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Whitfield NN, Hogan CA, Chenoweth J, Hansen J, Hsu EB, Humphries R, Mann E, May L, Michelson EA, Rothman R, Self WH, Smithline HA, Karita HCS, Steingrub JS, Swedien D, Weissman A, Wright DW, Liesenfeld O, Shapiro NI. A standardized protocol using clinical adjudication to define true infection status in patients presenting to the emergency department with suspected infections and/or sepsis. Diagn Microbiol Infect Dis 2024; 110:116382. [PMID: 38850687 DOI: 10.1016/j.diagmicrobio.2024.116382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/28/2024] [Accepted: 05/30/2024] [Indexed: 06/10/2024]
Abstract
In absence of a "gold standard", a standardized clinical adjudication process was developed for a registrational trial of a transcriptomic host response (HR) test. Two physicians independently reviewed clinical data to adjudicate presence and source of bacterial and viral infections in emergency department patients. Discordant cases were resolved by a third physician. Agreement among 955 cases was 74.1% (708/955) for bacterial, 75.6% (722/955) for viral infections, and 71.2% (680/955) overall. Most discordances were minor (85.2%; 409/480) versus moderate (11.7%; 56/480) or complete (3.3%; 16/480). Concordance levels were lowest for bacterial skin and soft tissue infections (8.2%) and for viral respiratory tract infections (4.5%). This robust adjudication process can be used to evaluate HR tests and other diagnostics by regulatory agencies and for educating clinicians, laboratorians, and clinical researchers. Clinicaltrials.gov NCT04094818. SUMMARY: Without a gold standard for evaluating host response tests, clinical adjudication is a robust reference standard that is essential to determine the true infection status in diagnostic registrational clinical studies.
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Affiliation(s)
| | | | - James Chenoweth
- Department of Emergency Medicine, University of California-Davis School of Medicine, Sacramento, California, USA
| | - Jonathan Hansen
- Department of Emergency Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Edbert B Hsu
- Department of Emergency Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Roger Humphries
- Department of Emergency Medicine, University of Kentucky College of Medicine, Lexington, Kentucky, USA
| | - Edana Mann
- Department of Emergency Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Larissa May
- Department of Emergency Medicine, University of California-Davis School of Medicine, Sacramento, California, USA
| | - Edward A Michelson
- Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, Department of Emergency Medicine, El Paso, Texas, USA
| | - Richard Rothman
- Department of Emergency Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Wesley H Self
- Department of Emergency Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Howard A Smithline
- Department of Emergency Medicine, University of Massachusetts Chan Medical School - Baystate, Springfield, Massachusetts, USA
| | | | - Jay S Steingrub
- Department of Critical Care Medicine, University of Massachusetts Chan Medical School - Baystate, Springfield, Massachusetts, USA
| | - Daniel Swedien
- Department of Emergency Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Alexandra Weissman
- Department of Emergency Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - David W Wright
- Department of Emergency Medicine, Emory University School of Medicine, Atlanta, Georgia
| | | | - Nathan I Shapiro
- Beth Israel Deaconess Medical Center, Emergency Medicine, Boston, Massachusetts, USA
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McCravy M, O’Grady N, Khan K, Betancourt-Quiroz M, Zaas AK, Treece AE, Yang Z, Que L, Henao R, Suchindran S, Ginsburg GS, Woods CW, McClain MT, Tsalik EL. Predictive signature of murine and human host response to typical and atypical pneumonia. BMJ Open Respir Res 2024; 11:e002001. [PMID: 39097412 PMCID: PMC11298752 DOI: 10.1136/bmjresp-2023-002001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 07/08/2024] [Indexed: 08/05/2024] Open
Abstract
BACKGROUND Pneumonia due to typical bacterial, atypical bacterial and viral pathogens can be difficult to clinically differentiate. Host response-based diagnostics are emerging as a complementary diagnostic strategy to pathogen detection. METHODS We used murine models of typical bacterial, atypical bacterial and viral pneumonia to develop diagnostic signatures and understand the host's response to these types of infections. Mice were intranasally inoculated with Streptococcus pneumoniae, Mycoplasma pneumoniae, influenza or saline as a control. Peripheral blood gene expression analysis was performed at multiple time points. Differentially expressed genes were used to perform gene set enrichment analysis and generate diagnostic signatures. These murine-derived signatures were externally validated in silico using human gene expression data. The response to S. pneumoniae was the most rapid and robust. RESULTS Mice infected with M. pneumoniae had a delayed response more similar to influenza-infected animals. Diagnostic signatures for the three types of infection had 0.94-1.00 area under the receiver operator curve (auROC). Validation in five human gene expression datasets revealed auROC of 0.82-0.96. DISCUSSION This study identified discrete host responses to typical bacterial, atypical bacterial and viral aetiologies of pneumonia in mice. These signatures validated well in humans, highlighting the conserved nature of the host response to these pathogen classes.
