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Microorganisms
Special Issues
Recent Advances in Diagnostic Microbiology
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Recent Advances in Diagnostic Microbiology

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

Deadline for manuscript submissions: 31 December 2026 | Viewed by 2390

Editor

Dr. Hin Fung Tsang

E-Mail Website
Guest Editor
Department of Clinical Laboratory and Pathology, Hong Kong Adventist Hospital, Hong Kong SAR, China
Interests: microbial metagenomics; molecular testing; infectious diseases
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue highlights significant innovations and methodologies that enhance the detection, identification, and characterization of pathogens. Key advancements include the integration of novel techniques, such as artificial intelligence (AI) and machine learning (ML), next-generation sequencing (NGS), and polymerase chain reaction (PCR), which allow for rapid and precise pathogen identification. These methods are particularly beneficial for high-throughput diagnostics and for identifying complex microbial communities in clinical settings. Additionally, recent findings on antimicrobial resistance (AMR) detection techniques receive special attention, emphasizing the urgency of developing diagnostics that can guide appropriate therapy and mitigate the AMR crisis. Furthermore, case studies illustrate the practical implementation of these advancements in laboratories, showcasing how they facilitate timely decisions in patient management. Overall, this Special Issue serves as a comprehensive overview of the current landscape in diagnostic microbiology, highlighting the essential role of technological progress in enhancing infectious disease diagnosis and management. We are pleased to invite original research articles, experiences, and reviews on recent advances in clinical diagnosis and management of infectious diseases.

Dr. Hin Fung Tsang
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-anonymized 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

  • innovations
  • diagnostic microbiology
  • infectious diseases
  • patient management
  • artificial intelligence
  • machine learning
  • next-generation sequencing
  • antimicrobial resistance

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

Published Papers (4 papers)

