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Microorganisms
Special Issues
Bacterial Infections in Clinical Settings
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Bacterial Infections in Clinical Settings

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Medical Microbiology".

Deadline for manuscript submissions: 31 August 2025 | Viewed by 4182

Special Issue Editor

Dr. Viera Lovayová

E-Mail Website
Guest Editor
Department of Medical and Clinical Microbiology, Faculty of Medicine, Pavol Jozef Šafárik University in Košice, 040 11 Kosice, Slovakia
Interests: antibiotic resistance; bacterial pathogens; infection

Special Issue Information

Dear Colleagues,

Bacterial infections remain a significant challenge in clinical settings, posing threats to patient health, increasing healthcare costs, and contributing to the growing problem of antibiotic resistance. This Special Issue aims to cover a comprehensive range of topics related to bacterial infections in clinical environments, from pathogenesis and diagnosis to treatment and prevention strategies.

The topics covered could include the following:

  1. Epidemiology of Bacterial Infections
    • Prevalence and incidence of bacterial infections in hospitals and clinics;
    • Surveillance methods and reporting systems;
    • Risk factors and vulnerable populations.
  2. Pathogenesis and Mechanisms of Infection
    • Molecular and cellular mechanisms of bacterial pathogenesis;
    • Host–pathogen interactions;
    • Biofilm formation and its clinical implications.
  3. Diagnosis of Bacterial Infections
    • Advances in diagnostic techniques (e.g., PCR, MALDI-TOF, next-generation sequencing);
    • Rapid diagnostic tests and point-of-care testing;
    • Challenges in diagnosing polymicrobial infections.
  4. Antibiotic Resistance
    • Mechanisms of antibiotic resistance;
    • Global trends and patterns in resistance;
    • Impact of antibiotic stewardship programs.
  5. Treatment Strategies
    • Novel antibiotics and alternative therapies;
    • Combination therapies;
    • Personalized medicine approaches for bacterial infections.
  6. Infection Control and Prevention
    • Hospital-acquired infections (HAIs) and their prevention;
    • Role of hand hygiene, sterilization, and disinfection;
    • Vaccination and prophylactic measures.
  7. Clinical Case Studies
    • Case reports and series highlighting unique or challenging bacterial infections;
    • Lessons learned and clinical implications.
  8. Public Health and Policy
    • Policies for controlling and preventing bacterial infections in healthcare settings;
    • The role of public health initiatives;
    • Economic impact of bacterial infections and cost-effective interventions.

Authors should submit original research articles, review articles, case reports, and short communications that address any aspect of bacterial infections in clinical settings. Contributions should be based on sound scientific methodologies and should provide a new perspective on the given topic.

The authors’ contributions to this Special Issue will contribute to improving our understanding and management of bacterial infections in clinical settings.

Dr. Viera Lovayová
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

  • bacterial pathogens
  • antibiotic resistance
  • nosocomial infections
  • sepsis
  • bacteremia
  • clinical diagnosis
  • infection control
  • microbiological culture
  • antibiotic therapy
  • pathogen identification
  • biofilms
  • gram-positive bacteria
  • gram-negative bacteria
  • Hospital-Acquired Infection (HAI)
  • Multidrug-Resistant Organisms (MDROs)
  • empirical therapy
  • clinical microbiology
  • prophylactic antibiotics
  • infectious disease epidemiology
  • antimicrobial stewardship

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

Published Papers (6 papers)

