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Cash-Goldwasser S, Beeson A, Marzec N, Ho DY, Hogan CA, Budvytiene I, Banaei N, Born DE, Gephart MH, Patel J, Dietrich EA, Nelson CA. Neuroinvasive Francisella tularensis Infection: Report of 2 Cases and Review of the Literature. Clin Infect Dis 2024; 78:S55-S63. [PMID: 38294117 DOI: 10.1093/cid/ciad719] [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] [Indexed: 02/01/2024] Open
Abstract
BACKGROUND Neuroinvasive infection with Francisella tularensis, the causative agent of tularemia, is rare. Establishing clinical suspicion is challenging if risk factors or clinical features classically associated with tularemia are absent. Tularemia is treatable with antibiotics; however, there are limited data to inform management of potentially fatal neuroinvasive infection. METHODS We collected epidemiologic and clinical data on 2 recent US cases of neuroinvasive F. tularensis infection, and performed a literature review of cases of neuroinvasive F. tularensis infection published after 1950. RESULTS One patient presented with focal neurologic deficits and brain lesions; broad-range molecular testing on resected brain tissue detected F. tularensis. The other patient presented with meningeal signs; tularemia was suspected based on animal exposure, and F. tularensis grew in cerebrospinal fluid (CSF) culture. Both patients received combination antibiotic therapy and recovered from infection. Among 16 published cases, tularemia was clinically suspected in 4 cases. CSF often displayed lymphocytic pleocytosis. Among cases with available data, CSF culture was positive in 13 of 16 cases, and F. tularensis antibodies were detected in 11 of 11 cases. Treatment typically included an aminoglycoside combined with either a tetracycline or a fluoroquinolone. Outcomes were generally favorable. CONCLUSIONS Clinicians should consider neuroinvasive F. tularensis infection in patients with meningitis and signs suggestive of tularemia or compatible exposures, lymphocyte-predominant CSF, unrevealing standard microbiologic workup, or lack of response to empiric bacterial meningitis treatment. Molecular testing, culture, and serologic testing can reveal the diagnosis. Favorable outcomes can be achieved with directed antibiotic treatment.
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Affiliation(s)
- Shama Cash-Goldwasser
- Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Amy Beeson
- Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado, USA
| | - Natalie Marzec
- Colorado Department of Public Health and Environment, Denver, Colorado, USA
| | - Dora Y Ho
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Catherine A Hogan
- Clinical Microbiology Laboratory, Stanford University Medical Center, Stanford, California, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Indre Budvytiene
- Clinical Microbiology Laboratory, Stanford University Medical Center, Stanford, California, USA
| | - Niaz Banaei
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
- Clinical Microbiology Laboratory, Stanford University Medical Center, Stanford, California, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Donald E Born
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Melanie H Gephart
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, California, USA
| | | | - Elizabeth A Dietrich
- Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado, USA
| | - Christina A Nelson
- Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado, USA
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Hogan CA, Miller S, Piantadosi A, Gaston DC, Simner PJ, Nash S, Babady NE. Which trial do we need? Plasma metagenomic next-generation sequencing to diagnose infections in patients with haematological malignancies and febrile neutropenia: proposal for a randomized-controlled trial. Clin Microbiol Infect 2023; 29:1474-1479. [PMID: 37244468 DOI: 10.1016/j.cmi.2023.05.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 05/18/2023] [Accepted: 05/20/2023] [Indexed: 05/29/2023]
Affiliation(s)
- Catherine A Hogan
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada; Department of Pathology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Steve Miller
- Delve Bio, San Francisco, CA, USA; Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Anne Piantadosi
- Emory University Department of Medicine, Division of Infectious Diseases, Atlanta, GA, USA; Emory University Department of Pathology and Laboratory Medicine, Atlanta, GA, USA
| | - David C Gaston
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Patricia J Simner
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Stephen Nash
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Solna, Sweden
| | - N Esther Babady
- Department of Pathology and Laboratory Medicine, Clinical Microbiology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Infectious Disease Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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Lo CKF, Plewes K, Sharma S, Low A, Su LD, Belga S, Salazar FV, Hajek J, Morshed M, Hogan CA. Plasmodium knowlesi Infection in Traveler Returning to Canada from the Philippines, 2023. Emerg Infect Dis 2023; 29:2177-2179. [PMID: 37735805 PMCID: PMC10521619 DOI: 10.3201/eid2910.230809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/23/2023] Open
Abstract
A 55-year-old man sought treatment for an uncomplicated febrile illness after returning to Canada from the Philippines. A suspected diagnosis of Plasmodium knowlesi infection was confirmed by PCR, and treatment with atovaquone/proguanil brought successful recovery. We review the evolving epidemiology of P. knowlesi malaria in the Philippines, specifically within Palawan Island.
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Pham J, Su LD, Hanson KE, Hogan CA. Sequence-based diagnostics and precision medicine in bacterial and viral infections: from bench to bedside. Curr Opin Infect Dis 2023; 36:228-234. [PMID: 37431553 DOI: 10.1097/qco.0000000000000936] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2023]
Abstract
PURPOSE OF REVIEW Nucleic acid sequence-based organism identification plays an important role in the diagnosis and management of transplant and cancer-associated infectious diseases. Here, we provide a high-level overview of advanced sequencing technologies, discuss test performance, and highlight unmet research needs with a focus on immunocompromised hosts. RECENT FINDINGS Next-generation sequencing (NGS) technologies are powerful tools with a growing role in managing immunocompromised patients with suspected infection. Targeted NGS (tNGS) can identify pathogens directly from patient specimens, especially for mixed samples, and has been used to detect resistance mutations in transplant-related viruses (e.g. CMV). Whole-genome sequencing (WGS) is increasingly used for outbreak investigations and infection control. Metagenomic NGS (mNGS) is useful for hypothesis-free testing and can simultaneously assess pathogens and host response to infection. SUMMARY NGS testing increases diagnostic yield relative to standard culture and Sanger sequencing but may be limited by high cost, turnaround times, and detection of unexpected organisms or commensals of uncertain significance. Close collaboration with the clinical microbiology laboratory and infectious diseases is recommended when NGS testing is considered. Additional research is required to understand which immunocompromised patients are most likely to benefit from NGS testing, and when testing should ideally be performed.
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Affiliation(s)
- Jonathan Pham
- Department of Pathology, University of Utah and ARUP Laboratories, Salt Lake City, Utah, USA
| | - LingHui David Su
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
| | - Kimberly E Hanson
- Department of Pathology, University of Utah and ARUP Laboratories, Salt Lake City, Utah, USA
- Department of Medicine, Division of Infectious Diseases, University of Utah, Salt Lake City, Utah, USA
| | - Catherine A Hogan
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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Cheung M, Yu D, Chan T, Chahil N, Tchao C, Slatnik M, Maruti S, Sidhu N, Scandrett B, Prystajecky N, Morshed MG, Hogan CA. The Brief Case: an Infectious Hazard of Hunting. J Clin Microbiol 2023; 61:e0062022. [PMID: 37078718 PMCID: PMC10117069 DOI: 10.1128/jcm.00620-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2023] Open
Affiliation(s)
- Martin Cheung
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, British Columbia, Canada
| | - Daisy Yu
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, British Columbia, Canada
| | - Tracy Chan
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, British Columbia, Canada
| | - Navdeep Chahil
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, British Columbia, Canada
| | - Christine Tchao
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, British Columbia, Canada
| | - Michael Slatnik
- Boundary District Hospital, Grand Forks, British Columbia, Canada
| | - Shobhit Maruti
- Interior Health Authority, Vernon, British Columbia, Canada
| | - Nina Sidhu
- Interior Health Authority, Vernon, British Columbia, Canada
| | - Brad Scandrett
- Centre for Food-borne and Animal Parasitology, Canadian Food Inspection Agency, Saskatoon, Saskatchewan, Canada
| | - Natalie Prystajecky
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Muhammad G. Morshed
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Catherine A. Hogan
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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Le AT, Wu M, Khan A, Phillips N, Rajpurkar P, Garland M, Magid K, Sibai M, Huang C, Sahoo MK, Bowen R, Cowan TM, Pinsky BA, Hogan CA. Targeted plasma metabolomics combined with machine learning for the diagnosis of severe acute respiratory syndrome virus type 2. Front Microbiol 2023; 13:1059289. [PMID: 37063449 PMCID: PMC10092816 DOI: 10.3389/fmicb.2022.1059289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 12/07/2022] [Indexed: 03/31/2023] Open
Abstract
IntroductionThe routine clinical diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is largely restricted to real-time reverse transcription quantitative PCR (RT-qPCR), and tests that detect SARS-CoV-2 nucleocapsid antigen. Given the diagnostic delay and suboptimal sensitivity associated with these respective methods, alternative diagnostic strategies are needed for acute infection.MethodsWe studied the use of a clinically validated liquid chromatography triple quadrupole method (LC/MS–MS) for detection of amino acids from plasma specimens. We applied machine learning models to distinguish between SARS-CoV-2-positive and negative samples and analyzed amino acid feature importance.ResultsA total of 200 samples were tested, including 70 from individuals with COVID-19, and 130 from negative controls. The top performing model overall allowed discrimination between SARS-CoV-2-positive and negative control samples with an area under the receiver operating characteristic curve (AUC) of 0.96 (95%CI 0.91, 1.00), overall sensitivity of 0.99 (95%CI 0.92, 1.00), and specificity of 0.92 (95%CI 0.85, 0.95).DiscussionThis approach holds potential as an alternative to existing methods for the rapid and accurate diagnosis of acute SARS-CoV-2 infection.
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Affiliation(s)
- Anthony T. Le
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Manhong Wu
- Department of Anesthesiology, Stanford University School of Medicine, Stanford, CA, United States
| | - Afraz Khan
- British Columbia Center for Disease Control Public Health Laboratory, Vancouver, BC, Canada
| | - Nicholas Phillips
- Stanford Computer Science Department, Stanford University, Stanford, CA, United States
| | - Pranav Rajpurkar
- Stanford Computer Science Department, Stanford University, Stanford, CA, United States
| | - Megan Garland
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Kayla Magid
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Mamdouh Sibai
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - ChunHong Huang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Malaya K. Sahoo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Raffick Bowen
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
- Stanford Biochemical Genetics Laboratory, Stanford Health Care, Palo Alto, CA, United States
| | - Tina M. Cowan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
- Clinical Chemistry and Immunology Laboratory, Stanford Health Care, Palo Alto, CA, United States
| | - Benjamin A. Pinsky
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
- Stanford Clinical Virology Laboratory, Stanford Health Care, Palo Alto, CA, United States
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Catherine A. Hogan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
- British Columbia Center for Disease Control Public Health Laboratory, Vancouver, BC, Canada
- Stanford Clinical Virology Laboratory, Stanford Health Care, Palo Alto, CA, United States
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
- *Correspondence: Catherine A. Hogan,
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Kostaki A, Wacker JW, Safarika A, Solomonidi N, Katsaros K, Giannikopoulos G, Koutelidakis IM, Hogan CA, Uhle F, Liesenfeld O, Sweeney TE, Giamarellos-Bourboulis EJ. A 29-MRNA HOST RESPONSE WHOLE-BLOOD SIGNATURE IMPROVES PREDICTION OF 28-DAY MORTALITY AND 7-DAY INTENSIVE CARE UNIT CARE IN ADULTS PRESENTING TO THE EMERGENCY DEPARTMENT WITH SUSPECTED ACUTE INFECTION AND/OR SEPSIS. Shock 2022; 58:224-230. [PMID: 36125356 PMCID: PMC9512237 DOI: 10.1097/shk.0000000000001970] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 03/09/2022] [Revised: 03/28/2022] [Accepted: 07/19/2022] [Indexed: 11/25/2022]
Abstract
ABSTRACT Background: Risk stratification of emergency department patients with suspected acute infections and/or suspected sepsis remains challenging. We prospectively validated a 29-messenger RNA host response classifier for predicting severity in these patients. Methods: We enrolled adults presenting with suspected acute infections and at least one vital sign abnormality to six emergency departments in Greece. Twenty-nine target host RNAs were quantified on NanoString nCounter and analyzed with the Inflammatix Severity 2 (IMX-SEV-2) classifier to determine risk scores as low, moderate, and high severity. Performance of IMX-SEV-2 for prediction of 28-day mortality was compared with that of lactate, procalcitonin, and quick sequential organ failure assessment (qSOFA). Results: A total of 397 individuals were enrolled; 38 individuals (9.6%) died within 28 days. Inflammatix Severity 2 classifier predicted 28-day mortality with an area under the receiver operator characteristics curve of 0.82 (95% confidence interval [CI], 0.74-0.90) compared with lactate, 0.66 (95% CI, 0.54-0.77); procalcitonin, 0.67 (95% CI, 0.57-0.78); and qSOFA, 0.81 (95% CI, 0.72-0.89). Combining qSOFA with IMX-SEV-2 improved prognostic accuracy from 0.81 to 0.89 (95% CI, 0.82-0.96). The high-severity (rule-in) interpretation band of IMX-SEV-2 demonstrated 96.9% specificity for predicting 28-day mortality, whereas the low-severity (rule-out) band had a sensitivity of 78.9%. Similarly, IMX-SEV-2 alone accurately predicted the need for day-7 intensive care unit care and further boosted overall accuracy when combined with qSOFA. Conclusions: Inflammatix Severity 2 classifier predicted 28-day mortality and 7-day intensive care unit care with high accuracy and boosted the accuracy of clinical scores when used in combination.
