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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Pathology, Diagnostics, and Therapeutics".

Deadline for manuscript submissions: closed (30 September 2024) | Viewed by 7231

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Prof. Dr. Stephen Bustin

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Medical Technology Research Institute, Anglia Ruskin University, Chelmsford CM1 1SQ, UK
Interests: qPCR; RT-qPCR; colorectal cancer; molecular staging; clostridium difficile; MRSA; aspergillus
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Special Issue Information

Dear Colleagues,

Nucleic acid-based diagnostics are pivotal at the crossroads of molecular biology and healthcare, enabling the identification of infectious diseases. Over the last few years, complementary technologies such as digital PCR (dPCR) and isothermal amplification methods have been introduced to complement traditional quantitative PCR (qPCR). Innovations encompass integrated microfluidic platforms, refined sample extraction, improved enzymes, creative primer designs, and multiplexing, thus enhancing speed and reliability. Bioinformatics and artificial intelligence augment accurate data analysis and results interpretation.

The COVID-19 pandemic has highlighted issues around sensitivity, specificity, and low viral loads, underscoring the complexities in diagnostic interpretation. Yet, amidst challenges like climate change and antibiotic resistance, nucleic acid amplification-based diagnostics (NAAT) continue to evolve with adaptability, sensitivity, and growing accessibility. However, as the field progresses, cautious results interpretation and transparent communication remain crucial to ensure the responsible use of these powerful tools.

This Special Issue aims to provide a broad overview across the molecular diagnostic landscape, with a special emphasis on the intersection of qPCR, dPCR, isothermal amplification methods, and emerging trends in infectious disease diagnostics. By exploring the advances, challenges, and potential applications, this Special Issue strives to contribute to the understanding and effective utilisation of these technologies in the context of healthcare and disease management.

Prof. Dr. Stephen Bustin
Guest Editor

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Published Papers (4 papers)

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Research

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9 pages, 1279 KiB

Open AccessArticle

Assessment of DNA/RNA Defend Pro: An Inactivating Sample Collection Buffer for Enhanced Stability, Extraction-Free PCR, and Rapid Antigen Testing of Nasopharyngeal Swab Samples

by Mikhail Claeys, Saif Al Obaidi, Karen Bruyland, Ilse Vandecandelaere and Jo Vandesompele

Int. J. Mol. Sci. 2024, 25(16), 9097; https://doi.org/10.3390/ijms25169097 - 22 Aug 2024

Viewed by 794

Abstract

This study comprehensively evaluated the DNA/RNA Defend Pro (DRDP) sample collection buffer, designed to inactivate and stabilize patient samples. The primary objectives were to assess DRDP’s efficacy in ensuring sample stability, facilitating extraction-free polymerase chain reaction (PCR), and ensuring compatibility with rapid antigen testing (RAT). Ninety-five diagnostic nasopharyngeal swab samples tested for influenza virus (influenza A), respiratory syncytial virus (RSV A), and/or severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were 10-fold diluted with DRDP and anonymized. Initial characterization and retesting of these samples using cobas Liat confirmed 88 samples as positive, validating the presence of viral targets. Results from rapid antigen testing showed lower sensitivity compared to nucleic acid amplification testing (NAAT) but maintained perfect specificity, with 40 out of 88 positive samples by cobas Liat also testing positive for RAT. Direct RT-qPCR of DRDP-diluted samples demonstrated robust compatibility, with 72 out of 88 samples positive for cobas Liat also testing positive by direct RT-qPCR. Non-concordant results could be explained by the 200-fold lower input of extraction-free NAAT. Stability testing involved incubating 31 positive samples at 4 °C, 20 °C, and 37 °C for 7 days, with extraction-free NAAT. DRDP guaranteed viral RNA stability at all temperatures for influenza A, SARS-CoV-2, and RSV A, showing stability up to 7 days at 4 °C. In conclusion, DRDP is an effective stabilizing medium compatible with direct RT-qPCR and rapid antigen testing and shows great potential for optimizing diagnostic processes, particularly in resource-limited or time-sensitive scenarios. Full article

(This article belongs to the Special Issue Nucleic Acid-Based Diagnostics for Infectious Diseases)

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16 pages, 460 KiB

Open AccessArticle

The Impact of Polymerase Chain Reaction Urine Testing on Clinical Decision-Making in the Management of Complex Urinary Tract Infections

by Julia Elia, Jason Hafron, Mara Holton, Connor Ervin, Mitchell B. Hollander and Deepak A. Kapoor

Int. J. Mol. Sci. 2024, 25(12), 6616; https://doi.org/10.3390/ijms25126616 - 16 Jun 2024

