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Laboratory Diagnosis and Epidemiology of Clinical Microbial Infections

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

Deadline for manuscript submissions: 30 June 2026 | Viewed by 5209

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Special Issue Editor

Dr. Vassiliki Pitiriga

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Department of Microbiology, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias Street, 11527 Athens, Greece
Interests: clinical infection; antibiotics
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Special Issue Information

Dear Colleagues,

Infectious diseases remain a significant global health challenge, driven by evolving microbial pathogens and increasing antimicrobial resistance. This Special Issue aims to highlight recent advances in the laboratory diagnosis and epidemiology of clinical microbial infections. We welcome contributions that explore emerging pathogens, novel diagnostic technologies, resistance mechanisms and epidemiological trends. By highlighting these aspects, this issue seeks to foster a deeper understanding of infectious disease dynamics and support the development of more effective strategies for the management of clinical microbial infections.

Dr. Vassiliki Pitiriga
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 250 words) can be sent to the Editorial Office for assessment.

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

infectious disease
laboratory diagnosis
epidemiology

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Published Papers (5 papers)

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Research

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13 pages, 268 KB

Open AccessArticle

Association of TLR4 Polymorphisms with Increased Susceptibility to Recurrent Vulvovaginal Candidiasis in Greek Women

by Maria Mavrouli, Chrysoula Verra, Athanasios Tsakris and John Routsias

Microorganisms 2026, 14(3), 727; https://doi.org/10.3390/microorganisms14030727 - 23 Mar 2026

Viewed by 551

Abstract

Recurrent vulvovaginal candidiasis (RVVC) affects 5–8% of women of reproductive age. Host genetic factors, particularly single nucleotide polymorphisms (SNPs) in Toll-like receptors (TLRs), may influence RVVC susceptibility by impairing vaginal mucosal antifungal immunity. The aim of this study was to assess the effect of SNPs in genes encoding TLRs on RVVC susceptibility. Τhe distribution of TLR2 Arg753Gln and TLR4 Asp299Gly/Thr399Ile polymorphisms in Greek women, including RVVC (n = 63), first-episode VVC (n = 37), Gardnerella vaginalis vaginitis (GV, n = 36) patients, and healthy controls (n = 61), was investigated using TaqMan SNP genotyping. Genotype and allele frequencies were analyzed under allelic and dominant models, with odds ratios (ORs), 95% confidence intervals (CIs), and linkage disequilibrium assessed. TLR4 Asp299Gly and Thr399Ile heterozygotes were significantly more frequent in RVVC patients compared with controls and affected RVVC susceptibility (OR: 5.57, 95% CI: 1.17–26.56, p: 0.0172; OR: 4.92, 95% CI: 1.02–23.78, p: 0.0306, respectively). No associations were observed for TLR2 Arg753Gln or for any SNP with GV or first-episode VVC. TLR4 variants co-segregated, indicating a haplotype effect. TLR4 haplotypes, rather than TLR2 polymorphism, confer increased RVVC susceptibility, supporting a genetically distinct, mucosal immunity-driven pathogenesis. Larger, ethnically diverse studies with functional assays are warranted to validate these findings and guide personalized prevention and treatment strategies. Full article

(This article belongs to the Special Issue Laboratory Diagnosis and Epidemiology of Clinical Microbial Infections)

19 pages, 1505 KB

Open AccessArticle

Species Identification, Virulence Factors, and Antifungal Resistance in Clinical Candida Isolates from ICU Patients

by Paola Aparecida Alves Ferreira, Lucas Daniel Cibolli Roso, Daniel Almeida Freitas, Ana Paula Pereira Bressani, Paulo Henrique da Cruz Ferreira, Emerson Cotta Bodevan, Cristiane Rocha Fagundes Moura, Rosane Freitas Schwan, Vanessa Amaral Mendonça, Karina Teixeira Magalhães-Guedes and Cíntia Lacerda Ramos

Microorganisms 2026, 14(1), 241; https://doi.org/10.3390/microorganisms14010241 - 21 Jan 2026

