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Zolotareva M, Cascalheira F, Caneiras C, Bárbara C, Caetano DM, Teixeira MC. In the flow of molecular miniaturized fungal diagnosis. Trends Biotechnol 2024:S0167-7799(24)00157-4. [PMID: 38987118 DOI: 10.1016/j.tibtech.2024.06.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 06/03/2024] [Accepted: 06/18/2024] [Indexed: 07/12/2024]
Abstract
The diagnosis of fungal infections presents several challenges and limitations, stemming from the similarities in symptomatology, diversity of underlying pathogenic species, complexity of fungal biology, and scarcity of rapid, affordable, and point-of-care approaches. In this review, we assess technological advances enabling the conversion of cutting-edge laboratory molecular diagnostic methods to cost-effective microfluidic devices. The most promising strategies toward the design of DNA sequence-based fungal diagnostic systems, capable of capturing and deciphering the highly informative DNA of the pathogen and adapted for resource-limited settings, are discussed, bridging fungal biology, molecular genetics, microfluidics, and biosensors.
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Affiliation(s)
- Maria Zolotareva
- Instituto de Engenharia de Sistemas e Computadores - Microsistemas e Nanotecnologias, INESC-, MN, 1000-029 Lisboa, Portugal; iBB - Institute for Bioengineering and Biosciences, Associate Laboratory Institute for Health and Bioeconomy - i4HB, 1049-001 Lisboa, Portugal
| | - Francisco Cascalheira
- Instituto de Engenharia de Sistemas e Computadores - Microsistemas e Nanotecnologias, INESC-, MN, 1000-029 Lisboa, Portugal; iBB - Institute for Bioengineering and Biosciences, Associate Laboratory Institute for Health and Bioeconomy - i4HB, 1049-001 Lisboa, Portugal
| | - Cátia Caneiras
- Environmental Health Institute (ISAMB), Faculdade de Medicina, Universidade de Lisboa, 1649-026 Lisboa, Portugal; Associate Laboratory TERRA, Faculty of Medicine, Universidade de Lisboa, 1649-026 Lisboa, Portugal; Egas Moniz Center for Interdisciplinary Research, Egas Moniz School of Health and Science, 2829-511 Almada, Portugal; Institute of Preventive Medicine and Public Health, Universidade de Lisboa, 1649-026 Lisboa, Portugal
| | - Cristina Bárbara
- Environmental Health Institute (ISAMB), Faculdade de Medicina, Universidade de Lisboa, 1649-026 Lisboa, Portugal; Associate Laboratory TERRA, Faculty of Medicine, Universidade de Lisboa, 1649-026 Lisboa, Portugal; Centro Hospitalar Universitário Lisboa Norte, 1600-190, Lisboa, Portugal
| | - Diogo Miguel Caetano
- Instituto de Engenharia de Sistemas e Computadores - Microsistemas e Nanotecnologias, INESC-, MN, 1000-029 Lisboa, Portugal; Department of Electrical and Computer Engineering, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisboa, Portugal.
| | - Miguel Cacho Teixeira
- iBB - Institute for Bioengineering and Biosciences, Associate Laboratory Institute for Health and Bioeconomy - i4HB, 1049-001 Lisboa, Portugal; Department of Bioengineering, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisboa, Portugal.