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Affiliation(s)
- Antigone Kostaki
- 4th Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, Greece
| | | | - Asimina Safarika
- 4th Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, Greece
| | - Nicky Solomonidi
- 4th Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, Greece
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Hogan CA, Hitchcock MM, Frost S, Kapphahn K, Holubar M, Tompkins LS, Banaei N. Clinical Outcomes of Treated and Untreated C. difficile PCR-Positive/Toxin-Negative Adult Hospitalized Patients: a Quasi-Experimental Noninferiority Study. J Clin Microbiol 2022; 60:e0218721. [PMID: 35611653 PMCID: PMC9199396 DOI: 10.1128/jcm.02187-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 04/21/2022] [Indexed: 12/31/2022] Open
Abstract
Clostridioides difficile infection (CDI) is routinely diagnosed by PCR, with or without toxin enzyme immunoassay testing. The role of therapy for positive PCR and negative toxin remains unclear. The objective of this study was to determine whether clinical outcomes of PCR+/cycle threshold-based toxin (CT-toxin)- individuals vary by result reporting and treatment strategy. We performed a quasiexperimental noninferiority study comparing clinical outcomes of PCR+/CT-toxin- individuals by reporting PCR result only (most patients treated) with reporting CT-toxin result only (most patients untreated) in a single-center, tertiary academic hospital. The primary outcome was symptomatic PCR+/CT-toxin+ conversion at 8 weeks. Secondary outcomes included 7-day diarrhea resolution, hospital length of stay, and 30-day all-cause mortality. A total of 663 PCR+/CT-toxin- test results were analyzed from 632 individuals with a median age of 61 years (interquartile range [IQR], 44 to 72) and 50.4% immunocompromised. Individuals in the preintervention group were more likely to have received CDI therapy than those in the intervention group (91.5 versus 15.1%; P < 0.001). Symptomatic toxin conversion at 8 weeks and hospital length of stay failed to establish the predefined thresholds for noninferiority. Lack of diarrhea resolution at 7 days and 30-day all-cause mortality was similar and established noninferiority (20.0 versus 13.7%; adjusted odds ratio [aOR], 0.57; 90% confidence interval [CI], 0.32 to 1.01; P = 0.1; and 8.6 versus 6.5%; aOR, 0.46; 90% CI, 0.20 to 1.04; P = 0.12). These data support the safety of withholding antibiotics for selected hospitalized individuals with suspected CDI but negative toxin.
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Affiliation(s)
- Catherine A. Hogan
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
- Clinical Microbiology Laboratory, Stanford Health Care, Stanford, California, USA
| | - Matthew M. Hitchcock
- Department of Medicine, Division of Infectious Diseases, Central Virginia VA Health Care System, Richmond, Virginia, USA
- Department of Internal Medicine, Division of Infectious Diseases, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
| | - Spencer Frost
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Kristopher Kapphahn
- Quantitative Sciences Unit, Stanford University School of Medicine, Stanford, California, USA
| | - Marisa Holubar
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
- Department of Quality, Patient Safety and Effectiveness, Stanford University School of Medicine, Stanford, California, USA
| | - Lucy S. Tompkins
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Niaz Banaei
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
- Clinical Microbiology Laboratory, Stanford Health Care, Stanford, California, USA
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
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Futai N, Fukazawa Y, Kashiwagi T, Tamaki S, Sakai R, Hogan CA, Murugesan K, Ramachandran A, Banaei N, Santiago JG. A modular and reconfigurable open-channel gated device for the electrokinetic extraction of cell-free DNA assays. Anal Chim Acta 2022; 1200:339435. [DOI: 10.1016/j.aca.2022.339435] [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] [Received: 08/20/2021] [Revised: 12/06/2021] [Accepted: 01/02/2022] [Indexed: 11/01/2022]
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Wang H, Hogan CA, Verghese M, Solis D, Sibai M, Huang C, Röltgen K, Stevens BA, Yamamoto F, Sahoo MK, Zehnder J, Boyd SD, Pinsky BA. SARS-CoV-2 Nucleocapsid Plasma Antigen for Diagnosis and Monitoring of COVID-19. Clin Chem 2021; 68:204-213. [PMID: 34605900 PMCID: PMC8522398 DOI: 10.1093/clinchem/hvab216] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [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: 05/30/2021] [Accepted: 09/10/2021] [Indexed: 11/30/2022]
Abstract
BACKGROUND Detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid antigen in blood has been described, but the diagnostic and prognostic role of antigenemia is not well understood. This study aimed to determine the frequency, duration, and concentration of nucleocapsid antigen in plasma and its association with coronavirus disease 2019 (COVID-19) severity. METHODS We utilized an ultrasensitive electrochemiluminescence immunoassay targeting SARS-CoV-2 nucleocapsid antigen to evaluate 777 plasma samples from 104 individuals with COVID-19. We compared plasma antigen to respiratory nucleic acid amplification testing (NAAT) in 74 individuals with COVID-19 from samples collected ±1 day of diagnostic respiratory NAAT and in 52 SARS-CoV-2-negative individuals. We used Kruskal-Wallis tests, multivariable logistic regression, and mixed-effects modeling to evaluate whether plasma antigen concentration was associated with disease severity. RESULTS Plasma antigen had 91.9% (95% CI 83.2%-97.0%) clinical sensitivity and 94.2% (84.1%-98.8%) clinical specificity. Antigen-negative plasma samples belonged to patients with later respiratory cycle thresholds (Ct) when compared with antigen-positive plasma samples. Median plasma antigen concentration (log10 fg/mL) was 5.4 (interquartile range 3.9-6.0) in outpatients, 6.0 (5.4-6.5) in inpatients, and 6.6 (6.1-7.2) in intensive care unit (ICU) patients. In models adjusted for age, sex, diabetes, and hypertension, plasma antigen concentration at diagnosis was associated with ICU admission [odds ratio 2.8 (95% CI 1.2-6.2), P=.01] but not with non-ICU hospitalization. Rate of antigen decrease was not associated with disease severity. CONCLUSIONS SARS-CoV-2 plasma nucleocapsid antigen exhibited comparable diagnostic performance to upper respiratory NAAT, especially among those with late respiratory Ct. In addition to currently available tools, antigenemia may facilitate patient triage to optimize intensive care utilization.
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Affiliation(s)
- Hannah Wang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Catherine A Hogan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Michelle Verghese
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Daniel Solis
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Mamdouh Sibai
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - ChunHong Huang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Katharina Röltgen
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Bryan A Stevens
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Fumiko Yamamoto
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Malaya K Sahoo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - James Zehnder
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Scott D Boyd
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Benjamin A Pinsky
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
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Wiredja D, Ritchie TA, Tam G, Hogan CA, Pinsky B, Shi RZ. Performance evaluation and optimized reporting workflow for HIV diagnostic screening and confirmatory tests in a low prevalence setting. J Clin Virol 2021; 145:105020. [PMID: 34736075 DOI: 10.1016/j.jcv.2021.105020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 07/08/2021] [Revised: 10/15/2021] [Accepted: 10/19/2021] [Indexed: 11/20/2022]
Abstract
BACKGROUND Our institution utilizes an antigen/antibody screening test followed by a confirmatory antibody assay for preliminary positive results. Given the low prevalence for HIV infections in our institution's county, we suspect that a substantial portion of the reactive screens are false positives. OBJECTIVES We aimed to characterize the false positivity rate of the HIV screening test performed at Stanford Health Care. In parallel, we modified our reporting workflow to release both the screening and confirmatory results simultaneously to mitigate the stress of a presumptive positive test. STUDY DESIGN We reviewed 45,296 eligible HIV screen specimens that underwent the Abbott ARCHITECT™ 4th generation HIV antigen/antibody combination assay between August 5, 2016 and March 16, 2021. Final sample signal/cutoff (S/CO) ratios ≥ 1 were deemed positive, which triggers a reflex order for the confirmatory Bio-Rad Geenius™ HIV 1/2 Supplemental Assay. Additional chart review was performed for positive screen cases with negative or indeterminate confirmatory results. RESULTS Our institution demonstrated a 0.28% (128/45,296) positive screen rate, with 12.5% (16/128) of these samples confirmed as false positives based on a negative HIV-1 RNA test. Median S/CO ratios of true positive screens were significantly higher than those with negative or indeterminate confirmatory tests (602.27vs 2.98; p = 0.0000323). We implemented a new synchronized reporting system for positive screens, which co-releases screen and confirmatory reports without compromise in the overall turnaround time. CONCLUSIONS Our study demonstrates a relatively high percentage of false positive screens. Subsequently, by providing a more complete picture up front, our new reporting pipeline may reduce anxiety of a stand-alone positive screen and optimize downstream clinical decision-making.
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Affiliation(s)
- Danica Wiredja
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States of America
| | - Todd A Ritchie
- Laboratory Information System, Stanford Health Care, Stanford, CA, United States of America
| | - Gordon Tam
- Stanford Clinical Virology Laboratory, Stanford Health Care, Stanford, CA, United States of America
| | | | - Benjamin Pinsky
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States of America; Stanford Clinical Virology Laboratory, Stanford Health Care, Stanford, CA, United States of America; Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, United States of America
| | - Run Zhang Shi
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States of America.
