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Bachmann TT, Mitsakakis K, Hays JP, van Belkum A, Russom A, Luedke G, Simonsen GS, Abel G, Peter H, Goossens H, Moran-Gilad J, Vila J, Becker K, Moons P, Sampath R, Peeling RW, Luz S, van Staa T, Di Gregori V. Expert guidance on target product profile development for AMR diagnostic tests. BMJ Glob Health 2023; 8:e012319. [PMID: 38114235 DOI: 10.1136/bmjgh-2023-012319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 11/10/2023] [Indexed: 12/21/2023] Open
Abstract
Diagnostics are widely considered crucial in the fight against antimicrobial resistance (AMR), which is expected to kill 10 million people annually by 2030. Nevertheless, there remains a substantial gap between the need for AMR diagnostics versus their development and implementation. To help address this problem, target product profiles (TPP) have been developed to focus developers' attention on the key aspects of AMR diagnostic tests. However, during discussion between a multisectoral working group of 51 international experts from industry, academia and healthcare, it was noted that specific AMR-related TPPs could be extended by incorporating the interdependencies between the key characteristics associated with the development of such TPPs. Subsequently, the working group identified 46 characteristics associated with six main categories (ie, Intended Use, Diagnostic Question, Test Description, Assay Protocol, Performance and Commercial). The interdependencies of these characteristics were then identified and mapped against each other to generate new insights for use by stakeholders. Specifically, it may not be possible for diagnostics developers to achieve all of the recommendations in every category of a TPP and this publication indicates how prioritising specific TPP characteristics during diagnostics development may influence (or not) a range of other TPP characteristics associated with the diagnostic. The use of such guidance, in conjunction with specific TPPs, could lead to more efficient AMR diagnostics development.
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Affiliation(s)
- Till T Bachmann
- Center for Inflammation Research, University of Edinburgh, Edinburgh, UK
| | - Konstantinos Mitsakakis
- Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Freiburg, Germany
- Hahn-Schickard, Freiburg, Germany
| | - John P Hays
- Department of Medical Microbiology & Infectious Diseases, Erasmus University Medical Centre (Erasmus MC), Rotterdam, Netherlands
| | - Alex van Belkum
- BioMérieux Open Innovation & Partnerships, La Balme Les Grottes, France
| | - Aman Russom
- Division of Nanobiotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
| | | | - Gunnar Skov Simonsen
- Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
- Faculty of Health Sciences, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Gyorgy Abel
- Division of Pathology and Laboratory Medicine, Lahey Hospital & Medical Center, Burlington, Massachusetts, USA
- Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
| | - Harald Peter
- Branch Bioanalytics and Bioprocesses, Fraunhofer Institute for Cell Therapy and Immunology, Potsdam, Germany
| | - Herman Goossens
- Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
- Department of Medical Microbiology, Antwerp University Hospital, Antwerp, Belgium
| | - Jacob Moran-Gilad
- Department of Health Policy and Management, School of Public Health, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Jordi Vila
- Department of Clinical Microbiology, Biomedical Diagnostic Centre (CDB), Hospital Clínic, School of Medicine, University of Barcelona, Barcelona, Spain
| | | | - Pieter Moons
- Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
- Department of Medical Microbiology, Antwerp University Hospital, Antwerp, Belgium
| | | | - Rosanna W Peeling
- Department of Clinical Research, London School of Hygiene and Tropical Medicine Faculty of Infectious and Tropical Diseases, London, UK
| | - Saturnino Luz
- Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Tjeerd van Staa
- Health eResearch Centre, Farr Institute for Health Informatics Research, University of Manchester, Manchester, UK
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Abstract
BACKGROUND Self-management is an important pillar for diabetes control and to achieve it, glucose self-monitoring devices are needed. Currently, there exist several different devices in the market and many others are being developed. However, whether these devices are suitable to be used in resource constrained settings is yet to be evaluated. AIMS To assess existing glucose monitoring tools and also those in development against the REASSURED which have been previously used to evaluate diagnostic tools for communicable diseases. METHODS We conducted a scoping review by searching PubMed for peer-review articles published in either English, Spanish or Portuguese in the last 5 years. We selected papers including information about devices used for self-monitoring and tested on humans with diabetes; then, the REASSURED criteria were used to assess them. RESULTS We found a total of 7 continuous glucose monitoring device groups, 6 non-continuous, and 6 devices in development. Accuracy varied between devices and most of them were either invasive or minimally invasive. Little to no evidence is published around robustness, affordability and delivery to those in need. However, when reviewing publicly available prices, none of the devices would be affordable for people living in low- and middle-income countries. CONCLUSIONS Available devices cannot be considered adapted for use in self-monitoring in resource constraints settings. Further studies should aim to develop less-invasive devices that do not require a large set of components. Additionally, we suggest some improvement in the REASSURED criteria such as the inclusion of patient-important outcomes to increase its appropriateness to assess non-communicable diseases devices.
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Affiliation(s)
- Jessica Hanae Zafra-Tanaka
- CRONICAS Centre of Excellence in
Chronic Diseases, Universidad Peruana Cayetano Heredia, Lima, Peru
- Jessica Hanae Zafra-Tanaka, MD, MSc,
CRONICAS Center of Excellence for Chronic Diseases, Universidad
Peruana Cayetano Heredia, Av. Armendáriz 497, Miraflores, Lima 18,
Perú.
| | - David Beran
- Division of Tropical and
Humanitarian Medicine, University of Geneva and Geneva University Hospitals,
Geneva, Switzerland
| | - Beatrice Vetter
- Foundation for Innovative New
Diagnostics, Geneva, Switzerland
| | | | - Antonio Bernabe-Ortiz
- CRONICAS Centre of Excellence in
Chronic Diseases, Universidad Peruana Cayetano Heredia, Lima, Peru
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Vidula H, McNitt S, Dennison C, Sampath R, Bjelic M, Sziveri Z, Alexis J, Gosev I, Caufield L, Goldenberg I. Safety and Efficacy of Home-Based Exercise Rehabilitation Using Remote Monitoring in New Left Ventricular Assist Device Recipients. J Heart Lung Transplant 2022. [DOI: 10.1016/j.healun.2022.01.151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Vetter B, Beran D, Boulle P, Chua A, de la Tour R, Hattingh L, Perel P, Roglic G, Sampath R, Woodman M, Perone SA. Development of a target product profile for a point-of-care cardiometabolic device. BMC Cardiovasc Disord 2021; 21:486. [PMID: 34627153 PMCID: PMC8501932 DOI: 10.1186/s12872-021-02298-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 09/30/2021] [Indexed: 11/26/2022] Open
Abstract
Introduction Multi-parameter diagnostic devices can simplify cardiometabolic disease diagnosis. However, existing devices may not be suitable for use in low-resource settings, where the burden of non-communicable diseases is high. Here we describe the development of a target product profile (TPP) for a point-of-care multi-parameter device for detection of biomarkers for cardiovascular disease and metabolic disorders, including diabetes, in primary care settings in low- and middle-income countries (LMICs). Methods A draft TPP developed by an expert group was reviewed through an online survey and semi-structured expert interviews to identify device characteristics requiring refinement. The draft TPP included 41 characteristics with minimal and optimal requirements; characteristics with an agreement level for either requirement of ≤ 85% in either the survey or among interviewees were further discussed by the expert group and amended as appropriate. Results Twenty people responded to the online survey and 18 experts participated in the interviews. Twenty-two characteristics had an agreement level of ≤ 85% in either the online survey or interviews. The final TPP defines the device as intended to be used for basic diagnosis and management of cardiometabolic disorders (lipids, glucose, HbA1c, and creatinine) as minimal requirement, and offering an expanded test menu for wider cardiometabolic disease management as optimal requirement. To be suitable, the device should be intended for level 1 healthcare settings or lower, used by minimally trained healthcare workers and allow testing using self-contained cartridges or strips without the need for additional reagents. Throughput should be one sample at a time in a single or multi-analyte cartridge, or optimally enable testing of several samples and analytes in parallel with random access. Conclusion This TPP will inform developers of cardiometabolic multi-parameter devices for LMIC settings, and will support decision makers in the evaluation of existing and future devices. Supplementary Information The online version contains supplementary material available at 10.1186/s12872-021-02298-7.
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Affiliation(s)
| | - David Beran
- Division of Tropical and Humanitarian Medicine, University of Geneva and Geneva University Hospitals (UNIGE/HUG), Geneva, Switzerland
| | | | - Arlene Chua
- Médecins Sans Frontières (MSF), Geneva, Switzerland
| | | | | | - Pablo Perel
- Centre for Global Chronic Conditions, London School of Hygiene and Tropical Medicine (LSHTM), London, UK
| | - Gojka Roglic
- Department for Noncommunicable Diseases, World Health Organization (WHO), Geneva, Switzerland
| | | | - Michael Woodman
- United Nations High Commissioner for Refugees (UNHCR), Geneva, Switzerland
| | - Sigiriya Aebischer Perone
- Division of Tropical and Humanitarian Medicine, University of Geneva and Geneva University Hospitals (UNIGE/HUG), Geneva, Switzerland.,International Committee of the Red Cross (ICRC), Geneva, Switzerland
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McGuire M, de Waal A, Karellis A, Janssen R, Engel N, Sampath R, Carmona S, Zwerling AA, Suarez MF, Pai NP. HIV self-testing with digital supports as the new paradigm: A systematic review of global evidence (2010-2021). EClinicalMedicine 2021; 39:101059. [PMID: 34430835 PMCID: PMC8367787 DOI: 10.1016/j.eclinm.2021.101059] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 07/06/2021] [Accepted: 07/15/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND HIV self-testing (HIVST) is recommended by the WHO as an innovative strategy to reach UNAIDS targets to end HIV by 2030. HIVST with digital supports is defined as the use of digital interventions (e.g., website-based, social media, mobile HIVST applications (apps), text messaging (SMS), digital vending machines (digital VMs)) to improve the efficiency and impact of HIVST. HIVST deployment and integration in health services is an emerging priority. We conducted a systematic review aiming to close the gap in evidence that summarizes the impact of digitally supported HIVST and to inform policy recommendations. METHODS We searched PubMed and Embase for articles and abstracts on HIVST with digital supports published during the period February 1st, 2010 to June 15th, 2021, following Cochrane guidelines and PRISMA methodology. We assessed feasibility, acceptability, preference, and impact outcomes across all populations and study designs. Metrics reported were willingness to use HIVST, preferences for HIVST delivery, proportion of first-time testers, HIVST uptake, HIVST kit return rate, and linkage to care. Heterogeneity of the interventions and reported metrics precluded us from conducting a meta-analysis. FINDINGS 46 studies were narratively synthesized, of which 72% were observational and 28% were RCTs. Half of all studies (54%, 25/46) assessed web-based innovations (e.g., study websites, videos, chatbots), followed by social media (26%, 12/46), HIVST-specific apps (7%, 3/46), SMS (9%, 4/46), and digital VMs (4%, 2/46). Web-based innovations were found to be acceptable (77-97%), preferred over in-person and hybrid options by more first-time testers (47-48%), highly feasible (93-95%), and were overall effective in supporting linkage to care (53-100%). Social media and app-based innovations also had high acceptability (87-95%) and linkage to care proportions (80-100%). SMS innovations increased kit return rates (54-94%) and HIVST uptake among hard-to-reach groups. Finally, digital VMs were highly acceptable (54-93%), and HIVST uptake was six times greater when using digital VMs compared to distribution by community workers. INTERPRETATION HIVST with digital supports was deemed feasible, acceptable, preferable, and was shown to increase uptake, engage first-time testers and hard-to-reach populations, and successfully link participants to treatment. Findings pave the way for greater use of HIVST interventions with digital supports globally.