Viewed by 748

Abstract

Candida spp. are important opportunistic human fungal pathogens. This study aimed to identify and characterize Candida spp. obtained from patients admitted to an Intensive Care Unit (ICU), focusing on virulence attributes and susceptibility to antifungal agents. A total of 131 isolates from oral and tracheobronchial secretions of adult ICU patients were evaluated. Phenotypic identification was performed using chromogenic culture media for Candida, followed by MALDI-TOF mass spectrometry, with representative isolates confirmed by ITS sequencing. Antifungal susceptibility to fluconazole, ketoconazole, and amphotericin B was determined only by the agar disk diffusion method, and virulence was assessed through esterase, DNase, protease, and hemolytic activity assays. C. albicans was the prevalent species, followed by C. tropicalis, C. krusei, C. glabrata, C. parapsilosis, C. dubliniensis, C. lusitaniae, and C. guilliermondii. Antifungal resistance rates reached 51.1% for fluconazole, 42.7% for ketoconazole, and 19.1% for amphotericin B, as determined by disk diffusion method. Overall, 64.9% of the isolates exhibited esterase activity, 18.3% DNase, 45.8% protease, and 67.2% exhibited hemolytic activity. Oral isolates were more frequent than tracheal isolates and demonstrated a higher prevalence of antifungal resistance and virulence traits. These findings underscore the epidemiological importance of characterizing Candida species in hospitals to better understand the yeast profile and to support adequate clinical management. Full article

(This article belongs to the Special Issue Laboratory Diagnosis and Epidemiology of Clinical Microbial Infections)

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19 pages, 2826 KB

Open AccessArticle

MACNeXt-Based Bacteria Species Detection

by Ozlem Aytac, Feray Ferda Senol, Tarik Kivrak, Zulal Asci Toraman, Mehmet Veysel Gun, Omer Faruk Goktas, Sengul Dogan and Turker Tuncer

Microorganisms 2025, 13(12), 2689; https://doi.org/10.3390/microorganisms13122689 - 25 Nov 2025

Viewed by 754

Abstract

Bacteria underpin human health, environmental balance, and industrial processes. Rapid and accurate identification is essential for diagnosis and responsible antibiotic use. Culture, biochemical tests, and microscopy are slow, expensive, and depend on expert judgment, which introduces subjectivity and errors. This research aims to recommend a new generation deep learning architecture for bacterial species classification. We curated a bacterial image dataset, and this dataset contains 18,221 microscopic images from 24 species under standard laboratory conditions. All images passed clarity and focus checks. We developed a compact CNN, the Multiple Activation Network (MACNeXt). The recommended MACNeXt preserves local feature extraction and improves representation with two activation functions (GELU and ReLU) and a multi-branch design. The aim is high accuracy with low computational cost for routine clinical use. MACNeXt achieved 90.97% accuracy, 89.63% precision, 88.64% recall, and 88.99% F1-score on the test set. The calculated results and findings showcase balanced and stable performance across species with an efficient, lightweight design since the introduced MACNeXt has about 4.4 million learnable parameters. The results of the MACNeXt openly demonstrate that this CNN is a compact, lightweight, and highly accurate CNN model. Full article

(This article belongs to the Special Issue Laboratory Diagnosis and Epidemiology of Clinical Microbial Infections)

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Review

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14 pages, 674 KB

Open AccessReview

Resistance of Uropathogens to Tebipenem: An Analysis of the Evidence from In Vitro Antimicrobial Susceptibility Studies

by Matthew E. Falagas, Christina-Maria Asimotou, Dimitrios S. Kontogiannis, Laura T. Romanos, Panagiota Poziou and Iva D. Tzvetanova

Microorganisms 2026, 14(3), 726; https://doi.org/10.3390/microorganisms14030726 - 23 Mar 2026