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Research

18 pages, 1404 KB  
Article
Diagnosis of Respiratory Infections Using Syndromic Panels: A Ct-Based Approach Beyond Qualitative Detection
by Maria Antonella Zingaropoli, Gianluca Bruno Tassone, Eleonora Coratti, Donatella Maria Rodio, Martina Bernassola, Roberta Campagna, Lucilla Caivano, Francesca Pulcinelli, Fabio Midulla, Gioacchino Galardo, Alessandra Pierangeli, Guido Antonelli and Ombretta Turriziani
Microorganisms 2026, 14(7), 1450; https://doi.org/10.3390/microorganisms14071450 - 30 Jun 2026
Viewed by 153
Abstract
This retrospective study, conducted between September 2023 and October 2025, evaluated age-related pathogen prevalence, seasonal dynamics, and cycle threshold (Ct) values in nasopharyngeal specimens from hospitalized subjects with suspected acute respiratory infections (ARIs) using the multiplex syndromic panel. A median-based Delta Ct was [...] Read more.
This retrospective study, conducted between September 2023 and October 2025, evaluated age-related pathogen prevalence, seasonal dynamics, and cycle threshold (Ct) values in nasopharyngeal specimens from hospitalized subjects with suspected acute respiratory infections (ARIs) using the multiplex syndromic panel. A median-based Delta Ct was calculated to define pathogen dominance in co-detections. A total of 2479 nasopharyngeal swabs were analyzed and 54.4% tested positive for at least one pathogen. Overall, the positivity rate and co-detections were found to be significantly higher in pediatric group than in the adult one (p < 0.0001 and p < 0.0001, respectively). Semi-quantitative analysis revealed that RSV and flu viruses maintained low Ct values irrespective of co-detection, whereas RV/EV, Adv, and human bocavirus (HBoV) exhibited significantly higher Ct values when co-detected. RV/EV showed higher Ct values versus human metapneumovirus A/B (p = 0.0014), human parainfluenza virus (p = 0.0007), flu virus (p = 0.0084) and RSV (p < 0.0001). Likewise, Adv demonstrated higher Ct values in comparison to RSV (p = 0.0046). Seasonal drivers typically dominate over persistent agents. Integrating semi-quantitative interpretation into syndromic panel reporting could enhance diagnostic stewardship, optimize antimicrobial use, and improve resource allocation in high-pressure clinical settings. Full article
(This article belongs to the Special Issue Recent Advances in Diagnostic Microbiology)
11 pages, 521 KB  
Article
QIAstat-Dx Syndromic Molecular Testing Versus Conventional Diagnostics in Acute Gastroenteritis: Impact on Pathogen Detection and Laboratory Workflow
by Fabio Formenti, Andrea Matucci, Martina Parisato, Marta Piccoli, Silvia Pasquetto, Milena Bernardi, Marco Venturini, Elena Pomari, Matteo Valerio, Cristina Mazzi, Marco Cavallini, Rebecca Passarelli Mantovani, Davide Treggiari, Chiara Piubelli and Francesca Perandin
Microorganisms 2026, 14(6), 1345; https://doi.org/10.3390/microorganisms14061345 - 16 Jun 2026
Viewed by 318
Abstract
Acute gastroenteritis is a common condition with a wide and often indistinguishable etiology, requiring laboratory support for an accurate diagnosis. Classical diagnostic methods, including stool culture and antigen-based tests, are limited by restricted pathogen coverage and variable sensitivity. In the present study, 548 [...] Read more.
Acute gastroenteritis is a common condition with a wide and often indistinguishable etiology, requiring laboratory support for an accurate diagnosis. Classical diagnostic methods, including stool culture and antigen-based tests, are limited by restricted pathogen coverage and variable sensitivity. In the present study, 548 stool samples from patients with suspected gastroenteritis were tested using the QIAstat-Dx Gastrointestinal Panel 2 and compared with stool culture and rotavirus/adenovirus antigen tests. The molecular panel showed a positivity rate of 50.4%, consistently higher than stool culture (12.6%) and antigen assays (12.3% for rotavirus and 4.4% for adenovirus). The most frequently detected pathogens included enteropathogenic Escherichia coli (15.3%), Campylobacter spp. (12.0%), and enteroaggregative E. coli (10.2%). Agreement between methods was good for bacterial pathogens but low for viral targets. Discordant viral results were often associated with low antigen cut-off index values and multiple pathogen detections by the molecular panel, suggesting potential limitations of antigen-based assays. Overall, the QIAstat-Dx Gastrointestinal Panel 2 improves pathogen detection and provides rapid, comprehensive diagnostic information, while a combined approach with conventional methods may represent the most appropriate strategy for optimizing patient management. Full article
(This article belongs to the Special Issue Recent Advances in Diagnostic Microbiology)
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13 pages, 360 KB  
Article
Intrapartum Molecular Detection of Group B Streptococcus: Real-World Evaluation of Multiple Point-of-Care Platforms and the Potential Role of Lysis Efficiency
by Mehdi Serrari, Lorenza Bianchi, Marie Tré-Hardy, Sara Törnblom-Paulander, Manon Alexandre, Arnaud Nevraumont, Ingrid Beukinga, Frédéric Buxant, Hamza Bensaoud and Laurent Blairon
Microorganisms 2026, 14(5), 1060; https://doi.org/10.3390/microorganisms14051060 - 8 May 2026
Viewed by 376
Abstract
Antenatal screening for Group B Streptococcus (GBS) does not always reflect intrapartum colonisation status, and rapid molecular point-of-care tests (POCT) have been developed to enable real-time detection during labour. This prospective single-centre study evaluated the performance of six molecular assays (easyNat, FlashDetect, GenDx, [...] Read more.
Antenatal screening for Group B Streptococcus (GBS) does not always reflect intrapartum colonisation status, and rapid molecular point-of-care tests (POCT) have been developed to enable real-time detection during labour. This prospective single-centre study evaluated the performance of six molecular assays (easyNat, FlashDetect, GenDx, GenPad, iPonatic, Revogene) and one antigen-based test (TZcheck) for intrapartum GBS detection under real-world conditions. Vaginal–rectal swabs were collected at admission from 104 women at ≥ 37 weeks of gestation and tested directly without prior enrichment, using conventional intrapartum culture as the reference standard. Diagnostic performance varied substantially across platforms, with positive percent agreement ranging from 0.0% to 80.6%, while negative percent agreement was generally high, except for GenDx. Seven culture-positive samples yielded negative results across all molecular assays, while one sample was consistently positive across multiple molecular platforms despite negative culture. Exploratory observations suggest that differences in lysis procedures may contribute to variability in assay performance, although this could not be formally assessed. These findings highlight the variability of intrapartum molecular POCT under routine conditions and underscore the need for cautious clinical interpretation and local validation prior to implementation. Full article
(This article belongs to the Special Issue Recent Advances in Diagnostic Microbiology)
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14 pages, 730 KB  
Article
Rapid Bacterial Identification and Quantitative Antimicrobial Susceptibility Assessment from Positive Blood Cultures to Optimize Bloodstream Infection Management
by Lucia Sliviaková Matúšková, Michala Vladárová and Elena Nováková
Microorganisms 2026, 14(3), 633; https://doi.org/10.3390/microorganisms14030633 - 11 Mar 2026
Viewed by 1035
Abstract
Bloodstream infection (BSI) is a serious clinical condition associated with high morbidity and mortality, requiring rapid identification of causative agents and timely antimicrobial susceptibility testing (AST). This study evaluated accelerated bacterial identification from positive blood culture samples using matrix-assisted laser desorption/ionization time-of-flight mass [...] Read more.
Bloodstream infection (BSI) is a serious clinical condition associated with high morbidity and mortality, requiring rapid identification of causative agents and timely antimicrobial susceptibility testing (AST). This study evaluated accelerated bacterial identification from positive blood culture samples using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) combined with two rapid processing approaches: a serum separation tube-based centrifugation method (SST method) and shortened cultivation on solid media. Rapid identification was followed by accelerated AST, performed either from a bacterial cell pellet (SST method) and from early-grown bacterial biomass (shortened cultivation protocol). The results were compared with those obtained using routine laboratory procedures. A total of 270 positive blood culture samples were analyzed, with 135 samples processed by each protocol. Both approaches achieved an identification success rate of 93.33%. Rapid AST using the SST method showed error rates of 0.51% minor errors, 0.57% major errors, and 0.23% very major errors, with an overall agreement of 98.69%. The shortened cultivation protocol demonstrated lower error rates (0.46% minor errors and 0.23% major errors) and an overall agreement of 99.31%. These findings confirm that MALDI-TOF MS enables reliable early identification of BSI pathogens and rapid AST, supporting timely optimization of antimicrobial therapy and early detection of multidrug-resistant strains. Full article
(This article belongs to the Special Issue Recent Advances in Diagnostic Microbiology)
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