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Affiliation(s)
- Madison McGuire
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, 1020 Pine Ave W, Montreal, QC H3A 1A2, Canada
- The Research Institute of the McGill University Health Centre, 1001 Decarie Blvd, 5252 blvd de Maisonneuve W., Montreal, QC H4A 3J1, Canada
| | - Anna de Waal
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, 1020 Pine Ave W, Montreal, QC H3A 1A2, Canada
- The Research Institute of the McGill University Health Centre, 1001 Decarie Blvd, 5252 blvd de Maisonneuve W., Montreal, QC H4A 3J1, Canada
| | - Angela Karellis
- The Research Institute of the McGill University Health Centre, 1001 Decarie Blvd, 5252 blvd de Maisonneuve W., Montreal, QC H4A 3J1, Canada
- Department of Medicine, McGill University, 3605 rue de la Montagne, Montréal, QC H3G 2M1, Canada
| | - Ricky Janssen
- Department of Health, Ethics and Society, Maastricht University, Postbus 616 6200 MD, Maastricht, the Netherland
| | - Nora Engel
- Department of Health, Ethics and Society, Maastricht University, Postbus 616 6200 MD, Maastricht, the Netherland
| | - Rangarajan Sampath
- Foundation for Innovative New Diagnostics, Chemin des Mines 9, Geneva 1202, Switzerland
| | - Sergio Carmona
- Foundation for Innovative New Diagnostics, Chemin des Mines 9, Geneva 1202, Switzerland
| | - Alice Anne Zwerling
- School of Epidemiology and Public Health, University of Ottawa, 600 Peter Morand Crescent, Ottawa, ON K1G 5Z, Canada
| | | | - Nitika Pant Pai
- The Research Institute of the McGill University Health Centre, 1001 Decarie Blvd, 5252 blvd de Maisonneuve W., Montreal, QC H4A 3J1, Canada
- Department of Medicine, McGill University, 3605 rue de la Montagne, Montréal, QC H3G 2M1, Canada
- Corresponding author at: The Research Institute of the McGill University Health Centre, 1001 Decarie Blvd, 5252 blvd de Maisonneuve W., Montreal, QC H4A 3J1, Canada.
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Staunton C, Hannay E, John O, Johnson M, Kadam R, Sampath R. The governance of personal data for COVID-19 response: perspective from the Access to COVID-19 Tools Accelerator. BMJ Glob Health 2021; 6:e006095. [PMID: 34059495 PMCID: PMC8169217 DOI: 10.1136/bmjgh-2021-006095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 05/14/2021] [Indexed: 11/03/2022] Open
Affiliation(s)
- Ciara Staunton
- Institute for Biomedicine, EURAC Research, Bolzano, Italy
- School of Law, Middlesex University, London, UK
| | | | - Oomen John
- George Institute for Global Health, UNSW, New Delhi, Delhi, India
- Prasanna School of Public Health, Manipal Academy of Higher Education, Manipal, India
| | - Michael Johnson
- The Global Fund to Fight AIDS Tuberculosis and Malaria, Grand-Saconnex, Genève, Switzerland
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Bernabé-Ortiz A, Zafra-Tanaka JH, Moscoso-Porras M, Sampath R, Vetter B, Miranda JJ, Beran D. Diagnostics and monitoring tools for noncommunicable diseases: a missing component in the global response. Global Health 2021; 17:26. [PMID: 33750391 PMCID: PMC7941936 DOI: 10.1186/s12992-021-00676-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 02/25/2021] [Indexed: 11/15/2022] Open
Abstract
A key component of any health system is the capacity to accurately diagnose individuals. One of the six building blocks of a health system as defined by the World Health Organization (WHO) includes diagnostic tools. The WHO’s Noncommunicable Disease Global Action Plan includes addressing the lack of diagnostics for noncommunicable diseases, through multi-stakeholder collaborations to develop new technologies that are affordable, safe, effective and quality controlled, and improving laboratory and diagnostic capacity and human resources. Many challenges exist beyond price and availability for the current tools included in the Package of Essential Noncommunicable Disease Interventions (PEN) for cardiovascular disease, diabetes and chronic respiratory diseases. These include temperature stability, adaptability to various settings (e.g. at high altitude), need for training in order to perform and interpret the test, the need for maintenance and calibration, and for Blood Glucose Meters non-compatible meters and test strips. To date the issues surrounding access to diagnostic and monitoring tools for noncommunicable diseases have not been addressed in much detail. The aim of this Commentary is to present the current landscape and challenges with regards to guidance from the WHO on diagnostic tools using the WHO REASSURED criteria, which define a set of key characteristics for diagnostic tests and tools. These criteria have been used for communicable diseases, but so far have not been used for noncommunicable diseases. Diagnostic tools have played an important role in addressing many communicable diseases, such as HIV, TB and neglected tropical diseases. Clearly more attention with regards to diagnostics for noncommunicable diseases as a key component of the health system is needed.
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Affiliation(s)
- Antonio Bernabé-Ortiz
- CRONICAS Centre of Excellence in Chronic Diseases, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Jessica H Zafra-Tanaka
- CRONICAS Centre of Excellence in Chronic Diseases, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Miguel Moscoso-Porras
- CRONICAS Centre of Excellence in Chronic Diseases, Universidad Peruana Cayetano Heredia, Lima, Peru.,School of Medicine "Alberto Hurtado", Universidad Peruana Cayetano Heredia, Lima, Peru
| | | | - Beatrice Vetter
- Foundation for Innovative and New Diagnostics, Geneva, Switzerland
| | - J Jaime Miranda
- CRONICAS Centre of Excellence in Chronic Diseases, Universidad Peruana Cayetano Heredia, Lima, Peru.,The George Institute for Global Health, UNSW, Sydney, Australia
| | - David Beran
- Division of Tropical and Humanitarian Medicine, University of Geneva and Geneva University Hospitals, Geneva, Switzerland.
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Boehme C, Hannay E, Sampath R. SARS-CoV-2 testing for public health use: core principles and considerations for defined use settings. Lancet Glob Health 2021; 9:e247-e249. [PMID: 33516282 PMCID: PMC7906635 DOI: 10.1016/s2214-109x(21)00006-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 01/04/2021] [Indexed: 12/12/2022]
Affiliation(s)
- Catharina Boehme
- Foundation for Innovative New Diagnostics (FIND), Geneva 1202, Switzerland
| | - Emma Hannay
- Foundation for Innovative New Diagnostics (FIND), Geneva 1202, Switzerland.
| | - Rangarajan Sampath
- Foundation for Innovative New Diagnostics (FIND), Geneva 1202, Switzerland
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9
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Pellé KG, Rambaud-Althaus C, D'Acremont V, Moran G, Sampath R, Katz Z, Moussy FG, Mehl GL, Dittrich S. Electronic clinical decision support algorithms incorporating point-of-care diagnostic tests in low-resource settings: a target product profile. BMJ Glob Health 2020; 5:e002067. [PMID: 32181003 PMCID: PMC7050342 DOI: 10.1136/bmjgh-2019-002067] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 12/17/2019] [Accepted: 01/27/2020] [Indexed: 11/29/2022] Open
Abstract
Health workers in low-resource settings often lack the support and tools to follow evidence-based clinical recommendations for diagnosing, treating and managing sick patients. Digital technologies, by combining patient health information and point-of-care diagnostics with evidence-based clinical protocols, can help improve the quality of care and the rational use of resources, and save patient lives. A growing number of electronic clinical decision support algorithms (CDSAs) on mobile devices are being developed and piloted without evidence of safety or impact. Here, we present a target product profile (TPP) for CDSAs aimed at guiding preventive or curative consultations in low-resource settings. This document will help align developer and implementer processes and product specifications with the needs of end users, in terms of quality, safety, performance and operational functionality. To identify the characteristics of CDSAs, a multidisciplinary group of experts (academia, industry and policy makers) with expertise in diagnostic and CDSA development and implementation in low-income and middle-income countries were convened to discuss a draft TPP. The TPP was finalised through a Delphi process to facilitate consensus building. An agreement greater than 75% was reached for all 40 TPP characteristics. In general, experts were in overwhelming agreement that, given that CDSAs provide patient management recommendations, the underlying clinical algorithms should be human-interpretable and evidence-based. Whenever possible, the algorithm’s patient management output should take into account pretest disease probabilities and likelihood ratios of clinical and diagnostic predictors. In addition, validation processes should at a minimum show that CDSAs are implementing faithfully the evidence they are based on, and ideally the impact on patient health outcomes. In terms of operational needs, CDSAs should be designed to fit within clinic workflows and function in connectivity-challenged and high-volume settings. Data collected through the tool should conform to local patient privacy regulations and international data standards.
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Affiliation(s)
- Karell G Pellé
- Foundation for Innovative New Diagnostics (FIND), Geneva, Switzerland
| | | | - Valérie D'Acremont
- Swiss Tropical and Public Health Institute, University of Basel, Basel, Switzerland
| | - Gretchen Moran
- Clinical and Laboratory Informatics, eHealth Africa, Kano, Nigeria
| | | | - Zachary Katz
- Foundation for Innovative New Diagnostics (FIND), Geneva, Switzerland
| | - Francis G Moussy
- Department of Essential Medicines and Health Products, World Health Organization, Geneva, Switzerland
| | - Garrett Livingston Mehl
- Department of Reproductive Health and Research, World Health Organization, Geneva, Switzerland
| | - Sabine Dittrich
- Foundation for Innovative New Diagnostics (FIND), Geneva, Switzerland
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Sampath R, Indumathi J. Automated computer aided system for early diagnosis of Alzheimer's disease by regional atrophy analysis in functional magnetic resonance imaging. IJBET 2020. [DOI: 10.1504/ijbet.2020.107205] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Abstract
According to the recent study, world-wide 40 million patients are affected by Alzheimer disease (AD) because it is one of the dangerous neurodegenerative disorders. This AD disease has less symptoms such as short term memory loss, mood swings, problem with language understanding and behavioral issues. Due to these low symptoms, AD disease is difficult to recognize in the early stage. So, the automated computer aided system need to be developed for recognizing the AD disease for minimizing the mortality rate. Initially, brain MRI image is collected from patients which are processed by applying different processing steps such as noise removal, segmentation, feature extraction, feature selection and classification. The captured MRI image has noise that is eliminated by applying the Lucy-Richardson approach which examines the each pixel in the image and removes the Gaussian noise which also eliminates the blur image. After eliminating the noise pixel from the image, affected region is segmented by Prolong adaptive exclusive analytical Atlas approach. From the segmented region, different GLCM statistical features are extracted and optimal features subset is selected by applying the hybrid wrapper filtering approach. This selected features are analyzed by N-fold cross validation approach which recognizes the AD related features successfully. Then the efficiency of the system is evaluated with the help of MATLAB based experimental results, in which Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset images are utilized for examining the efficiency in terms of sensitivity, specificity, ROC curve and accuracy.
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Affiliation(s)
| | - J Indumathi
- Department of Information Science and Technology, College of Engineering, Guindy, Anna University, Chennai, India
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Abstract
Tenofovir alafenamide fumarate is a recently developed prodrug of tenofovir, a nucleotide analogue reverse transcriptase inhibitor with potent inhibitory activity against HIV. The utility of a previously developed tenofovir prodrug, tenofovir disoproxil fumarate, had been hampered by renal and bone mineral adverse events. Tenofovir alafenamide fumarate overcomes the shortcomings of tenofovir disoproxil fumarate by delivering high intracellular concentrations of the parent drug, tenofovir, while substantially reducing systemic exposure. Tenofovir alafenamide fumarate is currently available as a component of three fixed-dose products: i) coformulation with emtricitabine; ii) coformulation with elvitegravir, cobicistat and emtricitabine; and iii) coformulation with rilpivirine and emtricitabine.
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Affiliation(s)
- R Sampath
- Division of Infectious Diseases, Mayo Clinic, Rochester, Minnesota, USA
| | - J Zeuli
- Department of Pharmacy, Mayo Clinic, Rochester, Minnesota, USA
| | - S Rizza
- Division of Infectious Diseases, Mayo Clinic, Rochester, Minnesota, USA
| | - Z Temesgen
- Division of Infectious Diseases, Mayo Clinic, Rochester, Minnesota, USA.