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12
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Caza M, Hogan CA, Jassem A, Prystajecky N, Hadzic A, Wilmer A. Evaluation of the clinical and analytical performance of the Seegene allplex™ SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). J Clin Virol 2021; 144:104996. [PMID: 34628158 PMCID: PMC8487322 DOI: 10.1016/j.jcv.2021.104996] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 06/21/2021] [Revised: 08/21/2021] [Accepted: 09/29/2021] [Indexed: 12/12/2022]
Abstract
Background High-throughput assays for the detection of SARS-CoV-2 variants of concern (VOC) and interest (VOI) are a diagnostic alternative when whole genome sequencing (WGS) is unavailable or limited. Objective This study evaluated the clinical and analytical performance of the Seegene Allplex™ SARS-CoV-2 Variants I assay, which detects the HV69/70 deletion, N501Y and E484K mutations of the S gene. Methods Genotyping was evaluated on -871 SARS-CoV-2 RNA positive specimens, 408 nasopharyngeal (NP) swabs and 463 saline gargle (SG) specimens, with WGS used as the reference standard. Analytical performance was assessed including stability, reproducibility, limit of detection (LOD), cross-reactivity and interference with various respiratory microorganisms. Results The clinical study revealed sensitivity of 100% (95% CI 99.27%–100%) and specificity of 100% (95% CI 98.99%–100%) for HV69/70 deletion, sensitivity of 100% (95% CI 99.55%–100%) and specificity of 100% (95% CI 93.73% – 100%) for N501Y, and sensitivity of 100% (95% CI 98.94% – 100%) and specificity of 98.10% (95% CI 96.53% – 99.08%) for E484K mutation. The E484Q mutation was detected in 10 specimens of the Kappa variant (B.1.627.1). Analytical performance demonstrated stability and reproducibility over 7 days, and LOD was calculated at 698 cp/mL for NP swab specimens, and 968 cp/mL for SG specimens. No interference or cross-reactivity with other microorganisms was noted. Conclusion The Allplex™ SARS-CoV-2 Variants I assay is acceptable for clinical use for the detection of variant of concern and variant of interest.
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Affiliation(s)
- Mélissa Caza
- Larissa Yarr Medical Microbiology Laboratory, Kelowna General Hospital, Kelowna, British Columbia, Canada.
| | - Catherine A Hogan
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, British Columbia, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Agatha Jassem
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, British Columbia, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Natalie Prystajecky
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, British Columbia, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Amir Hadzic
- Larissa Yarr Medical Microbiology Laboratory, Kelowna General Hospital, Kelowna, British Columbia, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Amanda Wilmer
- Larissa Yarr Medical Microbiology Laboratory, Kelowna General Hospital, Kelowna, British Columbia, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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13
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Hogan CA, Jassem AN, Sbihi H, Joffres Y, Tyson JR, Noftall K, Taylor M, Lee T, Fjell C, Wilmer A, Galbraith J, Romney MG, Henry B, Krajden M, Galanis E, Prystajecky N, Hoang LM. Rapid Increase in SARS-CoV-2 P.1 Lineage Leading to Codominance with B.1.1.7 Lineage, British Columbia, Canada, January-April 2021. Emerg Infect Dis 2021; 27:2802-2809. [PMID: 34388358 PMCID: PMC8544957 DOI: 10.3201/eid2711.211190] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Several severe acute respiratory syndrome coronavirus 2 variants of concern (VOCs) emerged in late 2020; lineage B.1.1.7 initially dominated globally. However, lineages B.1.351 and P.1 represent potentially greater risk for transmission and immune escape. In British Columbia, Canada, B.1.1.7 and B.1.351 were first identified in December 2020 and P.1 in February 2021. We combined quantitative PCR and whole-genome sequencing to assess relative contribution of VOCs in nearly 67,000 infections during the first 16 weeks of 2021 in British Columbia. B.1.1.7 accounted for <10% of screened or sequenced specimens early on, increasing to >50% by week 8. P.1 accounted for <10% until week 10, increased rapidly to peak at week 12, and by week 13 codominated within 10% of rates of B.1.1.7. B.1.351 was a minority throughout. This rapid expansion of P.1 but suppression of B.1.351 expands our understanding of population-level VOC patterns and might provide clues to fitness determinants for emerging VOCs.
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14
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Pinsky BA, Hogan CA. Carving Out a Niche for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Plasma RNA Testing. Clin Infect Dis 2021; 73:e803-e804. [PMID: 32941602 PMCID: PMC7543305 DOI: 10.1093/cid/ciaa1412] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 09/16/2020] [Indexed: 01/05/2023] Open
Affiliation(s)
- Benjamin A Pinsky
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA.,Clinical Virology Laboratory, Stanford Health Care, Stanford, California, USA.,Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Catherine A Hogan
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA.,Clinical Virology Laboratory, Stanford Health Care, Stanford, California, USA
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15
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Putney S, Theiss AH, Rajan NK, Deak E, Buie C, Ngo Y, Shah H, Yuan V, Botbol-Ponte E, Hoyos-Urias A, Knopfmacher O, Hogan CA, Banaei N, Herget MS. Novel electronic biosensor for automated inoculum preparation to accelerate antimicrobial susceptibility testing. Sci Rep 2021; 11:11360. [PMID: 34059754 PMCID: PMC8166823 DOI: 10.1038/s41598-021-90830-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 01/11/2021] [Accepted: 05/17/2021] [Indexed: 12/05/2022] Open
Abstract
A key predictor of morbidity and mortality for patients with a bloodstream infection is time to appropriate antimicrobial therapy. Accelerating antimicrobial susceptibility testing from positive blood cultures is therefore key to improving patient outcomes, yet traditional laboratory approaches can require 2–4 days for actionable results. The eQUANT—a novel instrument utilizing electrical biosensors—produces a standardized inoculum equivalent to a 0.5 McFarland directly from positive blood cultures. This proof-of-concept study demonstrates that eQUANT inocula prepared from clinically significant species of Enterobacterales were comparable to 0.5 McF inocula generated from bacterial colonies in both CFU/ml concentration and performance in antimicrobial susceptibility testing, with ≥ 95% essential and categorical agreement for VITEK2 and disk diffusion. The eQUANT, combined with a rapid, direct from positive blood culture identification technique, can allow the clinical laboratory to begin antimicrobial susceptibility testing using a standardized inoculum approximately 2–3 h after a blood culture flags positive. This has the potential to improve clinical practice by accelerating conventional antimicrobial susceptibility testing and the resulting targeted antibiotic therapy.
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Affiliation(s)
- Suzanne Putney
- Avails Medical Inc., 1455 Adams Drive, Menlo Park, CA, 94025, USA
| | - Andrew H Theiss
- Avails Medical Inc., 1455 Adams Drive, Menlo Park, CA, 94025, USA
| | - Nitin K Rajan
- Avails Medical Inc., 1455 Adams Drive, Menlo Park, CA, 94025, USA
| | - Eszter Deak
- Avails Medical Inc., 1455 Adams Drive, Menlo Park, CA, 94025, USA
| | - Creighton Buie
- Avails Medical Inc., 1455 Adams Drive, Menlo Park, CA, 94025, USA
| | - Yvonne Ngo
- Avails Medical Inc., 1455 Adams Drive, Menlo Park, CA, 94025, USA
| | - Hima Shah
- Avails Medical Inc., 1455 Adams Drive, Menlo Park, CA, 94025, USA
| | - Victoria Yuan
- Avails Medical Inc., 1455 Adams Drive, Menlo Park, CA, 94025, USA
| | | | | | - Oren Knopfmacher
- Avails Medical Inc., 1455 Adams Drive, Menlo Park, CA, 94025, USA
| | - Catherine A Hogan
- Stanford University School of Medicine, 3375 Hillview Ave, Palo Alto, CA, 94304, USA
| | - Niaz Banaei
- Stanford University School of Medicine, 3375 Hillview Ave, Palo Alto, CA, 94304, USA
| | - Meike S Herget
- Avails Medical Inc., 1455 Adams Drive, Menlo Park, CA, 94025, USA.
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16
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Hogan CA, Stevens BA, Sahoo MK, Huang C, Garamani N, Gombar S, Yamamoto F, Murugesan K, Kurzer J, Zehnder J, Pinsky BA. High Frequency of SARS-CoV-2 RNAemia and Association With Severe Disease. Clin Infect Dis 2021; 72:e291-e295. [PMID: 32965474 PMCID: PMC7543277 DOI: 10.1093/cid/ciaa1054] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [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: 06/09/2020] [Accepted: 07/27/2020] [Indexed: 11/13/2022] Open
Abstract
Background Detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in blood, also known as RNAemia, has been reported, but its prognostic implications are poorly understood. This study aimed to determine the frequency of SARS-CoV-2 RNA in plasma and its association with coronavirus disease 2019 (COVID-19) clinical severity. Methods An analytical cross-sectional study was performed in a single-center tertiary care institution and included consecutive inpatients and outpatients with confirmed COVID-19. The prevalence of SARS CoV-2 RNAemia and the strength of its association with clinical severity variables were examined and included intensive care unit (ICU) admission, invasive mechanical ventilation, and 30-day all-cause mortality. Results Paired nasopharyngeal and plasma samples were included from 85 patients. The median age was 55 years, and individuals with RNAemia were older than those with undetectable SARS-CoV-2 RNA in plasma (63 vs 50 years; P = .04). Comorbidities were frequent including obesity (37.6%), hypertension (30.6%), and diabetes mellitus (22.4%). RNAemia was detected in 28/85 (32.9%) of patients, including 22/28 (78.6%) who required hospitalization. In models adjusted for age, RNAemia was detected more frequently in individuals who developed severe disease including ICU admission (32.1 vs 14.0%; P = .04) and invasive mechanical ventilation (21.4% vs 3.5%; P = .02). All 4 deaths occurred in individuals with detectable RNAemia. An additional 121 plasma samples from 28 individuals with RNAemia were assessed longitudinally, and RNA was detected for a maximum duration of 10 days. Conclusions This study demonstrated a high proportion of SARS-CoV-2 RNAemia, and an association between RNAemia and clinical severity suggesting the potential utility of plasma viral testing as a prognostic indicator for COVID-19.
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Affiliation(s)
- Catherine A Hogan
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA.,Clinical Virology Laboratory, Stanford Health Care, Stanford, California, USA
| | - Bryan A Stevens
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA.,Clinical Virology Laboratory, Stanford Health Care, Stanford, California, USA
| | - Malaya K Sahoo
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - ChunHong Huang
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Natasha Garamani
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Saurabh Gombar
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Fumiko Yamamoto
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Kanagavel Murugesan
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Jason Kurzer
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - James Zehnder
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Benjamin A Pinsky
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA.,Clinical Virology Laboratory, Stanford Health Care, Stanford, California, USA.,Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
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17
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Hogan CA, Yang S, Garner OB, Green DA, Gomez CA, Dien Bard J, Pinsky BA, Banaei N. Clinical Impact of Metagenomic Next-Generation Sequencing of Plasma Cell-Free DNA for the Diagnosis of Infectious Diseases: A Multicenter Retrospective Cohort Study. Clin Infect Dis 2021; 72:239-245. [PMID: 31942944 DOI: 10.1093/cid/ciaa035] [Citation(s) in RCA: 137] [Impact Index Per Article: 45.7] [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: 09/12/2019] [Accepted: 01/13/2020] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Metagenomic next-generation sequencing (mNGS) of plasma cell-free DNA has emerged as an attractive diagnostic modality allowing broad-range pathogen detection, noninvasive sampling, and earlier diagnosis. However, little is known about its real-world clinical impact as used in routine practice. METHODS We performed a retrospective cohort study of all patients for whom plasma mNGS (Karius test) was performed for all indications at 5 United States institutions over 1.5 years. Comprehensive records review was performed, and standardized assessment of clinical impact of the mNGS based on the treating team's interpretation of Karius results and patient management was established. RESULTS A total of 82 Karius tests were evaluated from 39 (47.6%) adults and 43 (52.4%) children and a total of 53 (64.6%) immunocompromised patients. Karius positivity rate was 50 of 82 (61.0%), with 25 (50.0%) showing 2 or more organisms (range, 2-8). The Karius test results led to positive impact in 6 (7.3%), negative impact in 3 (3.7%), and no impact in 71 (86.6%), and was indeterminate in 2 (2.4%). Cases with positive Karius result and clinical impact involved bacteria and/or fungi but not DNA viruses or parasites. In 10 patients who underwent 16 additional repeated tests, only 1 was associated with clinical impact. CONCLUSIONS The real-world impact of the Karius test as currently used in routine clinical practice is limited. Further studies are needed to identify high-yield patient populations, define the complementary role of mNGS to conventional microbiological methods, and discern how best to integrate mNGS into current testing algorithms.
