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Diagnostics
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Microbiology Laboratory: Sample Collection and Diagnosis Advances
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Microbiology Laboratory: Sample Collection and Diagnosis Advances

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 (30 April 2024) | Viewed by 6609

Special Issue Editors

Prof. Dr. James P. Chambers

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Guest Editor
Department of Biology, University of Texas at San Antonio, San Antonio, TX 78249, USA
Interests: biochemistry; pathogen detection; virology; bacteriology; diagnostics; biosensors
Dr. Luke T. Daum

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Guest Editor
LuJo BioScience Laboratory, 1747 Citadel Plaza, Suite 201, San Antonio, TX 78209, USA
Interests: sample collection; nucleic acid extraction; qPCR; NGS; sequencing; molecular epidemiology; tuberculosis; influenza; SARS-CoV-2; diagnostics; point of care; rapid detection
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Infectious microbes continue to emerge, causing persistent infections, re-infections, and epidemics worldwide. Advances in the detection of nucleic acids, antigens, and protein assays, as well as the genomic characterization of drug susceptibility markers, have improved microbial diagnosis and treatment. Furthermore, innovations in sample collection, pre-processing, home collection, and point-of-care/decentralized testing have expanded the reach of microbial diagnosis to new patients, populations, and resource-challenged environments. We welcome the submission of manuscripts related to novel advances in the microbial diagnosis of infectious diseases, including but not limited to the fields of virology, bacteriology, mycology, and molecular epidemiology. Acceptable submission types include research articles, short research notes, and reviews.

Prof. Dr. James P. Chambers
Dr. Luke T. Daum
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

  • qPCR
  • NGS
  • sample collection
  • nucleic acid testing
  • rapid antigen testing
  • infectious diseases
  • virology
  • sequencing
  • point-of-care
  • diagnostics
  • bacteriology diagnosis
  • diagnostics
  • biosensors

Published Papers (5 papers)