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Affiliation(s)
- Matthew McCravy
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Nicholas O’Grady
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Kirin Khan
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | | | - Aimee K Zaas
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Amy E Treece
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Zhonghui Yang
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Loretta Que
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Ricardo Henao
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, North Carolina, USA
| | - Sunil Suchindran
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Geoffrey S Ginsburg
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Christopher W Woods
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Micah T McClain
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Ephraim L Tsalik
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
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3
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Thaden JT, Ahn R, Ruffin F, Gjertson DW, Hoffmann A, Fowler VG, Yeaman MR. Use of Transcriptional Signatures to Differentiate Pathogen-Specific and Treatment-Specific Host Responses in Patients With Bacterial Bloodstream Infections. J Infect Dis 2024; 229:1535-1545. [PMID: 38001039 PMCID: PMC11095544 DOI: 10.1093/infdis/jiad498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 10/26/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
BACKGROUND Clinical outcomes in bacterial bloodstream infections (BSIs) are influenced by bacterial species, host immunity, and antibiotic therapy. The mechanisms by which such factors influence outcomes are poorly understood. We aimed to identify bacterial- and antibiotic-specific host transcriptional signatures in patients with bacterial BSI. METHODS RNA sequencing was performed on blood samples from patients with BSI due to gram-negative (GN) versus gram-positive (GP) pathogens: Escherichia coli (n = 30) or Klebsiella pneumoniae (n = 28) versus methicillin-susceptible Staphylococcus aureus (MSSA) (n = 24) or methicillin-resistant S. aureus (MRSA) (n = 58). Patients were matched by age, sex, and race. RESULTS No significant host transcriptome differences were detected in patients with E. coli versus K. pneumoniae BSI, so these were considered together as GN BSI. Relative to S. aureus BSI, patients with GN BSI had increased activation of the classic complement system. However, the most significant signal was a reduction in host transcriptional signatures involving mitochondrial energy transduction and oxidative burst in MRSA versus MSSA. This attenuated host transcriptional signature remained after controlling for antibiotic therapy. CONCLUSIONS Given the importance of immune cellular energetics and reactive oxygen species in eliminating hematogenous or intracellular MRSA, these findings may offer insights into its persistence relative to other bacterial BSIs.
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Affiliation(s)
- Joshua T Thaden
- Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina, USA
| | - Richard Ahn
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, Los Angeles, California, USA
| | - Felicia Ruffin
- Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina, USA
| | - David W Gjertson
- Department of Biostatistics, University of California, Los Angeles, Los Angeles, California, USA
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Alexander Hoffmann
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, Los Angeles, California, USA
| | - Vance G Fowler
- Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina, USA
| | - Michael R Yeaman
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
- Department of Medicine, Divisions of Molecular Medicine and Infectious Diseases, Harbor-UCLA Medical Center, Torrance, California, USA
- Institute for Infection & Immunity, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, USA
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4
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Ivaska L, Herberg J, Sadarangani M. Distinguishing community-acquired bacterial and viral meningitis: Microbes and biomarkers. J Infect 2024; 88:106111. [PMID: 38307149 DOI: 10.1016/j.jinf.2024.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 01/16/2024] [Accepted: 01/22/2024] [Indexed: 02/04/2024]
Abstract
Diagnostic tools to differentiate between community-acquired bacterial and viral meningitis are essential to target the potentially lifesaving antibiotic treatment to those at greatest risk and concurrently spare patients with viral meningitis from the disadvantages of antibiotics. In addition, excluding bacterial meningitis and thus decreasing antibiotic consumption would be important to help reduce antimicrobial resistance and healthcare expenses. The available diagnostic laboratory tests for differentiating bacterial and viral meningitis can be divided microbiological pathogen-focussed methods and biomarkers of the host response. Bacterial culture-independent microbiological methods, such as highly multiplexed nucleic acid amplification tests, are rapidly making their way into the clinical practice. At the same time, more conventional host protein biomarkers, such as procalcitonin and C-reactive protein, are supplemented by newer proteomic and transcriptomic signatures. This review aims to summarise the current state and the recent advances in diagnostic methods to differentiate bacterial from viral meningitis.