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Affiliation(s)
- Catherine A Hogan
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA.,Clinical Microbiology Laboratory, Stanford Health Care, Stanford, California, USA.,Clinical Virology Laboratory, Stanford Health Care, Stanford, California, USA
| | - Shangxin Yang
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Omai B Garner
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Daniel A Green
- Department of Pathology, Columbia University Irving Medical Center, New York, New York, USA
| | - Carlos A Gomez
- Division of Infectious Diseases, Department of Medicine, University of Utah, Salt Lake City, Utah, USA
| | - Jennifer Dien Bard
- Department of Pathology, Children's Hospital of Los Angeles, Los Angeles, California, USA
| | - Benjamin A Pinsky
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA.,Clinical Microbiology Laboratory, Stanford Health Care, Stanford, California, USA.,Clinical Virology Laboratory, Stanford Health Care, Stanford, California, USA.,Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Niaz Banaei
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA.,Clinical Microbiology Laboratory, Stanford Health Care, Stanford, California, USA.,Clinical Virology Laboratory, Stanford Health Care, Stanford, California, USA.,Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
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18
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Affiliation(s)
- Catherine A Hogan
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA.,Clinical Microbiology Laboratory, Stanford Health Care, Stanford, California, USA.,Clinical Virology Laboratory, Stanford Health Care, Stanford, California, USA
| | - Benjamin A Pinsky
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA.,Clinical Microbiology Laboratory, Stanford Health Care, Stanford, California, USA.,Clinical Virology Laboratory, Stanford Health Care, Stanford, California, USA.,Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Niaz Banaei
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA.,Clinical Microbiology Laboratory, Stanford Health Care, Stanford, California, USA.,Clinical Virology Laboratory, Stanford Health Care, Stanford, California, USA.,Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
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19
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Wang H, Hogan CA, Verghese M, Solis D, Sibai M, Huang C, Zehnder J, Sahoo MK, Pinsky BA. Ultra-sensitive Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Antigen Detection for the Diagnosis of Coronavirus Disease 2019 (COVID-19) in Upper Respiratory Samples. Clin Infect Dis 2021; 73:2326-2328. [PMID: 33830203 PMCID: PMC8083502 DOI: 10.1093/cid/ciab063] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 12/21/2020] [Indexed: 12/23/2022] Open
Abstract
An ultra-sensitive severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid antigen assay (S-PLEX, MesoScale Diagnostics) was evaluated in 250 retrospective and 200 prospective upper respiratory specimens. In samples with cycle threshold <35, there was 95%–98% positive and 93%–96% negative percent agreement with reverse transcription-polymerase chain reaction. S-PLEX may provide a high-throughput alternative to nucleic acid-based testing for coronavirus disease 2019 (COVID-19) diagnosis.
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Affiliation(s)
- Hannah Wang
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Catherine A Hogan
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Michelle Verghese
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Daniel Solis
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Mamdouh Sibai
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - ChunHong Huang
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - James Zehnder
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Malaya K Sahoo
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Benjamin A Pinsky
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA.,Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
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20
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Lawrence L, Stevens BA, Sahoo MK, Huang C, Yamamoto F, Röltgen K, Wirz O, Zehnder J, Shi RZ, Boyd SD, Schoolnik G, Pinsky BA, Hogan CA. Plasma as an alternative COVID-19 diagnostic specimen in a hospitalized patient negative for SARS-CoV-2 by nasopharyngeal swab. Diagn Microbiol Infect Dis 2021; 100:115365. [PMID: 33865070 PMCID: PMC7930728 DOI: 10.1016/j.diagmicrobio.2021.115365] [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: 11/04/2020] [Revised: 02/28/2021] [Accepted: 02/28/2021] [Indexed: 12/05/2022]
Abstract
We present the case of an inpatient with pneumonia and repeatedly negative nasopharyngeal SARS-CoV-2 testing. In such challenging cases, alternative diagnostic options include lower respiratory tract and plasma SARS-CoV-2 RNA testing, of which the latter may be particularly useful where bronchoscopy is deferred due to clinical factors or transmission risk.
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Affiliation(s)
- Lauren Lawrence
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Bryan A Stevens
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Clinical Virology Laboratory, Stanford Health Care, Stanford, CA, USA
| | - Malaya K Sahoo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - ChunHong Huang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Fumiko Yamamoto
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Katharina Röltgen
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Oliver Wirz
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - James Zehnder
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Run-Zhang Shi
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Scott D Boyd
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Gary Schoolnik
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Benjamin A Pinsky
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Clinical Virology Laboratory, Stanford Health Care, Stanford, CA, USA; Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Catherine A Hogan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Clinical Virology Laboratory, Stanford Health Care, Stanford, CA, USA.
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21
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Senchyna F, Hogan CA, Murugesan K, Moreno A, Ho DY, Subramanian A, Schwenk HT, Budvytiene I, Costa HA, Gombar S, Banaei N. Clinical Accuracy and Impact of Plasma Cell-Free DNA Fungal PCR Panel for Non-Invasive Diagnosis of Fungal Infection. Clin Infect Dis 2021; 73:1677-1684. [PMID: 33606010 DOI: 10.1093/cid/ciab158] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 11/30/2020] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Invasive fungal infection (IFI) is a growing cause of morbidity and mortality in oncology and transplant patients. Diagnosis of IFI is often delayed due to need for invasive biopsy and low sensitivity of conventional diagnostic methods. Fungal cell-free DNA (cfDNA) detection in plasma is a novel testing modality for the non-invasive diagnosis of IFI. METHODS A novel bioinformatic pipeline was created to interrogate fungal genomes and identify multicopy sequences for cfDNA PCR targeting. A real-time PCR panel was developed for 12 genera and species most commonly causing IFI. Sensitivity and specificity of the fungal PCR panel were determined using plasma samples from patients with IFI and non-IFI controls. Clinical impact of fungal PCR panel was evaluated prospectively based on the treating team's interpretation of the results. RESULTS Overall, the sensitivity and specificity were 56.5% (65/115, 95% confidence interval [CI], 47.4%-65.2%) and 99.5% (2064/2075; 95% CI, 99.0%-99.7%), respectively. In the subset of patients with an optimized plasma volume (2mL), sensitivity was 69.6% (48/69; 95% CI, 57.9%-79.2%). Sensitivity was 91.7% (11/12; 95% CI, 62.5%-100%) for detection of Mucorales agents, 56.3% (9/16; 95% CI, 33.2%-76.9%) for Aspergillus species, and 84.6% (11/13; 95% CI, 56.5%-96.9%) for Candida albicans. In a prospective evaluation of 226 patients with suspected IFI, cfDNA testing was positive in 47 (20.8%) patients and resulted in a positive impact on clinical management in 20/47 (42.6%). CONCLUSIONS The fungal cfDNA PCR panel offers a non-invasive approach to early diagnosis of IFI, providing actionable results for personalized care.
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Affiliation(s)
- Fiona Senchyna
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Catherine A Hogan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.,Clinical Microbiology Laboratory, Stanford University Medical Center, Palo Alto, CA, USA
| | - Kanagavel Murugesan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Angel Moreno
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Dora Y Ho
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Aruna Subramanian
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Hayden T Schwenk
- Division of Infectious Diseases, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Indre Budvytiene
- Clinical Microbiology Laboratory, Stanford University Medical Center, Palo Alto, CA, USA
| | - Helio A Costa
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Saurabh Gombar
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Niaz Banaei
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.,Clinical Microbiology Laboratory, Stanford University Medical Center, Palo Alto, CA, USA.,Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
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22
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Broadhurst MJ, Garamani N, Hahn Z, Jiang B, Weber J, Huang C, Sahoo MK, Kurzer J, Hogan CA, Pinsky BA. Evaluation of a measles virus multiplex, triple-target real-time RT-PCR in three specimen matrices at a U.S. academic medical center. J Clin Virol 2021; 136:104757. [PMID: 33639409 DOI: 10.1016/j.jcv.2021.104757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 11/28/2020] [Revised: 01/24/2021] [Accepted: 02/03/2021] [Indexed: 11/17/2022]
Abstract
BACKGROUND Measles virus (MeV) is an important cause of acute febrile illness and pediatric mortality globally, with recent U.S. outbreaks associated with under-vaccination. MeV is highly contagious and timely diagnosis is critical to limit spread. RNA detection is the most sensitive method for acute measles diagnosis; however, MeV nucleic acid amplification assays are not widely available. METHODS We performed a diagnostic accuracy study of a triple-target, real-time RT-PCR (rRT-PCR) assay for simultaneous detection of MeV N, H, and L genes. RESULTS The MeV triple-target rRT-PCR was tested against serial dilutions (7.0-2.0 log10 copies/mL) of five MeV isolates representing circulating genotypes, and detected 98.7% (74/75) of nasopharyngeal (NP) swab dilutions, 100% (75/75) of plasma dilutions, and 85.3% (64/75) of urine dilutions. MeV RNA detection in urine was markedly improved with the addition of a nucleic acid stabilizing agent. A 95% lower limit of detection (LLOD) of < 3.0 log10 copies/mL was established in each specimen matrix. No cross-reactivity with relevant viruses or interfering substances were identified in specificity studies. The MeV triple-target rRT-PCR detected all three gene targets in a clinical NP swab from an individual with confirmed measles infection. Furthermore, pooled testing from 798 influenza A/B/RSV-negative pediatric NP swabs identified two specimens positive for MeV RNA, confirmed by N gene sequencing to represent shedding of the vaccine-type measles virus. CONCLUSIONS The MeV triple-target rRT-PCR assay showed high analytic sensitivity across circulating MeV genotypes in three clinically-relevant matrices. Implementation of this assay in the clinical laboratory may facilitate timely diagnosis of acute measles infection and implementation of appropriate infection control interventions.
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Affiliation(s)
- M Jana Broadhurst
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States
| | - Natasha Garamani
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States
| | - Zoe Hahn
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States
| | - Becky Jiang
- Clinical Virology Laboratory, Stanford Health Care, California, United States
| | - Jenna Weber
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States
| | - ChunHong Huang
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States
| | - Malaya K Sahoo
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States
| | - Jason Kurzer
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States
| | - Catherine A Hogan
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States; Clinical Virology Laboratory, Stanford Health Care, California, United States
| | - Benjamin A Pinsky
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States; Clinical Virology Laboratory, Stanford Health Care, California, United States; Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, United States.
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23
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Hogan CA, Huang C, Sahoo MK, Wang H, Jiang B, Sibai M, Holubar M, Mathew R, Zehnder J, Pinsky BA. Strand-Specific Reverse Transcription PCR for Detection of Replicating SARS-CoV-2. Emerg Infect Dis 2021; 27:632-635. [PMID: 33496233 PMCID: PMC7853532 DOI: 10.3201/eid2702.204168] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
We developed an assay that detects minus-strand RNA as a surrogate for actively replicating severe acute respiratory syndrome coronavirus 2. We detected minus-strand RNA in 41 persons with coronavirus disease up to 30 days after symptom onset. This assay might inform clinical decision-making about patient infectiousness.
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24
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Long DR, Gombar S, Hogan CA, Greninger AL, O’Reilly-Shah V, Bryson-Cahn C, Stevens B, Rustagi A, Jerome KR, Kong CS, Zehnder J, Shah NH, Weiss NS, Pinsky BA, Sunshine JE. Occurrence and Timing of Subsequent Severe Acute Respiratory Syndrome Coronavirus 2 Reverse-transcription Polymerase Chain Reaction Positivity Among Initially Negative Patients. Clin Infect Dis 2021; 72:323-326. [PMID: 33501950 PMCID: PMC7314163 DOI: 10.1093/cid/ciaa722] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 06/03/2020] [Indexed: 12/20/2022] Open
Abstract
Using data for 20 912 patients from 2 large academic health systems, we analyzed the frequency of severe acute respiratory syndrome coronavirus 2 reverse-transcription polymerase chain reaction test discordance among individuals initially testing negative by nasopharyngeal swab who were retested on clinical grounds within 7 days. The frequency of subsequent positivity within this window was 3.5% and was similar across institutions.