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Research

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19 pages, 2538 KiB  
Article
Validation of a New Duplex Real-Time Polymerase Chain Reaction for Chlamydia trachomatis DNA Detection in Ocular Swab Samples
by Joana da Felicidade Ribeiro Favacho, Keren Kariene Leite, Thiago Jacomasso, Aline Burda Farias, Luciano Chaves Franco Filho, Samara Tatielle Monteiro Gomes, Herald Souza dos Reis, Gardene Dourado Mota, Pedro Henrique de Caires Schluga, Walleyd Sami Tassi, Rita de Cássia Pontello Rampazzo, Sheila Kay West, Charlotte Ann Gaydos, Antonio José Ledo Alves da Cunha and Alexandre Dias Tavares Costa
Diagnostics 2024, 14(9), 892; https://doi.org/10.3390/diagnostics14090892 - 25 Apr 2024
Viewed by 338
Abstract
Trachoma is the world-leading infectious cause of preventable blindness and is caused by the bacteria Chlamydia trachomatis. In developing countries, diagnosis is usually based on clinical evaluation. Serological-based tests are cheaper than molecular-based ones, but the latter are more sensitive and specific. [...] Read more.
Trachoma is the world-leading infectious cause of preventable blindness and is caused by the bacteria Chlamydia trachomatis. In developing countries, diagnosis is usually based on clinical evaluation. Serological-based tests are cheaper than molecular-based ones, but the latter are more sensitive and specific. The present study developed a new duplex qPCR which concomitantly detects the C. trachomatis cryptic plasmid and the human 18S rRNA gene, with an LOD95% for C. trachomatis DNA of 13.04 genome equivalents per reaction. The new qPCR was tested using 50 samples from an endemic area and 12 from a non-endemic area that were previously characterized using direct immunofluorescence assay (DFA) and clinical evaluation. Among the 50 endemic samples, 3 were found to be positive by clinical evaluation (6%), 18 were found to be positive by DFA (36%), and 48 were found to be positive by qPCR (96%). Next, the new duplex qPCR was validated using 50 samples previously characterized by qPCR. Validation was carried out on a benchtop instrument (ABI7500) or on a portable point-of-care instrument (Q3-Plus), showing 95% specificity and 100% sensitivity. The ubiquitous presence of C. trachomatis DNA in samples from the endemic region confirms that constant monitoring is of paramount importance for the effective measurement of the elimination of trachoma. The newly developed duplex qPCR presented in this study, along with its validation in a portable qPCR system, constitutes important tools toward achieving this goal. Full article
(This article belongs to the Special Issue Microbiology Laboratory: Sample Collection and Diagnosis Advances)
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13 pages, 1940 KiB  
Article
A Lateral-Flow Device for the Rapid Detection of Scedosporium Species
by Genna E. Davies and Christopher R. Thornton
Diagnostics 2024, 14(8), 847; https://doi.org/10.3390/diagnostics14080847 - 19 Apr 2024
Viewed by 425
Abstract
Scedosporium species are human pathogenic fungi, responsible for chronic, localised, and life-threatening disseminated infections in both immunocompetent and immunocompromised individuals. The diagnosis of Scedosporium infections currently relies on non-specific CT, lengthy and insensitive culture from invasive biopsy, and the time-consuming histopathology of tissue [...] Read more.
Scedosporium species are human pathogenic fungi, responsible for chronic, localised, and life-threatening disseminated infections in both immunocompetent and immunocompromised individuals. The diagnosis of Scedosporium infections currently relies on non-specific CT, lengthy and insensitive culture from invasive biopsy, and the time-consuming histopathology of tissue samples. At present, there are no rapid antigen tests that detect Scedosporium-specific biomarkers. Here, we report the development of a rapid (30 min) and sensitive (pmol/L sensitivity) lateral-flow device (LFD) test, incorporating a Scedosporium-specific IgG1 monoclonal antibody (mAb), HG12, which binds to extracellular polysaccharide (EPS) antigens between ~15 kDa and 250 kDa secreted during the hyphal growth of the pathogens. The test is compatible with human serum and allows for the detection of the Scedosporium species most frequently reported as agents of human disease (Scedosporium apiospermum, Scedosporium aurantiacum, and Scedosporium boydii), with limits of detection (LODs) of the EPS biomarkers in human serum of ~0.81 ng/mL (S. apiospermum), ~0.94 ng/mL (S. aurantiacum), and ~1.95 ng/mL (S. boydii). The Scedosporium-specific LFD (ScedLFD) test therefore provides a potential novel opportunity for the detection of infections caused by different Scedosporium species. Full article
(This article belongs to the Special Issue Microbiology Laboratory: Sample Collection and Diagnosis Advances)
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9 pages, 443 KiB  
Communication
Clinical Evaluation of Xpert Xpress CoV-2/Flu/RSV plus and Alinity m Resp-4-Plex Assay
by Wai-Sing Chan, Kan-Pui Wong, Siu-Kei Yau, Ching-Yan Wong, Tsz-Ching Chan, Jeffrey Hung, Kristi Tsz-Wan Lai, Chin-Pang Leung, Candy Ling-Na Wang, Chun-Hang Au, Thomas Shek-Kong Wan, Edmond Shiu-Kwan Ma and Bone Siu-Fai Tang
Diagnostics 2024, 14(7), 683; https://doi.org/10.3390/diagnostics14070683 - 24 Mar 2024
Viewed by 647
Abstract
The performance of the Xpert Xpress CoV-2/Flu/RSV plus and Alinity m Resp-4-Plex Assays were evaluated using 167 specimens, including 158 human respiratory specimens and 9 external quality assessment program (EQAP) samples. For respiratory specimens, CoV-2/Flu/RSV plus exhibited perfect agreement with the standard-of-care (SOC) [...] Read more.
The performance of the Xpert Xpress CoV-2/Flu/RSV plus and Alinity m Resp-4-Plex Assays were evaluated using 167 specimens, including 158 human respiratory specimens and 9 external quality assessment program (EQAP) samples. For respiratory specimens, CoV-2/Flu/RSV plus exhibited perfect agreement with the standard-of-care (SOC) methods (Cohen’s κ: 1, 100% agreement). The overall positive and negative percent agreement (PPA and NPA) were 100%, with 95% confidence intervals of 96.50 to 100% and 85.70 to 100%, respectively. On the other hand, Resp-4-Plex revealed an almost perfect agreement with the SOC methods (Cohen’s κ: 0.92, 97.71% agreement). The overall PPA and NPA were 100% (95.76 to 100%) and 88.46% (70.20 to 96.82%), respectively. For EQAP samples, the results of CoV-2/Flu/RSV plus (9/9) and Resp-4-Plex (4/4) were concordant with the expected results. The experimental limit of detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was the lowest (25 copies/mL for both methods), and that of the respiratory syncytial virus was the highest (400 copies/mL for CoV-2/Flu/RSV plus and 100 copies/mL for Resp-4-Plex). Threshold cycle (Ct) value correlation showed a large positive linear association between CoV-2/Flu/RSV plus and Resp-4-Plex, with R-squared values of 0.92–0.97, and on average, the Ct values of CoV-2/Flu/RSV plus were higher than that of Resp-4-Plex by 1.86–2.78, except for Flu A1 target (−0.66). To conclude, the performance of both assay was comparable to the SOC methods for both upper and lower respiratory specimens. Implementation of these rapid assay may reinforce the diagnostic capacity for the post-pandemic co-circulation of SARS-CoV-2 and other respiratory viruses. Full article
(This article belongs to the Special Issue Microbiology Laboratory: Sample Collection and Diagnosis Advances)
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11 pages, 1159 KiB  
Article
Evaluation of the Diagnostic Performance of a SARS-CoV-2 and Influenza A/B Combo Rapid Antigen Test in Respiratory Samples
by Harika Öykü Dinç, Nuran Karabulut, Sema Alaçam, Hayriye Kırkoyun Uysal, Ferhat Osman Daşdemir, Mustafa Önel, Yeşim Tuyji Tok, Serhat Sirekbasan, Ali Agacfidan, Nesrin Gareayaghi, Hüseyin Çakan, Önder Yüksel Eryiğit and Bekir Kocazeybek
Diagnostics 2023, 13(5), 972; https://doi.org/10.3390/diagnostics13050972 - 03 Mar 2023
Cited by 7 | Viewed by 3866
Abstract
This study aimed to evaluate the performance characteristics of a rapid antigen test developed to detect SARS-CoV-2 (COVID-19), influenza A virus (IAV), and influenza B virus (IBV) (flu) compared with those of the real-time reverse transcription-polymerase chain reaction (rRT-PCR) method. One hundred SARS-CoV-2, [...] Read more.
This study aimed to evaluate the performance characteristics of a rapid antigen test developed to detect SARS-CoV-2 (COVID-19), influenza A virus (IAV), and influenza B virus (IBV) (flu) compared with those of the real-time reverse transcription-polymerase chain reaction (rRT-PCR) method. One hundred SARS-CoV-2, one hundred IAV, and twenty-four IBV patients whose diagnoses were confirmed by clinical and laboratory methods were included in the patient group. Seventy-six patients, who were negative for all respiratory tract viruses, were included as the control group. The Panbio™ COVID-19/Flu A&B Rapid Panel test kit was used in the assays. The sensitivity values of the kit were 97.5%, 97.9%, and 33.33% for SARS-CoV-2, IAV, and IBV, respectively, in samples with a viral load below 20 Ct values. The sensitivity values of the kit were 16.7%, 36.5%, and 11.11% for SARS-CoV-2, IAV, and IBV, respectively, in samples with a viral load above 20 Ct. The kit’s specificity was 100%. In conclusion, this kit demonstrated high sensitivity to SARS-CoV-2 and IAV for viral loads below 20 Ct values, but the sensitivity values were not compatible with PCR positivity for lower viral loads over 20 Ct values. Rapid antigen tests may be preferred as a routine screening tool in communal environments, especially in symptomatic individuals, when diagnosing SARS-CoV-2, IAV, and IBV with high caution. Full article
(This article belongs to the Special Issue Microbiology Laboratory: Sample Collection and Diagnosis Advances)
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Review

