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Article ; Online: The Impact of Patient Characteristics on Diagnostic Test Performance.

Kozlowski, Hannah N / Sindhwani, Shrey / Chan, Warren C W

Small methods

2022 Volume 6, Issue 2, Page(s) e2101233

Abstract: Diagnostic tests can detect diseases, monitor responses, and inform treatments. They are vital to the effective management of disease. There have been significant advances in the engineering of new diagnostic technologies. These technologies may forgo ... ...

Abstract	Diagnostic tests can detect diseases, monitor responses, and inform treatments. They are vital to the effective management of disease. There have been significant advances in the engineering of new diagnostic technologies. These technologies may forgo sample extraction, simplify readout, or automate processing. Many researchers design these diagnostics based on test performance in a limited sample subset. This approach ignores the intertwined relationship between patient characteristics and diagnostic test results. Yet, it is important to understand the clinical decision-making workflow and how the disease manifests in order to optimally design diagnostic tests. This review article explores the three aspects of incorporating patient characteristics to maximize diagnostic performance. 1) Characterize patient populations using patient demographics, disease prevalence, and other unique features. 2) Use the characteristics of the patient population to establish design requirements. 3) Determine the best use case since each case has different performance and target requirements. In this framework the clinical, technological, and unmet needs of a patient population shape the diagnostics design requirements. Following these steps will lead to maximal diagnostic performance and poise new diagnostics for real world use.
MeSH term(s)	Clinical Decision-Making ; Humans ; Molecular Diagnostic Techniques/methods ; Patient Selection ; Workflow
Language	English
Publishing date	2022-01-07
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ISSN	2366-9608
ISSN (online)	2366-9608
DOI	10.1002/smtd.202101233
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Genotyping SARS-CoV-2 Variants Using Ratiometric Nucleic Acid Barcode Panels.

Kozlowski, Hannah N / Malekjahani, Ayden / Li, Vanessa Y C / Lekuti, Ayokunle A / Perusini, Stephen / Bell, Natalie G / Voisin, Veronique / Pouyabahar, Delaram / Pai, Shraddha / Bader, Gary D / Mubareka, Samira / Gubbay, Jonathan B / Chan, Warren C W

Analytical chemistry

2023 Volume 95, Issue 14, Page(s) 5877–5885

Abstract: Designing diagnostic assays to genotype rapidly mutating viruses remains a challenge despite the overall improvements in nucleic acid detection technologies. RT-PCR and next-generation sequencing are unsuitable for genotyping during outbreaks or in point- ...

Abstract	Designing diagnostic assays to genotype rapidly mutating viruses remains a challenge despite the overall improvements in nucleic acid detection technologies. RT-PCR and next-generation sequencing are unsuitable for genotyping during outbreaks or in point-of-care detection due to their infrastructure requirements and longer turnaround times. We developed a quantum dot barcode multiplexing system to genotype mutated viruses. We designed multiple quantum dot barcodes to target conserved, wildtype, and mutated regions of SARS-CoV-2. We calculated ratios of the signal output from different barcodes that enabled SARS-CoV-2 detection and identified SARS-CoV-2 variant strains from a sample. We detected different sequence types, including conserved genes, nucleotide deletions, and single nucleotide substitutions. Our system detected SARS-CoV-2 patient specimens with 98% sensitivity and 94% specificity across 91 patient samples. Further, we leveraged our barcoding and ratio system to track the emergence of the N501Y SARS-CoV-2 mutation from December 2020 to May 2021 and demonstrated that the more transmissible N501Y mutation started to dominate infections by April 2021. Our barcoding and signal ratio approach can genotype viruses and track the emergence of viral mutations in a single diagnostic test. This technology can be extended to tracking other viruses. Combined with smartphone detection technologies, this assay can be adapted for point-of-care tracking of viral mutations in real time.
MeSH term(s)	Humans ; Nucleic Acids ; SARS-CoV-2/genetics ; COVID-19/diagnosis ; Genotype ; Nucleotides ; Mutation
Chemical Substances	Nucleic Acids ; Nucleotides
Language	English
Publishing date	2023-03-31
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.2c04630
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Article ; Online: Genotyping SARS-CoV‑2 Variants Using Ratiometric Nucleic Acid Barcode Panels

Kozlowski, Hannah N. / Malekjahani, Ayden / Li, Vanessa Y. C. / Lekuti, Ayokunle A. / Perusini, Stephen / Bell, Natalie G. / Voisin, Veronique / Pouyabahar, Delaram / Pai, Shraddha / Bader, Gary D. / Mubareka, Samira / Gubbay, Jonathan B. / Chan, Warren C. W.

