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Antibiotics
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Genetics and Antimicrobial Resistance in Pathogens of Hospital Importance
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Genetics and Antimicrobial Resistance in Pathogens of Hospital Importance

A special issue of Antibiotics (ISSN 2079-6382). This special issue belongs to the section "Genetic and Biochemical Studies of Antibiotic Activity and Resistance".

Deadline for manuscript submissions: 31 October 2025 | Viewed by 972

Special Issue Editor

Prof. Dr. Maria de Lourdes R.S. Cunha

E-Mail Website
Guest Editor
Department of Chemical and Biological Sciences, Institute of Biosciences, São Paulo State University (Unesp), Botucatu, SP, Brazil
Interests: Staphylococcus aureus; coagulase-negative staphylococci; antibiotic resistance; virulence factors; biofilm; molecular epidemiology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The emergence of multidrug-resistant organisms (MDROs) is becoming an increasingly serious threat to global public health, representing one of the greatest concerns of the World Health Organization (WHO). The clonal spread of resistant microorganisms between geographically distant regions has driven the increase in antibiotic resistance in recent years. Healthcare-Associated Infections (HAIs) are directly associated with the emergence of MDROs, a fact resulting from the exposure of patients to pathogenic microorganisms, the indiscriminate use of broad-spectrum antibiotics, and submission to invasive procedures. Antimicrobial resistance (AMR) occurs naturally over time through genetic mutations and exchanges, although these genetic events usually take place at low frequencies. However, the process of AMR emergence, dissemination, and persistence among bacteria has been accelerated due to the overuse or misuse of antimicrobials in the hospital settings. These resistance mechanisms have found a favorable environment in the modern hospital, a place with a high population of sensitive patients, intense pressure from the use of antibiotics that favors natural selection for resistance, and multiple opportunities for transmission. These organisms can spread through the care network, causing serious diseases and reducing therapeutic options. In this regard, The ESKAPEE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter species, and Escherichia coli) are listed as organisms of critical importance due to their MDR nature, consequently requiring the urgent development of new antibiotics. This Special Issue seeks manuscript submissions that further our understanding of basic and clinical research about genetics and antimicrobial resistance in the pathogens of hospital importance.

Prof. Dr. Maria de Lourdes R.S. Cunha
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. 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

  • ESKAPEE pathogens
  • antimicrobial resistance
  • multidrug-resistant organisms
  • genetics
  • resistance mechanisms

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Published Papers (2 papers)