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Farrell JJ, Wang H, Sampath R, Lowery KS, Bonomo RA. The effect of empiric antimicrobial treatment duration on detection of bacterial DNA in sterile surgical specimens. PLoS One 2017; 12:e0171074. [PMID: 28170436 PMCID: PMC5295705 DOI: 10.1371/journal.pone.0171074] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 01/15/2017] [Indexed: 11/18/2022] Open
Abstract
Initial antimicrobial treatment of patients with deep seated or invasive infections is typically empiric. Usually, cultures of specimens obtained from the suspected source of infection are performed to identify pathogens and guide continued antimicrobial treatment. When patients present with signs and symptoms of infection, but sterile body fluid or tissue specimens cannot be obtained in a timely fashion, growth of bacterial pathogens in culture may be inhibited following initiation of empiric antibiotic treatment. To address this clinical dilemma, we performed a prospective evaluation of conventional culture vs. PCR coupled to electrospray ionization mass spectrometry (PCR/ESI-MS) on sterile body fluids and tissues submitted to the diagnostic microbiology lab following initiation of empiric antibiotic treatment for patients with suspected infection. In this series of surgical samples, PCR/ESI-MS identified bacterial pathogen(s) in 56% (49/87) of patients with non-diagnostic cultures. Examination of patients stratified by antibiotic treatment duration demonstrated that PCR/ESI-MS sustains high rates of bacterial DNA detection over time by generalized estimating equation models (p<0.0001).
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Affiliation(s)
- John Joseph Farrell
- Department of Medicine, University of Illinois College of Medicine, Peoria, Illinois, United States of America
- Department of Laboratory Medicine, Division of Clinical Microbiology & Serology, OSF System Lab, Peoria, Illinois, United States of America
| | - Huaping Wang
- Department of Medicine, University of Illinois College of Medicine, Peoria, Illinois, United States of America
| | - Rangarajan Sampath
- Ibis Biosciences, an Abbott Company, Carlsbad, California, United States of America
| | - Kristin S. Lowery
- Ibis Biosciences, an Abbott Company, Carlsbad, California, United States of America
| | - Robert A. Bonomo
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, United States of America
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio, United States of America
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio, United States of America
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, Ohio, United States of America
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Evans S, Tran TTT, Hujer A, Hill C, Hujer KM, Mediavilla JR, Manca C, Domitrovic TN, Kreiswirth BN, Patel R, Jacobs MR, Perez F, Chen L, Sampath R, Hall T, Marzan C, Fowler V, Chambers H, Bonomo RA. Choosing Ceftazidime/Avibactam and Ceftolozane/Tazobactam as Empiric Therapies against Pseudomonas aeruginosa (Pa) using Rapid Molecular Diagnostics (RMDs): PRIMERS IV. Open Forum Infect Dis 2016. [DOI: 10.1093/ofid/ofw172.1598] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Scott Evans
- Department of Biostatistics and the Center for Biostatistics in AIDS Research, Harvard School of Public Health, Boston, Massachusetts
- Department of Biostatistics and the Center for Biostatistics in AIDS Research, Harvard School of Public Health, Boston, Massachusetts
| | - Thuy Tien T. Tran
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Department of Biostatistics and the Center for Biostatistics in AIDS Research, Harvard School of Public Health, Boston, Massachusetts
| | - Andrea Hujer
- Case Western Reserve University, Cleveland, Ohio
- Department of Biostatistics and the Center for Biostatistics in AIDS Research, Harvard School of Public Health, Boston, Massachusetts
| | - Carol Hill
- Duke Clinical Research Institute, Durham, North Carolina
- Department of Biostatistics and the Center for Biostatistics in AIDS Research, Harvard School of Public Health, Boston, Massachusetts
| | - Kristine M. Hujer
- Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio
- Department of Biostatistics and the Center for Biostatistics in AIDS Research, Harvard School of Public Health, Boston, Massachusetts
| | - Jose R. Mediavilla
- Public Health Research Institute, Rutgers University, Newark, New Jersey
- Department of Biostatistics and the Center for Biostatistics in AIDS Research, Harvard School of Public Health, Boston, Massachusetts
| | - Claudia Manca
- Public Health Research Institute - Rutgers University, Newark, New Jersey
- Department of Biostatistics and the Center for Biostatistics in AIDS Research, Harvard School of Public Health, Boston, Massachusetts
| | - T. Nicholas Domitrovic
- Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio
- Department of Biostatistics and the Center for Biostatistics in AIDS Research, Harvard School of Public Health, Boston, Massachusetts
| | - Barry N. Kreiswirth
- Public Health Research Institute Tuberculosis Center, Rutgers University, Newark, New Jersey
- Department of Biostatistics and the Center for Biostatistics in AIDS Research, Harvard School of Public Health, Boston, Massachusetts
| | - Robin Patel
- Divisions of Clinical Microbiology and Infectious Diseases, Mayo Clinic, Rochester, Minnesota
- Department of Biostatistics and the Center for Biostatistics in AIDS Research, Harvard School of Public Health, Boston, Massachusetts
| | - Michael R. Jacobs
- Case Western Reserve University/University Hospitals of Cleveland, Cleveland, Ohio
- Department of Biostatistics and the Center for Biostatistics in AIDS Research, Harvard School of Public Health, Boston, Massachusetts
| | - Federico Perez
- Louis Stokes Cleveland VA Medical Center, Cleveland, Ohio
- Department of Biostatistics and the Center for Biostatistics in AIDS Research, Harvard School of Public Health, Boston, Massachusetts
| | - Liang Chen
- Public Health Research Institute, Rutgers University, Newark, New Jersey
- Department of Biostatistics and the Center for Biostatistics in AIDS Research, Harvard School of Public Health, Boston, Massachusetts
| | - Rangarajan Sampath
- Ibis Biosciences, Inc., Carlsbad, California
- Department of Biostatistics and the Center for Biostatistics in AIDS Research, Harvard School of Public Health, Boston, Massachusetts
| | - Thomas Hall
- Ibis Biosciences, Carlsbad, California
- Department of Biostatistics and the Center for Biostatistics in AIDS Research, Harvard School of Public Health, Boston, Massachusetts
| | - Christine Marzan
- Ibis Biosciences, Carlsbad, California
- Department of Biostatistics and the Center for Biostatistics in AIDS Research, Harvard School of Public Health, Boston, Massachusetts
| | - Vance Fowler
- Duke University, Durham, North Carolina
- Department of Biostatistics and the Center for Biostatistics in AIDS Research, Harvard School of Public Health, Boston, Massachusetts
| | - Henry Chambers
- University of California, San Francisco, San Francisco, California
- Department of Biostatistics and the Center for Biostatistics in AIDS Research, Harvard School of Public Health, Boston, Massachusetts
| | - Robert A. Bonomo
- Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio
- Pharmacology, Molecular Biology, and Microbiology, Case Western Reserve University, Cleveland, Ohio
- Department of Biostatistics and the Center for Biostatistics in AIDS Research, Harvard School of Public Health, Boston, Massachusetts
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15
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O'Dwyer MJ, Starczewska MH, Schrenzel J, Zacharowski K, Ecker DJ, Sampath R, Brealey D, Singer M, Libert N, Wilks M, Vincent JL. The detection of microbial DNA but not cultured bacteria is associated with increased mortality in patients with suspected sepsis-a prospective multi-centre European observational study. Clin Microbiol Infect 2016; 23:208.e1-208.e6. [PMID: 27890455 DOI: 10.1016/j.cmi.2016.11.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Revised: 11/13/2016] [Accepted: 11/14/2016] [Indexed: 01/05/2023]
Abstract
OBJECTIVES Blood culture results inadequately stratify the mortality risk in critically ill patients with sepsis. We sought to establish the prognostic significance of the presence of microbial DNA in the bloodstream of patients hospitalized with suspected sepsis. METHODS We analysed the data collected during the Rapid Diagnosis of Infections in the Critically Ill (RADICAL) study, which compared a novel culture-independent PCR/electrospray ionization-mass spectrometry (ESI-MS) assay with standard microbiological testing. Patients were eligible for the study if they had suspected sepsis and were either hospitalized or were referred to one of nine intensive care units from six European countries. The blood specimen for PCR/ESI-MS assay was taken along with initial blood culture taken for clinical indications. RESULTS Of the 616 patients recruited to the RADICAL study, 439 patients had data on outcome, results of the blood culture and PCR/ESI-MS assay available for analysis. Positive blood culture and PCR/ESI-MSI result was found in 13% (56/439) and 40% (177/439) of patients, respectively. Either a positive blood culture (p 0.01) or a positive PCR/ESI-MS (p 0.005) was associated with higher SOFA scores on enrolment to the study. There was no difference in 28-day mortality observed in patients who had either positive or negative blood cultures (35% versus 32%, p 0.74). However, in patients with a positive PCR/ESI-MS assay, mortality was significantly higher in comparison to those with a negative result (42% versus 26%, p 0.001). CONCLUSIONS Presence of microbial DNA in patients with suspected sepsis might define a patient group at higher risk of death.
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Affiliation(s)
- M J O'Dwyer
- Department of Translational Medicine and Therapeutics, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK.
| | - M H Starczewska
- Adult Critical Care Unit, Royal London Hospital, Barts Health NHS Trust, London, UK
| | - J Schrenzel
- Genomic Research Laboratory, Department of Internal Medicine, Service of Infectious Diseases, University of Geneva Hospitals, Geneva, Switzerland
| | - K Zacharowski
- Klinik für Anästhesiologie, Intensivmedizin und Schmerztherapie, Universitätsklinikum Frankfurt, Frankfurt am Main, Germany
| | - D J Ecker
- Ibis Biosciences, Abbott, Carlsbad, CA, USA
| | - R Sampath
- Ibis Biosciences, Abbott, Carlsbad, CA, USA
| | - D Brealey
- Division of Critical Care, University College London Hospitals NIHR Biomedical Research Centre and Bloomsbury Institute of Intensive Care Medicine, University College Hospital, London, United Kingdom
| | - M Singer
- Division of Critical Care, University College London Hospitals NIHR Biomedical Research Centre and Bloomsbury Institute of Intensive Care Medicine, University College Hospital, London, United Kingdom
| | - N Libert
- Department of Anaesthesiology and Critical Care, Val de Grâce Military Hospital, Paris, France
| | - M Wilks
- Barts and The London School of Medicine and Dentistry, Queen Mary University of London and Barts Health NHS Trust, London, UK
| | - J-L Vincent
- Department of Intensive Care, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
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16
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Bartley P, Angelakis E, Raoult D, Sampath R, Bonomo RA, Jump RLP. Prosthetic Valve Endocarditis Caused by Bartonella henselae: A Case Report of Molecular Diagnostics Informing Nonsurgical Management. Open Forum Infect Dis 2016; 3:ofw202. [PMID: 27844027 PMCID: PMC5104973 DOI: 10.1093/ofid/ofw202] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Accepted: 09/19/2016] [Indexed: 12/14/2022] Open
Abstract
Identifying the pathogen responsible for culture-negative valve endocarditis often depends on molecular studies performed on surgical specimens. A patient with Ehlers-Danlos syndrome who had an aortic graft, a mechanical aortic valve, and a mitral anulloplasty ring presented with culture-negative prosthetic valve endocarditis and aortic graft infection. Research-based polymerase chain reaction (PCR)/electrospray ionization mass spectrometry on peripheral blood samples identified Bartonella henselae. Quantitative PCR targeting the16S-23S ribonucleic acid intergenic region and Western immunoblotting confirmed this result. This, in turn, permitted early initiation of pathogen-directed therapy and subsequent successful medical management of B henselae prosthetic valve endocarditis and aortic graft infection.