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Affiliation(s)
- Lauri Ivaska
- Department of Paediatrics and Adolescent Medicine, Turku University Hospital and University of Turku, Savitehtaankatu 5, 20521 Turku, Finland; InFLAMES Research Flagship Center, University of Turku, Kiinanmyllynkatu 10, 20520 Turku, Finland.
| | - Jethro Herberg
- Section of Paediatric Infectious Disease, Faculty of Medicine, Imperial College London, Norfolk Place, London, United Kingdom.
| | - Manish Sadarangani
- Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada; Vaccine Evaluation Center, BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada.
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5
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Ko ER, Reller ME, Tillekeratne LG, Bodinayake CK, Miller C, Burke TW, Henao R, McClain MT, Suchindran S, Nicholson B, Blatt A, Petzold E, Tsalik EL, Nagahawatte A, Devasiri V, Rubach MP, Maro VP, Lwezaula BF, Kodikara-Arachichi W, Kurukulasooriya R, De Silva AD, Clark DV, Schully KL, Madut D, Dumler JS, Kato C, Galloway R, Crump JA, Ginsburg GS, Minogue TD, Woods CW. Host-response transcriptional biomarkers accurately discriminate bacterial and viral infections of global relevance. Sci Rep 2023; 13:22554. [PMID: 38110534 PMCID: PMC10728077 DOI: 10.1038/s41598-023-49734-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 12/11/2023] [Indexed: 12/20/2023] Open
Abstract
Diagnostic limitations challenge management of clinically indistinguishable acute infectious illness globally. Gene expression classification models show great promise distinguishing causes of fever. We generated transcriptional data for a 294-participant (USA, Sri Lanka) discovery cohort with adjudicated viral or bacterial infections of diverse etiology or non-infectious disease mimics. We then derived and cross-validated gene expression classifiers including: 1) a single model to distinguish bacterial vs. viral (Global Fever-Bacterial/Viral [GF-B/V]) and 2) a two-model system to discriminate bacterial and viral in the context of noninfection (Global Fever-Bacterial/Viral/Non-infectious [GF-B/V/N]). We then translated to a multiplex RT-PCR assay and independent validation involved 101 participants (USA, Sri Lanka, Australia, Cambodia, Tanzania). The GF-B/V model discriminated bacterial from viral infection in the discovery cohort an area under the receiver operator curve (AUROC) of 0.93. Validation in an independent cohort demonstrated the GF-B/V model had an AUROC of 0.84 (95% CI 0.76-0.90) with overall accuracy of 81.6% (95% CI 72.7-88.5). Performance did not vary with age, demographics, or site. Host transcriptional response diagnostics distinguish bacterial and viral illness across global sites with diverse endemic pathogens.
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Affiliation(s)
- Emily R Ko
- Division of General Internal Medicine, Department of Medicine, Duke Regional Hospital, Duke University Health System, Duke University School of Medicine, 3643 N. Roxboro St., Durham, NC, 27704, USA.
