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Diagnostics
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Molecular Diagnostics of Infectious Diseases
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Molecular Diagnostics 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: closed (15 March 2023) | Viewed by 12356

Special Issue Editor

Prof. Dr. Chan Yean Yean

E-Mail Website
Guest Editor
Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
Interests: molecular microbiology; molecular diagnostic; biosensor
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The diagnosis of infectious diseases is critical in the management of patients especially those who are critically ill in order to prevent the adverse outcomes and reduce mortality by promptly starting the treatment. The infectious diseases like coronavirus diseases-2019 (COVID-19), tuberculosis (TB), shigellosis, bacterial infections, dengue and other mosquito-borne diseases, and human immunodeficiency virus (HIV) are the common examples of diseases which are badly affecting the humans worldwide. Apart from their diagnosis, the early detection of their potential treatment using various drugs is also mandatory. As, the antimicrobial resistance is a very well-known health related issues worldwide, there is a need to develop more suitable molecular candidates for the early detection of antimicrobial resistance among various bacteria.

The main objectives of this special issue are to provide an overview of current molecular techniques based early diagnosis in infectious diseases, antimicrobial resistance and antiviral resistance and to review the new possibilities of diagnostic candidates for early antimicrobial resistance detection and early diagnosis of infectious diseases.

The scope of the special issue can include but not be limited to:

  1. Diagnostic strategies in tuberculosis/dengue/malaria/COVID-19/infectious diseases
  2. Potential diagnostic biomarkers for infectious diseases
  3. Comparison of diagnostic techniques for bacterial infections
  4. Development of electrochemical genosensors for simultaneous detection of bacterial infections
  5. Bioinformatics based diagnostic tools for early detection of antimicrobial resistance

Prof. Dr. Chan Yean Yean
Guest Editor

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

  • molecular diagnostics
  • biosensors
  • bioinformatics based diagnosis
  • nanopore sequencing
  • whole genome sequencing
  • bacterial diagnosis
  • viral diagnosis
  • point of care testing
  • POCT
  • rapid diagnosis
  • early diagnosis
  • COVID-19 diagnosis
  • monkeypox diagnosis
  • diagnosis
  • diagnostics

Published Papers (6 papers)