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Research

15 pages, 2035 KiB  
Article
Comprehensive Genomic Analysis of Pseudomonas aeruginosa PSU9449 Isolated from a Clinical Case in Thailand
by Thitaporn Dechathai, Kamonnut Singkhamanan, Thunchanok Yaikhan, Sarunyou Chusri, Rattanaruji Pomwised, Monwadee Wonglapsuwan and Komwit Surachat
Antibiotics 2025, 14(6), 530; https://doi.org/10.3390/antibiotics14060530 - 22 May 2025
Viewed by 156
Abstract
Background/Objectives: Pseudomonas aeruginosa is one of the most significant multidrug-resistant bacteria. It poses considerable challenges in terms of treatment and causes hospital-acquired infections that lead to high morbidity and mortality. Colonization by P. aeruginosa in a patient without clinical signs of infection [...] Read more.
Background/Objectives: Pseudomonas aeruginosa is one of the most significant multidrug-resistant bacteria. It poses considerable challenges in terms of treatment and causes hospital-acquired infections that lead to high morbidity and mortality. Colonization by P. aeruginosa in a patient without clinical signs of infection is a concern in hospital settings, as it is an opportunistic pathogen and can potentially be a multidrug-resistant strain. The objective of this study was to characterize and provide a detailed genomic analysis of this strain of the P. aeruginosa PSU9449 genome, an isolate obtained from a patient at Songklanagarind Hospital, Thailand. Methods: Whole-genome sequencing (WGS) and bioinformatics analysis were employed to examine the genomic features of P. aeruginosa PSU9449. We performed sequence type (ST) determination through multilocus sequence typing (MLST), identified antimicrobial resistance genes (ARGs), virulence factor genes (VFGs), and analyzed the presence of mobile genetic elements (MGEs). Additionally, we compared the PSU9449 genome with strains from neighboring countries to understand its phylogenetic relationship. Results: The P. aeruginosa PSU9449 genome contained five insertion sequences and several ARGs, including fosA, aph (3’)-IIb, blaOXA-50, and catB7. It also harbored VFGs related to flagella (fli, fle, and flg), the type 6 secretion system (hcpA, tssA, and las), and the type 3 secretion system (exoS, exoU, and exoT). MLST identified PSU9449 as ST3777, which was reported in Thailand for the first time. Phylogenetic analysis based on core gene SNPs revealed that PSU9449 was closely related to P. aeruginosa HW001G from Malaysia and P. aeruginosa MyJU45 from Myanmar, forming a distinct clade. Conclusions: This study presents a comprehensive genomic analysis of P. aeruginosa PSU9449, shedding light on its genetic characteristics, antimicrobial resistance profile, and virulence potential. Interestingly, ST3777, the novel STs from the published genomes of P. aeruginosa in Thailand, were assigned in this study. The findings enhance valuable insights into the expanding knowledge of P. aeruginosa PSU9449 and highlight the importance of ongoing surveillance of its genetic diversity. Full article
(This article belongs to the Special Issue Genetics and Antimicrobial Resistance in Pathogens of Hospital Importance)
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20 pages, 8288 KiB  
Article
Molecular Characterization of Gram-Negative Bacilli Isolated from a Neonatal Intensive Care Unit and Phenotypic and Molecular Detection of ESBL and Carbapenemase
by Thaís Alves Barbosa, Maria Regina Bentlin, Lígia Maria Suppo de Souza Rugolo, João César Lyra, Adriano Martison Ferreira, Ana Cláudia Moro Lima dos Santos, Nathalia Bibiana Teixeira, Letícia Calixto Medeiros Romero, Carlos Magno Castelo Branco Fortaleza and Maria de Lourdes Ribeiro de Souza da Cunha
Antibiotics 2025, 14(4), 342; https://doi.org/10.3390/antibiotics14040342 - 27 Mar 2025
Viewed by 497
Abstract
Introduction: The increase in the rates of multidrug-resistant bacteria in healthcare environments has been recognized as a global public health problem. In view of the scarcity of data on the neonatal population, this study aimed to provide information on the genotypic and epidemiological [...] Read more.
Introduction: The increase in the rates of multidrug-resistant bacteria in healthcare environments has been recognized as a global public health problem. In view of the scarcity of data on the neonatal population, this study aimed to provide information on the genotypic and epidemiological characteristics of Gram-negative microorganisms isolated from colonization and infection sites in neonates admitted to a tertiary university center of high complexity. Methods: Enterobacterales and non-fermenting Gram-negative bacilli previously collected in a prospective cohort study were submitted to genotypic identification, detection of extended-spectrum β-lactamases (ESBL), carbapenemases and biofilm production, detection of specific virulence markers in Pseudomonas aeruginosa, and typing by pulsed-field gel electrophoresis. Results: The data found here revealed higher rates of infection by Klebsiella spp. and Serratia marcescens that caused bloodstream infection and pneumonia, respectively. In this study, high biofilm production was observed, with 95.0% of Enterobacterales and 100% of non-fermenting Gram-negative bacilli being producers. Most of the P. aeruginosa isolates carried pathogenicity factors such as alginate, hemolytic phospholipase C, exotoxin A, and rhamnolipids. The phenotypic analysis of ESBL revealed that 16 (5.3%) isolates produced these enzymes. Four of these isolates (66.7%) carried the CTX-M-9 gene, three (50%) carried the TEM gene, and one (16.7%) was positive for the SHV and CMY-2 genes. Univariate and multivariate Cox regression analyses were used to identify risk factors for colonization and infection by Gram-negative microorganisms. The results of multivariate analysis revealed that biofilm production by these microorganisms was associated with the persistence of colonization by the same pathogen in the newborn and increased by 75% the daily probability of the newborn developing infection. The production of ESBL also increased the daily probability of infection by 46.8 times. Conclusions: Enterobacterales showed average biofilm production, while the majority of non-fermenting Gram-negative bacilli were strong producers. The present data increase our knowledge of the molecular epidemiology of important Enterobacterales species, with emphasis on ESBL-producing Enterobacter cloacae and Klebsiella pneumoniae with emerging epidemiological potential in the neonatal intensive care unit of a tertiary university hospital. Furthermore, the results highlight the need for the monitoring and implementation of control measures and for restricting the use of broad-spectrum antibiotics. Full article
(This article belongs to the Special Issue Genetics and Antimicrobial Resistance in Pathogens of Hospital Importance)
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