New Advancements in Clinical Microbiology: Surveillance, Diagnosis, and Treatment

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 378

Special Issue Editors


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Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
Interests: antimicrobial resistance; whole-genome sequencing; genomic epidemiology
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Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
Interests: environmental microbiology; antimicrobial resistance; whole-genome sequence-based analysis

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UTA RAM One Health, Department of Food and Biotechnology Science and Engineering, Universidad Técnica de Ambato, Ambato 180103, Ecuador
Interests: environmental chemistry; antimicrobial resistance; water analysis
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1. School of Veterinary Medicine, Metropolitan University of Santos, Santos, Brazil
2. Department of Internal Medicine, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
Interests: veterinary microbiology; antimicrobial resistance; One Health
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Special Issue Information

Dear Colleagues,

Clinical microbiology has experienced significant advancements in surveillance, diagnostic methodologies, and treatment strategies, profoundly enhancing our capacity to manage infectious diseases. Innovations in molecular diagnostics, genomic sequencing, and bioinformatics have revolutionized pathogen detection and characterization, leading to more precise and timely interventions. These developments have not only improved patient outcomes but also bolstered our preparedness against emerging infectious threats.

This Special Issue, "New Advancements in Clinical Microbiology: Surveillance, Diagnosis, and Treatment", aims at exploring the latest developments in the field. We welcome original research articles, reviews, and communications encompassing varied aspects of pathogen detection, surveillance, and evolution, including, but not limited to, the following topics:

  • Innovations in Diagnostic Techniques: Exploring rapid molecular assays, point-of-care tests, and metagenomic sequencing to enhance the detection and identification of resistant pathogens.
  • Genomic Insights into Antimicrobial Resistance Mechanisms: Utilizing whole-genome sequencing to uncover genetic factors contributing to antimicrobial resistance, facilitating the development of targeted therapies.
  • Bioinformatics in Surveillance and Prediction: Employing artificial intelligence tools to analyze genomic data, predict resistance patterns, and inform public health strategies.
  • Clinical Implications and Treatment Strategies: Assessing the impact of antimicrobial resistance on clinical outcomes and evaluating novel therapeutic approaches, including combination therapies and antimicrobial stewardship programs.
  • Environmental factors and their impact on clinical microbiology and infectious diseases.

Prof. Dr. Zhi Ruan
Dr. João Pedro Rueda Furlan
Dr. William Ricardo Calero-Cáceres
Dr. Fábio P. Sellera
Guest Editors

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Keywords

  • clinical microbiology
  • surveillance
  • diagnostic methodologies
  • treatment strategies
  • molecular diagnostics
  • genomic sequencing
  • bioinformatics
  • pathogen detection
  • antimicrobial resistance
  • point-of-care tests

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Published Papers (1 paper)

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Research

22 pages, 1961 KiB  
Article
The Clinical Validity and Utility of PCR Compared to Conventional Culture and Sensitivity Testing for the Management of Complicated Urinary Tract Infections in Adults: A Secondary (Ad Hoc) Analysis of Pathogen Detection, Resistance Profiles, and Impact on Clinical Outcomes
by Moustafa Kardjadj, Tara W. Chang, Roel Chavez, DeAndre Derrick, Frank L. Spangler, Itoe P. Priestly, Lauren Y. Park and Thomas K. Huard
Microorganisms 2025, 13(4), 949; https://doi.org/10.3390/microorganisms13040949 - 20 Apr 2025
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Abstract
Clinical success in treating complicated urinary tract infections (cUTIs) depends on accurate pathogen detection, given the common occurrence of polymicrobial infections and antimicrobial resistance. This multicenter, randomized, investigator-blinded study compared polymerase chain reaction (PCR)-based diagnostics to conventional culture and sensitivity (C&S) testing in [...] Read more.
Clinical success in treating complicated urinary tract infections (cUTIs) depends on accurate pathogen detection, given the common occurrence of polymicrobial infections and antimicrobial resistance. This multicenter, randomized, investigator-blinded study compared polymerase chain reaction (PCR)-based diagnostics to conventional culture and sensitivity (C&S) testing in guiding the treatment of cUTIs. PCR identified polymicrobial infections in 43.52% of cases, a significantly higher rate than that observed with C&S (31.95%, p = 0.033). Patients in the C&S arms with undetected polymicrobial infections had a significantly higher clinical failure rate (33.33%, 14/42, p = 0.041) compared to those with concordant polymicrobial infection identification by both methods (22.22%, 12/54). PCR also detected additional pathogens in 54.44% (92/169) of cases in the C&S arm, where clinical failure was significantly higher when C&S missed pathogens (28.26% vs. 14.29%, p = 0.015). Similarly, when C&S failed to detect phenotypic resistance (compared to PCR), clinical failure occurred in 50% (16/42) of cases, compared to 13.22% (21/121, p = 0.001) when resistance detection was concordant (PCR and C&S). To further illustrate the clinical impact, patient-level case analyses are included to demonstrate how PCR-guided therapy improved pathogen detection and enabled more appropriate antimicrobial selection compared to C&S. These findings highlight the limitations of C&S in detecting polymicrobial infections, antimicrobial resistance, and hetero-resistance due to its limited clonal analysis, supporting the integration of PCR for more accurate diagnostics and optimized cUTI management. Full article
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