1
|
Miller JM, Binnicker MJ, Campbell S, Carroll KC, Chapin KC, Gonzalez MD, Harrington A, Jerris RC, Kehl SC, Leal SM, Patel R, Pritt BS, Richter SS, Robinson-Dunn B, Snyder JW, Telford S, Theel ES, Thomson RB, Weinstein MP, Yao JD. Guide to Utilization of the Microbiology Laboratory for Diagnosis of Infectious Diseases: 2024 Update by the Infectious Diseases Society of America (IDSA) and the American Society for Microbiology (ASM). Clin Infect Dis 2024:ciae104. [PMID: 38442248 DOI: 10.1093/cid/ciae104] [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: 02/09/2024] [Accepted: 02/21/2024] [Indexed: 03/07/2024] Open
Abstract
The critical nature of the microbiology laboratory in infectious disease diagnosis calls for a close, positive working relationship between the physician and the microbiologists who provide enormous value to the health care team. This document, developed by experts in both adult and pediatric laboratory and clinical medicine, provides information on which tests are valuable and in which contexts, and on tests that add little or no value for diagnostic decisions. Sections are divided into anatomic systems, including Bloodstream Infections and Infections of the Cardiovascular System, Central Nervous System Infections, Ocular Infections, Soft Tissue Infections of the Head and Neck, Upper Respiratory Infections, Lower Respiratory Tract infections, Infections of the Gastrointestinal Tract, Intraabdominal Infections, Bone and Joint Infections, Urinary Tract Infections, Genital Infections, and Skin and Soft Tissue Infections; or into etiologic agent groups, including arboviral Infections, Viral Syndromes, and Blood and Tissue Parasite Infections. Each section contains introductory concepts, a summary of key points, and detailed tables that list suspected agents; the most reliable tests to order; the samples (and volumes) to collect in order of preference; specimen transport devices, procedures, times, and temperatures; and detailed notes on specific issues regarding the test methods, such as when tests are likely to require a specialized laboratory or have prolonged turnaround times. In addition, the pediatric needs of specimen management are also addressed. There is redundancy among the tables and sections, as many agents and assay choices overlap. The document is intended to serve as a reference to guide physicians in choosing tests that will aid them to diagnose infectious diseases in their patients.
Collapse
Affiliation(s)
| | - Matthew J Binnicker
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Sheldon Campbell
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Karen C Carroll
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | | | - Mark D Gonzalez
- Department of Pathology, Children's Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Amanda Harrington
- Department of Pathology and Laboratory Medicine, Loyola University, Chicago, Illinois, USA
| | - Robert C Jerris
- Department of Pathology, Children's Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Sue C Kehl
- Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Sixto M Leal
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Bobbi S Pritt
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Division of Public Health, Infectious Diseases and Occupational Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Sandra S Richter
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Jacksonville, FL, USA
| | - Barbara Robinson-Dunn
- Department of Pathology and Laboratory Medicine (Ret), Beaumont Health, Royal Oak, Michigan, USA
| | - James W Snyder
- Department of Pathology and Laboratory Medicine, University of Louisville, Louisville, Kentucky, USA
| | - Sam Telford
- Department of Infectious Disease and Global Health, Tufts University, North Grafton, MA, USA
| | - Elitza S Theel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Richard B Thomson
- Emeritus Staff, NorthShore University Health System, Evanston, Illinois, USA
| | - Melvin P Weinstein
- Department of Pathology and Laboratory Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey, USA
| | - Joseph D Yao
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| |
Collapse
|
2
|
Streck NT, Espy MJ, Ferber MJ, Klee EW, Razonable RR, Gonzalez D, Sayada C, Heaton PR, Chou S, Binnicker MJ. Use of next-generation sequencing to detect mutations associated with antiviral drug resistance in cytomegalovirus. J Clin Microbiol 2023; 61:e0042923. [PMID: 37750719 PMCID: PMC10595055 DOI: 10.1128/jcm.00429-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 07/25/2023] [Indexed: 09/27/2023] Open
Abstract
Cytomegalovirus (CMV) is a significant cause of morbidity and mortality among immunocompromised hosts, including transplant recipients. Antiviral prophylaxis or treatment is used to reduce the incidence of CMV disease in this patient population; however, there is concern about increasing antiviral resistance. Detection of antiviral resistance in CMV was traditionally accomplished using Sanger sequencing of UL54 and UL97 genes, in which specific mutations may result in reduced antiviral activity. In this study, a novel next-generation sequencing (NGS) method was developed and validated to detect mutations in UL54/UL97 associated with antiviral resistance. Plasma samples (n = 27) submitted for antiviral resistance testing by Sanger sequencing were also analyzed using the NGS method. When compared to Sanger sequencing, the NGS assay demonstrated 100% (27/27) overall agreement for determining antiviral resistance/susceptibility and 88% (22/25) agreement at the level of resistance-associated mutations. The limit of detection of the NGS method was determined to be 500 IU/mL, and the lower threshold for detecting mutations associated with resistance was established at 15%. The NGS assay represents a novel laboratory tool that assists healthcare providers in treating patients who are infected with CMV harboring resistance-associated mutations and who may benefit from tailored antiviral therapy.
