Bacterial Infection and Antimicrobial Resistance

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

Deadline for manuscript submissions: closed (31 May 2026) | Viewed by 1327

Editors


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Guest Editor
Electronic Microscopy Center of the Institute of Biosciences of Botucatu, UNESP, Botucatu, Brazil
Interests: staphylococci; bacterial infection; antimicrobial resistance; biofilm; leprosy

E-Mail Website
Guest Editor
Department of Genetics, Microbiology and Immunology, Institute of Biosciences of Botucatu, UNESP, Botucatu, Brazil
Interests: Staphylococcus aureus; coagulase-negative staphylococci; antibiotic resistance; virulence factors; biofilm; molecular epidemiology
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Special Issue Information

Dear Colleagues,

Infections caused by pathogenic and opportunistic bacteria exert a profound impact on global public health. Bacterial infections constitute the second leading cause of mortality worldwide, a situation further exacerbated by the alarming rise in antimicrobial resistance (AMR)—a challenge that has become even more pressing in the aftermath of the COVID-19 pandemic.

Several bacterial species are recognized as major etiological agents of clinically significant infections, including Staphylococcus aureus (skin and soft tissue infections), Escherichia coli (urinary tract and kidney infections), Streptococcus pneumoniae (pneumonia and meningitis), Klebsiella pneumoniae (pneumonia and bloodstream infections), and Pseudomonas aeruginosa (pneumonia, urinary tract, and bloodstream infections). Other bacterial taxa, such as group B Streptococcus, Enterococcus spp., Neisseria spp., Haemophilus spp., Helicobacter pylori, and Chlamydia trachomatis, are less frequently implicated as primary causative agents of human infections.

The severity of infection is influenced not only by the virulence and pathogenic potential of the bacterial species but also by host-intrinsic factors, including immunocompromised status, extremes of age, and genetic background.

Antimicrobial resistance arises from a convergence of intrinsic genetic mechanisms and anthropogenic factors that accelerate its emergence and dissemination. Key drivers include the excessive and inappropriate use of antimicrobial agents in clinical and agricultural contexts, inadequate infection prevention and control practices, insufficient hygiene measures, and the circulation of substandard or falsified pharmaceuticals. At the molecular level, resistance develops through spontaneous mutations and horizontal gene transfer among bacterial populations. The selective pressure imposed by antimicrobial misuse further facilitates the survival and propagation of resistant strains, thereby intensifying the global AMR crisis.

This Special Issue seeks to showcase original research articles and comprehensive reviews that deepen current knowledge on bacterial infections and antimicrobial resistance, encompassing their emerging trends, molecular mechanisms, epidemiological patterns, and future perspectives for research, surveillance, and public health interventions.

Dr. Luiza Pinheiro-Hubinger-Stauffer
Prof. Dr. Maria de Lourdes Ribeiro de Souza da Cunha
Guest Editors

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Keywords

  • bacterial infections
  • Staphylococcus
  • Streptococcus
  • Escherichia coli
  • Klebsiella pneumoniae
  • Pseudomonas aeruginosa
  • antimicrobial resistance
  • mutations

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Published Papers (3 papers)