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21 pages, 2783 KiB  
Article
Resistance Genes and Virulence Factor Genes in Coagulase-Negative and Positive Staphylococci of the Staphylococcus intermedius Group (SIG) Isolated from the Dog Skin
by Simona Hisirová, Jana Koščová, Ján Király, Vanda Hajdučková, Patrícia Hudecová, Stanislav Lauko, Gabriela Gregová, Nikola Dančová, Júlia Koreneková and Viera Lovayová
Microorganisms 2025, 13(4), 735; https://doi.org/10.3390/microorganisms13040735 - 25 Mar 2025
Viewed by 404
Abstract
Staphylococci are common pathogens in dogs, causing a variety of dermatological problems. This study aimed to characterize the prevalence, antibiotic resistance, and biofilm-forming potential of Staphylococcus species isolated from the skin of shelter dogs. Overall, 108 samples were collected from the hairless skin [...] Read more.
Staphylococci are common pathogens in dogs, causing a variety of dermatological problems. This study aimed to characterize the prevalence, antibiotic resistance, and biofilm-forming potential of Staphylococcus species isolated from the skin of shelter dogs. Overall, 108 samples were collected from the hairless skin areas of dogs in a shelter over one year. Isolates were cultured using standard microbiological methods and identified through biochemical testing, MALDI-TOF MS, and multiplex PCR. A total of 67 Staphylococcus isolates were identified, with S. pseudintermedius being the most prevalent. Antibiotic susceptibility was assessed using disk diffusion and MIC methods, revealing high resistance to ampicillin, erythromycin, and tetracycline. Notably, 12 multidrug-resistant SIG (S. intermedius group; S. pseudintermedius) and 4 CoNS strains (coagulase-negative staphylococci; S. equorum) were identified. Biofilm production was evaluated using a crystal violet assay, showing variable biofilm-forming capabilities among isolates and PCR, to confirm genes associated with biofilm formation. These findings highlight the presence of multidrug-resistant Staphylococcus species in shelter dogs, emphasizing the need for careful monitoring and antibiotic stewardship to manage potential risks to both animal and human health. Full article
(This article belongs to the Special Issue Bacterial Infections in Clinical Settings)
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13 pages, 662 KiB  
Article
Comparative Analysis of Metagenomic Next-Generation Sequencing, Sanger Sequencing, and Conventional Culture for Detecting Common Pathogens Causing Lower Respiratory Tract Infections in Clinical Samples
by Qiaolian Yi, Ge Zhang, Tong Wang, Jin Li, Wei Kang, Jingjia Zhang, Yali Liu and Yingchun Xu
Microorganisms 2025, 13(3), 682; https://doi.org/10.3390/microorganisms13030682 - 18 Mar 2025
Viewed by 443
Abstract
Metagenomic next-generation sequencing (mNGS) has emerged as a revolutionary tool for infectious disease diagnostics. The necessity of mNGS in real-world clinical practice for common Lower Respiratory Tract Infections (LRTI) needs further evaluation. A total of 184 bronchoalveolar lavage fluid (BALF) samples and 322 [...] Read more.
Metagenomic next-generation sequencing (mNGS) has emerged as a revolutionary tool for infectious disease diagnostics. The necessity of mNGS in real-world clinical practice for common Lower Respiratory Tract Infections (LRTI) needs further evaluation. A total of 184 bronchoalveolar lavage fluid (BALF) samples and 322 sputa associated with LRTI were fully examined. The detection performance was compared between mNGS and standard microbiology culture, using Sanger sequencing as the reference method. 52.05% (165/317) of sputa showed identical results for all three methods. Compared to Sanger sequencing, the same results obtained by mNGS were 88.20% (284/322). In 2.80% (9/322) of cases, Sanger sequencing detected more microorganisms, while mNGS detected more in 9% (29/322) of cases. For BALF, 49.41% (85/172) of cases showed identical results for all three methods. In 91.30% (168/184) of cases, identical results were produced by both mNGS and Sanger sequencing. mNGS detected more species in 7.61% (14/184) of cases, whereas in 2.80% (2/184) instances, the Sanger sequencing detected more microorganisms than mNGS. In the 184 BALF samples, 66 samples were identified as having co-infections by mNGS, Sanger sequencing identified 64 samples, and cultures identified 22 samples. Our study demonstrates that mNGS offers a significant advantage over conventional culture methods in detecting co-infections. For common bacterial pathogens, conventional culture methods are sufficient for detection. However, mNGS provides comprehensive pathogen detection and is particularly useful for identifying rare and difficult-to-culture pathogens. Full article
(This article belongs to the Special Issue Bacterial Infections in Clinical Settings)
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13 pages, 290 KiB  
Communication
The Role of Physical Examination and Clinical Scores in Distinguishing Streptococcal Colonization from Pharyngitis in Pediatric Patients: Insights from a Common Clinical Scenario