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28 pages, 515 KiB  
Review
The Role and Value of Professional Rapid Testing of Acute Respiratory Infections (ARIs) in Europe: A Special Focus on the Czech Republic, Poland, and Romania
by Pavel Drevinek, Robert Flisiak, Roxana Nemes, Katya A. Nogales Crespo and Krzysztof Tomasiewicz
Diagnostics 2024, 14(6), 631; https://doi.org/10.3390/diagnostics14060631 - 16 Mar 2024
Viewed by 866
Abstract
This review aims to explore the role of professional diagnostic rapid testing of acute respiratory infections (ARIs), especially COVID-19 and influenza, ensuring proper disease management and treatment in Europe, and particularly in Czech Republic, Poland, and Romania. The paper was constructed based on [...] Read more.
This review aims to explore the role of professional diagnostic rapid testing of acute respiratory infections (ARIs), especially COVID-19 and influenza, ensuring proper disease management and treatment in Europe, and particularly in Czech Republic, Poland, and Romania. The paper was constructed based on a review of scientific evidence and national and international policies and recommendations, as well as a process of validation by four experts. The development of new testing technologies, treatment options, and increased awareness of the negative multidimensional impact of ARI profiles transformed differential diagnosis into a tangible and desirable reality. This review covers the following topics: (1) the multidimensional impact of ARIs, (2) ARI rapid diagnostic testing platforms and their value, (3) the policy landscape, (4) challenges and barriers to implementation, and (5) a set of recommendations illustrating a path forward. The findings indicate that rapid diagnostic testing, including at the point of care (POC), can have a positive impact on case management, antimicrobial and antibiotic stewardship, epidemiological surveillance, and decision making. Integrating this strategy will require the commitment of governments and the international and academic communities, especially as we identified room for improvement in the access and expansion of POC rapid testing in the focus countries and the inclusion of rapid testing in relevant policies. Full article
(This article belongs to the Special Issue Microbiology Laboratory: Sample Collection and Diagnosis Advances)
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