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Mosconi G, Fantini M, Righini M, Flachi M, Semprini S, Hu L, Chiappo F, Veterani B, Ambri K, Ferrini F, Milanesi C, Giudicissi A, La Manna G, Rigotti A, Buscaroli A, Sambri V, Cappuccilli M. Efficacy of SARS-CoV-2 Vaccination in Dialysis Patients: Epidemiological Analysis and Evaluation of the Clinical Progress. J Clin Med 2022; 11:jcm11164723. [PMID: 36012962 PMCID: PMC9410204 DOI: 10.3390/jcm11164723] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 07/24/2022] [Accepted: 08/01/2022] [Indexed: 12/16/2022] Open
Abstract
This study investigated the impact of the fourth COVID-19 pandemic wave on dialysis patients of Romagna territory, assessing the associations of vaccination status with infection risk, clinical severity and mortality. From November 2021 to February 2022, an epidemiological search was conducted on 829 patients under dialysis treatment for at least one month. The data were then analyzed with reference to the general population of the same area. A temporal comparison was also carried out with the previous pandemic waves (from March 2020 to October 2021). The epidemiological evolution over time in the dialysis population and in Romagna citizens replicated the global trend, as the peak of the fourth wave corresponded to the time of maximum diffusion of omicron variant (B.1.1.529). Of 771 prevalent dialysis patients at the beginning of the study, 109 (14.1%) contracted SARS-CoV-2 infection during the 4-month observation period. Vaccine adherence in the dialysis population of the reference area was above 95%. Compared to fully or partially vaccinated subjects, the unvaccinated ones showed a significantly higher proportion of infections (12.5% vs. 27.0% p = 0.0341), a more frequent need for hospitalization (22.2% vs. 50.0%) and a 3.3-fold increased mortality risk. These findings confirm the effectiveness of COVID-19 vaccines in keeping infectious risk under control and ameliorating clinical outcomes in immunocompromised patients.
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Affiliation(s)
- Giovanni Mosconi
- Nephrology and Dialysis Unit, AUSL Romagna Morgagni-Pierantoni Hospital, 47121 Forli, FC, Italy
- Correspondence: (G.M.); (F.C.); Tel.: +39-0543-735-312 (G.M.)
| | - Michela Fantini
- Local Healthcare Authority of Romagna (AUSL Romagna), 48121 Ravenna, RA, Italy
| | - Matteo Righini
- Nephrology and Dialysis Unit, AUSL Romagna S. Maria delle Croci Hospital, 48121 Ravenna, RA, Italy
| | - Marta Flachi
- Nephrology and Dialysis Unit, AUSL Romagna Infermi Hospital, 47923 Rimini, RN, Italy
| | - Simona Semprini
- Unit of Microbiology, AUSL Romagna Laboratory, 47023 Pievesestina, FC, Italy
| | - Lilio Hu
- Nephrology and Dialysis Unit, AUSL Romagna Morgagni-Pierantoni Hospital, 47121 Forli, FC, Italy
| | - Francesca Chiappo
- Nephrology and Dialysis Unit, AUSL Romagna Morgagni-Pierantoni Hospital, 47121 Forli, FC, Italy
- Correspondence: (G.M.); (F.C.); Tel.: +39-0543-735-312 (G.M.)
| | - Barbara Veterani
- Nephrology and Dialysis Unit, AUSL Romagna Morgagni-Pierantoni Hospital, 47121 Forli, FC, Italy
| | - Katia Ambri
- Nephrology and Dialysis Unit, AUSL Romagna Morgagni-Pierantoni Hospital, 47121 Forli, FC, Italy
| | - Franca Ferrini
- Nephrology and Dialysis Unit, AUSL Romagna Morgagni-Pierantoni Hospital, 47121 Forli, FC, Italy
| | - Catia Milanesi
- Nephrology and Dialysis Unit, AUSL Romagna Morgagni-Pierantoni Hospital, 47121 Forli, FC, Italy
| | - Antonio Giudicissi
- Nephrology and Dialysis Unit, AUSL Romagna Morgagni-Pierantoni Hospital, 47121 Forli, FC, Italy
| | - Gaetano La Manna