| | - Megan E Reller
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
- Durham Veterans Affairs Health Care System, Durham, NC, USA
- Duke Global Health Institute, Duke University, Durham, NC, USA
| | - L Gayani Tillekeratne
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
- Durham Veterans Affairs Health Care System, Durham, NC, USA
- Duke Global Health Institute, Duke University, Durham, NC, USA
- Department of Medicine, Faculty of Medicine, University of Ruhuna, Galle, Sri Lanka
| | - Champica K Bodinayake
- Duke Global Health Institute, Duke University, Durham, NC, USA
- Department of Medicine, Faculty of Medicine, University of Ruhuna, Galle, Sri Lanka
| | - Cameron Miller
- Clinical Research Unit, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Thomas W Burke
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Ricardo Henao
- Department of Biostatistics and Informatics, Duke University, Durham, NC, USA
| | - Micah T McClain
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
- Durham Veterans Affairs Health Care System, Durham, NC, USA
| | - Sunil Suchindran
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | | | - Adam Blatt
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Duke University School of Medicine, Durham, NC, USA
| | - Elizabeth Petzold
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Ephraim L Tsalik
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
- Danaher Diagnostics, Washington, DC, USA
| | - Ajith Nagahawatte
- Department of Microbiology, Faculty of Medicine, University of Ruhuna, Galle, Sri Lanka
| | - Vasantha Devasiri
- Department of Medicine, Faculty of Medicine, University of Ruhuna, Galle, Sri Lanka
| | - Matthew P Rubach
- Durham Veterans Affairs Health Care System, Durham, NC, USA
- Duke Global Health Institute, Duke University, Durham, NC, USA
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore, Singapore, Singapore
- Kilimanjaro Christian Medical Center, Moshi, Tanzania
| | - Venance P Maro
- Kilimanjaro Christian Medical Center, Moshi, Tanzania
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Bingileki F Lwezaula
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
- Maswenzi Regional Referral Hospital, Moshi, Tanzania
| | | | | | - Aruna D De Silva
- General Sir John Kotelawala Defence University, Colombo, Sri Lanka
| | - Danielle V Clark
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
- Austere Environments Consortium for Enhanced Sepsis Outcomes (ACESO), Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Ft. Detrick, MD, USA
| | - Kevin L Schully
- Austere Environments Consortium for Enhanced Sepsis Outcomes (ACESO), Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Ft. Detrick, MD, USA
| | - Deng Madut
- Durham Veterans Affairs Health Care System, Durham, NC, USA
- Duke Global Health Institute, Duke University, Durham, NC, USA
| | - J Stephen Dumler
- Joint Departments of Pathology, School of Medicine, Uniformed Services University, Bethesda, MD, USA
| | - Cecilia Kato
- Centers for Disease Control and Prevention, National Center for Emerging Zoonotic Infectious Diseases, Atlanta, USA
| | - Renee Galloway
- Centers for Disease Control and Prevention, National Center for Emerging Zoonotic Infectious Diseases, Atlanta, USA
| | - John A Crump
- Duke Global Health Institute, Duke University, Durham, NC, USA
- Department of Medicine, Faculty of Medicine, University of Ruhuna, Galle, Sri Lanka
- Kilimanjaro Christian Medical Center, Moshi, Tanzania
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
- Centre for International Health, University of Otago, Dunedin, New Zealand
| | - Geoffrey S Ginsburg
- Department of Medicine, Duke University School of Medicine, Durham, NC, USA
- National Institute of Health, Bethesda, MD, USA
| | - Timothy D Minogue
- Diagnostic Systems Division, USAMRIID, Fort Detrick, Frederick, MD, USA
| | - Christopher W Woods
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
- Durham Veterans Affairs Health Care System, Durham, NC, USA
- Duke Global Health Institute, Duke University, Durham, NC, USA
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6
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Rees CA, Kuppermann N, Florin TA. Community-Acquired Pneumonia in Children. Pediatr Emerg Care 2023; 39:968-976. [PMID: 38019716 DOI: 10.1097/pec.0000000000003070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
ABSTRACT Community-acquired pneumonia (CAP) is the most common cause of childhood mortality globally. In the United States, CAP is a leading cause of pediatric hospitalization and antibiotic use and is associated with substantial morbidity. There has been a dramatic shift in microbiological etiologies for CAP in children over time as pneumococcal pneumonia has become less common and viral etiologies have become predominant. There is no commonly agreed on approach to the diagnosis of CAP in children. When indicated, antimicrobial treatment should consist of narrow-spectrum antibiotics. In this article, we will describe the current understanding of the microbiological etiologies, clinical presentation, diagnostic approach, risk factors, treatment, and future directions in the diagnosis and management of pediatric CAP.
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Affiliation(s)
| | - Nathan Kuppermann
- Professor, Departments of Emergency Medicine and Pediatrics, University of California Davis Health, University of California Davis, School of Medicine, Sacramento, CA
| | - Todd A Florin
- Associate Professor, Department of Pediatrics, Northwestern University Feinberg School of Medicine and Division of Emergency Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL
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7
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Hanson KE, Banerjee R, Doernberg SB, Evans SR, Komarow L, Satlin MJ, Schwager N, Simner PJ, Tillekeratne LG, Patel R. Priorities and Progress in Diagnostic Research by the Antibacterial Resistance Leadership Group. Clin Infect Dis 2023; 77:S314-S320. [PMID: 37843119 PMCID: PMC10578045 DOI: 10.1093/cid/ciad541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2023] Open
Abstract
The advancement of infectious disease diagnostics, along with studies devoted to infections caused by gram-negative and gram-positive bacteria, is a top scientific priority of the Antibacterial Resistance Leadership Group (ARLG). Diagnostic tests for infectious diseases are rapidly evolving and improving. However, the availability of rapid tests designed to determine antibacterial resistance or susceptibility directly in clinical specimens remains limited, especially for gram-negative organisms. Additionally, the clinical impact of many new tests, including an understanding of how best to use them to inform optimal antibiotic prescribing, remains to be defined. This review summarizes the recent work of the ARLG toward addressing these unmet needs in the diagnostics field and describes future directions for clinical research aimed at curbing the threat of antibiotic-resistant bacterial infections.