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Affiliation(s)
- Patricia Bartley
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, and
| | | | | | | | - Robert A Bonomo
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, and; Departments of Pathology, Pharmacology, and Molecular Biology and Microbiology and Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio;; Geriatric Research Education and Clinical Center, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio
| | - Robin L P Jump
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, and; Geriatric Research Education and Clinical Center, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio
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17
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Bartley P, Angelakis E, Raoult D, Sampath R, Bonomo R, Jump R. Prosthetic Valve Endocarditis (PVE) Caused by Bartonella henselae: A Case Report of Molecular Methods to Diagnose and Inform Non-Surgical Management. Open Forum Infect Dis 2016. [DOI: 10.1093/ofid/ofw194.28] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Patricia Bartley
- Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Emmanouil Angelakis
- Unite De Recherche Sur Les Maladies Infectieuses Et Tropicales Emergentes, Aix-Marseille Université, Marseille, France
| | | | | | - Robert Bonomo
- Pharmacology, Molecular Biology, and Microbiology, Case Western Reserve University, Cleveland, Ohio; Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio
| | - Robin Jump
- Division of Infectious Diseases and HIV Medicine, Case Western Reserve University, Cleveland, Ohio; Geriatric Research Education and Clinical Center, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio
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18
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Ecker DJ, Drader JJ, Gutierrez J, Gutierrez A, Hannis JC, Schink A, Sampath R, Blyn LB, Eshoo MW, Hall TA, Tobarmosquera M, Jiang Y, Sannes-Lowery KA, Cummins LL, Libby B, Walcott DJ, Massire C, Ranken R, Manalili S, Ivy C, Melton R, Levene H, Harpin V, Li F, White N, Pear M, Ecker JA, Samant V, Knize D, Robbins D, Rudnick K, Hajjar F, Hofstadler SA. The Ibis T5000 Universal Biosensor: An Automated Platform for Pathogen Identification and Strain Typing. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.jala.2006.09.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
We describe a new approach to the sensitive and specific identification of bacteria, viruses, fungi, and protozoa based on broad-range PCR and high-performance mass spectrometry. The Ibis T5000 is based on technology developed for the Department of Defense known as T.I.G.E.R. (Triangulation Identification for the Genetic Evaluation of Risks) for pathogen surveillance. The technology uses mass spectrometry—derived base composition signatures obtained from PCR amplification of broadly conserved regions of the pathogen genomes to identify most organisms present in a sample. The process of sample analysis has been automated using a combination of commercially available and custom instrumentation. A software system known as T-Track manages the sample flow, signal analysis, and data interpretation and provides simplified result reports to the user. No specialized expertise is required to use the instrumentation. In addition to pathogen surveillance, the Ibis T5000 is being applied to reducing health care—associated infections (HAIs), emerging and pandemic disease surveillance, human forensics analysis, and pharmaceutical product and food safety, and will be used eventually in human infectious disease diagnosis. In this review, we describe the automated Ibis T5000 instrument and provide examples of how it is used in HAI control.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Feng Li
- Ibis Biosciences, Carlsbad, CA
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19
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Metzgar D, Frinder MW, Rothman RE, Peterson S, Carroll KC, Zhang SX, Avornu GD, Rounds MA, Carolan HE, Toleno DM, Moore D, Hall TA, Massire C, Richmond GS, Gutierrez JR, Sampath R, Ecker DJ, Blyn LB. The IRIDICA BAC BSI Assay: Rapid, Sensitive and Culture-Independent Identification of Bacteria and Candida in Blood. PLoS One 2016; 11:e0158186. [PMID: 27384540 PMCID: PMC4934770 DOI: 10.1371/journal.pone.0158186] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 06/10/2016] [Indexed: 12/12/2022] Open
Abstract
Bloodstream infection (BSI) and sepsis are rising in incidence throughout the developed world. The spread of multi-drug resistant organisms presents increasing challenges to treatment. Surviving BSI is dependent on rapid and accurate identification of causal organisms, and timely application of appropriate antibiotics. Current culture-based methods used to detect and identify agents of BSI are often too slow to impact early therapy and may fail to detect relevant organisms in many positive cases. Existing methods for direct molecular detection of microbial DNA in blood are limited in either sensitivity (likely the result of small sample volumes) or in breadth of coverage, often because the PCR primers and probes used target only a few specific pathogens. There is a clear unmet need for a sensitive molecular assay capable of identifying the diverse bacteria and yeast associated with BSI directly from uncultured whole blood samples. We have developed a method of extracting DNA from larger volumes of whole blood (5 ml per sample), amplifying multiple widely conserved bacterial and fungal genes using a mismatch- and background-tolerant PCR chemistry, and identifying hundreds of diverse organisms from the amplified fragments on the basis of species-specific genetic signatures using electrospray ionization mass spectrometry (PCR/ESI-MS). We describe the analytical characteristics of the IRIDICA BAC BSI Assay and compare its pre-clinical performance to current standard-of-care methods in a collection of prospectively collected blood specimens from patients with symptoms of sepsis. The assay generated matching results in 80% of culture-positive cases (86% when common contaminants were excluded from the analysis), and twice the total number of positive detections. The described method is capable of providing organism identifications directly from uncultured blood in less than 8 hours. Disclaimer: The IRIDICA BAC BSI Assay is not available in the United States.
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Affiliation(s)
- David Metzgar
- Ibis Biosciences, an Abbott Company, Carlsbad, California, United States of America
- * E-mail:
| | - Mark W. Frinder
- Ibis Biosciences, an Abbott Company, Carlsbad, California, United States of America
| | - Richard E. Rothman
- Department of Emergency Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Stephen Peterson
- Department of Emergency Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Karen C. Carroll
- The Johns Hopkins Hospital Clinical Microbiology Laboratory, Baltimore, Maryland, United States of America
| | - Sean X. Zhang
- The Johns Hopkins Hospital Clinical Microbiology Laboratory, Baltimore, Maryland, United States of America
| | - Gideon D. Avornu
- Department of Emergency Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Megan A. Rounds
- Ibis Biosciences, an Abbott Company, Carlsbad, California, United States of America
| | - Heather E. Carolan
- Ibis Biosciences, an Abbott Company, Carlsbad, California, United States of America
| | - Donna M. Toleno
- Ibis Biosciences, an Abbott Company, Carlsbad, California, United States of America
| | - David Moore
- Ibis Biosciences, an Abbott Company, Carlsbad, California, United States of America
| | - Thomas A. Hall
- Ibis Biosciences, an Abbott Company, Carlsbad, California, United States of America
| | - Christian Massire
- Ibis Biosciences, an Abbott Company, Carlsbad, California, United States of America
| | - Gregory S. Richmond
- Ibis Biosciences, an Abbott Company, Carlsbad, California, United States of America
| | - Jose R. Gutierrez
- Ibis Biosciences, an Abbott Company, Carlsbad, California, United States of America
| | - Rangarajan Sampath
- Ibis Biosciences, an Abbott Company, Carlsbad, California, United States of America
| | - David J. Ecker
- Ibis Biosciences, an Abbott Company, Carlsbad, California, United States of America
| | - Lawrence B. Blyn
- Ibis Biosciences, an Abbott Company, Carlsbad, California, United States of America
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Farrell JJ, Ikladios O, Wylie KM, O'Rourke LM, Lowery KS, Cromwell JS, Wylie TN, Melendez ELV, Makhoul Y, Sampath R, Bonomo RA, Storch GA. Enterovirus D68-associated acute respiratory distress syndrome in adult, United States, 2014. Emerg Infect Dis 2016; 21:914-6. [PMID: 25897542 PMCID: PMC4412249 DOI: 10.3201/eid2105.142033] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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21
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Farrell J, Melendez EV, Lowery K, Sampath R. Examination of Sterile Fluids for Unrecognized Secondary Pathogens From Patients on Antibiotic Treatment. Open Forum Infect Dis 2015. [DOI: 10.1093/ofid/ofv133.1285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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22
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Evans S, Jiang H, Hujer A, Hujer KM, Mediavilla J, Manca C, Hill C, Kreiswirth B, Patel R, Jacobs MR, Chen L, Sampath R, Hall T, Marzan C, Fowler VG, Chambers H, Bonomo RA. Informing Antibiotic Treatment Decisions: Evaluating Rapid Molecular Diagnostics (RMDs) to Identify Susceptibility and Resistance to Carbapenems Against Acinetobacter spp PRIMERS –III. Open Forum Infect Dis 2015. [DOI: 10.1093/ofid/ofv133.1157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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23
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Evans S, Jiang H, Hujer A, Hujer KM, Manca C, Hill C, Kreiswirth BN, Jacobs MR, Chen L, Sampath R, Hall T, Marzan C, Bonomo RA. Benefit/Risk Evaluation in Diagnostics: An Example Comparing Two Rapid Molecular Diagnostics Testing Imipemem Susceptibility in Acinetobacter spp. Open Forum Infect Dis 2015. [DOI: 10.1093/ofid/ofv133.1155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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24
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Evans SR, Hujer AM, Jiang H, Hujer KM, Hall T, Marzan C, Jacobs MR, Sampath R, Ecker DJ, Manca C, Chavda K, Zhang P, Fernandez H, Chen L, Mediavilla JR, Hill CB, Perez F, Caliendo AM, Fowler VG, Chambers HF, Kreiswirth BN, Bonomo RA. Rapid Molecular Diagnostics, Antibiotic Treatment Decisions, and Developing Approaches to Inform Empiric Therapy: PRIMERS I and II. Clin Infect Dis 2015; 62:181-9. [PMID: 26409063 DOI: 10.1093/cid/civ837] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 09/04/2015] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Rapid molecular diagnostic (RMD) platforms may lead to better antibiotic use. Our objective was to develop analytical strategies to enhance the interpretation of RMDs for clinicians. METHODS We compared the performance characteristics of 4 RMD platforms for detecting resistance against β-lactams in 72 highly resistant isolates of Escherichia coli and Klebsiella pneumoniae (PRIMERS I). Subsequently, 2 platforms were used in a blinded study in which a heterogeneous collection of 196 isolates of E. coli and K. pneumoniae (PRIMERS II) were examined. We evaluated the genotypic results as predictors of resistance or susceptibility against β-lactam antibiotics. We designed analytical strategies and graphical representations of platform performance, including discrimination summary plots and susceptibility and resistance predictive values, that are readily interpretable by practitioners to inform decision-making. RESULTS In PRIMERS I, the 4 RMD platforms detected β-lactamase (bla) genes and identified susceptibility or resistance in >95% of cases. In PRIMERS II, the 2 platforms identified susceptibility against extended-spectrum cephalosporins and carbapenems in >90% of cases; however, against piperacillin/tazobactam, susceptibility was identified in <80% of cases. Applying the analytical strategies to a population with 15% prevalence of ceftazidime-resistance and 5% imipenem-resistance, RMD platforms predicted susceptibility in >95% of cases, while prediction of resistance was 69%-73% for ceftazidime and 41%-50% for imipenem. CONCLUSIONS RMD platforms can help inform empiric β-lactam therapy in cases where bla genes are not detected and the prevalence of resistance is known. Our analysis is a first step in bridging the gap between RMDs and empiric treatment decisions.