by Victor Daniel Miron, Doina Anca Pleșca, Anuța Bilașco, Claudiu Filimon, Sigrid Covaci and Anca Cristina Drăgănescu
Microorganisms 2025, 13(3), 529; https://doi.org/10.3390/microorganisms13030529 - 27 Feb 2025
Viewed by 612
Abstract
The accurate differentiation between asymptomatic carriage with group A streptococcus (GAS) and active streptococcal pharyngitis is a complex task with important clinical and public health implications. This work aims to highlight the key strategies necessary for optimizing the diagnostic and therapeutic management of [...] Read more.
The accurate differentiation between asymptomatic carriage with group A streptococcus (GAS) and active streptococcal pharyngitis is a complex task with important clinical and public health implications. This work aims to highlight the key strategies necessary for optimizing the diagnostic and therapeutic management of pediatric pharyngitis. Clinical scores are essential tools for improving diagnostic accuracy. When combined with laboratory tests such as throat cultures and rapid antigen detection tests, these systems enable effective risk stratification of patients, supporting more precise treatment decisions. In addition to diagnostic strategies, the article underscores the importance of patient-centered communication, particularly with the families of pediatric patients. Clear, empathetic discussions about the condition, diagnostic rationale, and treatment plan help foster trust, enhance adherence to medical recommendations, and reduce anxiety related to potential complications. A critical outcome of these combined strategies is the reduction of unnecessary antibiotic use, which plays a pivotal role in preventing both overdiagnosis and overprescription. This, in turn, mitigates the growing threat of antimicrobial resistance, one of the most significant global health challenges. By integrating clinical expertise, standardized protocols, and effective communication, healthcare providers can promote judicious and effective management of streptococcal pharyngitis or asymptomatic carriage, contributing to improved individual and population health outcomes. Full article
(This article belongs to the Special Issue Bacterial Infections in Clinical Settings)
15 pages, 1496 KiB  
Article
Molecular Characterization of Carbapenem and Colistin Resistance in Klebsiella pneumoniae Isolates Obtained from Clinical Samples at a University Hospital Center in Algeria
by Riyane Rihane, Abla Hecini-Hannachi, Chafia Bentchouala, Kaddour Benlabed and Seydina M. Diene
Microorganisms 2024, 12(10), 1942; https://doi.org/10.3390/microorganisms12101942 - 25 Sep 2024
Viewed by 1589
Abstract
The current study aimed to determine the molecular mechanisms of carbapenem and colistin resistance among the clinical isolates of Klebsiella pneumoniae from hospitalized patients admitted to a university hospital in Eastern Algeria. In total, 124 non-duplicate isolates of K. pneumoniae were collected from [...] Read more.
The current study aimed to determine the molecular mechanisms of carbapenem and colistin resistance among the clinical isolates of Klebsiella pneumoniae from hospitalized patients admitted to a university hospital in Eastern Algeria. In total, 124 non-duplicate isolates of K. pneumoniae were collected from September 2018 to April 2019. Bacterial identification was performed using MALDI-TOF MS. The presence of extended spectrum β-lactamase (ESBL) genes, carbapenemase genes, chromosomal mutation and mcr genes in colistin-resistant K. pneumoniae were evaluated by PCR. ESBLs represented a rate of 49.1% and harbored blaCTX-M, blaTEM and blaSHV genes. Concerning carbapenems, 12 strains (9.6%) were resistant to ertapenem (MIC: 1–32 μg/mL), of which one strain (0.8%) was also resistant to imipenem (MIC: 32 μg/mL). Among these strains, nine (75%) harbored blaOXA-48 gene. Seven strains (5.6%) expressed resistance to colistin (MIC: 2–32 μg/mL), of which two harbored mcr-8 and mgrB genes simultaneously. The existence of a double resistance to colistin in the same strain is new in Algeria, and this could raise concerns about the increase in levels of resistance to this antibiotic (MIC: 32 μg/mL). The mgrB gene alone was observed in five isolates (71.4%), including two strains harboring blaOXA-48. This is the first report revealing the presence of K. pneumoniae strains carrying the blaOXA-48 gene as well as a mutation in the mgrB gene. Large-scale surveillance and effective infection control measures are also urgently needed to prevent the outbreak of various carbapenem- and colistin-resistant isolates. Full article
(This article belongs to the Special Issue Bacterial Infections in Clinical Settings)
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12 pages, 257 KiB  
Case Report
Abiotrophia defectiva and Granulicatella: A Literature Review on Prosthetic Joint Infection and a Case Report on A. defectiva PJI and Concurrent Native Valve Endocarditis
by Cristina Seguiti, Edda Piacentini, Angelica Fraghì, Mattia Zappa, Elia Croce, Angelo Meloni, Marco Cirillo, Clarissa Ferrari, Chiara Zani, David Belli, Tony Sabatini and Paolo Colombini