Analytical Chemistry. 2023 Mar. 31, v. 95, no. 14 p.5877-5885

2023

Abstract	Designing diagnostic assays to genotype rapidly mutating viruses remains a challenge despite the overall improvements in nucleic acid detection technologies. RT-PCR and next-generation sequencing are unsuitable for genotyping during outbreaks or in point-of-care detection due to their infrastructure requirements and longer turnaround times. We developed a quantum dot barcode multiplexing system to genotype mutated viruses. We designed multiple quantum dot barcodes to target conserved, wildtype, and mutated regions of SARS-CoV-2. We calculated ratios of the signal output from different barcodes that enabled SARS-CoV-2 detection and identified SARS-CoV-2 variant strains from a sample. We detected different sequence types, including conserved genes, nucleotide deletions, and single nucleotide substitutions. Our system detected SARS-CoV-2 patient specimens with 98% sensitivity and 94% specificity across 91 patient samples. Further, we leveraged our barcoding and ratio system to track the emergence of the N501Y SARS-CoV-2 mutation from December 2020 to May 2021 and demonstrated that the more transmissible N501Y mutation started to dominate infections by April 2021. Our barcoding and signal ratio approach can genotype viruses and track the emergence of viral mutations in a single diagnostic test. This technology can be extended to tracking other viruses. Combined with smartphone detection technologies, this assay can be adapted for point-of-care tracking of viral mutations in real time.
Keywords	Severe acute respiratory syndrome coronavirus 2 ; analytical chemistry ; barcoding ; genotype ; genotyping ; infrastructure ; mobile telephones ; mutation ; nucleic acids ; patients ; point-of-care systems ; quantum dots
Language	English
Dates of publication	2023-0331
Size	p. 5877-5885.
Publishing place	American Chemical Society
Document type	Article ; Online
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.2c04630
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: A Colorimetric Test to Differentiate Patients Infected with Influenza from COVID-19.

Kozlowski, Hannah N / Abdou Mohamed, Mohamed A / Kim, Jisung / Bell, Natalie G / Zagorovsky, Kyryl / Mubareka, Samira / Chan, Warren C W

Small structures

2021 Volume 2, Issue 8, Page(s) 2100034

Abstract: Patients infected with SARS-CoV-2 and influenza display similar symptoms, but treatment requirements are different. Clinicians need to accurately distinguish SARS-CoV-2 from influenza to provide appropriate treatment. Here, the authors develope a color- ... ...

Abstract	Patients infected with SARS-CoV-2 and influenza display similar symptoms, but treatment requirements are different. Clinicians need to accurately distinguish SARS-CoV-2 from influenza to provide appropriate treatment. Here, the authors develope a color-based technique to differentiate between patients infected with SARS-CoV-2 and influenza A using a nucleic acid enzyme-gold nanoparticle (GNP) molecular test requiring minimal equipment. The MNAzyme and GNP probes are designed to be robust to viral mutations. Conserved regions of the viral genomes are targeted, and two MNAzymes are created for each virus. The ability of the system to distinguish between SARS-CoV-2 and influenza A using 79 patient samples is tested. When detecting SARS-CoV-2 positive patients, the clinical sensitivity is 90%, and the specificity is 100%. When detecting influenza A, the clinical sensitivity and specificity are 93% and 100%, respectively. The high clinical performance of the MNAzyme-GNP assay shows that it can be used to help clinicians choose effective treatments.
Language	English
Publishing date	2021-06-06
Publishing country	Germany
Document type	Journal Article
ISSN	2688-4062
ISSN (online)	2688-4062
DOI	10.1002/sstr.202100034
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Article ; Online: COVID-19: a pandemic experience that illuminates potential reforms to health research.

Kozlowski, Hannah N / Farkouh, Michael E / Irwin, Meredith S / Radvanyi, Laszlo G / Schimmer, Aaron D / Tabori, Uri / Rosenblum, Norman D

EMBO molecular medicine

2020 Volume 12, Issue 11, Page(s) e13278

Abstract: COVID-19 has halted research around the globe and forced researchers out of their laboratories. Non-emergency medical appointments were canceled. Ongoing clinical trials were challenged to create new modes of operation while public pressure mounted to ... ...