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Research

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8 pages, 532 KiB  
Communication
Evaluation of the BioFire® FilmArray® Pneumonia Panel with Conventional Bacterial Culture in Conjunction with Leukocyte Esterase Test
by In Young Yoo, Hyun Soo Seok, Joo An Kwon, Jongmin Lee, Sungjin Jo, Soo Young Kim and Yeon-Joon Park
Diagnostics 2023, 13(11), 1847; https://doi.org/10.3390/diagnostics13111847 - 25 May 2023
Cited by 1 | Viewed by 1294
Abstract
We evaluated the performance of the BioFire® FilmArray® Pneumonia panel (PN-panel) in detecting bacterial pathogens by comparing it to cultures and to the usefulness of the leukocyte esterase (LE) urine strip test. Between January and June 2022, a total of 67 [...] Read more.
We evaluated the performance of the BioFire® FilmArray® Pneumonia panel (PN-panel) in detecting bacterial pathogens by comparing it to cultures and to the usefulness of the leukocyte esterase (LE) urine strip test. Between January and June 2022, a total of 67 sputum specimens were obtained from community-acquired pneumonia patients. The PN-panel and LE test were performed simultaneously with conventional cultures. The pathogen detection rates of the PN-panel and culture were 40/67 (59.7%) and 25/67 (37.3%), respectively. The concordance rate between the PN-panel and culture was high (76.9%) when the bacterial burden was high (107 copies/mL), but it was low (8.6%) when it was 104−6 copies/mL, irrespective of the sputum quality. According to the LE positivity, the overall culture positive rate and PN-panel positive rate were significantly higher among the LE-positive specimens (23/45, 31/45) than among the LE-negative specimens (2/21, 8/21). Moreover, the difference in concordance rate between the PN-panel test and culture was significant according to the LE positivity, but not the Gram stain grading. In conclusion, the PN-panel showed high concordance when the bacterial burden was high (107 copies/mL) and ancillary use of LE test will be helpful in interpreting the PN-panel results, especially when the copy number of bacterial pathogens is low. Full article
(This article belongs to the Special Issue Molecular Diagnostics of Infectious Diseases)
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13 pages, 916 KiB  
Article
Comparative Clinical Evaluation of a Novel FluA/FluB/SARS-CoV-2 Multiplex LAMP and Commercial FluA/FluB/SARS-CoV-2/RSV RT-qPCR Assays
by Hyunseul Jee, Seoyeon Park, Junmin Lee, Chae Seung Lim and Woong Sik Jang
Diagnostics 2023, 13(8), 1432; https://doi.org/10.3390/diagnostics13081432 - 16 Apr 2023
Viewed by 1584
Abstract
Influenza and coronaviruses cause highly contagious respiratory diseases that cause millions of deaths worldwide. Public health measures implemented during the current coronavirus disease (COVID-19) pandemic have gradually reduced influenza circulation worldwide. As COVID-19 measures have relaxed, it is necessary to monitor and control [...] Read more.
Influenza and coronaviruses cause highly contagious respiratory diseases that cause millions of deaths worldwide. Public health measures implemented during the current coronavirus disease (COVID-19) pandemic have gradually reduced influenza circulation worldwide. As COVID-19 measures have relaxed, it is necessary to monitor and control seasonal influenza during this COVID-19 pandemic. In particular, the development of rapid and accurate diagnostic methods for influenza and COVID-19 is of paramount importance because both diseases have significant public health and economic impacts. To address this, we developed a multi-loop-mediated isothermal amplification (LAMP) kit capable of simultaneously detecting influenza A/B and SARS-CoV-2. The kit was optimized by testing various ratios of primer sets for influenza A/B (FluA/FluB) and SARS-CoV-2 and internal control (IC). The FluA/FluB/SARS-CoV-2 multiplex LAMP assay showed 100% specificity for uninfected clinical samples and sensitivities of 90.6%, 86.89%, and 98.96% for LAMP kits against influenza A, influenza B, and SARS-CoV-2 clinical samples, respectively. Finally, the attribute agreement analysis for clinical tests indicated substantial agreement between the multiplex FluA/FluB/SARS-CoV-2/IC LAMP and commercial AllplexTM SARS-CoV-2/FluA/FluB/RSV assays. Full article
(This article belongs to the Special Issue Molecular Diagnostics of Infectious Diseases)
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11 pages, 1370 KiB  
Article
Serial Changes in Blood-Cell-Count-Derived and CRP-Derived Inflammatory Indices of COVID-19 Patients
by Maryam B. Khadzhieva, Alesya S. Gracheva, Olesya B. Belopolskaya, Yulia V. Chursinova, Ivan V. Redkin, Mikhail V. Pisarev and Artem N. Kuzovlev
Diagnostics 2023, 13(4), 746; https://doi.org/10.3390/diagnostics13040746 - 16 Feb 2023
Cited by 4 | Viewed by 1646
Abstract
The aim of the study was to investigate the serial changes in inflammatory indices derived from blood cell counts and C-reactive protein (CRP) levels in COVID-19 patients with good and poor outcomes. We retrospectively analyzed the serial changes in the inflammatory indices in [...] Read more.
The aim of the study was to investigate the serial changes in inflammatory indices derived from blood cell counts and C-reactive protein (CRP) levels in COVID-19 patients with good and poor outcomes. We retrospectively analyzed the serial changes in the inflammatory indices in 169 COVID-19 patients. Comparative analyses were performed on the first and last days of a hospital stay or death and serially from day 1 to day 30 from the symptom onset. On admission, non-survivors had higher CRP to lymphocytes ratio (CLR) and multi-inflammatory index (MII) values than survivors, while at the time of discharge/death, the largest differences were found for the neutrophil to lymphocyte ratio (NLR), systemic inflammation response index (SIRI), and MII. A significant decrease in NLR, CLR, and MII by the time of discharge was documented in the survivors, and a significant increase in NLR was documented in the non-survivors. The NLR was the only one that remained significant from days 7–30 of disease in intergroup comparisons. The correlation between the indices and the outcome was observed starting from days 13–15. The changes in the index values over time proved to be more helpful in predicting COVID-19 outcomes than those measured on admission. The values of the inflammatory indices could reliably predict the outcome no earlier than days 13–15 of the disease. Full article
(This article belongs to the Special Issue Molecular Diagnostics of Infectious Diseases)
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15 pages, 4922 KiB  
Article
A Nanoplex PCR Assay for the Simultaneous Detection of Vancomycin- and Linezolid-Resistant Genes in Enterococcus
by Yusuf Wada, Azian Harun, Chan Yean Yean and Abdul Rahman Zaidah
Diagnostics 2023, 13(4), 722; https://doi.org/10.3390/diagnostics13040722 - 14 Feb 2023
Cited by 2 | Viewed by 1278
Abstract
Background: Enterococci are Gram-positive cocci found in the guts of humans and animals. The goal of this research is to develop a multiplex PCR assay that can detect the Enterococcus genus, four VRE genes, and three LZRE genes simultaneously. Methods: Primers used in [...] Read more.
Background: Enterococci are Gram-positive cocci found in the guts of humans and animals. The goal of this research is to develop a multiplex PCR assay that can detect the Enterococcus genus, four VRE genes, and three LZRE genes simultaneously. Methods: Primers used in this study were specifically designed for the detection of 16S rRNA of Enterococcus genus, vanA—vanB—vanC—vanD for vancomycin, cfr methyltransferase, and optrA, and poxtA, as well as an adenosine triphosphate-binding cassette (ABC) transporter for linezolid. A Vibrio cholerae ctxA (internal amplification control) was included. Optimization of primer concentrations and PCR components was also done. This was followed by evaluating the sensitivity and specificity of the optimized multiplex PCR. Results: Final Primer concentrations were optimized as follows: 16S rRNA is 1.0 pmol/μL, vanA is 1.0 pmol/μL, optrA is 1.0 pmol/μL, cfr is 1.0 pmol/μL, poxtA is 0.1 pmol/μL, vanB is 0.08 pmol/μL, ctxA is 0.07 pmol/μL, vanC is 0.8 pmol/μL, and vanD is 0.1 pmol/μL. Further, the optimized concentrations for MgCl2, dNTPs and Taq DNA polymerase were 2.5 mM, 0.16 mM, and 0.75 units respectively, and an annealing temperature of 64.5 °C. Conclusions: The developed multiplex PCR is sensitive and species-specific. The development of a multiplex PCR assay that will take into account all known VRE genes and linezolid mutation is highly recommended. Full article
(This article belongs to the Special Issue Molecular Diagnostics of Infectious Diseases)
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Review