Microorganisms 2025, 13(5), 1113; https://doi.org/10.3390/microorganisms13051113 - 12 May 2025
Viewed by 265
Abstract
Together with Granulicatella spp., A. defectiva was formerly classified within the group of nutritionally variant streptococci (NVS). NVS-related endocarditis has been associated with higher rates of complications, bacteriological failure, and mortality compared to other streptococci, partially due to challenges related to timely and [...] Read more.
Together with Granulicatella spp., A. defectiva was formerly classified within the group of nutritionally variant streptococci (NVS). NVS-related endocarditis has been associated with higher rates of complications, bacteriological failure, and mortality compared to other streptococci, partially due to challenges related to timely and accurate identification. PJI caused by A. defectiva are rarely reported, and standardized management strategies have not yet been established. We describe a case of a 68-year-old man with concomitant A. defectiva PJI and native mitral valve endocarditis. The patient was managed conservatively for endocarditis and subsequently underwent a two-stage arthroplasty of the infected prosthetic knee. A. defectiva was identified using MALDI-TOF mass spectrometry on both synovial fluid and blood cultures. As penicillin susceptibility data were not available, the patient was treated with vancomycin at a dose of 2 g/day, resulting in a favorable clinical response. In addition, we performed a literature review on A. defectiva and Granulicatella PJI. Despite the limited number of reported cases in the literature, the findings suggest a potential correlation between clinical outcomes and antimicrobial treatment duration. Further comprehensive studies are needed to establish standardized management strategies for A. defectiva and Granulicatella PJI. Full article
(This article belongs to the Special Issue Bacterial Infections in Clinical Settings)
12 pages, 2789 KiB  
Case Report
Primary Axillary Actinomycosis: A Case Report on the Integration of Culture and Molecular Diagnostics for Accurate Diagnosis of Polymicrobial Infections
by Junko Tezuka, Noriyuki Abe and Hiroshi Tanabe
Microorganisms 2025, 13(3), 671; https://doi.org/10.3390/microorganisms13030671 - 17 Mar 2025
Viewed by 388
Abstract
Actinomycosis is a chronic suppurative granulomatous disease caused by Actinomyces spp. Although cutaneous actinomycosis is rare, dermatologists must consider it due to its potential coexistence with other pathogens, often as part of polymicrobial infections. We present a rare case of primary axillary cutaneous [...] Read more.
Actinomycosis is a chronic suppurative granulomatous disease caused by Actinomyces spp. Although cutaneous actinomycosis is rare, dermatologists must consider it due to its potential coexistence with other pathogens, often as part of polymicrobial infections. We present a rare case of primary axillary cutaneous actinomycosis in a young woman, likely triggered by cosmetic axillary hair removal and home shaving practices. Histological examination revealed characteristics of actinomycosis, including sulfur granules and Gram-positive filamentous structures. Bacterial cultures failed to isolate Actinomyces, but identified Staphylococcus epidermidis, S. aureus (MRSA), and Corynebacterium simulans, suggesting a polymicrobial infection contributing to the inflammatory response. Molecular analysis of DNA extracted from formalin-fixed paraffin-embedded (FFPE) tissue yielded a 675 bp PCR product using Actinomyces-specific primers. BLAST analysis confirmed the species as A. gerencseriae, establishing the diagnosis of actinomycosis. However, a 1000 bp PCR product obtained using universal 16S rDNA primers could not be sequenced successfully, likely due to the presence of multiple bacterial species. Notably, Actinomyces was detected only through molecular methods, while bacterial cultures identified the aforementioned bacteria. This discrepancy between FFPE-PCR results and bacterial culture findings demonstrates a key challenge in the microbiological diagnosis of polymicrobial infections. This case highlights the importance of integrating histopathological, microbiological, and molecular techniques for accurate pathogen identification in polymicrobial infections. The failure to detect Actinomyces in bacterial cultures, despite its presence in FFPE-PCR, suggests that conventional culture methods alone may be insufficient for diagnosing such infections. Extended culture durations, selective anaerobic culture techniques, and molecular diagnostic methods are essential for a comprehensive evaluation. Recognizing Actinomyces as more than a contaminant is important for timely diagnosis and effective treatment. Increased awareness of its potential involvement in polymicrobial infection should improve clinical outcomes. Full article
(This article belongs to the Special Issue Bacterial Infections in Clinical Settings)
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