- Nephrology Dialysis and Renal Transplant Unit, IRCCS-Azienda Ospedaliero-Universitaria di Bologna, Alma Mater Studiorum University of Bologna, 40138 Bologna, BO, Italy
| | - Angelo Rigotti
- Nephrology and Dialysis Unit, AUSL Romagna Infermi Hospital, 47923 Rimini, RN, Italy
| | - Andrea Buscaroli
- Nephrology and Dialysis Unit, AUSL Romagna S. Maria delle Croci Hospital, 48121 Ravenna, RA, Italy
| | - Vittorio Sambri
- Unit of Microbiology, AUSL Romagna Laboratory, 47023 Pievesestina, FC, Italy
| | - Maria Cappuccilli
- Nephrology Dialysis and Renal Transplant Unit, IRCCS-Azienda Ospedaliero-Universitaria di Bologna, Alma Mater Studiorum University of Bologna, 40138 Bologna, BO, Italy
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Marble HD, Bard AZ, Mizrachi MM, Lennerz JK. Temporary Regulatory Deviations and the Coronavirus Disease 2019 (COVID-19) PCR Labeling Update Study Indicate What Laboratory-Developed Test Regulation by the US Food and Drug Administration (FDA) Could Look Like. J Mol Diagn 2021; 23:1207-1217. [PMID: 34538703 PMCID: PMC8444018 DOI: 10.1016/j.jmoldx.2021.07.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 06/20/2021] [Accepted: 07/01/2021] [Indexed: 12/23/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) response necessitated innovations and a series of regulatory deviations that also affected laboratory-developed tests (LDTs). To examine real-world consequences and specify regulatory paradigm shifts, legislative proposals were aligned on a common timeline with Emergency Use Authorization (EUA) of LDTs and the US Food and Drug Administration (FDA)-orchestrated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) labeling update study. The initial EUA adoption by LDT developers shows that the FDA can have oversight over LDTs. We used efficiency-corrected microcosting of our EUA PCR assay to estimate the national cost of the labeling update study to $0.3 to $1.4 million US dollars. Labeling update study performance data showed lower average detection limits in commercial in vitro diagnostic (IVD) assays versus LDTs (32,000 ± 75,000 versus 71,000 ± 147,000 nucleic acid amplification tests/mL; P = 0.04); however, comparison also shows that FDA review of IVD assays and LDTs did not prevent differences between initial and labeling update performance (IVD assay, P < 0.0001; LDT, P = 0.003). The regulatory shifts re-emphasized that both commercial tests and LDTs rely heavily on laboratory competence and procedures; however, lack of performance data on authorized tests, when clinically implemented, precludes assessment of the benefit related to regulatory review. Temporary regulatory deviations during the pandemic and regulatory science tools (ie, reference material) have generated valuable real-world evidence to inform pending legislation regarding LDT regulation.
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Affiliation(s)
- Hetal D Marble
- Center for Integrated Diagnostics, Department of Pathology, Massachusetts General Hospital/Harvard Medical School, Boston, Massachusetts
| | - Adam Z Bard
- Center for Integrated Diagnostics, Department of Pathology, Massachusetts General Hospital/Harvard Medical School, Boston, Massachusetts
| | - Mark M Mizrachi
- Center for Autoimmune Musculoskeletal and Hematopoietic Diseases, Institute of Molecular Medicine, The Feinstein Institutes for Medical Research, Manhasset, New York; Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, New York
| | - Jochen K Lennerz
- Center for Integrated Diagnostics, Department of Pathology, Massachusetts General Hospital/Harvard Medical School, Boston, Massachusetts.