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25 pages, 2571 KiB  
Review
Evolution of the Probe-Based Loop-Mediated Isothermal Amplification (LAMP) Assays in Pathogen Detection
by Xiaoling Zhang, Yongjuan Zhao, Yi Zeng and Chiyu Zhang
Diagnostics 2023, 13(9), 1530; https://doi.org/10.3390/diagnostics13091530 - 24 Apr 2023
Cited by 7 | Viewed by 3938
Abstract
Loop-mediated isothermal amplification (LAMP), as the rank one alternative to a polymerase chain reaction (PCR), has been widely applied in point-of-care testing (POCT) due to its rapid, simple, and cost-effective characteristics. However, it is difficult to achieve real-time monitoring and multiplex detection with [...] Read more.
Loop-mediated isothermal amplification (LAMP), as the rank one alternative to a polymerase chain reaction (PCR), has been widely applied in point-of-care testing (POCT) due to its rapid, simple, and cost-effective characteristics. However, it is difficult to achieve real-time monitoring and multiplex detection with the traditional LAMP method. In addition, these approaches that use turbidimetry, sequence-independent intercalating dyes, or pH-sensitive indicators to indirectly reflect amplification can result in false-positive results if non-specific amplification occurs. To fulfill the needs of specific target detection and one-pot multiplex detection, a variety of probe-based LAMP assays have been developed. This review focuses on the principles of these assays, summarizes their applications in pathogen detection, and discusses their features and advantages over the traditional LAMP methods. Full article
(This article belongs to the Special Issue Molecular Diagnostics of Infectious Diseases)
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Other

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8 pages, 1116 KiB  
Brief Report
Evaluation of a ddPCR Commercial Assay for the Absolute Quantification of the Monkeypox Virus West Africa in Clinical Samples
by Elena Pomari, Antonio Mori, Silvia Accordini, Annalisa Donini, Maddalena Cordioli, Evelina Tacconelli and Concetta Castilletti
Diagnostics 2023, 13(7), 1349; https://doi.org/10.3390/diagnostics13071349 - 04 Apr 2023
Cited by 2 | Viewed by 1418
Abstract
Background: Monkeypox virus (MPXV) is a double-stranded DNA virus belonging to the orthopoxvirus genus in the family Poxviridae. Distinct clades are identified: the clade I belonging to the Central African (or Congo Basin) clade and the subclades IIa and IIb belonging to [...] Read more.
Background: Monkeypox virus (MPXV) is a double-stranded DNA virus belonging to the orthopoxvirus genus in the family Poxviridae. Distinct clades are identified: the clade I belonging to the Central African (or Congo Basin) clade and the subclades IIa and IIb belonging to the West African clade. Here, a commercial droplet digital PCR (ddPCR) assay was evaluated for the quantification of the MPXV West Africa clade in clinical samples. Methods: The ddPCR reaction was assessed as a duplex assay using RPP30 as an internal amplification control. A total of 60 clinical specimens were tested, 40 positives (skin lesions, n=10; rectal swabs, n = 10; pharyngeal swabs, n = 10; and whole blood, n = 10), and 20 negatives (n = 5 for each biological matrix) were found at the routine molecular diagnostics (orthopoxvirus qPCR followed by confirmation with Sanger sequencing). To evaluate the analytical sensitivity, the ddPCR reaction was first analyzed on serial dilutions of synthetic DNA spiked in water and in negative biological matrices, achieving a limit of detection of 3.5 copy/µL. Results: Regarding the clinical samples, compared to routine molecular diagnostics, the ddPCR duplex assay showed 100% of specificity for all biological matrices and 100% sensitivity (10/10) for lesions, 100% (10/10) for rectal swabs, 90% (9/10) for pharyngeal swabs, and 60% (6/10) for whole blood. Conclusion: Overall, our data showed that the commercial ddPCR assay allowed the DNA detection of MPXV in 87.5% (35/40) of our cohort, highlighting useful technical indications for the different specimens with a potential greatest performance for skin lesions and rectal swabs. Full article
(This article belongs to the Special Issue Molecular Diagnostics of Infectious Diseases)
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