Viewed by 878

Abstract

While urinary polymerase chain reaction (PCR) testing is effective in organism identification in patients with complex urinary tract infections (cUTI), limited data exists on the clinical usefulness of this test. We serially surveyed physicians treating symptomatic patients with cUTI both at presentation and after PCR, and urine culture (UC) results were available to ascertain how the test results modified the therapy. A total of 96 unique surveys completed by 21 providers were included in the data analysis. The mean age for female and male patients was 69.4 ± 15.5 and 71.6 ± 12.7 years, respectively. The test positivity and line–item concordance for UC and PCR were consistent with prior reports. The PCR results modified or confirmed treatment in 59/96 (61.5%) and 25/96 (26.0%) of the cases, respectively, with 12/29 (41.4%) and 47/67 (70.1%) having negative and positive PCR results, respectively, resulting in treatment change (difference 28.7%, p < 0.01). Of these, 55/59 (57.3%) were alterations in the antibiotic regimen. PCR use to modify treatment was similar across providers and not statistically different when stratified by patient age, gender, or prior empiric therapy. In 31/59 (52.5%) of the cases, the PCR results modified the treatment where UC would not; conversely, UC would have modified the treatment in 3/37 (8.1%) of the cases where PCR did not (difference 44.4%, p < 0.01). We find that PCR test results are used by clinicians in managing cUTI, and use of this test provides an opportunity to improve antibiotic stewardship in this difficult-to-treat subset of patients. Full article

(This article belongs to the Special Issue Nucleic Acid-Based Diagnostics for Infectious Diseases)

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19 pages, 3864 KiB

Open AccessArticle

FlashPCR: Revolutionising qPCR by Accelerating Amplification through Low ∆T Protocols

by Stephen A. Bustin, Sara Kirvell, Tania Nolan and Gregory L. Shipley

Int. J. Mol. Sci. 2024, 25(5), 2773; https://doi.org/10.3390/ijms25052773 - 28 Feb 2024

Cited by 1 | Viewed by 2570

Abstract

Versatility, sensitivity, and accuracy have made the real-time polymerase chain reaction (qPCR) a crucial tool for research, as well as diagnostic applications. However, for point-of-care (PoC) use, traditional qPCR faces two main challenges: long run times mean results are not available for half an hour or more, and the requisite high-temperature denaturation requires more robust and power-demanding instrumentation. This study addresses both issues and revises primer and probe designs, modified buffers, and low ∆T protocols which, together, speed up qPCR on conventional qPCR instruments and will allow for the development of robust, point-of-care devices. Our approach, called “FlashPCR”, uses a protocol involving a 15-second denaturation at 79 °C, followed by repeated cycling for 1 s at 79 °C and 71 °C, together with high Tm primers and specific but simple buffers. It also allows for efficient reverse transcription as part of a one-step RT-qPCR protocol, making it universally applicable for both rapid research and diagnostic applications. Full article

(This article belongs to the Special Issue Nucleic Acid-Based Diagnostics for Infectious Diseases)

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Review

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32 pages, 1277 KiB

Open AccessReview

Enhancing Clinical Utility: Utilization of International Standards and Guidelines for Metagenomic Sequencing in Infectious Disease Diagnosis

by Chau-Ming Kan, Hin Fung Tsang, Xiao Meng Pei, Simon Siu Man Ng, Aldrin Kay-Yuen Yim, Allen Chi-Shing Yu and Sze Chuen Cesar Wong

Int. J. Mol. Sci. 2024, 25(6), 3333; https://doi.org/10.3390/ijms25063333 - 15 Mar 2024

Cited by 3 | Viewed by 2364

Abstract

Metagenomic sequencing has emerged as a transformative tool in infectious disease diagnosis, offering a comprehensive and unbiased approach to pathogen detection. Leveraging international standards and guidelines is essential for ensuring the quality and reliability of metagenomic sequencing in clinical practice. This review explores the implications of international standards and guidelines for the application of metagenomic sequencing in infectious disease diagnosis. By adhering to established standards, such as those outlined by regulatory bodies and expert consensus, healthcare providers can enhance the accuracy and clinical utility of metagenomic sequencing. The integration of international standards and guidelines into metagenomic sequencing workflows can streamline diagnostic processes, improve pathogen identification, and optimize patient care. Strategies in implementing these standards for infectious disease diagnosis using metagenomic sequencing are discussed, highlighting the importance of standardized approaches in advancing precision infectious disease diagnosis initiatives. Full article

(This article belongs to the Special Issue Nucleic Acid-Based Diagnostics for Infectious Diseases)

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