Surveillance of Carbapenem-Resistant Microbes and Strategies to Combat Them

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: 15 September 2026 | Viewed by 2093

Special Issue Editors


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Guest Editor
1. Laboratorio de Resistencia Bacteriana, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Departamento de Microbiología, Inmunología, Biotecnología y Genética, Universidad de Buenos Aires; Facultad de Farmacia y Bioquímica, Buenos Aires, Argentina
2. Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
Interests: antimicrobial resistance (AMR); microbial genomics, genomic epidemiology of carbapenem-resistant enterobacterales, and hypervirulent Klebsiella pneumoniae, plasmids harboring bla CARBAPENEMASES; high-risk clones

E-Mail Website
Guest Editor
1. Laboratorio de Resistencia Bacteriana, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Departamento de Microbiología, Inmunología, Biotecnología y Genética, Universidad de Buenos Aires; Facultad de Farmacia y Bioquímica, Buenos Aires, Argentina
2. Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
Interests: antimicrobial resistance (AMR); epidemiology of carbapenem-resistant enterobacterales; detection of carbapenemases-producing critical pathogens; mobile genetic elements.

Special Issue Information

Dear Colleagues,

Antimicrobial resistance (AMR) constitutes a global concern and is one of the main threats to public health in the 21st century. The massive, often abusive, use of antibiotics in human and veterinary medicine and food production threatens their future usefulness. This has led us towards a post-antibiotic era, in which common infections could be fatal again. Gram-negative bacteria resistant to last-resort antibiotics, such as Acinetobacter baumannii, and various pathogens in the Enterobacterales order, are considered to be a critical priority by the World Health Organization. They are frequently involved in severe infections/diseases, cause hospital outbreaks, and can spread in clinical settings. They have developed high-level resistance to carbapenems but are often resistant to other first-line antibiotics such as clinical β-lactamase inhibitors and fluoroquinolones, becoming difficult-to-treat pathogens. The transfer of resistance genes among them has been decisive for the high levels of resistance they have reached. Additionally, clonal expansion and the presence of high-risk clones have been recognized among these pathogens. The surveillance of these resistant pathogens is essential for providing early warnings about emerging issues, identifying new resistance markers, and adapting resistance mechanisms’ detection methods and antibiotic use to minimize therapeutic failures. This Special Issue aims to provide the latest research on the prevalence, resistance mechanisms, and control strategies of carbapenem-resistant pathogens in clinical settings. Through the analysis of critical pathogens, we aim to deepen our understanding of the factors driving resistance and to inspire the development of more effective solutions.

In this Special Issue, original research articles and reviews are welcome. Research areas may include (but are not limited to) the following:

  • Surveillance of carbapenem-resistant Enterobacterales and A. baumanii.
  • Characterization of plasmids harboring carbapenemases-coding genes.
  • Detection and prevalence of carbapenem-resistant mechanisms.
  • Rapid identification of carbapenem-resistant pathogens.

Dr. Daniela Cejas
Dr. Marcela Radice
Guest Editors

Manuscript Submission Information

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Keywords

  • antibiotic resistance
  • epidemiology
  • carbapenemases
  • carbapenem resistance
  • enterobacterales
  • acinetobacter baumannii
  • resistance plasmids
  • surveillance
  • genomics
  • high-risk clones

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Published Papers (2 papers)

