Clinical Microbiology and Related Diseases

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

Deadline for manuscript submissions: closed (31 August 2025) | Viewed by 2837

Special Issue Editor


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Guest Editor
Department Pathology & Laboratory Medicine and Medicine, Section of Microbiology and Division of Infectious Diseases, University of Calgary, 9-3535 Research Rd NW, Calgary, AB, Canada
Interests: beta-lactamases; carbapenem-resistant enterobacteriaceae; klebsiella pneumoniae; beta lactamase; enterobacteriaceae; extended spectrum beta lactamase; streptococcus agalactiae; group a streptococcal infection; newborn

Special Issue Information

Dear Colleagues,

The testing of human specimens in clinical microbiology laboratories is the cornerstone of not only infectious disease diagnoses but outbreak detection and surveillance. Global conditions are increasing the emergence of new diseases and accelerating evolving changes in many pathogens; most notable is the continued emergence of new types of antibiotic resistance. Diagnostic and public health laboratories worldwide continue to mount major efforts to keep abreast of the rapidly changing clinical requirements and increased demands for testing. At the same time, these facilities have been undergoing transformation from traditional culture-based whole cell methods to advanced technologies, including proteomics and genomics analyses. This transition has been challenging due to the simultaneous implementation of automation, information systems and artificial intelligence within workflows already struggling to meet increasing patient care demands with less experienced staff. Advanced technologies are also driving extensive taxonomic change within human pathogenic microbes, leading to the renaming of existing pathogens, the transfer of important genus and species to new ones and the discovery of new pathogens. Although the transformation in clinical testing is allowing more timely, accurate microbial diagnoses to be made, translational research is required to establish the clinical outcomes of these advances, including, but not limited to, the clinical and epidemiological picture of new and emerging pathogens and pathogen traits.

The aim of this Special Issue of Microorganisms is to present a picture of the major technological challenges facing clinical microbiology laboratories. Manuscripts covering major emerging pathogens, the use of MALDI-TOF MS for pathogen identification, pathogen identification using molecular methods, metagenomics, pathogen taxonomy and the impacts of automation, information technology and artificial intelligence to improve diagnostic and surveillance capabilities will be of interest.

Prof. Dr. Deirdre Church
Guest Editor

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Keywords

  • clinical microbiology
  • infectious diseases
  • emerging pathogens
  • outbreak surveillance
  • MALDI-TOF MS
  • pathogen detection
  • pathogen identification
  • metagenomics
  • pathogen taxonomy
  • diagnosis

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Published Papers (1 paper)

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Research

17 pages, 374 KB  
Article
Detection of Pathogens by a Novel User-Developed Broad-Range BR 16S PCR rRNA Polymerase Chain Reaction/Gene Sequencing Assay: Multiyear Experience in a Large Canadian Healthcare Zone
by Thomas Griener, Barbara Chow and Deirdre Church
Microorganisms 2026, 14(1), 240; https://doi.org/10.3390/microorganisms14010240 - 20 Jan 2026
Abstract
Between 2015 and 2022, we evaluated a novel broad-range (BR) 16S PCR rDNA PCR/Sanger sequencing assay to improve diagnosis of invasive infections in culture-negative specimens. Using dual-priming oligonucleotides (DPO), this assay analyzed ribosomal DNA from sterile fluids or tissues. A total of 762 [...] Read more.
Between 2015 and 2022, we evaluated a novel broad-range (BR) 16S PCR rDNA PCR/Sanger sequencing assay to improve diagnosis of invasive infections in culture-negative specimens. Using dual-priming oligonucleotides (DPO), this assay analyzed ribosomal DNA from sterile fluids or tissues. A total of 762 specimens were analyzed from 661 patients: 61% had negative cultures and BR 16S PCR tests; 35% had negative cultures but positive BR 16S PCR tests; and only 4% had negative cultures with indeterminate BR 16S PCR results. After resolution of indeterminate BR 16S PCR results (i.e., 29 negative, 1 false-positive, and 1 positive) the assay showed a sensitivity of 98.26% (95% CI = 96.00–99.43%), specificity of 99.79% (95% CI: 99.82–99.99%), positive predictive value of 99.65% (95% CI: 97.56–99.95%), negative predictive value of 98.94% (95% CI: 97.51–99.55%), and accuracy of 99.21% (95% CI: 98.28–99.71%) for a disease prevalence of 38.10% (95% CI: 34.62–41.66%). Gram stain purulence predicted the BR 16S PCR result better (69.4%) than organisms (24.6%), but the latter had a higher PPV (78.5%). Increased peripheral WBC (86.1%) or CRP (71.8%) predicted positive BR 16S PCR results. Our DPO BR 16S PCR assay improved pathogen detection over culture and minimized contamination. Broad range 16S rDNA PCR/sequencing (BR 16S PCR) is an important diagnostic technique in cases with invasive infection due to fastidious or uncultivatable pathogens. However, appropriate case selection, the quality of clinical specimen, and the specific assay primers affect its performance. Our novel BR 16S PCR assay uses unique dual-priming oligonucleotides (DPO) primers and fast protocols for rapid, optimal detection of bacterial pathogens, while minimizing contamination. Fast BR 16S PCR assay reports occurred within 24–48 h. BR 16S PCR and culture analyzed a diverse range of clinical specimens from patients with invasive infections. BR 16S PCR demonstrated a high performance for accurately detecting pathogens, ruling out infections, and minimizing contamination. BR 16S PCR detection of a pathogen allowed the appropriate clinical management of one-third of patients in this cohort. BR 16S PCR is an essential tool for the clinical management of patients with invasive infection when primary cultures are negative or contaminated. Full article
(This article belongs to the Special Issue Clinical Microbiology and Related Diseases)
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