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Affiliation(s)
- Scott R Evans
- Center for Biostatistics in AIDS Research and the Department of Biostatistics, Harvard University, Boston, Massachusetts
| | - Andrea M Hujer
- Department of Medicine, Case Western Reserve University School of Medicine Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio
| | - Hongyu Jiang
- Center for Biostatistics in AIDS Research and the Department of Biostatistics, Harvard University, Boston, Massachusetts
| | - Kristine M Hujer
- Department of Medicine, Case Western Reserve University School of Medicine Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio
| | - Thomas Hall
- Ibis Biosciences, an Abbott Company, Carlsbad, California
| | | | - Michael R Jacobs
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | | | - David J Ecker
- Ibis Biosciences, an Abbott Company, Carlsbad, California
| | - Claudia Manca
- Public Health Research Institute Center, New Jersey Medical School-Rutgers University, Newark
| | - Kalyan Chavda
- Public Health Research Institute Center, New Jersey Medical School-Rutgers University, Newark
| | - Pan Zhang
- Weill Cornell Medical College, New York, New York
| | | | - Liang Chen
- Public Health Research Institute Center, New Jersey Medical School-Rutgers University, Newark
| | - Jose R Mediavilla
- Public Health Research Institute Center, New Jersey Medical School-Rutgers University, Newark
| | - Carol B Hill
- Duke Clinical Research Institute, Duke University Medical Center, Durham, North Carolina
| | - Federico Perez
- Department of Medicine, Case Western Reserve University School of Medicine Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio
| | - Angela M Caliendo
- Department of Medicine, Alpert Medical School of Brown University, Providence, Rhode Island
| | - Vance G Fowler
- Duke Clinical Research Institute, Duke University Medical Center, Durham, North Carolina Division of Infectious Diseases, Department of Medicine, Duke University Medical Center, Durham, North Carolina
| | | | - Barry N Kreiswirth
- Public Health Research Institute Center, New Jersey Medical School-Rutgers University, Newark
| | - Robert A Bonomo
- Department of Medicine, Case Western Reserve University School of Medicine Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio Departments of Pharmacology, Molecular Biology and Microbiology, Biochemistry, and Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio
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25
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Perreten V, Endimiani A, Thomann A, Wipf JR, Rossano A, Bodmer M, Raemy A, Sannes-Lowery KA, Ecker DJ, Sampath R, Bonomo RA. Corrigendum to “Evaluation of PCR electrospray-ionization mass spectrometry for rapid molecular diagnosis of bovine mastitis” (J. Dairy Sci. 96:3611–3620). J Dairy Sci 2015. [DOI: 10.3168/jds.2015-98-1-0718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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26
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MacCallum N, Brealey D, Libert N, Pugin J, Picard-Maureau M, Sampath R, Ecker D, Singer M, Vincent JL. A RADICAL APPROACH TO DIAGNOSING INFECTION. Intensive Care Med Exp 2015. [PMCID: PMC4797822 DOI: 10.1186/2197-425x-3-s1-a4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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27
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Farrell JJ, Hujer AM, Sampath R, Bonomo RA. Salvage microbiology: opportunities and challenges in the detection of bacterial pathogens following initiation of antimicrobial treatment. Expert Rev Mol Diagn 2014; 15:349-60. [PMID: 25523281 DOI: 10.1586/14737159.2015.989216] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Broad-range 16S ribosomal RNA gene PCR coupled with Sanger sequencing was originally employed by soil scientists and was subsequently adapted for clinical applications. PCR coupled with electrospray ionization mass spectrometry has also progressed from initial applications in the detection of organisms from environmental samples into the clinical realm and has demonstrated promise in detection of pathogens in clinical specimens obtained from patients with suspected infection but negative cultures. We review studies of multiplex PCR, 16S ribosomal RNA gene PCR and sequencing and PCR coupled with electrospray ionization mass spectrometry for detection of bacteria in specimens that were obtained from patients during or after administration of antibiotic treatment, and examine the role of each for assisting in antimicrobial treatment and stewardship efforts. Following an exploration of the available data in this field, we discuss the opportunities that the preliminary investigations reveal, as well as the challenges faced with the implementation of these strategies in clinical practice.
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Affiliation(s)
- John J Farrell
- Department of Medicine, Division of Infectious Disease, University of Illinois College of Medicine, 723 N.E. Glen Oak Ave. Peoria, IL 61603, USA
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28
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Brealey D, Libert N, Pugin J, O'Dwyer M, Zacharowski K, Mikaszewska-Sokolewicz M, Maureau MP, Ecker DJ, Sampath R, Singer M, Vincent JL. RADICAL study: rapid diagnosis of suspected bloodstream infections from direct blood testing using PCR/ESI-MS. Crit Care 2014. [PMCID: PMC4273894 DOI: 10.1186/cc14064] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Vazquez Melendez EL, Farrell JJ, Hujer AM, Lowery KS, Sampath R, Bonomo RA. Culture negative empyema in a critically ill child: an opportunity for rapid molecular diagnostics. BMC Anesthesiol 2014; 14:107. [PMID: 25484623 PMCID: PMC4258007 DOI: 10.1186/1471-2253-14-107] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 11/10/2014] [Indexed: 12/25/2022] Open
Abstract
Background Nucleic acid amplification technologies (NAAT) are advancing our ability to make rapid molecular diagnoses in patients with serious culture negative infections. This is the first report of PCR coupled to electrospray ionization mass spectrometry use in the evaluation of complicated community acquired pneumonia in a pediatric patient. Case presentation We present a case of culture negative empyema in a critically ill, Caucasian, 2-year-old girl who was treated with broad-spectrum empiric antibiotics, in which the length of stay was prolonged by adverse effects of the empiric antibiotic treatment. PCR coupled to electrospray ionization mass spectrometry was applied to culture negative fluid and tissue samples from the patient in order to determine the etiology of the empyema. Conclusions Using this method, Streptococcus mitis/viridans was identified as the pathogen. A retrospective review of cases of empyema in children at our institution found that 87.5% of cases were negative for identification of a pathogen and antibiotics were administered to 100% of cases prior to collecting pleural fluid for culture. Understanding the role of Streptococcus mitis/viridans group in the etiology of empyema using an advanced NAAT coupled with mass spectrometry can enlighten clinicians as to the impact of this pathogen in community acquired pneumonia and help assist with antibiotic stewardship.
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Affiliation(s)
- Elsa L Vazquez Melendez
- Departments of Medicine & Pediatrics, University of Illinois School of Medicine, 530 N.E. Glen Oak Ave, Peoria, IL 61603 USA
| | - John J Farrell
- Department of Medicine, University of Illinois School of Medicine, Peoria, IL USA
| | - Andrea M Hujer
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Research Service, 10701 East Blvd, Cleveland, Ohio 44106 USA ; Department of Medicine, Case Western Reserve University, Cleveland, OH USA
| | | | | | - Robert A Bonomo
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Research Service, 10701 East Blvd, Cleveland, Ohio 44106 USA ; Department of Medicine, Case Western Reserve University, Cleveland, OH USA ; Departments of Pharmacology and Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH USA
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30
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Bacconi A, Richmond GS, Baroldi MA, Laffler TG, Blyn LB, Carolan HE, Frinder MR, Toleno DM, Metzgar D, Gutierrez JR, Massire C, Rounds M, Kennel NJ, Rothman RE, Peterson S, Carroll KC, Wakefield T, Ecker DJ, Sampath R. Improved sensitivity for molecular detection of bacterial and Candida infections in blood. J Clin Microbiol 2014; 52:3164-74. [PMID: 24951806 PMCID: PMC4313132 DOI: 10.1128/jcm.00801-14] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 06/06/2014] [Indexed: 12/29/2022] Open
Abstract
The rapid identification of bacteria and fungi directly from the blood of patients with suspected bloodstream infections aids in diagnosis and guides treatment decisions. The development of an automated, rapid, and sensitive molecular technology capable of detecting the diverse agents of such infections at low titers has been challenging, due in part to the high background of genomic DNA in blood. PCR followed by electrospray ionization mass spectrometry (PCR/ESI-MS) allows for the rapid and accurate identification of microorganisms but with a sensitivity of about 50% compared to that of culture when using 1-ml whole-blood specimens. Here, we describe a new integrated specimen preparation technology that substantially improves the sensitivity of PCR/ESI-MS analysis. An efficient lysis method and automated DNA purification system were designed for processing 5 ml of whole blood. In addition, PCR amplification formulations were optimized to tolerate high levels of human DNA. An analysis of 331 specimens collected from patients with suspected bloodstream infections resulted in 35 PCR/ESI-MS-positive specimens (10.6%) compared to 18 positive by culture (5.4%). PCR/ESI-MS was 83% sensitive and 94% specific compared to culture. Replicate PCR/ESI-MS testing from a second aliquot of the PCR/ESI-MS-positive/culture-negative specimens corroborated the initial findings in most cases, resulting in increased sensitivity (91%) and specificity (99%) when confirmed detections were considered true positives. The integrated solution described here has the potential to provide rapid detection and identification of organisms responsible for bloodstream infections.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Megan Rounds
- Ibis Biosciences, Inc., Carlsbad, California, USA
| | | | - Richard E Rothman
- Department of Emergency Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Stephen Peterson
- Department of Emergency Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Karen C Carroll
- The Johns Hopkins Hospital Clinical Microbiology Laboratory, Baltimore, Maryland, USA
| | - Teresa Wakefield
- The Johns Hopkins Hospital Clinical Microbiology Laboratory, Baltimore, Maryland, USA
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31
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Farrell JJ, Kasper DJ, Taneja D, Baman S, O׳Rourke LM, Lowery KS, Sampath R, Bonomo RA, Peterson SW. Acute respiratory distress caused by Neosartorya udagawae. Med Mycol Case Rep 2014; 6:1-5. [PMID: 25379388 PMCID: PMC4216325 DOI: 10.1016/j.mmcr.2014.07.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 07/14/2014] [Accepted: 07/17/2014] [Indexed: 11/24/2022] Open
Abstract
We describe the first reported case of acute respiratory distress syndrome (ARDS) attributed to Neosartorya udagawae infection. This mold grew rapidly in cultures of multiple respiratory specimens from a previously healthy 43-year-old woman. Neosartorya spp. are a recently recognized cause of invasive disease in immunocompromised patients that can be mistaken for their sexual teleomorph, Aspergillus fumigatus. Because the cultures were sterile, phenotypic identification was not possible. DNA sequencing of ITS, calmodulin and β-tubulin genes supported identification of Neosartorya udagawae. Our case is the first report of ARDS associated with Neosartorya sp. infection and defines a new clinical entity.
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Affiliation(s)
- John J Farrell
- Department of Medicine, Division of Infectious Disease, University of Illinois School of Medicine, Peoria, IL 61604, USA
| | - Douglas J Kasper
- Department of Medicine, Division of Infectious Disease, University of Illinois School of Medicine, Peoria, IL 61604, USA
| | - Deepak Taneja
- Department of Medicine, Division of Pulmonary Medicine, Saint Francis Medical Center, Peoria, IL 61604, USA
| | - Sudhakar Baman
- Department of Laboratory Medicine, Saint Francis Medical Center, Peoria, IL 61604, USA
| | - Lindsay M O׳Rourke
- Department of Laboratory Medicine, Saint Francis Medical Center, Peoria, IL 61604, USA
| | | | | | - Robert A Bonomo
- Departments of Medicine, Pharmacology and Molecular Microbiology Case Western Reserve University, Cleveland, OH 44106, USA ; Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH 44106, USA
| | - Stephen W Peterson
- Bacterial Foodborne Pathogens and Mycology, National Center for Agricultural Utilization Research, US Department of Agriculture, 1815 North University Street, Peoria, IL 61604, USA
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32
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Hellberg RS, Li F, Sampath R, Yasuda IJ, Carolan HE, Wolfe JM, Brown MK, Alexander RC, Williams-Hill DM, Martin WB. Rapid detection and differentiation of human noroviruses using RT-PCR coupled to electrospray ionization mass spectrometry. Food Microbiol 2014; 44:71-80. [PMID: 25084648 DOI: 10.1016/j.fm.2014.05.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 04/25/2014] [Accepted: 05/25/2014] [Indexed: 11/26/2022]
Abstract
The goal of this study was to develop an assay for the detection and differentiation of noroviruses using RT-PCR followed by electrospray ionization mass spectrometry (ESI-MS). Detection of hepatitis A virus was also considered. Thirteen primer pairs were designed for use in this assay and a reference database was created using GenBank sequences and reference norovirus samples. The assay was tested for inclusivity and exclusivity using 160 clinical norovirus samples, 3 samples of hepatitis A virus and 3 other closely related viral strains. Results showed that the assay was able to detect norovirus with a sensitivity of 92% and a specificity of 100%. Norovirus identification at the genogroup level was correct for 98% of samples detected by the assay and for 75% of a subset of samples (n = 32) compared at the genotype level. Identification of norovirus genotypes is expected to improve as more reference samples are added to the database. The assay was also capable of detecting and genotyping hepatitis A virus in all 3 samples tested. Overall, the assay developed here allows for detection and differentiation of noroviruses within one working day and may be used as a tool in surveillance efforts or outbreak investigations.
