Antimicrobial Resistance and Epidemiological Study of Clinically Relevant Pathogens

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 May 2025 | Viewed by 16123

Special Issue Editors


E-Mail Website
Guest Editor
Department of Microbiology, “Victor Babes” University of Medicine and Pharmacy, Timisoara, Romania
Interests: antimicrobials; antibiotic resistance; microbiology; healthcare associated infections; COVID-19; SARS-CoV-2
Special Issues, Collections and Topics in MDPI journals
Department of Microbiology, “George Emil Palade” University of Medicine, Pharmacy, Sciences and Technology, Targu Mures, Romania
Interests: bacteriology; molecular biology; mycology; virology; antimicrobial activity
Special Issues, Collections and Topics in MDPI journals

E-Mail Website
Guest Editor
Department of Microbiology, “Victor Babes” University of Medicine and Pharmacy, Timisoara, Romania
Interests: antibacterial resistance; hospital-acquired infections; new antimicrobial compounds
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The escalating threat of bacterial resistance poses a significant challenge in contemporary healthcare, leading to critical clinical implications that profoundly impact treatment options. In recent years, infections caused by multidrug-resistant organisms (MDROs) have become endemic in numerous healthcare facilities, resulting in hospital-acquired outbreaks reported globally. Several factors contribute to the varying prevalence of MDRO acquisition across departments, including individual patient risk factors such as underlying diseases, recent hospital admissions, the presence of vascular catheters, major surgeries, and recent antibiotic therapies.

Local factors further influence MDRO acquisition, such as excessive bed occupancy, inadequate patient isolation rooms, high patient-to-nurse ratios, and suboptimal compliance with standard precautions, including hand hygiene and environmental decontamination. There is a growing interest in understanding the role of the environment in patient MDRO acquisition, shedding light on bacterial adaptability, exemplified by the production of bacterial biofilm to facilitate adherence.

Advances in genotyping methods, particularly whole genome sequencing, offer exciting opportunities to trace the spread of microorganisms either between patients or from the environment to a patient. In this context, we invite contributions for our Special Issue, with a focus on, but not limited to, the following topics:

  • The molecular characterization of multidrug-resistant bacteria;
  • Correlation between antibiotic use and resistance patterns;
  • The identification of risk factors for acquired multidrug resistance;
  • The evaluation of local trends in multidrug-resistant bacteria;
  • The investigation of novel methods for rapid resistance detection;
  • The assessment of antimicrobial activity of new compounds;
  • The relationship between the environment and resistant pathogens.

We encourage submissions of both original research and review articles. Your valuable contributions will significantly advance our understanding of bacterial multidrug resistance and antimicrobial activity.

Dr. Florin George Horhat
Dr. Adrian Man
Dr. Delia Muntean
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 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. 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

  • antibacterial activity
  • antimicrobial resistance
  • infections
  • multidrug-resistant pathogens
  • virulence gene expression
  • drug discovery
  • epidemiological study

Benefits of Publishing in a Special Issue

  • Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
  • Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
  • Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
  • External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
  • e-Book format: Special Issues with more than 10 articles can be published as dedicated e-books, ensuring wide and rapid dissemination.

Further information on MDPI's Special Issue policies can be found here.

Published Papers (8 papers)

Order results
Result details
Select all
Export citation of selected articles as:

Research

Jump to: Review, Other

16 pages, 248 KiB  
Article
Rapid Syndromic Testing: A Key Strategy for Antibiotic Stewardship in ICU Patients with Pneumonia
by Silvana Vulpie, Monica Licker, Oana Izmendi, Delia Muntean, Diana Lungeanu, Beatrice Sarah Zembrod, Iasmina Maria Hancu, Ovidiu Bedreag, Dorel Sandesc, Romanita Jumanca and Luminita Mirela Baditoiu
Antibiotics 2025, 14(5), 426; https://doi.org/10.3390/antibiotics14050426 - 23 Apr 2025
Viewed by 172
Abstract
Background/Objectives: According to the European Centre for Disease Prevention and Control, improved antimicrobial stewardship programs (ASPs) combined with rapid diagnostic tests could potentially prevent thousands of deaths caused by multidrug-resistant organisms annually. This study aimed to compare the results obtained using the Unyvero [...] Read more.
Background/Objectives: According to the European Centre for Disease Prevention and Control, improved antimicrobial stewardship programs (ASPs) combined with rapid diagnostic tests could potentially prevent thousands of deaths caused by multidrug-resistant organisms annually. This study aimed to compare the results obtained using the Unyvero system/hospital-acquired pneumonia (HPN) panel with those obtained using classic microbiological diagnostic methods to evaluate the potential of introducing this rapid diagnostic test into routine diagnosis and improving local ASPs. Methods: A single-center, observational, cross-sectional, analytical study was performed; it included patients admitted to the intensive care unit (ICU) with the presumptive diagnosis of community- or hospital-acquired pneumonia. One hundred non-repetitive endotracheal aspirates were collected and subjected to analysis using both methods. The concordance between the results obtained via the standard-of-care (SoC) culture and Unyvero was analyzed. Results: Of the results generated using Unyvero/HPN, 51% were fully concordant with those obtained via culture, 48% were partially concordant, and only 1% represented failure. It was also more efficient in identifying multiple organisms in a single sample than the SoC culture (1.32 versus 1.1 per sample). The three most common isolates identified via both methods were Acinetobacter baumannii, Klebsiella pneumoniae, and Pseudomonas aeruginosa. The most common resistance markers identified with Unyvero were sul1 (41%), tem and ndm (25%), and kpc, imp, vim, and gyrA87 (2% of results). Conclusions: Unyvero/HPN, if associated with appropriate diagnostic stewardship, could be used to manage critically ill patients to ensure an appropriate ASP. Full article
23 pages, 1188 KiB  
Article
Mechanical Ventilator-Associated Pneumonia in the COVID-19 Pandemic Era: A Critical Challenge in the Intensive Care Units
by Mircea Stoian, Adina Andone, Sergiu Rareș Bândilă, Danusia Onișor, Sergiu Ștefan Laszlo, Gabriela Lupu, Alina Danielescu, Dragoș-Florin Baba, Anca Meda Văsieșiu, Andrei Manea and Adina Stoian
Antibiotics 2025, 14(1), 28; https://doi.org/10.3390/antibiotics14010028 - 3 Jan 2025
Cited by 3 | Viewed by 1720
Abstract
Background/Objectives: Ventilator-associated pneumonia (VAP) is the most common nosocomial infection encountered in the intensive care unit (ICU) and is associated with prolonged hospitalization and increased mortality. We evaluated the causative pathogens involved and their resistance to the major classes of antibiotics in patients [...] Read more.
Background/Objectives: Ventilator-associated pneumonia (VAP) is the most common nosocomial infection encountered in the intensive care unit (ICU) and is associated with prolonged hospitalization and increased mortality. We evaluated the causative pathogens involved and their resistance to the major classes of antibiotics in patients with VAP and assessed the differences between patients with and without coronavirus disease 2019 (COVID-19). Materials and Methods: This study was a single-center, cross-sectional, retrospective analysis involving 122 patients who were hospitalized in the ICU of Târgu Mureș County Clinical Hospital from 1 April 2021, to 1 April 2023. This study compares patients with VAP in COVID-19 and non-COVID-19 groups, examining the clinical progression, duration of ventilation and hospitalization, mortality, pathogen distribution, and the emergence of multidrug-resistant strains. Results: A length of stay in the ICU exceeding 11.5 days was associated with the development of multidrug-resistant (MDR) infections (AUC: 0.708, p < 0.001). Similarly, a duration of MV exceeding 196 h was associated with MDR acquisition (AUC: 0.695, p = 0.002). Additionally, a Clinical Pulmonary Infection Score (CPIS) greater than 5 was associated with MDR development (AUC: 0.854, p < 0.001) in the whole group of patients. The most commonly isolated strains were Acinetobacter spp., Pseudomonas spp., Klebsiella spp., and Staphylococcus aureus. Among non-COVID-19 patients, there was a notably higher frequency of MDR Acinetobacter baumannii. A bacterial resistance to carbapenems was found in Acinetobacter spp. (51.6%), Klebsiella spp. (22.6%), and Pseudomonas spp. (25.8%). Conclusions: COVID-19 patients experienced longer ventilation, higher mortality, and an increased risk of developing MDR. Carbapenem resistance was universal in Acinetobacter spp. and Klebsiella pneumoniae, whereas resistance in Pseudomonas aeruginosa was more prevalent among non-COVID-19 patients. The Clinical Pulmonary Infection Score (CPIS) strongly correlates with developing MDR pathogens in both patient groups. Full article
Show Figures