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Research

22 pages, 2638 KB  
Article
Antimicrobial Resistance and Comparative Genome Analysis of High-Risk Escherichia coli Strains Isolated from Ventilator-Associated Pneumonia Cases in Egyptian ICUs
by Shaymaa Yusuf, Mona H. Abdel-Rahim, Omnia El-Badawy, Safy Hadiya, Amany G. Thabit, Radwa Abdelwahab, Heba A. Hammad, Shabaan H. Ahmed, Mohamed Samir, Xiaoqiang Liu, Douglas F. Browning and Sherine A. Aly
Microorganisms 2026, 14(7), 1438; https://doi.org/10.3390/microorganisms14071438 - 30 Jun 2026
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Abstract
Escherichia coli is increasingly recognised as an important cause of ventilator-associated pneumonia (VAP), particularly in intensive care units (ICUs) with high antimicrobial selective pressure. Unlike classical respiratory pathogens, ICU-associated E. coli often originates from the patient’s intestinal microbiota and harbours a complex mobilome [...] Read more.
Escherichia coli is increasingly recognised as an important cause of ventilator-associated pneumonia (VAP), particularly in intensive care units (ICUs) with high antimicrobial selective pressure. Unlike classical respiratory pathogens, ICU-associated E. coli often originates from the patient’s intestinal microbiota and harbours a complex mobilome enriched with antimicrobial resistance determinants. In this study, a total of 200 nosocomial endotracheal aspirate samples were aseptically collected from patients admitted to the Respiratory ICU at Assiut University hospital. Antimicrobial susceptibility testing, serotyping and screening for various virulence and antimicrobial resistance genes (e.g., extended-spectrum β-lactamase (ESBL) and carbapenems genes) were carried out. In total, E. coli isolates were recovered from 54/200 (27%) endotracheal aspirates, with a high prevalence of multidrug resistance (MDR) observed (74.1%). Resistance to β-lactams was common with phenotypic evidence suggestive of ESBL production detected in 64.8% of isolates. Genome sequencing of three MDR E. coli isolates confirmed that they carried multiple antimicrobial resistance genes, which included ESBL genes (e.g., blaCTX-M-15 and blaTEM-1B). Each strain was also found to be high-risk extraintestinal pathogenic E. coli (ExPEC) clones, belonging to either sequence type ST131 or ST405. These findings support an endogenous infection model for VAP, whereby ICU selective pressure favours highly mobile, multidrug-resistant E. coli lineages adapted for extraintestinal survival. The high production of ESBLs and the prevalence of carbapenemase genes highlight the urgent need for molecular surveillance and antimicrobial stewardship strategies for the control of such high-priority pathogens in this part of the world. Full article
(This article belongs to the Special Issue Bacterial Infection and Antimicrobial Resistance)
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15 pages, 294 KB  
Article
Microbial Profile and Antimicrobial Resistance Patterns in Chronic Lower Limb Ulcers: Evidence from a Brazilian Dermatology Referral Center
by Silas Matheus Brosco de Toledo Piza, Regina Maldonado Poz Bernardo, Claudia Alessandra de Lima Ramos, Maria de Lourdes Ribeiro de Souza da Cunha, Patricia Sammarco Rosa, Antônio Carlos Ceribelli Martelli and Luiza Pinheiro-Hubinger-Stauffer
Microorganisms 2026, 14(6), 1199; https://doi.org/10.3390/microorganisms14061199 - 26 May 2026
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Abstract
Chronic ulcers are characterized by impaired tissue repair and frequently harbor antimicrobial-resistant microorganisms, worsening clinical outcomes. The objective of this study is to identify microbial agents in chronic ulcers treated at the Lauro de Souza Lima Institute Wound Care Outpatient Clinic and to [...] Read more.
Chronic ulcers are characterized by impaired tissue repair and frequently harbor antimicrobial-resistant microorganisms, worsening clinical outcomes. The objective of this study is to identify microbial agents in chronic ulcers treated at the Lauro de Souza Lima Institute Wound Care Outpatient Clinic and to evaluate their antimicrobial susceptibility profiles and β-lactamase production. Samples (swab and biopsy) from patients treated at the Lauro de Souza Lima Institute were analyzed. Susceptibility was assessed by disk diffusion. ESBL and AmpC production were confirmed by PCR targeting blaTEM, blaSHV, blaCTX-M1, and blaCMY-2. In Staphylococcus spp., oxacillin and clindamycin resistance were evaluated and confirmed by mecA and ermAC. From 33 patients (mean age 63.4 years), 116 isolates were obtained, mainly Pseudomonas aeruginosa (27%), Proteus mirabilis (18%), and Staphylococcus aureus (13%). P. aeruginosa showed high resistance, with 48% MDR and 29% PDR. Among Enterobacterales, 19% were ESBL producers and 17% AmpC, with 56% carrying blaCMY-2. In Staphylococcus, 33% were oxacillin-resistant and 50% expressed MLSb phenotype. P. aeruginosa was identified as the most prevalent pathogen, with frequent MDR/PDR phenotypes. Resistance genes exhibited a discrepancy between genotypic and phenotypic profiles, suggesting the presence of unexpressed resistance that may be inducible during treatment. Full article
(This article belongs to the Special Issue Bacterial Infection and Antimicrobial Resistance)
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19 pages, 945 KB  
Article
Patterns, Associated Factors, and Anatomical Concordance of Nasal and Throat Staphylococcus aureus Carriage Among Community-Dwelling Adults in Germany
by Alexander Martens, Markus Schauer, Mohamad Motevalli and Brigitte König
Microorganisms 2026, 14(5), 1053; https://doi.org/10.3390/microorganisms14051053 - 8 May 2026
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Abstract
Despite its clinical importance, Staphylococcus aureus colonization in community populations remains insufficiently understood. This study aimed to determine the prevalence, anatomical distribution (nasal versus throat), and antimicrobial resistance patterns of Staphylococcus aureus colonization in healthy community-dwelling adults and to identify demographic and clinical [...] Read more.
Despite its clinical importance, Staphylococcus aureus colonization in community populations remains insufficiently understood. This study aimed to determine the prevalence, anatomical distribution (nasal versus throat), and antimicrobial resistance patterns of Staphylococcus aureus colonization in healthy community-dwelling adults and to identify demographic and clinical factors associated with carriage. A cross-sectional study was conducted among 100 community-dwelling adults in Germany, yielding 200 nasal/throat samples. Staphylococcal isolates were identified using MALDI-TOF MS, and antimicrobial susceptibility was determined according to EUCAST guidelines. MRSA and PVL genes were assessed using molecular assays, and genetic relatedness was evaluated by rep-PCR. Associations with demographic and clinical variables were analyzed using multivariable logistic regression in R. Staphylococcus aureus carriage prevalence was 39%, higher in the nose (33%) than the throat (19%), with rare MRSA (3%) and no PVL detection. Significant nasal–throat discordance was observed (p < 0.01), with a fair agreement between sites (κ = 0.34). Resistance patterns among Staphylococcus aureus isolates were dominated by penicillin G resistance (47%), while 35% remained fully susceptible, and multidrug resistance was rare (6%). Multivariable analyses indicated no strong associations between overall, nasal, or throat carriage and age, sex, recent antibiotic use, or other clinical exposures (p > 0.05), with wide confidence intervals, potentially reflecting limited statistical power and only modest model discrimination (AUC 0.65–0.68). These findings indicate that community Staphylococcus aureus colonization is potentially marked by modest prevalence, substantial anatomical discordance, and a low-risk resistance profile, while common demographic and clinical factors contributed little to explaining carriage patterns. Full article
(This article belongs to the Special Issue Bacterial Infection and Antimicrobial Resistance)
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