monitor asymptomatic K. pneumoniae colonization through surveillance protocols, especially for intensive care and [...] Read more.
Klebsiella pneumoniae represent a common invasive infection etiological agent, whose potential carbapenem-resistance and hypermucoviscosity complicate the patient’s management. Infection development often derives from gastrointestinal colonization; thus, it is fundamental to monitor asymptomatic K. pneumoniae colonization through surveillance protocols, especially for intensive care and immunocompromised patients. We described a six-month routine screening protocol from the Policlinico of Catania (Italy), while blood samples were collected from the same patients only in cases of a systemic infection suspicion. All the patients who had dissemination episodes were furtherly investigated through next-generation sequencing, analyzing both colonizing and disseminating strains. This study documents emerging invasive sequence types such as ST101, ST307, and ST395, mainly revealing blaNDM or blaKPC genes, along with siderophores and hyperproduction capsule markers as virulence factors. Most of the detected factors are presumably related to a specific plasmid content, which are extremely varied and rich. In conclusion, active surveillance through sequencing is essential to enhance awareness of local epidemiology within high-risk multi-drug resistance areas. A random sequencing analysis on the most warning microorganisms could enhance sequence typing (ST) awareness within specific settings, allowing for better prevention control strategies on their eventual persistence or diffusion. Full article
(This article belongs to the Special Issue Antimicrobial Resistance (AMR) Diagnostics and Genomic/Molecular Epidemiology of Multidrug-Resistant Isolates)
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