Figure 1

15 pages, 448 KiB  
Article
The Profile of Bacterial Infections in a Burn Unit during and after the COVID-19 Pandemic Period
by Corina Musuroi, Silvia-Ioana Musuroi, Luminita Baditoiu, Zorin Crainiceanu, Delia Muntean, Adela Voinescu, Oana Izmendi, Alexandra Sirmon and Monica Licker
Antibiotics 2024, 13(9), 823; https://doi.org/10.3390/antibiotics13090823 - 30 Aug 2024
Cited by 2 | Viewed by 1555
Abstract
Infections represent a major complication for burn-injured patients. The aim of this study was to highlight the changes in the incidence and antimicrobial resistance of bacterial strains isolated from burn patients, at the end of the COVID-19 pandemic, in relation to the antibiotics [...] Read more.
Infections represent a major complication for burn-injured patients. The aim of this study was to highlight the changes in the incidence and antimicrobial resistance of bacterial strains isolated from burn patients, at the end of the COVID-19 pandemic, in relation to the antibiotics used during the pandemic. A comparative analysis of the demographic data and the microorganisms identified in the clinical samples of two groups of burn patients admitted to a university hospital in Romania was carried out. The first group consisted of 48 patients and the second of 69 patients, hospitalized in January–August 2020 and 2023, respectively. The bacterial species with the highest incidence were S. aureus, A. baumannii, Pseudomonas spp. The significant changes between 2023 and 2020 are reflected in the increase in the frequency of non-fermentative Gram-negative bacteria, especially S. maltophilia, and the increase in antimicrobial resistance of Pseudomonas and Klebsiella spp. Klebsiella spp. did not change in frequency (7%), but there was a significant increase in the incidence of K. pneumoniae strains with pan-drug resistant behaviour to antibiotics (40%), including colistin. The phenomenon can be explained by the selection of specimens carrying multiple resistance genes, as a result of antibiotic treatment during the COVID-19 period. The post-pandemic antimicrobial resistance detected in burn patients indicates the need for permanent surveillance of the resistance trends, primarily due to the limited therapeutic options available for these patients. Full article
Show Figures

Figure 1

11 pages, 1347 KiB  
Article
Antibiotic Resistance Trends in Uropathogens during the COVID-19 Pandemic in Western Romania: A Cross-Sectional Study
by Elena Hogea, Alexandra Cristina Muntean, Felix Bratosin, Iulia Georgiana Bogdan, Oana Plavitu, Adelina Fratutu, Cristian Oancea, Mihai Calin Bica, Delia Muntean, Ingrid Hrubaru, Zoran Laurentiu Popa and Adrian Cosmin Ilie
Antibiotics 2024, 13(6), 512; https://doi.org/10.3390/antibiotics13060512 - 30 May 2024
Viewed by 1507
Abstract
The emergence and spread of antimicrobial resistance have been significant global health challenges, exacerbated by the COVID-19 pandemic. As healthcare systems faced unprecedented pressures, the management of non-COVID conditions, including urinary tract infections (UTIs), also encountered obstacles due to changes in microbial flora [...] Read more.
The emergence and spread of antimicrobial resistance have been significant global health challenges, exacerbated by the COVID-19 pandemic. As healthcare systems faced unprecedented pressures, the management of non-COVID conditions, including urinary tract infections (UTIs), also encountered obstacles due to changes in microbial flora and antibiotic usage patterns. This cross-sectional study aimed to characterize the antimicrobial resistance trends among bacterial uropathogens isolated from patients in the Western region of Romania, between January 2020 and December 2022. The objectives were to map the resistance patterns and observe the pandemic’s influence on antimicrobial resistance, particularly among enterobacterial Gram-negative species, to guide treatment and infection control strategies. From a total of 2472 urine samples collected during the study period, 378 positive samples were analyzed. This study found that Escherichia coli was the most commonly isolated uropathogen, making up 46.3% of the cases (n = 175), with Klebsiella pneumoniae at 20.6% (n = 78). There was a high resistance of Klebsiella pneumoniae to several antibiotics, while carbapenemase production increased to 52.5% and extended-spectrum beta-lactamase (ESBL) present in 24.3% of the strains. Escherichia coli showed high resistance rates to amoxicillin–clavulanic acid (from 45.4% in 2020 to 53.8% in 2022) and trimethoprim/sulfamethoxazole (from 27.5% in 2020 to 47.2% in 2022). The increasing trend of antimicrobial resistance noted during the pandemic, especially in Gram-negative enterobacterial species, highlights the urgent need for robust infection control measures and rational antibiotic use. This study underscores the critical importance of continuous surveillance to adapt antibiotic therapies effectively and prevent the further spread of resistance, thereby ensuring effective management of UTIs in the evolving healthcare landscape influenced by the pandemic. Full article
Show Figures