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Affiliation(s)
- Kimberly E Hanson
- Division of Infectious Diseases, Department of Medicine, University of Utah, Salt Lake City, Utah, USA
- Division of Clinical Microbiology, Department of Pathology, University of Utah, Salt Lake City, Utah, USA
| | - Ritu Banerjee
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Sarah B Doernberg
- Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Scott R Evans
- Department of Biostatistics, George Washington University, Washington, DC, USA
| | - Lauren Komarow
- George Washington University Biostatistics Center, Rockville, Maryland, USA
| | - Michael J Satlin
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Nyssa Schwager
- Duke Clinical Research Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - Patricia J Simner
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - L Gayani Tillekeratne
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
- Duke Global Health Institute, Duke University, Durham, North Carolina, USA
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Division of Public Health, Infectious Diseases, and Occupational Medicine, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
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8
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Quach HQ, Goergen KM, Grill DE, Haralambieva IH, Ovsyannikova IG, Poland GA, Kennedy RB. Virus-specific and shared gene expression signatures in immune cells after vaccination in response to influenza and vaccinia stimulation. Front Immunol 2023; 14:1168784. [PMID: 37600811 PMCID: PMC10436507 DOI: 10.3389/fimmu.2023.1168784] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 07/18/2023] [Indexed: 08/22/2023] Open
Abstract
Background In the vaccine era, individuals receive multiple vaccines in their lifetime. Host gene expression in response to antigenic stimulation is usually virus-specific; however, identifying shared pathways of host response across a wide spectrum of vaccine pathogens can shed light on the molecular mechanisms/components which can be targeted for the development of broad/universal therapeutics and vaccines. Method We isolated PBMCs, monocytes, B cells, and CD8+ T cells from the peripheral blood of healthy donors, who received both seasonal influenza vaccine (within <1 year) and smallpox vaccine (within 1 - 4 years). Each of the purified cell populations was stimulated with either influenza virus or vaccinia virus. Differentially expressed genes (DEGs) relative to unstimulated controls were identified for each in vitro viral infection, as well as for both viral infections (shared DEGs). Pathway enrichment analysis was performed to associate identified DEGs with KEGG/biological pathways. Results We identified 2,906, 3,888, 681, and 446 DEGs in PBMCs, monocytes, B cells, and CD8+ T cells, respectively, in response to influenza stimulation. Meanwhile, 97, 120, 20, and 10 DEGs were identified as gene signatures in PBMCs, monocytes, B cells, and CD8+ T cells, respectively, upon vaccinia stimulation. The majority of DEGs identified in PBMCs were also found in monocytes after either viral stimulation. Of the virus-specific DEGs, 55, 63, and 9 DEGs occurred in common in PBMCs, monocytes, and B cells, respectively, while no DEGs were shared in infected CD8+ T cells after influenza and vaccinia. Gene set enrichment analysis demonstrated that these shared DEGs were over-represented in innate signaling pathways, including cytokine-cytokine receptor interaction, viral protein interaction with cytokine and cytokine receptor, Toll-like receptor signaling, RIG-I-like receptor signaling pathways, cytosolic DNA-sensing pathways, and natural killer cell mediated cytotoxicity. Conclusion Our results provide insights into virus-host interactions in different immune cells, as well as host defense mechanisms against viral stimulation. Our data also highlights the role of monocytes as a major cell population driving gene expression in ex vivo PBMCs in response to viral stimulation. The immune response signaling pathways identified in this study may provide specific targets for the development of novel virus-specific therapeutics and improved vaccines for vaccinia and influenza. Although influenza and vaccinia viruses have been selected in this study as pathogen models, this approach could be applicable to other pathogens.