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Affiliation(s)
- Rosalee S Hellberg
- Chapman University, Schmid College of Science and Technology, Food Science and Nutrition, One University Drive, Orange, CA 92866, USA.
| | - Feng Li
- Ibis Biosciences, Abbott, 2251 Faraday Ave., Suite 150, Carlsbad, CA 92008, USA
| | - Rangarajan Sampath
- Ibis Biosciences, Abbott, 2251 Faraday Ave., Suite 150, Carlsbad, CA 92008, USA
| | - Irene J Yasuda
- Ibis Biosciences, Abbott, 2251 Faraday Ave., Suite 150, Carlsbad, CA 92008, USA
| | - Heather E Carolan
- Ibis Biosciences, Abbott, 2251 Faraday Ave., Suite 150, Carlsbad, CA 92008, USA
| | - Julia M Wolfe
- Orange County Public Health Laboratory, 1729 West 17th Street, Santa Ana, CA 92706, USA
| | - Michael K Brown
- Orange County Public Health Laboratory, 1729 West 17th Street, Santa Ana, CA 92706, USA
| | - Richard C Alexander
- Orange County Public Health Laboratory, 1729 West 17th Street, Santa Ana, CA 92706, USA
| | - Donna M Williams-Hill
- U.S. Food and Drug Administration, Office of Regulatory Affairs, Pacific Regional Laboratory Southwest, 19701 Fairchild, Irvine, CA 92612, USA
| | - William B Martin
- U.S. Food and Drug Administration, Office of Regulatory Affairs, Pacific Regional Laboratory Southwest, 19701 Fairchild, Irvine, CA 92612, USA
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Chen J, Fu Y, Ju L, Miao X, Shen Y, He L, Wang W, Jin J, Shao L, Sampath R, Ecker DJ, Zhang Y, Li M, Cheng X, Zhang W. Detection and identification of viral pathogens in patients with hand, foot, and mouth disease by multilocus PCR, reverse-transcription PCR and electrospray ionization mass spectrometry. J Clin Virol 2014; 59:115-9. [DOI: 10.1016/j.jcv.2013.11.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 11/11/2013] [Accepted: 11/18/2013] [Indexed: 11/25/2022]
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Deyde VM, Sampath R, Gubareva LV. RT-PCR/electrospray ionization mass spectrometry approach in detection and characterization of influenza viruses. Expert Rev Mol Diagn 2014; 11:41-52. [DOI: 10.1586/erm.10.107] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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35
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Kecojevic A, Ranken R, Ecker DJ, Massire C, Sampath R, Blyn LB, Hsieh YH, Rothman RE, Gaydos CA. Rapid PCR/ESI-MS-based molecular genotyping of Staphylococcus aureus from nasal swabs of emergency department patients. BMC Infect Dis 2014; 14:16. [PMID: 24405766 PMCID: PMC3937163 DOI: 10.1186/1471-2334-14-16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 01/06/2014] [Indexed: 11/14/2022] Open
Abstract
Background A limitation of both culture-based and molecular methods of screening for staphylococcal infection is that current tests determine only the presence or absence of colonization with no information on the colonizing strain type. A technique that couples polymerase chain reaction to mass spectrometry (PCR/ESI-MS) has recently been developed and an assay validated to identify and genotype S. aureus and coagulase-negative staphylococci (CoNS). Methods This study was conducted to determine the rates, risk factors, and molecular genotypes of colonizing Staphylococcus aureus in adult patients presenting to an inner-city academic emergency department. Participants completed a structured questionnaire to assess hospital and community risks for infection with methicillin-resistant S. aureus (MRSA). Nasal swabs were analyzed by PCR/ESI-MS to identify and genotype S. aureus and CoNS. Results Of 200 patients evaluated, 59 were colonized with S. aureus; 27 of these were methicillin-resistant strains. Twenty-four of the 59 S. aureus carriers were co-colonized with a CoNS and 140 of the 200 patients were colonized exclusively with CoNS. The molecular genotypes of the 59 S. aureus strains were diverse; 21 unique molecular genotypes belonging to seven major clonal complexes were identified. Eighty-five of 200 patients carried strains with high-level mupirocin resistance. Of these eighty-five participants, 4 were colonized exclusively with S. aureus, 16 were co-colonized with S. aureus and CoNS, and 65 were colonized exclusively with CoNS. Conclusion The prevalence of S. aureus and methicillin-resistant S. aureus colonization in a random sample of patients seeking care in Emergency Department was 29.5% and 13.5%, respectively. A substantial fraction of the S. aureus-colonized patients were co-colonized with CoNS and high-level mupirocin-resistant CoNS. Determining the molecular genotype of S. aureus during intake screening may prove valuable in the future if certain molecular genotypes become associated with increased infection risk.
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Affiliation(s)
- Aleksandar Kecojevic
- Department of Community Health and Prevention, Drexel University School of Public Health, Philadelphia, PA, USA.
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36
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Metzgar D, Lovari R, Ray K, Baynes D, Drapp D, Frinder M, Vijesurier R, Stemler M, Ofsaiof R, Carolan H, Welk J, Toleno D, Ranken R, Hall TA, Massire C, Sampath R, Blyn LB, Goveia J, Schneider G. Analytical characterization of an assay designed to detect and identify diverse agents of disseminated viral infection. J Clin Virol 2013; 59:177-83. [PMID: 24440177 DOI: 10.1016/j.jcv.2013.12.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 12/14/2013] [Accepted: 12/18/2013] [Indexed: 11/30/2022]
Abstract
BACKGROUND Diverse viruses often reactivate in or infect cancer patients, patients with immunocompromising infections or genetic conditions, and transplant recipients undergoing immunosuppressive therapy. These infections can disseminate, leading to death, transplant rejection, and other severe outcomes. OBJECTIVES To develop and characterize an assay capable of inclusive and accurate identification of diverse potentially disseminating viruses directly from plasma specimens. STUDY DESIGN We developed a PCR/electrospray ionization mass spectrometry (PCR/ESI-MS) assay designed to simultaneously detect and identify adenovirus, enterovirus, polyomaviruses JC and BK, parvovirus B19, HSV-1, HSV-2, VZV, EBV, CMV, and herpesviruses 6-8 in plasma specimens. The assay performance was characterized analytically, and the results from clinical plasma samples were compared to the results obtained from single-analyte real time PCR tests currently used in clinical practice. RESULTS The assay demonstrated sensitivity and specificity to diverse strains of the targeted viral families and robustness to interfering substances and potentially cross reacting organisms. The assay yielded 94% sensitivity when testing clinical plasma samples previously identified as positive using standard-of-care real-time PCR tests for a single target virus (available samples included positive samples for 11 viruses targeted by the assay). CONCLUSIONS The assay functioned as designed, providing simultaneous broad-spectrum detection and identification of diverse agents of disseminated viral infection. Among 156 clinical samples tested, 37 detections were made in addition to the detections matching the initial clinical positive results.
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Affiliation(s)
- David Metzgar
- Ibis Biosciences, a Division of Abbott, 2251 Faraday Ave, Ste 150, Carlsbad, CA 92008, United States.
| | - Robert Lovari
- Ibis Biosciences, a Division of Abbott, 2251 Faraday Ave, Ste 150, Carlsbad, CA 92008, United States
| | - Keith Ray
- Ibis Biosciences, a Division of Abbott, 2251 Faraday Ave, Ste 150, Carlsbad, CA 92008, United States
| | - Darcie Baynes
- Ibis Biosciences, a Division of Abbott, 2251 Faraday Ave, Ste 150, Carlsbad, CA 92008, United States
| | - Darren Drapp
- Ibis Biosciences, a Division of Abbott, 2251 Faraday Ave, Ste 150, Carlsbad, CA 92008, United States
| | - Mark Frinder
- Ibis Biosciences, a Division of Abbott, 2251 Faraday Ave, Ste 150, Carlsbad, CA 92008, United States
| | - Roy Vijesurier
- Ibis Biosciences, a Division of Abbott, 2251 Faraday Ave, Ste 150, Carlsbad, CA 92008, United States
| | - Michelle Stemler
- Ibis Biosciences, a Division of Abbott, 2251 Faraday Ave, Ste 150, Carlsbad, CA 92008, United States
| | - Reuben Ofsaiof
- Ibis Biosciences, a Division of Abbott, 2251 Faraday Ave, Ste 150, Carlsbad, CA 92008, United States
| | - Heather Carolan
- Ibis Biosciences, a Division of Abbott, 2251 Faraday Ave, Ste 150, Carlsbad, CA 92008, United States
| | - Joseph Welk
- Ibis Biosciences, a Division of Abbott, 2251 Faraday Ave, Ste 150, Carlsbad, CA 92008, United States
| | - Donna Toleno
- Ibis Biosciences, a Division of Abbott, 2251 Faraday Ave, Ste 150, Carlsbad, CA 92008, United States
| | - Raymond Ranken
- Ibis Biosciences, a Division of Abbott, 2251 Faraday Ave, Ste 150, Carlsbad, CA 92008, United States
| | - Thomas A Hall
- Ibis Biosciences, a Division of Abbott, 2251 Faraday Ave, Ste 150, Carlsbad, CA 92008, United States
| | - Christian Massire
- Ibis Biosciences, a Division of Abbott, 2251 Faraday Ave, Ste 150, Carlsbad, CA 92008, United States
| | - Rangarajan Sampath
- Ibis Biosciences, a Division of Abbott, 2251 Faraday Ave, Ste 150, Carlsbad, CA 92008, United States
| | - Lawrence B Blyn
- Ibis Biosciences, a Division of Abbott, 2251 Faraday Ave, Ste 150, Carlsbad, CA 92008, United States
| | - Jon Goveia
- Ibis Biosciences, a Division of Abbott, 2251 Faraday Ave, Ste 150, Carlsbad, CA 92008, United States
| | - George Schneider
- Ibis Biosciences, a Division of Abbott, 2251 Faraday Ave, Ste 150, Carlsbad, CA 92008, United States
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Metzgar D, Sampath R, Rounds MA, Ecker DJ. The value and validation of broad spectrum biosensors for diagnosis and biodefense. Virulence 2013; 4:752-8. [PMID: 24128433 PMCID: PMC3925709 DOI: 10.4161/viru.26652] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 09/25/2013] [Accepted: 09/29/2013] [Indexed: 12/05/2022] Open
Abstract
Broad spectrum biosensors capable of identifying diverse organisms are transitioning from the realm of research into the clinic. These technologies simultaneously capture signals from a wide variety of biological entities using universal processes. Specific organisms are then identified through bioinformatic signature-matching processes. This is in contrast to currently accepted molecular diagnostic technologies, which utilize unique reagents and processes to detect each organism of interest. This paradigm shift greatly increases the breadth of molecular diagnostic tools with little increase in biochemical complexity, enabling simultaneous diagnostic, epidemiologic, and biothreat surveillance capabilities at the point of care. This, in turn, offers the promise of increased biosecurity and better antimicrobial stewardship. Efficient realization of these potential gains will require novel regulatory paradigms reflective of the generalized, information-based nature of these assays, allowing extension of empirical data obtained from readily available organisms to support broader reporting of rare, difficult to culture, or extremely hazardous organisms.
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Affiliation(s)
- David Metzgar
- Ibis Biosciences; An Abbott Company; Carlsbad, CA USA
| | | | | | - David J Ecker
- Ibis Biosciences; An Abbott Company; Carlsbad, CA USA
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38
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Laffler TG, Cummins LL, McClain CM, Quinn CD, Toro MA, Carolan HE, Toleno DM, Rounds MA, Eshoo MW, Stratton CW, Sampath R, Blyn LB, Ecker DJ, Tang YW. Enhanced diagnostic yields of bacteremia and candidemia in blood specimens by PCR-electrospray ionization mass spectrometry. J Clin Microbiol 2013; 51:3535-41. [PMID: 23966503 PMCID: PMC3889730 DOI: 10.1128/jcm.00876-13] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 08/08/2013] [Indexed: 12/20/2022] Open
Abstract
A prospective study was performed to determine the value of direct molecular testing of whole blood for detecting the presence of culturable and unculturable bacteria and yeasts in patients with suspected bloodstream infections. A total of 464 adult and pediatric patients with positive blood cultures matched with 442 patients with negative blood cultures collected during the same period were recruited during a 10-month study. PCR amplification coupled with electrospray ionization mass spectrometry (PCR-ESI-MS) plus blood culture reached an overall agreement of 78.6% in the detection and species-level identification of bacterial and candidal pathogens. Of 33 culture-negative/PCR-ESI-MS-positive specimens, 31 (93.9%) were judged to be truly bacteremic and/or candidemic based on a medical chart review and analytical metrics. Among the 15 culture-positive specimens in which PCR-ESI-MS detected additional bacterial or yeast species, 66.7% and 20.0% of the additional positive specimens by PCR-ESI-MS were judged to be truly or possibly bacteremic and/or candidemic, respectively. Direct analysis of blood samples by PCR-ESI-MS rapidly detects bacterial and yeast pathogens in patients with bloodstream infections. When used in conjunction with blood culture, PCR-ESI-MS enhances the diagnostics of septicemia by shortening test turnaround time and improving yields.
