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Diagnostics
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DNA Sequencing of Infectious Diseases
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DNA Sequencing of Infectious Diseases

A special issue of Diagnostics (ISSN 2075-4418). This special issue belongs to the section "Diagnostic Microbiology and Infectious Disease".

Deadline for manuscript submissions: 30 September 2025 | Viewed by 1654

Special Issue Editors

Prof. Dr. Edward R. B. Moore

E-Mail Website
Guest Editor
1. Department of Infectious Diseases, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
2. Department of Clinical Microbiology, Sahlgrenska University Hospital, Guldhedsgatan 10a, Gothenburg, Sweden
Interests: microbial evolution and phylogeny; bacterial systematics and taxonomy; bacterial identification; molecular bacterial diagnostics; diagnostics of infectious diseases; anti-microbial resistance
Special Issues, Collections and Topics in MDPI journals
Dr. Daniel Jaén Luchoro

E-Mail Website
Guest Editor
Department of Infectious Diseases, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
Interests: molecular bacterial diagnostics; bacterial identification; bacterial systematics and taxonomy
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The Special Issue delves into the critical role of DNA sequencing in infectious disease diagnostics and screening. Highlighting rapidly evolving advancements, DNA sequencing technology has enabled the rapid and precise identification of pathogens through methods such as whole-genome sequencing and targeted amplicon sequencing. These techniques provide crucial insights into disease transmission, evolution, and virulence, enabling earlier diagnoses and tailored, more effective treatments. Thia Special Issue also underscores the importance of screening high-risk populations for early detection and prevention, ultimately contributing to improved patient outcomes and global disease control.

Prof. Dr. Edward R. B. Moore
Dr. Daniel Jaén Luchoro
Guest Editors

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. Diagnostics is an international peer-reviewed open access semimonthly 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 2600 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

  • DNA sequencing
  • infectious disease
  • diagnostics
  • screening
  • whole-genome sequencing
  • targeted amplicon sequencing

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Published Papers (2 papers)

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Research

12 pages, 1514 KiB  
Article
Genomic Characterization of Multidrug-Resistant Acinetobacter baumannii in Pneumonia Patients in Kazakhstan
by Vitaliy Strochkov, Vyacheslav Beloussov, Shynggys Orkara, Alyona Lavrinenko, Maxim Solomadin, Sergey Yegorov and Nurlan Sandybayev
Diagnostics 2025, 15(6), 704; https://doi.org/10.3390/diagnostics15060704 - 12 Mar 2025
Viewed by 804
Abstract
Background/Objectives: Acinetobacter baumannii is an increasingly significant nosocomial pathogen causing severe infections globally. The emergence of multidrug-resistant A. baumannii strains has raised concerns about the efficacy of current treatment options. This study aimed to investigate the molecular epidemiology and antimicrobial resistance patterns [...] Read more.
Background/Objectives: Acinetobacter baumannii is an increasingly significant nosocomial pathogen causing severe infections globally. The emergence of multidrug-resistant A. baumannii strains has raised concerns about the efficacy of current treatment options. This study aimed to investigate the molecular epidemiology and antimicrobial resistance patterns of A. baumannii isolates from Kazakhstan. Methods: We collected nine A. baumannii isolates in 2022–2023 in Karaganda, Kazakhstan, which were then subjected to whole-genome sequencing (WGS) using the IonTorrent platform for genome characterization. Multilocus sequence typing (MLST) was used to classify the isolates into distinct clonal complexes. In addition, antibiotic susceptibility testing was conducted using the standard methods for a range of antibiotics commonly used against A. baumannii. Results: Our results revealed a high degree of genomic diversity among isolates from Kazakhstan, with multiple distinct classes identified: ST78 (n = 4, 44.4%), ST15 (n = 2, 22.2%), ST2 (n = 2, 22.2%), and ST193 (n = 1, 11%). MLST analysis showed that ST78Pas/1104Oxf (harboring blaOXA-72 and blaOXA-90 genes) were prevalent among the multidrug-resistant isolates. Based on the results of MLST, KL, and OCL, the analyzed isolates were assigned to specific international clones: IC2—ST2(Pas)-KL2/168-OCL1, IC4—ST15(Pas)-KL9-OCL7, and IC6—ST78(Pas)-KL49-OCL1. Notably, these isolates exhibited resistance to multiple antibiotics including meropenem, imipenem, gentamicin, amikacin, and ciprofloxacin. Conclusions: This study highlighted the complex molecular epidemiology of A. baumannii in Kazakhstan over a two-year period, underscoring the need for targeted surveillance strategies to monitor antimicrobial resistance patterns. The emergence and dissemination of multidrug-resistant strains within this timeframe emphasizes the importance of whole-genome sequencing as a diagnostic tool and underscores the challenges posed by these infections. Full article
(This article belongs to the Special Issue DNA Sequencing of Infectious Diseases)
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14 pages, 456 KiB  
Article
Implementation of Multi-Criteria Decision-Making for Selecting Most Effective Genome Sequencing Technology
by Ayse Arikan, Berna Uzun and Murat Sayan
Diagnostics 2025, 15(6), 665; https://doi.org/10.3390/diagnostics15060665 - 10 Mar 2025
Viewed by 528
Abstract
Background/Objectives: In recent years, molecular diagnosis has become increasingly critical in identifying human pathogens with unknown genes. Methods: An innovative approach, the fuzzy-based preference ranking organization method for enrichment evaluation (PROMETHEE) technique, one of the most effective multi-criteria decision-making (MCDM) methods, was used [...] Read more.
Background/Objectives: In recent years, molecular diagnosis has become increasingly critical in identifying human pathogens with unknown genes. Methods: An innovative approach, the fuzzy-based preference ranking organization method for enrichment evaluation (PROMETHEE) technique, one of the most effective multi-criteria decision-making (MCDM) methods, was used to evaluate criteria, including portability, generation type, max read/run, max output data/run, processing time/run, read length, accuracy, diagnostic sensitivity, test minimum loading volume, test cost/run, instrument cost, error rate, throughput capability, ability to sequence the large whole genome, small whole genome, and exome and large panel, mutation detection ability, whole-genome sequencing with single-stranded sequencing, and single-stranded sequencing accuracy, to determine the most suitable sequencing technology. Results: Based on the analysis, the Avidite Base Chemistry (ABC), Nanopore, and Illumina sequencing platforms sequentially emerged as the most favorable options based on their net flows of 0.0346, 0.0041, and 0.0003, respectively. Conclusions: Our findings provide important data to facilitate the selection of genome detection technologies. Through the use of innovative approaches, complex evaluations can be analyzed and the right choices can be made. Importantly, the technique has a degree of subjectivity, so varying conditions may lead to different findings. Full article
(This article belongs to the Special Issue DNA Sequencing of Infectious Diseases)
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