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Affiliation(s)
- Huy Quang Quach
- Mayo Clinic Vaccine Research Group, Division of General Internal Medicine, Mayo Clinic, Rochester, MN, United States
| | - Krista M. Goergen
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, United States
| | - Diane E. Grill
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, United States
| | - Iana H. Haralambieva
- Mayo Clinic Vaccine Research Group, Division of General Internal Medicine, Mayo Clinic, Rochester, MN, United States
| | - Inna G. Ovsyannikova
- Mayo Clinic Vaccine Research Group, Division of General Internal Medicine, Mayo Clinic, Rochester, MN, United States
| | - Gregory A. Poland
- Mayo Clinic Vaccine Research Group, Division of General Internal Medicine, Mayo Clinic, Rochester, MN, United States
| | - Richard B. Kennedy
- Mayo Clinic Vaccine Research Group, Division of General Internal Medicine, Mayo Clinic, Rochester, MN, United States
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Tsalik EL, Rouphael NG, Sadikot RT, Rodriguez-Barradas MC, McClain MT, Wilkins DM, Woods CW, Swamy GK, Walter EB, El Sahly HM, Keitel WA, Mulligan MJ, Tuyishimire B, Serti E, Hamasaki T, Evans SR, Ghazaryan V, Lee MS, Lautenbach E. Efficacy and safety of azithromycin versus placebo to treat lower respiratory tract infections associated with low procalcitonin: a randomised, placebo-controlled, double-blind, non-inferiority trial. THE LANCET. INFECTIOUS DISEASES 2023; 23:484-495. [PMID: 36525985 PMCID: PMC10040424 DOI: 10.1016/s1473-3099(22)00735-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/24/2022] [Accepted: 10/27/2022] [Indexed: 12/15/2022]
Abstract
BACKGROUND Lower respiratory tract infections are frequently treated with antibiotics, despite a viral cause in many cases. It remains unknown whether low procalcitonin concentrations can identify patients with lower respiratory tract infection who are unlikely to benefit from antibiotics. We aimed to compare the efficacy and safety of azithromycin versus placebo to treat lower respiratory tract infections in patients with low procalcitonin. METHODS We conducted a randomised, placebo-controlled, double-blind, non-inferiority trial at five health centres in the USA. Adults aged 18 years or older with clinically suspected non-pneumonia lower respiratory tract infection and symptom duration from 24 h to 28 days were eligible for enrolment. Participants with a procalcitonin concentration of 0·25 ng/mL or less were randomly assigned (1:1), in blocks of four with stratification by site, to receive over-encapsulated oral azithromycin 250 mg or matching placebo (two capsules on day 1 followed by one capsule daily for 4 days). Participants, non-study clinical providers, investigators, and study coordinators were masked to treatment allocation. The primary outcome was efficacy of azithromycin versus placebo in terms of clinical improvement at day 5 in the intention-to-treat population. The non-inferiority margin was -12·5%. Solicited adverse events (abdominal pain, vomiting, diarrhoea, allergic reaction, or yeast infections) were recorded as a secondary outcome. This trial is registered with ClinicalTrials.gov, NCT03341273. FINDINGS Between Dec 8, 2017, and March 9, 2020, 691 patients were assessed for eligibility and 499 were enrolled and randomly assigned to receive azithromycin (n=249) or placebo (n=250). Clinical improvement at day 5 was observed in 148 (63%, 95% CI 54 to 71) of 238 participants with full data in the placebo group and 155 (69%, 61 to 77) of 227 participants with full data in the azithromycin group in the intention-to-treat analysis (between-group difference -6%, 95% CI -15 to 2). The 95% CI for the difference did not meet the non-inferiority margin. Solicited adverse events and the severity of solicited adverse events were not significantly different between groups at day 5, except for increased abdominal pain associated with azithromycin (47 [23%, 95% CI 18 to 29] of 204 participants) compared with placebo (35 [16%, 12 to 21] of 221; between-group difference -7% [95% CI -15 to 0]; p=0·066). INTERPRETATION Placebo was not non-inferior to azithromycin in terms of clinical improvement at day 5 in adults with lower respiratory tract infection and a low procalcitonin concentration. After accounting for both the rates of clinical improvement and solicited adverse events at day 5, it is unclear whether antibiotics are indicated for patients with lower respiratory tract infection and a low procalcitonin concentration. FUNDING National Institute of Allergy and Infectious Diseases, bioMérieux.