Viewed by 514

Abstract

Tebipenem is a new carbapenem antibiotic that binds to penicillin-binding proteins (PBPs). Given the need for effective antibiotics against multidrug-resistant (MDR) bacteria, this review evaluated the in vitro antimicrobial activity of tebipenem against Gram-negative and Gram-positive bacteria, focusing on uropathogens. Five resources (Google Scholar, Web of Science, Embase, Scopus, and PubMed) were used to identify relevant articles. Of the 1322 articles identified, 9 relevant studies were included, which evaluated 12,501 Gram-negative and 122 Gram-positive pathogens. All nine studies (100%) assessed the activity of tebipenem against Escherichia coli, with an MIC₉₀ value range of 0.015–>4 mg/L. Seven studies (77.8%) included Klebsiella pneumoniae, with an MIC₉₀ value range of 0.015–0.5 mg/L. Six studies (66.7%) reported data on Proteus mirabilis, with an MIC₉₀ value range of ≤0.125–0.5 mg/L. Two studies (22.2%) evaluated the activity of tebipenem against Enterococcus faecalis, with MIC₉₀ of 1 mg/L among vancomycin-susceptible isolates and 32 mg/L in isolates with not-reported mechanisms of resistance. Two studies (22.2%) evaluated the activity of tebipenem against Enterococcus faecium, with MIC₉₀ of >4 mg/L among both vancomycin-susceptible and vancomycin-resistant isolates and MIC₉₀ of 128 mg/L among isolates with no resistance mechanism reported. Tebipenem demonstrated good activity against Enterobacterales, such as E. coli and K. pneumoniae. The antimicrobial agent exhibited higher MICs and a higher proportion of resistance among P. mirabilis isolates. Tebipenem could be effective for outpatient treatment of infections caused by MDR Gram-negative pathogens. However, given its potential to exert selective pressure for the development of antimicrobial resistance, it should be considered for patients with cUTIs when none of the first-line treatment options demonstrate in vitro antimicrobial activity. Full article

(This article belongs to the Special Issue Laboratory Diagnosis and Epidemiology of Clinical Microbial Infections)

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Other

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30 pages, 500 KB

Open AccessSystematic Review

Role of Lipidomics in Respiratory Tract Infections: A Systematic Review of Emerging Evidence

by Vasiliki E. Georgakopoulou, Konstantinos Dodos and Vassiliki C. Pitiriga

Microorganisms 2025, 13(9), 2190; https://doi.org/10.3390/microorganisms13092190 - 19 Sep 2025

Cited by 1 | Viewed by 2175

Abstract

Lower respiratory tract infections (LRTIs) remain a major cause of global morbidity and mortality, yet accurate pathogen identification and risk stratification continue to pose clinical challenges. Lipidomics—the comprehensive analysis of lipid species within biological systems—has emerged as a promising tool to unravel host–pathogen interactions and reveal novel diagnostic and prognostic biomarkers. This systematic review synthesizes evidence from nine original studies applying mass spectrometry-based lipidomic profiling in human LRTIs, including community-acquired pneumonia (CAP), ventilator-associated pneumonia (VAP), and coronavirus disease 2019 (COVID-19). Across diverse study designs, sample types, and analytical platforms, consistent alterations in lipid metabolism were observed. Perturbations in phospholipid classes, particularly phosphatidylcholines (PCs) and lysophosphatidylcholines (LPCs), were frequently associated with disease severity and immune activation. The ratios of PC to LPC and phosphatidylethanolamine (PE) to lysophosphatidylethanolamine (LPE) emerged as markers of inflammatory remodeling. Sphingolipids—including sphingomyelins (SMs) and sphingosine-1-phosphate (S1P)—were identified as key modulators of monocyte and neutrophil activation. Fatty acid–derived lipid mediators such as oxylipins (e.g., 12,13-epoxyoctadecenoic acid and 15-hydroxyeicosatetraenoic acid) and acylcarnitines reflected pathogen-specific immune responses and mitochondrial dysfunction. Several lipid-based classifiers demonstrated superior diagnostic and prognostic performance compared to conventional clinical scores, including the CURB-65 and pneumonia severity index. However, significant heterogeneity in experimental design, lipid identification workflows, and reporting standards limits inter-study comparability. While preliminary findings support the integration of lipidomics into infectious disease research, larger multi-omic and longitudinal studies are required. This review provides the first comprehensive synthesis of lipidomic alterations in human LRTIs and highlights their emerging translational relevance. Full article

(This article belongs to the Special Issue Laboratory Diagnosis and Epidemiology of Clinical Microbial Infections)

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