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Diagnostics
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Applications of Next-Generation Sequencing Technologies for the Diagnosis and Management...
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Applications of Next-Generation Sequencing Technologies for the Diagnosis and Management 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 2024 | Viewed by 3287

Special Issue Editors

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
Dr. Sze Chuen Cesar Wong

E-Mail Website
Guest Editor
Department of Applied Biology & Chemical Technology, Hong Kong Polytechnic University, Hong Kong SAR, China
Interests: colorectal cancer; CRC; genetic testing

Special Issue Information

Dear Colleagues,

Since the advent of sequencing technologies and emergence of different sequencing platforms, the use of next-generation sequencing (NGS) technologies for the clinical diagnosis of infectious diseases has increased. NGS technologies allow the comprehensive, high-throughput, and massively parallel detection of any pathogens, ranging from viruses to bacteria to fungi to parasites in specimens. Moreover, it has also been applied broadly and successfully in epidemiological studies, such as those on disease origin tracing. In this Special Issue, we are pleased to invite original research articles, experiences, and reviews on applications of NGS for the clinical diagnosis and management of infectious diseases. We believe these will have a considerable impact on the future development of accurate diagnostic technologies and precise management of infectious diseases. We look forward to receiving your contributions.

Dr. Hin Fung Tsang
Dr. Sze Chuen Cesar Wong
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

  • NGS
  • sequencing
  • diagnostic microbiology
  • infectious diseases

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Published Papers (2 papers)

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Research

10 pages, 1346 KiB  
Article
The Impact of Next-Generation Sequencing Added to Multiplex PCR on Antibiotic Stewardship in Critically Ill Patients with Suspected Pneumonia
by Kendall Kling, Chao Qi, Richard G. Wunderink and Chiagozie Pickens
Diagnostics 2024, 14(13), 1388; https://doi.org/10.3390/diagnostics14131388 - 29 Jun 2024
Viewed by 628
Abstract
Introduction: In patients with suspected pneumonia who are tested with respiratory culture and multiplex PCR, the potential added benefit of next-generation sequencing technologies is unknown. Methods: This was a single-center, retrospective study in which residual bronchoalveolar lavage (BAL) specimens were retrieved from hospitalized [...] Read more.
Introduction: In patients with suspected pneumonia who are tested with respiratory culture and multiplex PCR, the potential added benefit of next-generation sequencing technologies is unknown. Methods: This was a single-center, retrospective study in which residual bronchoalveolar lavage (BAL) specimens were retrieved from hospitalized patients. We compared its research-use-only Respiratory Pathogen Illumina Panel (RPIP) results to culture and BioFire® FilmArray Pneumonia Panel (BioFire® PN) results from critically ill patients. Results: In total, 47 BAL specimens from 47 unique patients were included. All BAL samples were tested with culture and multiplex PCR. In total, 38 of the 47 BALs were consistent with a clinical picture of pneumonia per chart review. Additional testing of the 38 samples with the RPIP identified a new bacterium in 20 patients, a new virus in 4 patients, a new bacterium plus virus in 4 patients, and no additional organisms in 10 patients. In 17 (44.5%) of these patients, the RPIP results could have indicated an antibiotic addition. Compared with cultures, the RPIP had an overall sensitivity of 64% and specificity of 98%, with a 0% sensitivity for fungus and 14% sensitivity for mycobacteria. Compared with BioFire® PN, the RPIP was 70% sensitive and 99% specific, with a 74% sensitivity for bacteria and 33% sensitivity for viruses. The RPIP was 29% more sensitive for HAP/VAP bacterial targets compared with CAP. Conclusions: Emerging NGS technologies such as the RPIP may have a role in identifying the etiology of pneumonia, even when patients have BAL culture and multiplex PCR results available. Similar to prior studies evaluating RPIP, our study showed this platform lacked sensitivity when compared with cultures, particularly for fungi and mycobacteria. However, the high specificity of the test can be leveraged when clinicians are seeking to rule out certain infections. Full article
(This article belongs to the Special Issue Applications of Next-Generation Sequencing Technologies for the Diagnosis and Management of Infectious Diseases)
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12 pages, 679 KiB  
Article
Menstrual Blood as a Diagnostic Specimen for Human Papillomavirus Genotyping and Genital Tract Infection Using Next-Generation Sequencing as a Novel Diagnostic Tool
by Hin-Fung Tsang, Yui-Shing Cheung, Chi-Shing Allen Yu, Chung-Sum Sammy Chan, Chi-Bun Thomas Wong, Kay-Yuen Aldrin Yim, Xiaomeng Pei and Sze-Chuen Cesar Wong
Diagnostics 2024, 14(7), 686; https://doi.org/10.3390/diagnostics14070686 - 25 Mar 2024
Cited by 1 | Viewed by 2197
Abstract
Background: Menstrual blood (MB) is a convenient specimen type that can be self-collected easily and non-invasively by women. This study assessed the potential application of MB as a diagnostic specimen to detect genital tract infections (GTIs) and human papillomavirus (HPV) infections in women. [...] Read more.
Background: Menstrual blood (MB) is a convenient specimen type that can be self-collected easily and non-invasively by women. This study assessed the potential application of MB as a diagnostic specimen to detect genital tract infections (GTIs) and human papillomavirus (HPV) infections in women. Method: Genomic DNA was extracted from MB samples. Pacific Bioscience (Pacbio) 16S ribosomal DNA (rDNA) high-fidelity (HiFi) long-read sequencing and HPV PCR were performed. Results: MB samples were collected from women with a pathological diagnosis of CIN1, CIN2, CIN3 or HPV infection. The sensitivity and positive predictive value (PPV) of high-risk HPV detection using MB were found to be 66.7%. A shift in vaginal flora and a significant depletion in Lactobacillus spp. in the vaginal microbiota communities were observed in the MB samples using 16S rDNA sequencing. Conclusions: In this study, we demonstrated that MB is a proper diagnostic specimen of consideration for non-invasive detection of HPV DNA and genotyping using PCR and the diagnosis of GTIs using metagenomic next-generation sequencing (mNGS). MB testing is suitable for all women who menstruate and this study has opened up the possibility of the use of MB as a diagnostic specimen to maintain women’s health. Full article
(This article belongs to the Special Issue Applications of Next-Generation Sequencing Technologies for the Diagnosis and Management of Infectious Diseases)
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