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Affiliation(s)
- Dustin R Long
- Division of Critical Care Medicine, Department of Anesthesiology and Pain Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Saurabh Gombar
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Catherine A Hogan
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
- Clinical Virology Laboratory, Stanford Health Care, Stanford, California, USA
| | - Alexander L Greninger
- Department of Laboratory Medicine, University of Washington School of Medicine, Seattle, Washington, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Vikas O’Reilly-Shah
- Department of Anesthesiology and Pain Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Chloe Bryson-Cahn
- Division of Allergy and Infectious Diseases, University of Washington School of Medicine, Seattle, Washington, USA
| | - Bryan Stevens
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
- Clinical Virology Laboratory, Stanford Health Care, Stanford, California, USA
| | - Arjun Rustagi
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Keith R Jerome
- Department of Laboratory Medicine, University of Washington School of Medicine, Seattle, Washington, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Christina S Kong
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - James Zehnder
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Nigam H Shah
- Center for Biomedical Informatics Research, Stanford University, Stanford, California, USA
| | - Noel S Weiss
- Department of Epidemiology, University of Washington School of Public Health, Seattle, Washington, USA
| | - Benjamin A Pinsky
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
- Clinical Virology Laboratory, Stanford Health Care, Stanford, California, USA
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Jacob E Sunshine
- Department of Anesthesiology and Pain Medicine, University of Washington School of Medicine, Seattle, Washington, USA
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25
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Röltgen K, Powell AE, Wirz OF, Stevens BA, Hogan CA, Najeeb J, Hunter M, Wang H, Sahoo MK, Huang C, Yamamoto F, Manohar M, Manalac J, Otrelo-Cardoso AR, Pham TD, Rustagi A, Rogers AJ, Shah NH, Blish CA, Cochran JR, Jardetzky TS, Zehnder JL, Wang TT, Narasimhan B, Gombar S, Tibshirani R, Nadeau KC, Kim PS, Pinsky BA, Boyd SD. Defining the features and duration of antibody responses to SARS-CoV-2 infection associated with disease severity and outcome. Sci Immunol 2020; 5:eabe0240. [PMID: 33288645 PMCID: PMC7857392 DOI: 10.1126/sciimmunol.abe0240] [Citation(s) in RCA: 325] [Impact Index Per Article: 81.3] [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: 07/27/2020] [Revised: 10/05/2020] [Accepted: 12/03/2020] [Indexed: 12/11/2022]
Abstract
SARS-CoV-2-specific antibodies, particularly those preventing viral spike receptor binding domain (RBD) interaction with host angiotensin-converting enzyme 2 (ACE2) receptor, can neutralize the virus. It is, however, unknown which features of the serological response may affect clinical outcomes of COVID-19 patients. We analyzed 983 longitudinal plasma samples from 79 hospitalized COVID-19 patients and 175 SARS-CoV-2-infected outpatients and asymptomatic individuals. Within this cohort, 25 patients died of their illness. Higher ratios of IgG antibodies targeting S1 or RBD domains of spike compared to nucleocapsid antigen were seen in outpatients who had mild illness versus severely ill patients. Plasma antibody increases correlated with decreases in viral RNAemia, but antibody responses in acute illness were insufficient to predict inpatient outcomes. Pseudovirus neutralization assays and a scalable ELISA measuring antibodies blocking RBD-ACE2 interaction were well correlated with patient IgG titers to RBD. Outpatient and asymptomatic individuals' SARS-CoV-2 antibodies, including IgG, progressively decreased during observation up to five months post-infection.
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Affiliation(s)
- Katharina Röltgen
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Abigail E Powell
- Stanford ChEM-H and Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Oliver F Wirz
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Bryan A Stevens
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Catherine A Hogan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Javaria Najeeb
- Department of Structural Biology, Stanford University, Stanford, USA
| | | | - Hannah Wang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Malaya K Sahoo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - ChunHong Huang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Fumiko Yamamoto
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Monali Manohar
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Stanford University, Stanford, CA, USA
- Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA, USA
| | - Justin Manalac
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Tho D Pham
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Blood Center, Palo Alto, CA, USA
| | - Arjun Rustagi
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA
| | - Angela J Rogers
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Stanford University, Stanford, CA, USA
| | - Nigam H Shah
- Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, California, USA
| | - Catherine A Blish
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | | | - James L Zehnder
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Taia T Wang
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Balasubramanian Narasimhan
- Department of Statistics, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Sciences, Stanford University, Stanford, CA, USA
| | - Saurabh Gombar
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Robert Tibshirani
- Department of Statistics, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Sciences, Stanford University, Stanford, CA, USA
| | - Kari C Nadeau
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Stanford University, Stanford, CA, USA
- Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA, USA
| | - Peter S Kim
- Stanford ChEM-H and Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Benjamin A Pinsky
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA
| | - Scott D Boyd
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
- Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA, USA
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26
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Stevens B, Hogan CA, Sahoo MK, Huang C, Garamani N, Zehnder J, Kurzer J, Pinsky BA. Comparison of a Point-of-Care Assay and a High-Complexity Assay for Detection of SARS-CoV-2 RNA. J Appl Lab Med 2020; 5:1307-1312. [PMID: 32761092 PMCID: PMC7454585 DOI: 10.1093/jalm/jfaa135] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 07/15/2020] [Indexed: 11/21/2022]
Abstract
Background Numerous nucleic acid amplification assays utilizing different target genes of the SARS-CoV-2 genome have received emergency use authorization (EUA) by the United States Food and Drug Administration (FDA). Limited data are available comparing the test performance characteristics of these assays. Methods A diagnostic comparison study was performed to evaluate the performance of the Cepheid Xpert Xpress SARS-CoV-2 assay compared to the Hologic Panther Fusion SARS-CoV-2 assay using clinical nasopharyngeal specimens. Agreement between the two assays was assessed by overall, positive, and negative percent agreement and Cohen’s kappa coefficient. Results A total of 104 (54 positive and 50 negative) clinical nasopharyngeal samples were tested by both assays. Using the Panther Fusion as a reference standard, the Xpert demonstrated an overall agreement of 99.0% (95% confidence interval (CI): 94.8 – 100), positive percent agreement of 98.1% (95% CI: 90.1 – 100), and a negative percent agreement of 100% (95% CI: 94.2 – 100). The kappa coefficient was 0.98 (95% CI: 0.94 – 1.0). One sample positive by the Panther Fusion with a cycle threshold (Ct) of 38.6 was found to be reproducibly negative by the Xpert assay. Conclusions The Cepheid Xpert Xpress SARS-CoV-2 assay provides test performance comparable to the Hologic Panther Fusion SARS-CoV-2 assay while offering laboratories rapid, on-demand testing capacity.
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Affiliation(s)
- Bryan Stevens
- Department of Pathology, Stanford University School of Medicine, Stanford, CA.,Clinical Virology Laboratory, Stanford Health Care, Stanford, CA
| | - Catherine A Hogan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA.,Clinical Virology Laboratory, Stanford Health Care, Stanford, CA
| | - Malaya K Sahoo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA
| | - ChunHong Huang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA
| | - Natasha Garamani
- Department of Pathology, Stanford University School of Medicine, Stanford, CA
| | - James Zehnder
- Department of Pathology, Stanford University School of Medicine, Stanford, CA
| | - Jason Kurzer
- Department of Pathology, Stanford University School of Medicine, Stanford, CA
| | - Benjamin A Pinsky
- Department of Pathology, Stanford University School of Medicine, Stanford, CA.,Clinical Virology Laboratory, Stanford Health Care, Stanford, CA.,Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA
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27
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Hogan CA, Gombar S, Wang H, Röltgen K, Shi RZ, Holubar M, Chang SI, Lee GM, Boyd SD, Zehnder J, Pinsky BA. Large-Scale Testing of Asymptomatic Healthcare Personnel for Severe Acute Respiratory Syndrome Coronavirus 2. Emerg Infect Dis 2020; 27. [PMID: 33256889 PMCID: PMC7774535 DOI: 10.3201/eid2701.203892] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Large-scale, 1-time testing of >12,000 asymptomatic healthcare personnel in California, USA, during April–June 2020 showed that prevalence of severe acute respiratory syndrome coronavirus 2 was low (<1%). Testing might identify asymptomatic and presymptomatic persons, including some with high viral burden, enabling prompt implementation of measures to limit nosocomial spread.
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28
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Wang H, Hogan CA, Miller JA, Sahoo MK, Huang C, Mfuh KO, Sibai M, Zehnder J, Hickey B, Sinnott-Armstrong N, Pinsky BA. Performance of Nucleic Acid Amplification Tests for Detection of Severe Acute Respiratory Syndrome Coronavirus 2 in Prospectively Pooled Specimens. Emerg Infect Dis 2020; 27. [PMID: 33183494 PMCID: PMC7774575 DOI: 10.3201/eid2701.203379] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Pooled nucleic acid amplification tests for severe acute respiratory syndrome coronavirus 2 could increase availability of testing at decreased cost. However, the effect of dilution on analytical sensitivity through sample pooling has not been well characterized. We tested 1,648 prospectively pooled specimens by using 3 nucleic acid amplification tests for severe acute respiratory syndrome coronavirus 2: a laboratory-developed real-time reverse transcription PCR targeting the envelope gene, and 2 commercially available Panther System assays targeting open reading frame 1ab. Positive percent agreement (PPA) of pooled versus individual testing ranged from 71.7% to 82.6% for pools of 8 and from 82.9% to 100.0% for pools of 4. We developed and validated an independent stochastic simulation model to estimate effects of dilution on PPA and efficiency of a 2-stage pooled real-time reverse transcription PCR testing algorithm. PPA was dependent on the proportion of tests with positive results, cycle threshold distribution, and assay limit of detection.
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29
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Röltgen K, Wirz OF, Stevens BA, Powell AE, Hogan CA, Najeeb J, Hunter M, Sahoo MK, Huang C, Yamamoto F, Manalac J, Otrelo-Cardoso AR, Pham TD, Rustagi A, Rogers AJ, Shah NH, Blish CA, Cochran JR, Nadeau KC, Jardetzky TS, Zehnder JL, Wang TT, Kim PS, Gombar S, Tibshirani R, Pinsky BA, Boyd SD. SARS-CoV-2 Antibody Responses Correlate with Resolution of RNAemia But Are Short-Lived in Patients with Mild Illness. medRxiv 2020:2020.08.15.20175794. [PMID: 32839786 PMCID: PMC7444305 DOI: 10.1101/2020.08.15.20175794] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
SARS-CoV-2-specific antibodies, particularly those preventing viral spike receptor binding domain (RBD) interaction with host angiotensin-converting enzyme 2 (ACE2) receptor, could offer protective immunity, and may affect clinical outcomes of COVID-19 patients. We analyzed 625 serial plasma samples from 40 hospitalized COVID-19 patients and 170 SARS-CoV-2-infected outpatients and asymptomatic individuals. Severely ill patients developed significantly higher SARS-CoV-2-specific antibody responses than outpatients and asymptomatic individuals. The development of plasma antibodies was correlated with decreases in viral RNAemia, consistent with potential humoral immune clearance of virus. Using a novel competition ELISA, we detected antibodies blocking RBD-ACE2 interactions in 68% of inpatients and 40% of outpatients tested. Cross-reactive antibodies recognizing SARS-CoV RBD were found almost exclusively in hospitalized patients. Outpatient and asymptomatic individuals' serological responses to SARS-CoV-2 decreased within 2 months, suggesting that humoral protection may be short-lived.