Abstract	COVID-19 has halted research around the globe and forced researchers out of their laboratories. Non-emergency medical appointments were canceled. Ongoing clinical trials were challenged to create new modes of operation while public pressure mounted to find therapeutic options against COVID-19. Yet, the inability to conduct research during COVID-19 was overcome with cooperation, resource sharing, and compassion, which provides important lessons on how to improve health related research as we enter a new normal.
MeSH term(s)	COVID-19/epidemiology ; COVID-19/pathology ; COVID-19/prevention & control ; COVID-19/virology ; Empathy ; Humans ; Information Dissemination ; Intersectoral Collaboration ; Pandemics ; Research ; SARS-CoV-2/isolation & purification
Keywords	covid19
Language	English
Publishing date	2020-10-19
Publishing country	England
Document type	Journal Article
ZDB-ID	2467145-9
ISSN	1757-4684 ; 1757-4676
ISSN (online)	1757-4684
ISSN	1757-4676
DOI	10.15252/emmm.202013278
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Article ; Online: COVID‐19

Hannah N Kozlowski / Michael E Farkouh / Meredith S Irwin / Laszlo G Radvanyi / Aaron D Schimmer / Uri Tabori / Norman D Rosenblum

EMBO Molecular Medicine, Vol 12, Iss 11, Pp n/a-n/a (2020)

a pandemic experience that illuminates potential reforms to health research

2020

Abstract: COVID‐19 has halted research around the globe and forced researchers out of their laboratories. Non‐emergency medical appointments were canceled. Ongoing clinical trials were challenged to create new modes of operation while public pressure mounted to ... ...

Abstract	COVID‐19 has halted research around the globe and forced researchers out of their laboratories. Non‐emergency medical appointments were canceled. Ongoing clinical trials were challenged to create new modes of operation while public pressure mounted to find therapeutic options against COVID‐19. Yet, the inability to conduct research during COVID‐19 was overcome with cooperation, resource sharing, and compassion, which provides important lessons on how to improve health related research as we enter a new normal.
Keywords	Medicine (General) ; R5-920 ; Genetics ; QH426-470
Language	English
Publishing date	2020-11-01T00:00:00Z
Publisher	Wiley
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Granuloma in the explanted lungs: Infectious causes and impact on post-lung transplant mycobacterial infection.

Kabbani, Dima / Kozlowski, Hannah N / Cervera, Carlos / Chaparro, Cecilia / Singer, Lianne / Rotstein, Coleman / Keshavjee, Shaf / Husain, Shahid

Transplant infectious disease : an official journal of the Transplantation Society

2020 Volume 22, Issue 3, Page(s) e13262

Abstract: Introduction: The significance of granuloma in explanted lungs of lung transplant recipients (LTR) on the development of post-transplant mycobacterial infection is unclear.: Methods: A retrospective review comparing LTRs and heart-lung transplant (H- ... ...

Abstract	Introduction: The significance of granuloma in explanted lungs of lung transplant recipients (LTR) on the development of post-transplant mycobacterial infection is unclear. Methods: A retrospective review comparing LTRs and heart-lung transplant (H-LTR) recipients with granuloma in the explanted lungs between 2000 and 2012 (excluding those LTRs with granuloma due to sarcoidosis) and LTRs or H-LTRs without granuloma. Patients were followed for 2 years post-transplant. Results: A total of 144 LTRs and 4 H-LTRs with granulomas (75 necrotizing and 73 non-necrotizing) and a comparator cohort of 144 LTRs and 4 H-LTRs without granuloma were analyzed. In LTRs with granulomas, identification of infectious organisms was more common by histopathology (35 AFB and 22 fungal) compared to cultures (six NTM and seven fungal) taken around time of the transplant. LTRs with granulomas were more likely to have pre-transplant non-tuberculous mycobacteria (NTM) infection compared to LTRs without granuloma; P < .01. In the multivariate analysis, having granuloma or positive mycobacterial cultures at time of transplant were associated with increased risk of post-transplant mycobacterial infection (HR = 1.8 95% CI [1.024-3.154]; P = .041 and HR = 2.083 95% CI [1.011-4.292]; P = .047). Although there was a trend toward increase mycobacterial disease in those with granulomas P = .056, there was no difference in survival post-transplantation between those with or without granuloma in the explanted lung; P = .886. Conclusion: The presence of granuloma in the explanted lungs of LTRs or positive mycobacterial cultures at time of transplant is associated with an increased risk of mycobacterial infection post-transplant.
MeSH term(s)	Female ; Granuloma/complications ; Granuloma/microbiology ; Heart-Lung Transplantation/adverse effects ; Humans ; Lung Diseases/microbiology ; Lung Transplantation/adverse effects ; Male ; Middle Aged ; Mycobacterium/isolation & purification ; Mycobacterium Infections, Nontuberculous/etiology ; Postoperative Complications/etiology ; Retrospective Studies ; Risk Factors
Language	English
Publishing date	2020-02-26
Publishing country	Denmark
Document type	Comparative Study ; Journal Article
ZDB-ID	1476094-0
ISSN	1399-3062 ; 1398-2273
ISSN (online)	1399-3062
ISSN	1398-2273
DOI	10.1111/tid.13262
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Article ; Online: Diagnosing Antibiotic Resistance Using Nucleic Acid Enzymes and Gold Nanoparticles.