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Affiliation(s)
| | | | - Colt M. McClain
- Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | | | | | | | | | | | | | | | | | | | | | - Yi-Wei Tang
- Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Memorial Sloan-Kettering Cancer Center, New York, New York, USA
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Shen J, Wang F, Li F, Housley R, Carolan H, Yasuda I, Burrows E, Binet R, Sampath R, Zhang J, Allard MW, Meng J. Rapid Identification and Differentiation of Non-O157 Shiga Toxin–ProducingEscherichia coliUsing Polymerase Chain Reaction Coupled to Electrospray Ionization Mass Spectrometry. Foodborne Pathog Dis 2013; 10:737-43. [DOI: 10.1089/fpd.2012.1469] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Jinling Shen
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province, China
- Department of Nutrition and Food Science, University of Maryland, College Park, Maryland
- Zhangjiagang Entry-Exit Inspection and Quarantine Bureau, Zhangjiagang, Jiangsu Province, China
| | - Fei Wang
- Department of Nutrition and Food Science, University of Maryland, College Park, Maryland
| | - Feng Li
- Ibis Biosciences, Abbott, Carlsbad, California
| | | | | | | | - Erik Burrows
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland
| | - Rachel Binet
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland
| | | | | | - Marc W. Allard
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland
| | - Jianghong Meng
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province, China
- Department of Nutrition and Food Science, University of Maryland, College Park, Maryland
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40
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Sarovich DS, Colman RE, Price EP, Massire C, Von Schulze AT, Waddell V, Anderson SM, Ecker DJ, Liguori AP, Engelthaler DM, Sampath R, Keim P, Eshoo MW, Wagner DM. Molecular genotyping of Acinetobacter spp. isolated in Arizona, USA, using multilocus PCR and mass spectrometry. J Med Microbiol 2013; 62:1295-1300. [PMID: 23741021 DOI: 10.1099/jmm.0.052381-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Acinetobacter spp. are a diverse group of Gram-negative bacteria frequently implicated in nosocomial infections. Genotypic methods have been instrumental in studying Acinetobacter, but few offer high resolution, rapid turnaround time, technical ease and high inter-laboratory reproducibility, which has hampered understanding of disease incidence, transmission patterns and diversity within this genus. Here, we further evaluated multilocus PCR electrospray ionization/mass spectrometry (PCR/ESI-MS), a method that is simple and robust, and provides both species characterization and strain-level resolution of Acinetobacter spp. on a single platform. We examined 125 Acinetobacter isolates from 21 hospitals, laboratories and medical centres spanning four counties in Arizona, USA, using PCR/ESI-MS. We compared PCR/ESI-MS with an in-house amplified fragment length polymorphism (AFLP) genotyping scheme. PCR/ESI-MS demonstrated that Acinetobacter spp. from Arizonan hospitals had similar species and strain distributions to other US civilian hospitals. Furthermore, we showed that the PCR/ESI-MS and AFLP genotypes were highly congruent, with the former having the advantages of robust inter-laboratory reproducibility, rapid turnaround time and simple experimental set-up and data analysis. PCR/ESI-MS is an effective and high-throughput platform for strain typing of Acinetobacter baumannii and for identification of other Acinetobacter spp., including the emerging nosocomial pathogens Acinetobacter pittii and Acinetobacter nosocomialis.
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Affiliation(s)
- Derek S Sarovich
- Menzies School of Health Research, Darwin, NT 0810, Australia.,Northern Arizona University, Center for Microbial Genetics and Genomics, Flagstaff, AZ 86011, USA
| | - Rebecca E Colman
- Northern Arizona University, Center for Microbial Genetics and Genomics, Flagstaff, AZ 86011, USA
| | - Erin P Price
- Menzies School of Health Research, Darwin, NT 0810, Australia.,Northern Arizona University, Center for Microbial Genetics and Genomics, Flagstaff, AZ 86011, USA
| | | | - Alex T Von Schulze
- Northern Arizona University, Center for Microbial Genetics and Genomics, Flagstaff, AZ 86011, USA
| | - Victor Waddell
- Arizona Department of Health Services, Phoenix, AZ 85007, USA
| | | | | | - Andrew P Liguori
- Northern Arizona University, Center for Microbial Genetics and Genomics, Flagstaff, AZ 86011, USA
| | | | | | - Paul Keim
- Translational Genomics Research Institute, Flagstaff, AZ 86001, USA.,Northern Arizona University, Center for Microbial Genetics and Genomics, Flagstaff, AZ 86011, USA
| | | | - David M Wagner
- Northern Arizona University, Center for Microbial Genetics and Genomics, Flagstaff, AZ 86011, USA
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41
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Perreten V, Endimiani A, Thomann A, Wipf JR, Rossano A, Bodmer M, Raemy A, Sannes-Lowery KA, Ecker DJ, Sampath R, Bonomo RA. Evaluation of PCR electrospray-ionization mass spectrometry for rapid molecular diagnosis of bovine mastitis. J Dairy Sci 2013; 96:3611-20. [DOI: 10.3168/jds.2012-6124] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 02/22/2013] [Indexed: 01/16/2023]
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Jordana-Lluch E, Carolan HE, Giménez M, Sampath R, Ecker DJ, Quesada MD, Mòdol JM, Arméstar F, Blyn LB, Cummins LL, Ausina V, Martró E. Rapid diagnosis of bloodstream infections with PCR followed by mass spectrometry. PLoS One 2013; 8:e62108. [PMID: 23626775 PMCID: PMC3633912 DOI: 10.1371/journal.pone.0062108] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Accepted: 03/19/2013] [Indexed: 01/30/2023] Open
Abstract
Achieving a rapid microbiological diagnosis is crucial for decreasing morbidity and mortality of patients with a bloodstream infection, as it leads to the administration of an appropriate empiric antimicrobial therapy. Molecular methods may offer a rapid alternative to conventional microbiological diagnosis involving blood culture. In this study, the performance of a new technology that uses broad-spectrum PCR coupled with mass spectrometry (PCR/ESI-MS) was evaluated for the detection of microorganisms directly from whole blood. A total of 247 whole blood samples and paired blood cultures were prospectively obtained from 175 patients with a suspicion of sepsis. Both sample types were analyzed using the PCR/ESI-MS technology, and the results were compared with those obtained by conventional identification methods. The overall agreement between conventional methods and PCR/ESI-MS performed in blood culture aliquots was 94.2% with 96.8% sensitivity and 98.5% specificity for the molecular method. When comparing conventional methods with PCR/ESI-MS performed in whole blood specimens, the overall agreement was 77.1% with 50% sensitivity and 93.8% specificity for the molecular method. Interestingly, the PCR/ESI-MS technology led to the additional identification of 13 pathogens that were not found by conventional methods. Using the PCR/ESI-MS technology the microbiological diagnosis of bloodstream infections could be anticipated in about half of the patients in our setting, including a small but significant proportion of patients newly diagnosed. Thus, this promising technology could be very useful for the rapid diagnosis of sepsis in combination with traditional methods.
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Affiliation(s)
- Elena Jordana-Lluch
- Microbiology Department, Fundació Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Heather E. Carolan
- Ibis Biosciences, an Abbott company, Carlsbad, California, United States of America
| | - Montserrat Giménez
- Microbiology Department, Fundació Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Rangarajan Sampath
- Ibis Biosciences, an Abbott company, Carlsbad, California, United States of America
| | - David J. Ecker
- Ibis Biosciences, an Abbott company, Carlsbad, California, United States of America
| | - M. Dolores Quesada
- Microbiology Department, Fundació Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Josep M. Mòdol
- Emergency Room, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Fernando Arméstar
- Intensive Care Unit, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Lawrence B. Blyn
- Ibis Biosciences, an Abbott company, Carlsbad, California, United States of America
| | - Lendell L. Cummins
- Ibis Biosciences, an Abbott company, Carlsbad, California, United States of America
| | - Vicente Ausina
- Microbiology Department, Fundació Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
- CIBER Enfermedades Respiratorias (CIBERES), Bunyola, Spain
- * E-mail:
| | - Elisa Martró
- Microbiology Department, Fundació Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
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Duncan D, Vogler A, Wolcott M, Li F, Sarovich D, Birdsell D, Watson L, Hall T, Sampath R, Housley R, Blyn L, Hofstadler S, Ecker D, Keim P, Wagner D, Eshoo M. Identification and typing of Francisella tularensis
with a highly automated genotyping assay. Lett Appl Microbiol 2012; 56:128-34. [DOI: 10.1111/lam.12022] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 10/24/2012] [Accepted: 10/29/2012] [Indexed: 01/21/2023]
Affiliation(s)
- D.D. Duncan
- Ibis Biosciences, an Abbott company; Carlsbad CA USA
| | - A.J. Vogler
- Center for Microbial Genetics and Genomics; Northern Arizona University; Flagstaff AZ USA
| | - M.J. Wolcott
- United States Army Medical Research Institute of Infectious Diseases; Fort Detrick MD USA
| | - F. Li
- Ibis Biosciences, an Abbott company; Carlsbad CA USA
| | - D.S. Sarovich
- Center for Microbial Genetics and Genomics; Northern Arizona University; Flagstaff AZ USA
| | - D.N. Birdsell
- Center for Microbial Genetics and Genomics; Northern Arizona University; Flagstaff AZ USA
| | - L.M. Watson
- Center for Microbial Genetics and Genomics; Northern Arizona University; Flagstaff AZ USA
| | - T.A. Hall
- Ibis Biosciences, an Abbott company; Carlsbad CA USA
| | - R. Sampath
- Ibis Biosciences, an Abbott company; Carlsbad CA USA
| | - R. Housley
- Ibis Biosciences, an Abbott company; Carlsbad CA USA
| | - L.B. Blyn
- Ibis Biosciences, an Abbott company; Carlsbad CA USA
| | | | - D.J. Ecker
- Ibis Biosciences, an Abbott company; Carlsbad CA USA
| | - P. Keim
- Center for Microbial Genetics and Genomics; Northern Arizona University; Flagstaff AZ USA
| | - D.M. Wagner
- Center for Microbial Genetics and Genomics; Northern Arizona University; Flagstaff AZ USA
| | - M.W. Eshoo
- Ibis Biosciences, an Abbott company; Carlsbad CA USA
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Abstract
AIM (1) To investigate the recurrence of periocular basal cell carcinoma (BCC) reported as completely excised on histology. (2) To identify risks associated with recurrence. (3) To recommend a rational follow-up protocol. METHODS This is a cohort study by case note review of consecutive patients undergoing excision of periocular BCC between 2000 and 2006 at University Hospitals of Leicester. All lesions were excised with 3 mm clinical margin and the defect reconstructed only after the excision margin was declared clear. RESULTS A total of 413 episodes of surgical excision were recorded for 270 patients over the 7-year period of 2000-2006. All of them have 5 years follow-up. Mean age 73.7 (±12.5). In all, 67% were nodular BCC and 45.4% located in the lower eyelid. The main outcome measure was the recurrence rate. None of the patients with primary nodular BCC suffered recurrence. The recurrence rate for primary morphoeaform BCC following complete excision is 3.8%. In total, 8.1% of patients had several lesions simultaneously whereas 7.8% patients had BCC in multiple locations subsequently (metachronous). Three patients who had previously recurrent BCC (rBCC) treated elsewhere or not using this method had orbital/lacrimal drainage system involvement requiring exenteration. CONCLUSION We recommend that patients with a single, completely excised primary solid or nodular BCC can be discharged after one 6-monthly review, although they should be instructed to monitor for the development of further lesions. The incidence of recurrence for primary morphoeaform BCC is 3.8% and for rBCC is 3.6% over 5 years and these patients should stay under review for this period.