Figure 1

20 pages, 3859 KiB  
Article
Prevalence of Infections and Antimicrobial Resistance of ESKAPE Group Bacteria Isolated from Patients Admitted to the Intensive Care Unit of a County Emergency Hospital in Romania
by Alina-Simona Bereanu, Rareș Bereanu, Cosmin Mohor, Bogdan Ioan Vintilă, Ioana Roxana Codru, Ciprian Olteanu and Mihai Sava
Antibiotics 2024, 13(5), 400; https://doi.org/10.3390/antibiotics13050400 - 27 Apr 2024
Cited by 17 | Viewed by 4582
Abstract
The ESKAPE group (Enterococcus faecium, Staphylococcus aureus, Klebsiella Pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp.) is a group of bacteria very difficult to treat due to their high ability to acquire resistance to antibiotics and are the [...] Read more.
The ESKAPE group (Enterococcus faecium, Staphylococcus aureus, Klebsiella Pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp.) is a group of bacteria very difficult to treat due to their high ability to acquire resistance to antibiotics and are the main cause of nosocomial infections worldwide, posing a threat to global public health. Nosocomial infections with MDR bacteria are found mainly in Intensive Care Units, due to the multitude of maneuvers and invasive medical devices used, the prolonged antibiotic treatments, the serious general condition of these critical patients, and the prolonged duration of hospitalization. Materials and Methods: During a period of one year, from January 2023 to December 2023, this cross-sectional study was conducted on patients diagnosed with sepsis admitted to the Intensive Care Unit of the Sibiu County Emergency Clinical Hospital. Samples taken were tracheal aspirate, catheter tip, pharyngeal exudate, wound secretion, urine culture, blood culture, and peritoneal fluid. Results: The most common bacteria isolated from patients admitted to our Intensive Care Unit was Klebsiella pneumoniae, followed by Acinetobacter baumanii and Pseudomonas aeruginosa. Gram-positive cocci (Enterococcus faecium and Staphilococcus aureus) were rarely isolated. Most of the bacteria isolated were MDR bacteria. Conclusions: The rise of antibiotic and antimicrobial resistance among strains in the nosocomial environment and especially in Intensive Care Units raises serious concerns about limited treatment options. Full article
Show Figures

Figure 1

29 pages, 3565 KiB  
Article
Inhibition of Clinical MRSA Isolates by Coagulase Negative Staphylococci of Human Origin
by Ellen Twomey, Paula M. O’Connor, Aidan Coffey, Maija Kiste, Caitriona M. Guinane, Colin Hill, Des Field and Máire Begley
Antibiotics 2024, 13(4), 338; https://doi.org/10.3390/antibiotics13040338 - 8 Apr 2024
Viewed by 2060
Abstract
Staphylococcus aureus is frequently highlighted as a priority for novel drug research due to its pathogenicity and ability to develop antibiotic resistance. Coagulase-negative staphylococci (CoNS) are resident flora of the skin and nares. Previous studies have confirmed their ability to kill and prevent [...] Read more.
Staphylococcus aureus is frequently highlighted as a priority for novel drug research due to its pathogenicity and ability to develop antibiotic resistance. Coagulase-negative staphylococci (CoNS) are resident flora of the skin and nares. Previous studies have confirmed their ability to kill and prevent colonization by S. aureus through the production of bioactive substances. This study screened a bank of 37 CoNS for their ability to inhibit the growth of methicillin-resistant S. aureus (MRSA). Deferred antagonism assays, growth curves, and antibiofilm testing performed with the cell-free supernatant derived from overnight CoNS cultures indicated antimicrobial and antibiofilm effects against MRSA indicators. Whole genome sequencing and BAGEL4 analysis of 11 CoNS isolates shortlisted for the inhibitory effects they displayed against MRSA led to the identification of two strains possessing complete putative bacteriocin operons. The operons were predicted to encode a nukacin variant and a novel epilancin variant. From this point, strains Staphylococcus hominis C14 and Staphylococcus epidermidis C33 became the focus of the investigation. Through HPLC, a peptide identical to previously characterized nukacin KQU-131 and a novel epilancin variant were isolated from cultures of C14 and C33, respectively. Mass spectrometry confirmed the presence of each peptide in the active fractions. Spot-on-lawn assays demonstrated both bacteriocins could inhibit the growth of an MRSA indicator. The identification of natural products with clinically relevant activity is important in today’s climate of escalating antimicrobial resistance and a depleting antibiotic pipeline. These findings also highlight the prospective role CoNS may play as a source of bioactive substances with activity against critical pathogens. Full article
Show Figures