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Affiliation(s)
- Ephraim L Tsalik
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, USA; Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, USA; Emergency Medicine Service, Durham VA Health Care System, Durham, NC, USA.
| | - Nadine G Rouphael
- Hope Clinic of the Emory Vaccine Center, Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Ruxana T Sadikot
- Atlanta VA Health Care System, Atlanta, GA, USA; Medical Service, VA Nebraska-Western Iowa Health Care System, Omaha, NE, USA; Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE, USA
| | - Maria C Rodriguez-Barradas
- Infectious Diseases Section, Michael E DeBakey VA Medical Center and Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Micah T McClain
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, USA; Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, USA; Medical Service, Durham VA Health Care System, Durham, NC, USA
| | | | - Christopher W Woods
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, USA; Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, USA; Medical Service, Durham VA Health Care System, Durham, NC, USA
| | - Geeta K Swamy
- Department of Obstetrics and Gynecology, Duke University School of Medicine, Durham, NC, USA; Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Emmanuel B Walter
- Department of Pediatrics, Duke University School of Medicine, Durham, NC, USA; Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Hana M El Sahly
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA; Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Wendy A Keitel
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA; Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Mark J Mulligan
- Hope Clinic of the Emory Vaccine Center, Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA; Division of Infectious Diseases and Immunology, NYU Langone Health, New York, NY, USA
| | | | | | - Toshimitsu Hamasaki
- Biostatistics Center, Milken Institute School of Public Health, George Washington University, Rockville, MD, USA; Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, George Washington University, Rockville, MD, USA
| | - Scott R Evans
- Biostatistics Center, Milken Institute School of Public Health, George Washington University, Rockville, MD, USA; Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, George Washington University, Rockville, MD, USA
| | - Varduhi Ghazaryan
- Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Marina S Lee
- Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Ebbing Lautenbach
- Division of Infectious Diseases, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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10
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Patel R, Tsalik EL, Evans S, Fowler VG, Doernberg SB. Clinically Adjudicated Reference Standards for Evaluation of Infectious Diseases Diagnostics. Clin Infect Dis 2023; 76:938-943. [PMID: 36262037 PMCID: PMC10226744 DOI: 10.1093/cid/ciac829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/06/2022] [Accepted: 10/13/2022] [Indexed: 11/13/2022] Open
Abstract
Lack of a gold standard can present a challenge for evaluation of diagnostic test accuracy of some infectious diseases tests, particularly when the test's accuracy potentially exceeds that of its predecessors. This approach may measure agreement with an imperfect reference, rather than correctness, because the right answer is unknown. Solutions consist of multitest comparators, including those that involve a test under evaluation if multiple new tests are being evaluated together, using latent class modeling, and clinically adjudicated reference standards. Clinically adjudicated reference standards may be considered as comparator methods when no predefined test or composite of tests is sufficiently accurate; they emulate clinical practice in that multiple data pieces are clinically assessed together.
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Affiliation(s)
- Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Division of Public Health, Infectious Diseases and Occupational Medicine, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Ephraim L Tsalik
- Emergency Medicine Service, Durham VA Health Care System, Durham, North Carolina, USA
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
- Danaher Diagnostics, Washington, District of Columbia, USA
| | - Scott Evans
- Biostatistics Center and the Department of Biostatistics and Bioinformatics, George Washington Milken Institute School of Public Health, George Washington University, Washington, District of Columbia, USA
| | - Vance G Fowler
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
- Duke Clinical Research Institute, Durham, North Carolina, USA
| | - Sarah B Doernberg
- Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, California, USA
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11
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de la Fuente A, García-Mateo N, Bermejo-Martin JF. Prime-time for clinical use of transcriptomics for differentiating viral from bacterial respiratory infection. Eur J Clin Invest 2023; 53:e13967. [PMID: 36748118 DOI: 10.1111/eci.13967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 02/03/2023] [Accepted: 02/05/2023] [Indexed: 02/08/2023]
Affiliation(s)
- Amanda de la Fuente
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca (IBSAL), Gerencia Regional de Salud de Castilla y León, Salamanca, Spain.,CIBER de Enfermedades Respiratorias, CB22/06/00035, Instituto de Salud Carlos III, Madrid, Spain