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Affiliation(s)
- Katharina Röltgen
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Oliver F. Wirz
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Bryan A. Stevens
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Abigail E. Powell
- Stanford ChEM-H and Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Catherine A. Hogan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Javaria Najeeb
- Department of Structural Biology, Stanford University, Stanford, USA
| | | | - Malaya K. Sahoo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - ChunHong Huang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Fumiko Yamamoto
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Justin Manalac
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Tho D. Pham
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Blood Center, Palo Alto, CA, USA
| | - Arjun Rustagi
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA
| | - Angela J. Rogers
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Stanford University, Stanford, CA, USA
| | - Nigam H. Shah
- Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, California, USA
| | - Catherine A. Blish
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | - Kari C. Nadeau
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Stanford University, Stanford, CA, USA
- Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA, USA
| | | | - James L. Zehnder
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Taia T. Wang
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Peter S. Kim
- Stanford ChEM-H and Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Saurabh Gombar
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Robert Tibshirani
- Department of Biomedical Data Sciences, Stanford University, Stanford, CA, USA
- Department of Statistics, Stanford University, Stanford, CA, USA
| | - Benjamin A. Pinsky
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA
| | - Scott D. Boyd
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA, USA
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30
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Gombar S, Chang M, Hogan CA, Zehnder J, Boyd S, Pinsky BA, Shah NH. Persistent detection of SARS-CoV-2 RNA in patients and healthcare workers with COVID-19. J Clin Virol 2020; 129:104477. [PMID: 32505778 PMCID: PMC7260561 DOI: 10.1016/j.jcv.2020.104477] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 05/26/2020] [Indexed: 12/20/2022]
Abstract
BACKGROUND Current guidelines for returning health care workers (HCW) to service after a positive SARS-CoV-2 RT-PCR test and ceasing of transmission precautions for patients is based on two general strategies. A test-based strategy that requires negative respiratory RT-PCR tests obtained after the resolution of symptoms. Alternatively, due to the limited availability of testing, many sites employ a symptom-based strategy that recommends excluding HCW from the workforce and keeping patients on contact precautions until a fixed period of time has elapsed from symptom recovery. The underlying assumption of the symptom-based strategy is that waiting for a fixed period of time is a surrogate for negative RT-PCR testing, which itself is a surrogate for the absence of shedding infectious virus. OBJECTIVES To better understand the appropriate length of symptom based return to work and contact precaution strategies. STUDY DESIGN We performed an observational analysis of 150 patients and HCW that transitioned from RT-PCR SARS-CoV-2 positive to negative over the course of 2 months at a US academic medical center. RESULTS We found that the average time to transition from RT-PCR positive to negative was 24 days after symptom onset and 10 % remained positive even 33 days after symptom onset. No difference was seen in HCW and patients. CONCLUSIONS These findings suggest until definitive evidence of the length of infective viral shedding is obtained that the fixed length of time before returning to work or ceasing contract precautions be revised to over one-month.
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Affiliation(s)
- Saurabh Gombar
- Department of Pathology, School of Medicine, Stanford, CA, United States.
| | - Marcello Chang
- Department of Medicine (Biomedical Informatics), School of Medicine, Stanford, CA, United States
| | - Catherine A Hogan
- Department of Pathology, School of Medicine, Stanford, CA, United States
| | - James Zehnder
- Department of Pathology, School of Medicine, Stanford, CA, United States; Department of Medicine (Hematology), School of Medicine, Stanford, CA, United States
| | - Scott Boyd
- Department of Pathology, School of Medicine, Stanford, CA, United States
| | - Benjamin A Pinsky
- Department of Pathology, School of Medicine, Stanford, CA, United States
| | - Nigam H Shah
- Department of Medicine (Biomedical Informatics), School of Medicine, Stanford, CA, United States
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Abstract
To investigate the possibility of earlier cases of severe acute respiratory syndrome coronavirus 2 infection than previously recognized, we retrospectively tested pooled samples from 1,700 persons with respiratory signs/symptoms seen at Stanford Health Care, Palo Alto, California, USA, during the last 2 months of 2019. We found no evidence of earlier infection.
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32
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Abstract
This study describes findings of novel coronavirus testing on pooled nasopharyngeal and bronchoalveolar lavage samples taken from patients who had negative results by routine respiratory virus testing to see if pooling samples could increase testing throughput and efficiency and facilitate early detection of community COVID-19 transmission.
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Affiliation(s)
- Catherine A. Hogan
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Malaya K. Sahoo
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Benjamin A. Pinsky
- Department of Pathology, Stanford University School of Medicine, Stanford, California
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33
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Long DR, Gombar S, Hogan CA, Greninger AL, OReilly Shah V, Bryson-Cahn C, Stevens B, Rustagi A, Jerome KR, Kong CS, Zehnder J, Shah NH, Weiss NS, Pinsky BA, Sunshine J. Occurrence and Timing of Subsequent SARS-CoV-2 RT-PCR Positivity Among Initially Negative Patients. medRxiv 2020. [PMID: 32511542 DOI: 10.1101/2020.05.03.20089151] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
BACKGROUND SARS-CoV-2 reverse transcriptase polymerase chain reaction (RT-PCR) testing remains the cornerstone of laboratory-based identification of patients with COVID-19. As the availability and speed of SARS-CoV-2 testing platforms improve, results are increasingly relied upon to inform critical decisions related to therapy, use of personal protective equipment, and workforce readiness. However, early reports of RT-PCR test performance have left clinicians and the public with concerns regarding the reliability of this predominant testing modality and the interpretation of negative results. In this work, two independent research teams report the frequency of discordant SARS-CoV-2 test results among initially negative, repeatedly tested patients in regions of the United States with early community transmission and access to testing. METHODS All patients at the University of Washington (UW) and Stanford Health Care undergoing initial testing by nasopharyngeal (NP) swab between March 2nd and April 7th, 2020 were included. SARS-CoV-2 RT-PCR was performed targeting the N, RdRp, S, and E genes and ORF1ab, using a combination of Emergency Use Authorization laboratory-developed tests and commercial assays. Results through April 14th were extracted to allow for a complete 7-day observation period and an additional day for reporting. RESULTS A total of 23,126 SARS-CoV-2 RT-PCR tests (10,583 UW, 12,543 Stanford) were performed in 20,912 eligible patients (8,977 UW, 11,935 Stanford) undergoing initial testing by NP swab; 626 initially test-negative patients were re-tested within 7 days. Among this group, repeat testing within 7 days yielded a positive result in 3.5% (4.3% UW, 2.8% Stanford) of cases, suggesting an initial false negative RT-PCR result; the majority (96.5%) of patients with an initial negative result who warranted reevaluation for any reason remained negative on all subsequent tests performed within this window. CONCLUSIONS Two independent research teams report the similar finding that, among initially negative patients subjected to repeat SARS-CoV-2 RT-PCR testing, the occurrence of a newly positive result within 7 days is uncommon. These observations suggest that false negative results at the time of initial presentation do occur, but potentially at a lower frequency than is currently believed. Although it is not possible to infer the clinical sensitivity of NP SARS-CoV-2 RT-PCR testing using these data, they may be used in combination with other reports to guide the use and interpretation of this common testing modality.
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Bulterys PL, Garamani N, Stevens B, Sahoo MK, Huang C, Hogan CA, Zehnder J, Pinsky BA. Comparison of a laboratory-developed test targeting the envelope gene with three nucleic acid amplification tests for detection of SARS-CoV-2. J Clin Virol 2020; 129:104427. [PMID: 32535398 PMCID: PMC7207111 DOI: 10.1016/j.jcv.2020.104427] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 05/03/2020] [Accepted: 05/05/2020] [Indexed: 11/18/2022]
Abstract
Four nucleic acid amplification tests for SARS-CoV-2 RNA demonstrated comparable performance using clinical specimens. A limited number of discrepancies were observed in specimens with low viral loads. The isothermal amplification assay was slightly less sensitive but was one hour faster than the other methods. Assay selection requires consideration of test performance, instrument/reagent availability, turnaround and throughput.
Background Numerous nucleic acid amplification tests, including real-time, reverse transcription PCR (rRT-PCR) and isothermal amplification methods, have been developed to detect SARS-CoV-2 RNA, including many that have received emergency use authorization (EUA). There is a need to assess their test performance relative to one another. Objectives The aim of this study was to compare the test performance of a high complexity laboratory-developed rRT-PCR EUA from Stanford Health Care (SHC) targeting the SARS-CoV-2 envelope (E) gene with other tests: the Atila isothermal amplification assay targeting the nucleocapsid (N) gene and open reading frame 1ab (ORF1ab), the Altona E and spike (S) multiplex, real-time RT-PCR, and the US Centers for Disease Control and Prevention (CDC) N1 and N2 rRT-PCRs. Study Design A diagnostic comparison study was performed by testing nasopharyngeal samples from persons under investigation for coronavirus disease 2019 (COVID-19). Assay performance was assessed by percent agreement and Cohen’s kappa coefficient. Results Positive percent agreement with the SHC EUA reference assay was 82.8 % (95 % confidence interval (CI) 65.0 to 92.9) for Atila, 86.7 % (95 % CI 69.7 to 95.3) for the Altona E and S targets, and 86.7 % (95 % CI 69.7 to 95.3) and 90.0 % (95 % CI 73.6 to 97.3), for the CDC N1 and N2 targets, respectively. All assays demonstrated 100 % negative percent agreement. Kappa coefficients ranged from 0.86 to 0.92, indicating excellent agreement. Conclusions Performance was comparable among the SARS-CoV-2 nucleic acid amplification methods tested, with a limited number of discrepancies observed in specimens with low viral loads.
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Affiliation(s)
- Philip L Bulterys
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Natasha Garamani
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Bryan Stevens
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Clinical Virology Laboratory, Stanford Health Care, Stanford, CA, USA
| | - Malaya K Sahoo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - ChunHong Huang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Catherine A Hogan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Clinical Virology Laboratory, Stanford Health Care, Stanford, CA, USA
| | - James Zehnder
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Benjamin A Pinsky
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Clinical Virology Laboratory, Stanford Health Care, Stanford, CA, USA; Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
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Hogan CA, Sahoo MK, Huang C, Garamani N, Stevens B, Zehnder J, Pinsky BA. Five-minute point-of-care testing for SARS-CoV-2: Not there yet. J Clin Virol 2020; 128:104410. [PMID: 32403009 PMCID: PMC7194071 DOI: 10.1016/j.jcv.2020.104410] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 04/28/2020] [Indexed: 11/27/2022]
Affiliation(s)
- Catherine A Hogan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Clinical Virology Laboratory, Stanford Health Care, Stanford, CA, USA
| | - Malaya K Sahoo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - ChunHong Huang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Natasha Garamani
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Bryan Stevens
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Clinical Virology Laboratory, Stanford Health Care, Stanford, CA, USA
| | - James Zehnder
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Benjamin A Pinsky
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Clinical Virology Laboratory, Stanford Health Care, Stanford, CA, USA; Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
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Hogan CA, Sahoo MK, Huang C, Garamani N, Stevens B, Zehnder J, Pinsky BA. Comparison of the Panther Fusion and a laboratory-developed test targeting the envelope gene for detection of SARS-CoV-2. J Clin Virol 2020; 127:104383. [PMID: 32353760 PMCID: PMC7195328 DOI: 10.1016/j.jcv.2020.104383] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 04/18/2020] [Accepted: 04/21/2020] [Indexed: 01/04/2023]
Abstract
BACKGROUND Numerous nucleic acid amplification assays have recently received emergency use authorization (EUA) for the diagnosis of SARS-CoV-2 infection, and there is a need to assess their test performance relative to one another. OBJECTIVES The aim of this study was to compare the test performance of the Hologic Panther Fusion SARS-CoV-2 assay targeting two regions of open reading frame 1ab (ORF1ab) to a high complexity molecular-based, laboratory-developed EUA from Stanford Health Care (SHC) targeting the SARS-CoV-2 envelope (E) gene. STUDY DESIGN We performed a diagnostic comparison study by testing nasopharyngeal samples on the two assays. Assay agreement was assessed by overall percent agreement and Cohen's kappa coefficient. RESULTS A total of 184 nasopharyngeal samples were tested using the two assays, of which 180 showed valid results and were included for the comparative analysis. Overall percent agreement between the assays was 98.3 % (95 % confidence interval (CI) 95.2-99.7) and kappa coefficient was 0.97 (95 % CI 0.93-1.0). One sample was detected on the SHC laboratory developed test (LDT) and not on the Panther Fusion, and had a Ct of 35.9. Conversely, 2 samples were detected on the Panther Fusion and not on the LDT, and had Ct values of 37.2 and 36.6. CONCLUSION The Panther Fusion SARS-CoV-2 assay and the SHC LDT perform similarly on clinical nasopharyngeal swab specimens. Other considerations, including reagent availability, turnaround time, labor requirements, cost and instrument throughput should guide the decision of which assay to perform.