Abdou Mohamed, Mohamed A / Kozlowski, Hannah N / Kim, Jisung / Zagorovsky, Kyryl / Kantor, Melinda / Feld, Jordan J / Mubareka, Samira / Mazzulli, Tony / Chan, Warren C W

ACS nano

2021 Volume 15, Issue 6, Page(s) 9379–9390

Abstract: The rapid and accurate detection of antimicrobial resistance is critical to limiting the spread of infections and delivering effective treatments. Here, we developed a rapid, sensitive, and simple colorimetric nanodiagnostic platform to identify disease- ... ...

Abstract	The rapid and accurate detection of antimicrobial resistance is critical to limiting the spread of infections and delivering effective treatments. Here, we developed a rapid, sensitive, and simple colorimetric nanodiagnostic platform to identify disease-causing pathogens and their associated antibiotic resistance genes within 2 h. The platform can detect bacteria from different biological samples (
MeSH term(s)	Anti-Bacterial Agents/pharmacology ; Anti-Bacterial Agents/therapeutic use ; Drug Resistance, Microbial ; Gold ; Humans ; Metal Nanoparticles ; Methicillin-Resistant Staphylococcus aureus/genetics ; Microbial Sensitivity Tests ; Nucleic Acids ; Staphylococcal Infections/drug therapy
Chemical Substances	Anti-Bacterial Agents ; Nucleic Acids ; Gold (7440-57-5)
Language	English
Publishing date	2021-05-10
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1936-086X
ISSN (online)	1936-086X
DOI	10.1021/acsnano.0c09902
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Diagnosing COVID-19: The Disease and Tools for Detection.

Udugama, Buddhisha / Kadhiresan, Pranav / Kozlowski, Hannah N / Malekjahani, Ayden / Osborne, Matthew / Li, Vanessa Y C / Chen, Hongmin / Mubareka, Samira / Gubbay, Jonathan B / Chan, Warren C W

ACS nano

2020 Volume 14, Issue 4, Page(s) 3822–3835

Abstract: COVID-19 has spread globally since its discovery in Hubei province, China in December 2019. A combination of computed tomography imaging, whole genome sequencing, and electron microscopy were initially used to screen and identify SARS-CoV-2, the viral ... ...

Abstract	COVID-19 has spread globally since its discovery in Hubei province, China in December 2019. A combination of computed tomography imaging, whole genome sequencing, and electron microscopy were initially used to screen and identify SARS-CoV-2, the viral etiology of COVID-19. The aim of this review article is to inform the audience of diagnostic and surveillance technologies for SARS-CoV-2 and their performance characteristics. We describe point-of-care diagnostics that are on the horizon and encourage academics to advance their technologies beyond conception. Developing plug-and-play diagnostics to manage the SARS-CoV-2 outbreak would be useful in preventing future epidemics.
MeSH term(s)	Betacoronavirus/pathogenicity ; COVID-19 ; COVID-19 Testing ; Clinical Laboratory Techniques ; Coronavirus Infections/diagnosis ; Humans ; Mobile Applications ; Nucleic Acid Amplification Techniques ; Pandemics ; Pneumonia, Viral/diagnosis ; Point-of-Care Testing ; Population Surveillance ; Real-Time Polymerase Chain Reaction ; SARS-CoV-2 ; Smartphone ; Tomography, X-Ray Computed ; Viral Proteins/analysis
Chemical Substances	Viral Proteins
Keywords	covid19
Language	English
Publishing date	2020-03-30
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ISSN	1936-086X
ISSN (online)	1936-086X
DOI	10.1021/acsnano.0c02624
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: COVID-19: a pandemic experience that illuminates potential reforms to health research

Kozlowski, Hannah N / Farkouh, Michael E / Irwin, Meredith S / Radvanyi, Laszlo G / Schimmer, Aaron D / Tabori, Uri / Rosenblum, Norman D

EMBO Mol Med

Abstract	COVID-19 has halted research around the globe and forced researchers out of their laboratories. Non-emergency medical appointments were canceled. Ongoing clinical trials were challenged to create new modes of operation while public pressure mounted to find therapeutic options against COVID-19. Yet, the inability to conduct research during COVID-19 was overcome with cooperation, resource sharing, and compassion, which provides important lessons on how to improve health related research as we enter a new normal.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #805239
Database	COVID19

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