| | - Nadia García-Mateo
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca (IBSAL), Gerencia Regional de Salud de Castilla y León, Salamanca, Spain
| | - Jesús F Bermejo-Martin
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca (IBSAL), Gerencia Regional de Salud de Castilla y León, Salamanca, Spain.,CIBER de Enfermedades Respiratorias, CB22/06/00035, Instituto de Salud Carlos III, Madrid, Spain.,School of Medicine, Universidad de Salamanca, Salamanca, Spain
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12
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Scott J, Deresinski S. Use of biomarkers to individualize antimicrobial therapy duration: a narrative review. Clin Microbiol Infect 2023; 29:160-164. [PMID: 36096429 DOI: 10.1016/j.cmi.2022.08.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 08/28/2022] [Accepted: 08/31/2022] [Indexed: 02/07/2023]
Abstract
BACKGROUND Reducing the overuse of antimicrobials is imperative for the sake of minimizing antimicrobial-associated adverse effects, optimizing resource utilization, and curtailing the rise in multidrug-resistant organisms. Biomarkers reflect the host responses to infection and may assist with minimizing unnecessary antimicrobial usage. OBJECTIVES To review the literature pertaining to the performance of biomarkers specifically used to guide the duration of antimicrobial therapy (AMT). SOURCES Randomized controlled trials, observational studies, and meta-analyses assessing biomarker-guided approaches to AMT decision-making and their impact on the duration of therapy were reviewed. CONTENT Several randomized controlled trials and real-world observational studies have shown that a procalcitonin (PCT)-guided strategy can help clinicians individualize the duration of AMT, particularly among non-critically ill patients hospitalized with suspected respiratory tract infections when using a PCT cut-off value of <0.25 μg/L and critically ill patients with respiratory tract infections or undifferentiated sepsis when using a PCT cut-off value of <0.5 μg/L or ≥80% decline in the peak level. C-reactive protein is a non-specific marker of inflammation that may also assist with an early discontinuation of AMT; however, data are limited. Haematological biomarkers are prone to variance between individuals and are often influenced by medications and non-infectious conditions, making them less reliable for the purposes of AMT decision-making. Novel biomarkers such as multi-protein signatures and host gene expression tests have shown promise as tools to better differentiate between bacterial and non-bacterial infections; clinical studies are needed to determine whether they can be used to help optimize the duration of AMT. IMPLICATIONS Studies have demonstrated that a PCT-guided strategy, when utilized appropriately, can help guide clinicians to individualize and often reduce the duration of AMT, especially in patients hospitalized with respiratory tract infections and those admitted to the intensive care unit with suspected respiratory tract infections or sepsis. The impact of utilizing other biomarkers is less clear and requires further study.
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Affiliation(s)
- Jake Scott
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA, USA.
| | - Stan Deresinski
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA, USA
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13
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Ko ER, Tsalik EL. A New Era in Host Response Biomarkers to Guide Precision Medicine for Infectious Diseases. J Pediatric Infect Dis Soc 2022; 11:477-479. [PMID: 35964237 DOI: 10.1093/jpids/piac081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 07/21/2022] [Indexed: 11/14/2022]
Affiliation(s)
- Emily R Ko
- Section of Hospital Medicine, Division of General Internal Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Ephraim L Tsalik
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA.,Danaher Diagnostics, Washington DC, USA
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14
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Watkins RR. Antibiotic stewardship in the era of precision medicine. JAC Antimicrob Resist 2022; 4:dlac066. [PMID: 35733911 PMCID: PMC9209748 DOI: 10.1093/jacamr/dlac066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Antimicrobial resistance (AMR) continues to spread at an alarming rate worldwide. Novel approaches are needed to mitigate its deleterious impact on antibiotic efficacy. Antibiotic stewardship aims to promote the appropriate use of antibiotics through evidence-based interventions. One paradigm is precision medicine, a medical model in which decisions, practices, interventions, and therapies are adapted to the individual patient based on their predicted response or risk of disease. Precision medicine approaches hold promise as a way to improve outcomes for patients with myriad illnesses, including infections such as bacteraemia and pneumonia. This review describes the latest advances in precision medicine as they pertain to antibiotic stewardship, with an emphasis on hospital-based antibiotic stewardship programmes. The impact of the COVID-19 pandemic on AMR and antibiotic stewardship, gaps in the scientific evidence, and areas for further research are also discussed.
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Affiliation(s)
- Richard R Watkins
- Department of Medicine, Northeast Ohio Medical University , Rootstown, OH , USA
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