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Affiliation(s)
- Catherine A Hogan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Clinical Virology Laboratory, Stanford Health Care, Stanford, CA, USA
| | - Malaya K Sahoo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - ChunHong Huang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Natasha Garamani
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Bryan Stevens
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Clinical Virology Laboratory, Stanford Health Care, Stanford, CA, USA
| | - James Zehnder
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Benjamin A Pinsky
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Clinical Virology Laboratory, Stanford Health Care, Stanford, CA, USA; Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
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Jones VG, Mills M, Suarez D, Hogan CA, Yeh D, Segal JB, Nguyen EL, Barsh GR, Maskatia S, Mathew R. COVID-19 and Kawasaki Disease: Novel Virus and Novel Case. Hosp Pediatr 2020; 10:537-540. [PMID: 32265235 DOI: 10.1542/hpeds.2020-0123] [Citation(s) in RCA: 500] [Impact Index Per Article: 125.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In the midst of the coronavirus disease 2019 (COVID-19) pandemic, we are seeing widespread disease burden affecting patients of all ages across the globe. However, much remains to be understood as clinicians, epidemiologists, and researchers alike are working to describe and characterize the disease process while caring for patients at the frontlines. We describe the case of a 6-month-old infant admitted and diagnosed with classic Kawasaki disease, who also screened positive for COVID-19 in the setting of fever and minimal respiratory symptoms. The patient was treated per treatment guidelines, with intravenous immunoglobulin and high-dose aspirin, and subsequently defervesced with resolution of her clinical symptoms. The patient's initial echocardiogram was normal, and she was discharged within 48 hours of completion of her intravenous immunoglobulin infusion, with instruction to quarantine at home for 14 days from the date of her positive test results for COVID-19. Further study of the clinical presentation of pediatric COVID-19 and the potential association with Kawasaki disease is warranted, as are the indications for COVID-19 testing in the febrile infant.
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Affiliation(s)
- Veena G Jones
- Division of Pediatric Hospital Medicine, Palo Alto Foundation Medical Group and .,Palo Alto Medical Foundation Research Institute, Palo Alto Medical Foundation, Sutter Health, Palo Alto, California; and
| | - Marcos Mills
- Divisions of Pediatric Cardiology and.,Department of Pediatrics, Stanford Medicine, Stanford University, Stanford, California
| | - Dominique Suarez
- Division of Pediatric Hospital Medicine, Palo Alto Foundation Medical Group and
| | | | - Debra Yeh
- Department of Pediatrics, Stanford Medicine, Stanford University, Stanford, California
| | - J Bradley Segal
- Department of Pediatrics, Stanford Medicine, Stanford University, Stanford, California
| | - Elizabeth L Nguyen
- Department of Pediatrics, Stanford Medicine, Stanford University, Stanford, California
| | - Gabrielle R Barsh
- Department of Pediatrics, Stanford Medicine, Stanford University, Stanford, California
| | - Shiraz Maskatia
- Divisions of Pediatric Cardiology and.,Department of Pediatrics, Stanford Medicine, Stanford University, Stanford, California
| | - Roshni Mathew
- Department of Pediatrics, Stanford Medicine, Stanford University, Stanford, California.,Pediatric Infectious Disease and
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Hitchcock MM, Holubar M, Hogan CA, Tompkins LS, Banaei N. Dual Reporting of Clostridioides difficile PCR and Predicted Toxin Result Based on PCR Cycle Threshold Reduces Treatment of Toxin-Negative Patients without Increases in Adverse Outcomes. J Clin Microbiol 2019; 57:e01288-19. [PMID: 31511334 PMCID: PMC6812995 DOI: 10.1128/jcm.01288-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 09/05/2019] [Indexed: 12/21/2022] Open
Abstract
Nucleic acid amplification tests are commonly used to diagnose Clostridioides difficile infection (CDI). Two-step testing with a toxin enzyme immunoassay is recommended to discriminate between infection and colonization but requires additional resources. Prior studies showed that PCR cycle threshold (CT ) can predict toxin positivity with high negative predictive value. Starting in October 2016, the predicted toxin result (CT-toxin) based on a validated cutoff was routinely reported at our facility. To evaluate the clinical efficacy of this reporting, all adult patients with positive GeneXpert PCR results from October 2016 through October 2017 underwent a chart review to measure the recurrence of or conversion to a CT-toxin+ result and 30-day all-cause mortality. There were 482 positive PCR tests in 430 unique patients, 282 CT-toxin+ and 200 CT-toxin- Patient characteristics were similar at testing, though CT-toxin+ patients had higher white blood cell (WBC) counts (12.5 × 103 versus 9.3 × 103 cells/μl; P = 0.001). All cases (n = 21) of fulminant CDI had a CT-toxin+ result. Index CT-toxin+ patients were significantly more likely to have a CT-toxin+ result within 90 days than CT-toxin- patients (17.4% [n = 49] versus 8.0% [n = 16], respectively; P = 0.003). Thirty-day all-cause mortality was higher in CT-toxin- patients (11.1% versus 6.8%; P = 0.1), though no deaths in CT-toxin- patients were directly attributable to CDI. Of the 200 CT-toxin- patients, 51.5% (n = 103) were treated for CDI. The rates of conversion to a CT-toxin+ result (8.8% versus 7.2%; P = 0.8) and all-cause mortality (8.8% versus 13.4%; P = 0.3) were similar between treated and untreated CT-toxin- patients, respectively. CT -based toxin prediction may identify patients at higher risk for CDI-related complications and reduce treatment among CT-toxin- patients.
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Affiliation(s)
- Matthew M Hitchcock
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Marisa Holubar
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Catherine A Hogan
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
- Clinical Microbiology Laboratory, Stanford Health Care, Stanford, California, USA
| | - Lucy S Tompkins
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Niaz Banaei
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
- Clinical Microbiology Laboratory, Stanford Health Care, Stanford, California, USA
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Hitchcock MM, Hogan CA, Budvytiene I, Banaei N. Reproducibility of positive results for rare pathogens on the FilmArray GI Panel. Diagn Microbiol Infect Dis 2019; 95:10-14. [PMID: 31029490 DOI: 10.1016/j.diagmicrobio.2019.03.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [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: 01/23/2019] [Revised: 03/23/2019] [Accepted: 03/24/2019] [Indexed: 12/27/2022]
Abstract
Though the FilmArray GI Panel has a reported aggregate specificity and reproducibility of >97% and > 99%, respectively, the reproducibility is less understood in clinical practice. We measured the reproducibility of positive results for low-prevalence pathogens. Samples with positive results for selected targets were repeated using a different FilmArray module. Overall, 331 of 373 (89%) results were reproducible. Giardia lamblia (57/57, 100%), Cryptosporidium spp. (61/63, 97%), Cyclospora cayetanensis (34/35, 97%), Plesiomonas shigelloides (17/18, 94%), and Rotavirus A (76/77, 99%) were highly reproducible, while Adenovirus F40/41 (38/54, 70%), Vibrio spp. (8/10, 80%), V. cholerae (3/8, 37.5%), and Yersinia enterocolitica (36/50, 72%) were poorly reproducible. Review of 38 patients with nonreproducible results showed that 19 (50%) had evidence of gastroenteritis and only 6 (16%) had possible infection with the organism that showed a nonreproducible result. Higher false-positive rates with certain targets on FAGP emphasize the need for diagnostic stewardship.
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Affiliation(s)
- Matthew M Hitchcock
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Catherine A Hogan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Clinical Microbiology Laboratory, Stanford Health Care, Stanford, CA, USA
| | - Indre Budvytiene
- Clinical Microbiology Laboratory, Stanford Health Care, Stanford, CA, USA
| | - Niaz Banaei
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Clinical Microbiology Laboratory, Stanford Health Care, Stanford, CA, USA.
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Hogan CA, Watz N, Budvytiene I, Banaei N. Rapid antimicrobial susceptibility testing by VITEK®2 directly from blood cultures in patients with Gram-negative rod bacteremia. Diagn Microbiol Infect Dis 2019; 94:116-121. [PMID: 30711413 DOI: 10.1016/j.diagmicrobio.2019.01.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [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: 10/22/2018] [Revised: 12/28/2018] [Accepted: 01/01/2019] [Indexed: 10/27/2022]
Abstract
OBJECTIVE Optimizing therapy for bacteremia is currently limited by the 1-2-day turnaround time required for antimicrobial susceptibility testing (AST). Here, we assess a rapid AST method with VITEK®2 (bioMérieux, France) directly from positive blood cultures. METHODS Patient-derived positive blood cultures with Gram-negative rods identified as Enterobacteriaceae and Pseudomonas aeruginosa were prospectively tested, and other blood culture bottles were spiked with carbapenem-resistant Enterobacteriaceae (CRE). Positive cultures were subjected to red blood cell lysis and centrifugation, and setup on VITEK®2. RESULTS A total of 109 patient blood cultures and 52 spiked blood cultures were tested. Overall, essential agreement was 97.7% [95% confidence interval (CI) 96.4-99.0], and categorical agreement was 96.8% (95% CI 95.0-98.6). Mean turnaround time from setup to susceptibility results for Enterobacteriaceae in the clinical cultures was 9.0 (±1.3) h. CONCLUSIONS Direct susceptibility testing of blood cultures by VITEK®2 for Enterobacteriaceae is an accurate, practical, and inexpensive diagnostic strategy for rapid automated AST.
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Affiliation(s)
- C A Hogan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Clinical Microbiology Laboratory, Stanford University Medical Center, Palo Alto, CA, USA
| | - N Watz
- Clinical Microbiology Laboratory, Stanford University Medical Center, Palo Alto, CA, USA
| | - I Budvytiene
- Clinical Microbiology Laboratory, Stanford University Medical Center, Palo Alto, CA, USA
| | - N Banaei
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Clinical Microbiology Laboratory, Stanford University Medical Center, Palo Alto, CA, USA; Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
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Abstract
INTRODUCTION Respiratory syncytial virus (RSV) is a leading cause of acute respiratory infections. The clinical manifestations of RSV are indistinguishable from other etiologies of acute respiratory infection. Therefore, accurate and timely laboratory testing is needed to impact clinical management. There are now multiple rapid, low-complexity, commercially available assays for RSV. These tests present significant performance advantages compared to older antigen detection tests. Accurate and rapid diagnosis of RSV has the potential for enabling timely cessation of unnecessary antibiotics and implementation of good infection control practices. Furthermore, a recently approved RSV diagnostic assay can reduce the test turnaround time to 13 min or less. Areas covered: The authors aim to review the importance of rapid and accurate testing for RSV and will describe the available molecular RSV diagnostic assays approved for use at the point-of-care. Expert commentary: Further independent evaluations are needed to confirm that the accuracy of the low-complexity assays is indeed similar to reverse transcriptase polymerase chain reaction across the age spectrum, and in immunosuppressed hosts. In the future, the challenge will be to achieve a balance between increasingly sophisticated multiplex diagnostic platforms and tests that are sufficiently simple to be used at the point-of-care.