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Dugdale CM, Anahtar MN, Chiosi JJ, Lazarus JE, McCluskey SM, Ciaranello AL, Gogakos T, Little BP, Branda JA, Shenoy ES, Walensky RP, Zachary KC, Hooper DC, Turbett SE, Hyle EP. Clinical, Laboratory, and Radiologic Characteristics of Patients With Initial False-Negative Severe Acute Respiratory Syndrome Coronavirus 2 Nucleic Acid Amplification Test Results. Open Forum Infect Dis 2021; 8:ofaa559. [PMID: 34164560 PMCID: PMC7717411 DOI: 10.1093/ofid/ofaa559] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 11/10/2020] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Concerns about false-negative (FN) severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleic acid amplification tests (NAATs) have prompted recommendations for repeat testing if suspicion for coronavirus disease 2019 (COVID-19) infection is moderate to high. However, the frequency of FNs and patient characteristics associated with FNs are poorly understood. METHODS We retrospectively reviewed test results from 15 011 adults who underwent ≥1 SARS-CoV-2 NAATs; 2699 had an initial negative NAAT and repeat testing. We defined FNs as ≥1 negative NAATs followed by a positive NAAT within 14 days during the same episode of illness. We stratified subjects with FNs by duration of symptoms before the initial FN test (≤5 days versus >5 days) and examined their clinical, radiologic, and laboratory characteristics. RESULTS Sixty of 2699 subjects (2.2%) had a FN result during the study period. The weekly frequency of FNs among subjects with repeat testing peaked at 4.4%, coinciding with peak NAAT positivity (38%). Most subjects with FNs had symptoms (52 of 60; 87%) and chest radiography (19 of 32; 59%) consistent with COVID-19. Of the FN NAATs, 18 of 60 (30%) were performed early (ie, ≤1 day of symptom onset), and 18 of 60 (30%) were performed late (ie, >7 days after symptom onset) in disease. Among 17 subjects with 2 consecutive FNs on NP NAATs, 9 (53%) provided lower respiratory tract (LRT) specimens for testing, all of which were positive. CONCLUSIONS Our findings support repeated NAATs among symptomatic patients, particularly during periods of higher COVID-19 incidence. The LRT testing should be prioritized to increase yield among patients with high clinical suspicion for COVID-19.
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Affiliation(s)
- Caitlin M Dugdale
- Medical Practice Evaluation Center, Department of Medicine, Massachusetts
General Hospital, Boston, Massachusetts, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General
Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Melis N Anahtar
- Department of Pathology, Massachusetts General Hospital, Boston,
Massachusetts, USA
| | - John J Chiosi
- Medical Practice Evaluation Center, Department of Medicine, Massachusetts
General Hospital, Boston, Massachusetts, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General
Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Jacob E Lazarus
- Division of Infectious Diseases, Department of Medicine, Massachusetts General
Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Suzanne M McCluskey
- Medical Practice Evaluation Center, Department of Medicine, Massachusetts
General Hospital, Boston, Massachusetts, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General
Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Andrea L Ciaranello
- Medical Practice Evaluation Center, Department of Medicine, Massachusetts
General Hospital, Boston, Massachusetts, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General
Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Tasos Gogakos
- Department of Pathology, Massachusetts General Hospital, Boston,
Massachusetts, USA
| | - Brent P Little
- Department of Radiology, Massachusetts General Hospital, Boston,
Massachusetts, USA
| | - John A Branda
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Pathology, Massachusetts General Hospital, Boston,
Massachusetts, USA
| | - Erica S Shenoy
- Division of Infectious Diseases, Department of Medicine, Massachusetts General
Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Infection Control Unit, Massachusetts General Hospital, Boston,
Massachusetts, USA
| | - Rochelle P Walensky
- Medical Practice Evaluation Center, Department of Medicine, Massachusetts
General Hospital, Boston, Massachusetts, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General
Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Kimon C Zachary
- Division of Infectious Diseases, Department of Medicine, Massachusetts General
Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Infection Control Unit, Massachusetts General Hospital, Boston,
Massachusetts, USA
| | - David C Hooper
- Division of Infectious Diseases, Department of Medicine, Massachusetts General
Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Infection Control Unit, Massachusetts General Hospital, Boston,
Massachusetts, USA
| | - Sarah E Turbett
- Division of Infectious Diseases, Department of Medicine, Massachusetts General
Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Pathology, Massachusetts General Hospital, Boston,
Massachusetts, USA
| | - Emily P Hyle
- Medical Practice Evaluation Center, Department of Medicine, Massachusetts
General Hospital, Boston, Massachusetts, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General
Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
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