Figure 1

Review

Jump to: Research, Other

23 pages, 926 KiB  
Review
The Synergy of Machine Learning and Epidemiology in Addressing Carbapenem Resistance: A Comprehensive Review
by Aikaterini Sakagianni, Christina Koufopoulou, Petros Koufopoulos, Georgios Feretzakis, Dimitris Kalles, Evgenia Paxinou, Pavlos Myrianthefs and Vassilios S. Verykios
Antibiotics 2024, 13(10), 996; https://doi.org/10.3390/antibiotics13100996 - 21 Oct 2024
Cited by 4 | Viewed by 2109
Abstract
Background/Objectives: Carbapenem resistance poses a significant threat to public health by undermining the efficacy of one of the last lines of antibiotic defense. Addressing this challenge requires innovative approaches that can enhance our understanding and ability to combat resistant pathogens. This review aims [...] Read more.
Background/Objectives: Carbapenem resistance poses a significant threat to public health by undermining the efficacy of one of the last lines of antibiotic defense. Addressing this challenge requires innovative approaches that can enhance our understanding and ability to combat resistant pathogens. This review aims to explore the integration of machine learning (ML) and epidemiological approaches to understand, predict, and combat carbapenem-resistant pathogens. It examines how leveraging large datasets and advanced computational techniques can identify patterns, predict outbreaks, and inform targeted intervention strategies. Methods: The review synthesizes current knowledge on the mechanisms of carbapenem resistance, highlights the strengths and limitations of traditional epidemiological methods, and evaluates the transformative potential of ML. Real-world applications and case studies are used to demonstrate the practical benefits of combining ML and epidemiology. Technical and ethical challenges, such as data quality, model interpretability, and biases, are also addressed, with recommendations provided for overcoming these obstacles. Results: By integrating ML with epidemiological analysis, significant improvements can be made in predictive accuracy, identifying novel patterns in disease transmission, and designing effective public health interventions. Case studies illustrate the benefits of interdisciplinary collaboration in tackling carbapenem resistance, though challenges such as model interpretability and data biases must be managed. Conclusions: The combination of ML and epidemiology holds great promise for enhancing our capacity to predict and prevent carbapenem-resistant infections. Future research should focus on overcoming technical and ethical challenges to fully realize the potential of these approaches. Interdisciplinary collaboration is key to developing sustainable strategies to combat antimicrobial resistance (AMR), ultimately improving patient outcomes and safeguarding public health. Full article
Show Figures

Figure 1

Other

Jump to: Research, Review

27 pages, 1698 KiB  
Systematic Review
Bacterial Infections, Trends, and Resistance Patterns in the Time of the COVID-19 Pandemic in Romania—A Systematic Review
by Dan Dumitru Vulcanescu, Iulia Cristina Bagiu, Cecilia Roberta Avram, Licinia Andrada Oprisoni, Sonia Tanasescu, Teodora Sorescu, Razvan Susan, Monica Susan, Virgiuliu Bogdan Sorop, Mircea Mihai Diaconu, Tiberiu Liviu Dragomir, Octavia Oana Harich, Razvan Mihai Horhat, Stefania Dinu and Florin George Horhat
Antibiotics 2024, 13(12), 1219; https://doi.org/10.3390/antibiotics13121219 - 14 Dec 2024
Cited by 2 | Viewed by 1746
Abstract
Background: The COVID-19 pandemic has intensified concerns over bacterial infections and antimicrobial resistance, particularly in Romania. This systematic review explores bacterial infection patterns and resistance during the pandemic to address critical gaps in knowledge. Methods: A systematic review, following PRISMA guidelines, was conducted [...] Read more.
Background: The COVID-19 pandemic has intensified concerns over bacterial infections and antimicrobial resistance, particularly in Romania. This systematic review explores bacterial infection patterns and resistance during the pandemic to address critical gaps in knowledge. Methods: A systematic review, following PRISMA guidelines, was conducted using databases such as PubMed and Scopus, focusing on studies of bacterial infections from 2020 to 2022. Articles on bacterial infections in Romanian patients during the pandemic were analyzed for demographic data, bacterial trends, and resistance profiles. Results: A total of 87 studies were included, detailing over 20,000 cases of bacterial infections. The review found that Gram-negative bacteria, particularly Escherichia coli and Klebsiella pneumoniae, were the most frequently identified pathogens, alongside Gram-positive Staphylococcus aureus and Enterococcus spp. Multidrug resistance (MDR) was noted in 24% of the reported strains, with common resistance to carbapenems and cephalosporins. Conclusions: The pandemic has amplified the complexity of managing bacterial infections, particularly in critically ill patients. The rise in MDR bacteria underscores the need for stringent antimicrobial stewardship and infection control measures. Continuous monitoring of bacterial trends and resistance profiles will be essential to improve treatment strategies in post-pandemic healthcare settings. Full article
Show Figures

Figure 1

Back to TopTop