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Affiliation(s)
- Catherine A Hogan
- a Division of Infectious Diseases, Department of Microbiology , McGill University Health Centre , Montréal , Canada.,b Department of Pathology , Stanford University School of Medicine , Stanford , CA , USA.,c Clinical Microbiology Laboratory , Stanford University Medical Center , Palo Alto , CA , USA
| | - Chelsea Caya
- d Infectious Diseases and Immunity in Global Health Program , Research Institute of the McGill University Health Centre , CA , USA
| | - Jesse Papenburg
- e Division of Pediatric Infectious Diseases, Departments of Microbiology and Pediatrics , McGill University Health Centre , CA , USA
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Hogan CA, Puri L, Gore G, Pai M. Impact of fluoroquinolone treatment on delay of tuberculosis diagnosis: A systematic review and meta-analysis. J Clin Tuberc Other Mycobact Dis 2016; 6:1-7. [PMID: 31723692 PMCID: PMC6850236 DOI: 10.1016/j.jctube.2016.12.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [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: 11/08/2016] [Revised: 12/03/2016] [Accepted: 12/08/2016] [Indexed: 11/17/2022] Open
Abstract
Background Fluoroquinolones are among the most commonly used antibiotics for the treatment of respiratory infections. Because fluoroquinolones show bactericidal activity against Mycobacterium tuberculosis, there is concern that their use can delay the diagnosis of tuberculosis. We conducted a systematic review and meta-analysis to assess whether empiric treatment with fluoroquinolones delays the diagnosis and treatment of tuberculosis in patients with respiratory tract infections. Objectives The primary objective was to assess the delay in days in the diagnosis and treatment of tuberculosis, among patients who received quinolones, compared to those who received non-fluoroquinolone antibiotics. Methods We included studies of adult patients treated with fluoroquinolones prior to a confirmed diagnosis of tuberculosis. We performed a literature search of 7 databases (including PubMed, Embase and Cochrane Library) with no language restrictions. We calculated an unweighted mean of estimate of difference in delay across all studies. For the studies for which the estimate was available as a mean with standard deviation, a weighted average using a random effects meta-analysis model was estimated. Results A total of 3983 citations were identified from the literature search; of these, 17 articles were selected for full-text review. A total of 10 studies were retained for the synthesis. These included 7 retrospective cohort studies and 3 case-control studies. Only one of these studies was from a high TB burden country, South Africa. The most commonly used fluoroquinolones were levofloxacin, gemifloxacin and moxifloxacin. The unweighted average of difference in delay between the fluoroquinolone group and non-fluoroquinolone group was 12.9 days (95% CI 6.1-19.7). When these differences were pooled using a random effects model, the weighted estimate was 10.9 days (95% CI 4.2-17.6). When stratified by acid-fast smear status, the delay was consistently greater in the smear-negative group. Conclusion Although results are variable, the use of fluoroquinolones in patients with respiratory infections seems to delay the diagnosis of TB by nearly two weeks. Consistent with the International Standards for TB Care, their use should be avoided when tuberculosis is suspected.
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Affiliation(s)
- Catherine A Hogan
- McGill International Tuberculosis Centre & Department of Epidemiology, Biostatistics and Occupational Health, McGill University. 1020 Pine Ave West, Montreal, QC H3A 1A2, Canada
| | - Lekha Puri
- McGill International Tuberculosis Centre & Department of Epidemiology, Biostatistics and Occupational Health, McGill University. 1020 Pine Ave West, Montreal, QC H3A 1A2, Canada
| | - Genevieve Gore
- Schulich Library of Science and Engineering, McGill University. 809 Sherbrooke St. West, Montreal, QC H3A 0C1, Canada
| | - Madhukar Pai
- McGill International Tuberculosis Centre & Department of Epidemiology, Biostatistics and Occupational Health, McGill University. 1020 Pine Ave West, Montreal, QC H3A 1A2, Canada.,Manipal McGill Center for Infectious Diseases, Manipal University, Manipal, India
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Hogan CA, Iles J, Frost EH, Giroux G, Cassar O, Gessain A, Dion MJ, Ilunga V, Rambaut A, Yengo-Ki-Ngimbi AÉ, Behets F, Pybus OG, Pépin J. Epidemic History and Iatrogenic Transmission of Blood-borne Viruses in Mid-20th Century Kinshasa. J Infect Dis 2016; 214:353-60. [PMID: 26768251 DOI: 10.1093/infdis/jiw009] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 11/13/2015] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The human immunodeficiency virus type 1 (HIV-1) pandemic was ignited in Léopoldville (now known as Kinshasa), in the former Belgian Congo. Factors that jump-started its early expansion remain unclear. Nonlethal hepatitis C virus (HCV) and human T-cell lymphotropic virus (HTLV-1) can be used to investigate past iatrogenic transmission. METHODS We undertook a cross-sectional study of elderly inhabitants of Kinshasa, with serological assays, amplification, and sequencing. Risk factors were assessed through logistic regression. Phylogenetic methods reconstructed the genetic history of HCV. RESULTS A total of 217 of 839 participants (25.9%) were HCV seropositive; 26 (3.1%) were HTLV-1-seropositive. Amplification products were obtained from 118 HCV-seropositive participants; subtypes 4k (in 47 participants) and 4r (in 38) were most common. Independent risk factors for HCV subtype 4r seropositivity were intramuscular tuberculosis therapy, intravenous injections at hospital A, intravenous injections before 1960, and injections at a colonial-era venereology clinic. Intravenous injections at hospital B and antimalarials were associated with HCV subtype 4k seropositivity. Risk factors for HTLV-1 seropositivity included intravenous injections at hospitals C or D and transfusions. Evolutionary analysis of viral sequences revealed independent exponential amplification of HCV subtypes 4r and 4k from the 1950s onward. CONCLUSIONS Iatrogenic transmission of HCV and HTLV-1 occurred in mid-20th century Kinshasa, at the same time and place HIV-1 emerged. Iatrogenic routes may have contributed to the early establishment of the pandemic.
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Affiliation(s)
| | | | | | | | - Olivier Cassar
- Institut Pasteur Centre National de la Recherche Scientifique, UMR 3569, Paris, France
| | - Antoine Gessain
- Institut Pasteur Centre National de la Recherche Scientifique, UMR 3569, Paris, France
| | | | | | | | | | - Frieda Behets
- Programme ESP/UNC-DRC University of North Carolina, Chapel Hill
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Alizadeh RI, Eckhoff DG, Samson MM, Doucette TK, Hogan CA, Bach JM. Axial and rotational alignment of the leg. Biomed Sci Instrum 2004; 40:290-6. [PMID: 15133973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
The axial and rotational alignments of the lower extremity are commonly referenced independently, with minimal research on whether coexistent axial and rotational malalignment cause pathologies. The present study analyzed whether a correlation exists between the axial and rotational alignments of the leg. The methodology to measure both alignments was adapted for computer tomography. Fifty patients were analyzed at five reference images to determine axial and rotational alignment. The reference images included the femoral head, the femoral shaft (at the level of the lesser trochanter), the distal femur, the proximal tibia, and the ankle joint. Axial alignment was calculated by using horizontal and vertical measurements of the location of the femoral head, the distal femur, and the ankle joint. Rotational alignments of femur, knee, and tibia were calculated using four angles: proximal femoral, distal femoral, proximal tibial, and ankle joint angles defined relative to a fixed reference. Pearson correlation analysis between axial alignment and the three mentioned rotational alignments were calculated. The correlation coefficient values ranged between -0.15-0.07 when comparing axial to rotational alignment, indicating that a week correlation exists between the two alignments. Though these results were derived using highly reproducible methods, the hypothesis of an existing correlation between the axial and rotational alignments of the leg was rejected. These findings allow for an improved understanding of lower extremity mechanics, which merit importance when considering pathologies of the leg and the surgical techniques that could ultimately benefit patients suffering from these pathologies.
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Affiliation(s)
- R I Alizadeh
- University of Colorado Health Sciences Center, Department of Orthopaedics, Colorado School of Mines, Division of Engineering, USA
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Fong CT, Wang M, Young EC, Hogan CA, Tallents RH, Kyrkanides S, Liptak GS, Sanger JA, Frisina RD. Microtia associated with the Kabuki (Niikawa-Kuroki) syndrome. Otolaryngol Head Neck Surg 2001; 125:557-8. [PMID: 11700460 DOI: 10.1067/mhn.2001.116780] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- C T Fong
- University of Rochester School of Medicine, Rochester, New York 14642, USA.
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Abstract
The present study was a systematic investigation of the benefit of providing hearing-impaired listeners with audible high-frequency speech information. Five normal-hearing and nine high-frequency hearing-impaired listeners identified nonsense syllables that were low-pass filtered at a number of cutoff frequencies. As a means of quantifying audibility for each condition, Articulation Index (AI) was calculated for each condition for each listener. Most hearing-impaired listeners demonstrated an improvement in speech recognition as additional audible high-frequency information was provided. In some cases for more severely impaired listeners, increasing the audibility of high-frequency speech information resulted in no further improvement in speech recognition, or even decreases in speech recognition. A new measure of how well hearing-impaired listeners used information within specific frequency bands called "efficiency" was devised. This measure compared the benefit of providing a given increase in speech audibility to a hearing-impaired listener to the benefit observed in normal-hearing listeners for the same increase in speech audibility. Efficiencies were calculated using the old AI method and the new AI method (which takes into account the effects of high speech presentation levels). There was a clear pattern in the results suggesting that as the degree of hearing loss at a given frequency increased beyond 55 dB HL, the efficacy of providing additional audibility to that frequency region was diminished, especially when this degree of hearing loss was present at frequencies of 4000 Hz and above. A comparison of analyses from the "old" and "new" AI procedures suggests that some, but not all, of the deficiencies of speech recognition in these listeners was due to high presentation levels.
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Affiliation(s)
- C A Hogan
- Department of Surgery, University of Rochester, New York 14642, USA
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Neill WA, Branch LG, De Jong G, Smith NE, Hogan CA, Corcoran PJ, Jette AM, Balasco EM, Osberg S. Cardiac disability. The impact of coronary heart disease on patients' daily activities. Arch Intern Med 1985; 145:1642-7. [PMID: 4026494 DOI: 10.1001/archinte.145.9.1642] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We studied 100 men with clinically stable coronary heart disease. Their capacity for exertion as defined by treadmill test was compared with the physical and social avocational activities they carried out in their daily routine, as reported by them. Exercise capacity (treadmill time) was strongly correlated with a physician's independent assessment of symptomatic status (anginal history). Although participation in some relatively strenuous elective activities was related slightly to exercise capacity, participation in many household duties and social undertakings bore no relationship to exercise capacity or to other measures of the severity of the underlying heart disease. The patients' own perceptions of their cardiac limitation varied for different activities and for some activities it was determined as much by their own concern and outside advice as by cardiac symptoms. Decreased capacity for exertion seems to exert surprisingly little influence on a cardiac patient's daily routine and interventions aimed at altering one of these measures of performance will not necessarily affect the other.
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Piotrowicz SR, Hogan CA, Shore RA, Pszenny AA. Variability in the distribution of weak acid leachable cadmium, chromium, copper, iron, nickel, lead, and zinc in the sediments of the Georges Bank/Gulf of Maine region [USA]. Environ Sci Technol 1981; 15:1067-1072. [PMID: 22284111 DOI: 10.1021/es00091a006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
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