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Affiliation(s)
- S F Ho
- Department of Ophthalmology, Leicester Royal Infirmary, Leicester, UK.
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45
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Abstract
BACKGROUND Antiphospholipid syndrome (APS) is defined as the presence of venous or arterial thrombosis, and/or recurrent miscarriage with evidence of antiphospholipid antibodies (aPL). In both primary and secondary APS, ocular and neurophthalmic manifestations such as retinal arteritis, retinal venous occlusion, ischemic optic neuropathy, transient loss of vision - amaurosis fugax, diplopia have been reported. MATERIALS AND METHODS We present an unusual case of APS in a healthy 24-year old male who had isolated ocular presentation with recurrent right periocular oedema and non-healing ulceration of the biopsy site without systemic involvement. Ocular examinations and investigations including inflammatory markers were normal. CONCLUSION Atypical presentations of APS may result in initial difficulty in making diagnosis.
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Affiliation(s)
- A Rahim
- University Hospital Leicester, Leicester, Leicester, UK.
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46
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Crowder CD, Matthews HE, Rounds MA, Li F, Schutzer SE, Sampath R, Sampath R, Hofstadler SA, Ecker DJ, Eshoo MW. Detection of heartworm infection in dogs via PCR amplification and electrospray ionization mass spectrometry of nucleic acid extracts from whole blood samples. Am J Vet Res 2012; 73:854-9. [PMID: 22620700 DOI: 10.2460/ajvr.73.6.854] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
OBJECTIVE To develop and evaluate a rapid and accurate assay involving PCR amplification and electrospray ionization mass spectrometry of nucleic acid extracts from whole blood samples for the detection of Dirofilaria immitis infection in dogs. SAMPLE Whole blood nucleic acid extracts from 29 dogs experimentally infected with D immitis (and in which circulating D immitis antigen was detected) and 10 uninfected dogs. PROCEDURES 16 of the 29 whole blood samples from infected dogs were examined at the time of collection for circulating microfilaria. Nucleic acids were extracted from all whole blood specimens and underwent PCR amplification with 12 PCR primer pairs designed to detect a wide range of pathogens (including the Wolbachia endosymbiont of D immitis) and electrospray ionization mass spectrometry. RESULTS On the basis of assay results, heartworm infection was detected in 13 of 13 antigen-positive dogs of unknown microfilaria status, 11 of 11 antigen-positive dogs with circulating microfilaria, 0 of 3 antigen-positive dogs tested at 3 months after larval infection, 0 of 2 antigen-positive dogs with occult infections, and 0 of 10 uninfected dogs. CONCLUSIONS AND CLINICAL RELEVANCE With the assay under investigation, it was possible to identify D immitis infection in dogs with circulating microfilaria via detection of the obligate Wolbachia endosymbiont of D immitis. It was not possible to identify dogs with occult infections, which suggested that circulating microfilaria must be present to detect infection with this assay, although further studies would be required to verify that finding.
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47
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Jacob D, Sauer U, Housley R, Washington C, Sannes-Lowery K, Ecker DJ, Sampath R, Grunow R. Rapid and high-throughput detection of highly pathogenic bacteria by Ibis PLEX-ID technology. PLoS One 2012; 7:e39928. [PMID: 22768173 PMCID: PMC3386907 DOI: 10.1371/journal.pone.0039928] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Accepted: 06/04/2012] [Indexed: 11/18/2022] Open
Abstract
In this manuscript, we describe the identification of highly pathogenic bacteria using an assay coupling biothreat group-specific PCR with electrospray ionization mass spectrometry (PCR/ESI-MS) run on an Ibis PLEX-ID high-throughput platform. The biothreat cluster assay identifies most of the potential bioterrorism-relevant microorganisms including Bacillus anthracis, Francisella tularensis, Yersinia pestis, Burkholderia mallei and pseudomallei, Brucella species, and Coxiella burnetii. DNA from 45 different reference materials with different formulations and different concentrations were chosen and sent to a service screening laboratory that uses the PCR/ESI-MS platform to provide a microbial identification service. The standard reference materials were produced out of a repository built up in the framework of the EU funded project "Establishment of Quality Assurances for Detection of Highly Pathogenic Bacteria of Potential Bioterrorism Risk" (EQADeBa). All samples were correctly identified at least to the genus level.
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Affiliation(s)
| | | | - Roberta Housley
- Ibis Biosciences, Inc., an Abbott Company, Carlsbad, California, United States of America
| | | | | | - David J. Ecker
- Ibis Biosciences, Inc., an Abbott Company, Carlsbad, California, United States of America
| | - Rangarajan Sampath
- Ibis Biosciences, Inc., an Abbott Company, Carlsbad, California, United States of America
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48
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Sampath R, Mulholland N, Blyn LB, Massire C, Whitehouse CA, Waybright N, Harter C, Bogan J, Miranda MS, Smith D, Baldwin C, Wolcott M, Norwood D, Kreft R, Frinder M, Lovari R, Yasuda I, Matthews H, Toleno D, Housley R, Duncan D, Li F, Warren R, Eshoo MW, Hall TA, Hofstadler SA, Ecker DJ. Comprehensive biothreat cluster identification by PCR/electrospray-ionization mass spectrometry. PLoS One 2012; 7:e36528. [PMID: 22768032 PMCID: PMC3387173 DOI: 10.1371/journal.pone.0036528] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Accepted: 04/02/2012] [Indexed: 11/18/2022] Open
Abstract
Technology for comprehensive identification of biothreats in environmental and clinical specimens is needed to protect citizens in the case of a biological attack. This is a challenge because there are dozens of bacterial and viral species that might be used in a biological attack and many have closely related near-neighbor organisms that are harmless. The biothreat agent, along with its near neighbors, can be thought of as a biothreat cluster or a biocluster for short. The ability to comprehensively detect the important biothreat clusters with resolution sufficient to distinguish the near neighbors with an extremely low false positive rate is required. A technological solution to this problem can be achieved by coupling biothreat group-specific PCR with electrospray ionization mass spectrometry (PCR/ESI-MS). The biothreat assay described here detects ten bacterial and four viral biothreat clusters on the NIAID priority pathogen and HHS/USDA select agent lists. Detection of each of the biothreat clusters was validated by analysis of a broad collection of biothreat organisms and near neighbors prepared by spiking biothreat nucleic acids into nucleic acids extracted from filtered environmental air. Analytical experiments were carried out to determine breadth of coverage, limits of detection, linearity, sensitivity, and specificity. Further, the assay breadth was demonstrated by testing a diverse collection of organisms from each biothreat cluster. The biothreat assay as configured was able to detect all the target organism clusters and did not misidentify any of the near-neighbor organisms as threats. Coupling biothreat cluster-specific PCR to electrospray ionization mass spectrometry simultaneously provides the breadth of coverage, discrimination of near neighbors, and an extremely low false positive rate due to the requirement that an amplicon with a precise base composition of a biothreat agent be detected by mass spectrometry.
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Affiliation(s)
- Rangarajan Sampath
- Ibis Biosciences, Abbott, Carlsbad, California, United States of America.
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49
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Jeng K, Massire C, Zembower TR, Deyde VM, Gubareva LV, Hsieh YH, Rothman RE, Sampath R, Penugonda S, Metzgar D, Blyn LB, Hardick J, Gaydos CA. Monitoring seasonal influenza A evolution: rapid 2009 pandemic H1N1 surveillance with an reverse transcription-polymerase chain reaction/electro-spray ionization mass spectrometry assay. J Clin Virol 2012; 54:332-6. [PMID: 22673129 DOI: 10.1016/j.jcv.2012.05.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Revised: 04/16/2012] [Accepted: 05/01/2012] [Indexed: 11/29/2022]
Abstract
BACKGROUND The emergence of the pandemic H1N1 influenza strain in 2009 reinforced the need for improved influenza surveillance efforts. A previously described influenza typing assay that utilizes RT-PCR coupled to electro-spray ionization mass spectrometry (ESI-MS) played an early role in the discovery of the pandemic H1N1 influenza strain, and has potential application for monitoring viral genetic diversity in ongoing influenza surveillance efforts. OBJECTIVES To determine the analytical sensitivity of RT-PCR/ESI-MS influenza typing assay for identifying the pandemic H1N1 strain and describe its ability to assess viral genetic diversity. STUDY DESIGN Two sets of pandemic H1N1 samples, 190 collected between April and June of 2009, and 69 collected between October 2009 and January 2010, were processed by the RT-PCR/ESI-MS influenza typing assay, and the spectral results were compared to reference laboratory results and historical sequencing data from the Nucleotide Database of the National Center for Biotechnology Information (NCBI). RESULTS Strain typing concordance with reference standard testing was 100% in both sample sets, and the assay demonstrated a significant increase in influenza genetic diversity, from 10.5% non-wildtype genotypes in early samples to 69.9% in late samples (P<0.001). An NCBI search demonstrated a similar increase, from 13.4% to 45.2% (P<0.001). CONCLUSIONS This comparison of early versus late influenza samples analyzed by RT-PCR/ESI-MS demonstrates the influenza typing assay's ability as a universal influenza detection platform to provide high-fidelity pH1N1 strain identification over time, despite increasing genetic diversity in the circulating virus. The genotyping data can also be leveraged for high-throughput influenza surveillance.
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Affiliation(s)
- Kevin Jeng
- Johns Hopkins University, Baltimore, MD, USA.
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50
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Koster F, Gouveia K, Zhou Y, Lowery K, Russell R, MacInnes H, Pollock Z, Layton RC, Cromwell J, Toleno D, Pyle J, Zubelewicz M, Harrod K, Sampath R, Hofstadler S, Gao P, Liu Y, Cheng YS. Exhaled aerosol transmission of pandemic and seasonal H1N1 influenza viruses in the ferret. PLoS One 2012; 7:e33118. [PMID: 22509254 PMCID: PMC3317934 DOI: 10.1371/journal.pone.0033118] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Accepted: 02/04/2012] [Indexed: 11/26/2022] Open
Abstract
Person-to-person transmission of influenza viruses occurs by contact (direct and fomites) and non-contact (droplet and small particle aerosol) routes, but the quantitative dynamics and relative contributions of these routes are incompletely understood. The transmissibility of influenza strains estimated from secondary attack rates in closed human populations is confounded by large variations in population susceptibilities. An experimental method to phenotype strains for transmissibility in an animal model could provide relative efficiencies of transmission. We developed an experimental method to detect exhaled viral aerosol transmission between unanesthetized infected and susceptible ferrets, measured aerosol particle size and number, and quantified the viral genomic RNA in the exhaled aerosol. During brief 3-hour exposures to exhaled viral aerosols in airflow-controlled chambers, three strains of pandemic 2009 H1N1 strains were frequently transmitted to susceptible ferrets. In contrast one seasonal H1N1 strain was not transmitted in spite of higher levels of viral RNA in the exhaled aerosol. Among three pandemic strains, the two strains causing weight loss and illness in the intranasally infected 'donor' ferrets were transmitted less efficiently from the donor than the strain causing no detectable illness, suggesting that the mucosal inflammatory response may attenuate viable exhaled virus. Although exhaled viral RNA remained constant, transmission efficiency diminished from day 1 to day 5 after donor infection. Thus, aerosol transmission between ferrets may be dependent on at least four characteristics of virus-host relationships including the level of exhaled virus, infectious particle size, mucosal inflammation, and viral replication efficiency in susceptible mucosa.
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Affiliation(s)
- Frederick Koster
- Program in Applied Science, Lovelace Respiratory Research Institute, Albuquerque, New Mexico, United States of America.
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