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Research

15 pages, 1247 KB  
Article
Epidemiological Insights into Carbapenem-Resistant Enterobacterales Throughout the COVID-19 Pandemic in Buenos Aires, Argentina
by Francisco González-Espinosa, Francisco Magariños, Sofía Ciminello, Roque Figueroa-Espinosa, María Sol Haim, Tomas Poklepovich, Nicolas Potente, Cecilia Ormazabal, Gabriel Gutkind, Daniela Cejas and Marcela Radice
Antibiotics 2026, 15(3), 273; https://doi.org/10.3390/antibiotics15030273 - 6 Mar 2026
Viewed by 751
Abstract
Background: Carbapenem-resistant Enterobacterales (CRE) are a global public health concern, with carbapenem-resistant Klebsiella pneumoniae (CR-Kp) recognised as the highest-priority pathogen. This study aimed to investigate the epidemiological features of CRE isolates throughout the COVID-19 pandemic in Buenos Aires, Argentina. Methods: A [...] Read more.
Background: Carbapenem-resistant Enterobacterales (CRE) are a global public health concern, with carbapenem-resistant Klebsiella pneumoniae (CR-Kp) recognised as the highest-priority pathogen. This study aimed to investigate the epidemiological features of CRE isolates throughout the COVID-19 pandemic in Buenos Aires, Argentina. Methods: A prospective study was conducted in two hospitals from 2019 to 2022, recovering all CRE from inpatients. Antimicrobial susceptibility was performed by automated and/or manual tests, according to CLSI. β-lactamases detection was performed using Multiplex PCR and MALDI-TOF MS. Kp typing was assessed by multiplex PCR and/or MLST based on WGS. Results: 22% (359/1594) were CRE, predominantly CR-Kp. Overall, high non-susceptibility (NS) rates were observed in both centres. NS remained largely stable in HA, except for a significant increase in colistin NS, whereas HB showed a rise in NS to multiple antimicrobials over time. A significant shift from multidrug-resistant to extensively drug-resistant and difficult-to-treat phenotypes was observed across the study periods. Out of 359 CRE, blaKPC was confirmed in 141, blaNDM in 170, and blaKPC + blaNDM in 20 isolates. Before the COVID-19 pandemic, KPC was the main carbapenemase in HB, while NDM was already the prevalent one in HA. In 2022, both enzymes showed similar prevalence. blaKPC-2 and blaNDM-5 were the prevalent alleles in K. pneumoniae. Before the COVID-19 pandemic, K. pneumoniae epidemiology varied by hospital, characterised by clonal diversity; however, in 2022, CG258-tonB79 drove the epidemiology in both hospitals. Conclusions: A more extensive resistance phenotype among CRE was evidenced throughout the COVID-19 pandemic, driven by carbapenemase-producing K. pneumoniae. NDM-5 and KPC-2 were the main carbapenemases identified. A temporal shift in carbapenemase prevalence was observed in each hospital, converging in similar frequencies of KPC and NDM by 2022 across both centres. This scenario was driven by the active dissemination of K. pneumoniae ST258. Full article
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18 pages, 2151 KB  
Article
Silent Waterborne Carriers of Carbapenem-Resistant Gram-Negative Bacilli and Antimicrobial Resistance Genes in Rio de Janeiro’s Aquatic Ecosystems
by Laura Brandão Martins, Marcos Tavares Carneiro, Kéren Vieira-Alcântara, Thiago Pavoni Gomes Chagas and Viviane Zahner
Antibiotics 2026, 15(2), 115; https://doi.org/10.3390/antibiotics15020115 - 23 Jan 2026
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Abstract
Background/Objectives: Water pollution caused by human activities disrupts ecosystems and promotes the spread of antimicrobial resistance genes (ARGs), posing a public health threat. This study investigated the presence of resistant Gram-negative bacteria and resistance genes in water from two sites occasionally exposed [...] Read more.
Background/Objectives: Water pollution caused by human activities disrupts ecosystems and promotes the spread of antimicrobial resistance genes (ARGs), posing a public health threat. This study investigated the presence of resistant Gram-negative bacteria and resistance genes in water from two sites occasionally exposed to domestic and hospital effluents, the Carioca River (CR) and Rodrigo de Freitas Lagoon (RFL), both used for recreation. Methods: Physicochemical parameters and coliform levels were measured. Bacterial isolates were identified by Matrix-Assisted Laser Desorption Ionization–Time-of-Flight Mass Spectrometry (MALDI-TOF MS) and tested for antimicrobial susceptibility using disk diffusion. The Minimum Inhibitory Concentration (MIC) was determined using the E-test® and broth microdilution methods. PCR was used to detect carbapenem resistance and other ARGs from the DNA of bacterial isolates obtained from water samples. Results: CR presented signs of environmental degradation, with low dissolved oxygen and high coliform counts. One Citrobacter braakii isolate showed resistance to all tested antimicrobials, raising concern for untreatable infections. Carbapenem-resistant isolates accounted for 49.4% of the total, harboring blaKPC (20%), blaTEM (5%), blaVIM (5%), and blaSPM (5%). The intl1 gene was found in 10% of isolates, indicating potential horizontal gene transfer. Conclusions: The findings from a one-day sampling reveal the presence of multidrug-resistant bacteria that carry antimicrobial resistance genes in polluted aquatic systems. These highlight the connection between water contamination and antimicrobial resistance. The evidence underscores the urgent need for environmental monitoring and effective management strategies to reduce public health risks. Full article
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