Collapse
Affiliation(s)
- Nicholas T. Streck
- Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
| | - Mark J. Espy
- Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
| | - Matthew J. Ferber
- Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | - Eric W. Klee
- Division of Biomedical Statistics and Informatics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Raymund R. Razonable
- Division of Public Health, Infectious Diseases and Occupational Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | | | | | - Phillip R. Heaton
- Health Partners Medical Laboratory and Pathology Services, Bloomington, Minnesota, USA
| | - Sunwen Chou
- Research Service, Department of Veterans Affairs Medical Center, Portland, Oregon, USA
| | | |
Collapse
|
3
|
Gaensbauer JT, Fernholz EC, Hiskey LM, Binnicker MJ, Corsini Campioli C. Comparison of two assays to diagnose herpes simplex virus in patients with central nervous system infections. J Clin Virol 2023; 166:105528. [PMID: 37390620 DOI: 10.1016/j.jcv.2023.105528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/23/2023] [Accepted: 06/25/2023] [Indexed: 07/02/2023]
Abstract
BACKGROUND Multiplex PCR panels are frequently used for detecting the diagnosis of central nervous system infection, but have demonstrated lower sensitivity for herpes simplex virus (HSV) compared to targeted PCRs. Providers in our institution frequently order both multiplex (BioFire Meningitis/Encephalitis Panel (MEP)) and targeted HSV PCR (Diasorin Simplexa HSV-1/2 Direct), allowing comparison of assay performance in practice and a unique clinical characterization of patients with concordant positive or discordant results. METHODS We retrospectively analyzed all HSV testing performed using the two assays simultaneously in a large multi-center institution between 12/10/2018 and 6/6/2022. We described and compared laboratory, diagnostic and therapeutic data between patients with positive results on both assays with patients with discordant results. RESULTS 1,387 patients were tested with both assays, of which 25 were positive on at least one assay. Eleven (44%) had discordant results; 9 were targeted-PCR-positive/MEP-negative and 2 were targeted-PCR-negative/MEP-positive. Compared with patients with concordant positive results, discordant targeted PCR-positive/MEP-negative patients had a higher PCR cycle threshold value (i.e., >35) and milder illness characterized by lower CSF WBC counts (4 vs 152; p = 0.032), fewer MRI abnormalities (37.5% vs. 87.5%; p = 0.039), HSV meningoencephalitis as primary discharge diagnosis (33% vs. 100%; p<0.0001) and were more often treated with oral medication or none at all. CONCLUSIONS Patients with discordant targeted PCR-positive/MEP-negative results represent a population with milder clinical disease. These findings will help clinicians and laboratorians determine when both targeted HSV and multiplex assays should be performed simultaneously and identify patients for whom a multiplex PCR may suffice, despite lower assay sensitivity.
Collapse
Affiliation(s)
- J T Gaensbauer
- Department of Pediatric and Adolescent Medicine, Division of Pediatric Infectious Diseases, USA.
| | - E C Fernholz
- Department of Laboratory Medicine and Pathology, Division of Clinical Microbiology, Mayo Clinic, Rochester, USA
| | - L M Hiskey
- Department of Pediatric and Adolescent Medicine, Division of Pediatric Infectious Diseases, USA
| | - M J Binnicker
- Department of Laboratory Medicine and Pathology, Division of Clinical Microbiology, Mayo Clinic, Rochester, USA
| | | |
Collapse
|
4
|
Shirley JD, Bennett SA, Binnicker MJ. Current regulatory landscape for viral point-of-care testing in the United States. J Clin Virol 2023; 164:105492. [PMID: 37210882 DOI: 10.1016/j.jcv.2023.105492] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 05/12/2023] [Accepted: 05/13/2023] [Indexed: 05/23/2023]
Abstract
Historically, the diagnosis of viral infections has been accomplished using a combination of laboratory-based methods, including culture, serology, antigen-based tests, and molecular (e.g., real-time PCR) assays. Although these methods provide an accurate way to detect viral pathogens, testing in a centralized laboratory may delay results, which could impact patient diagnosis and management. Point-of-care tests, including antigen- and molecular-based assays, have been developed to assist with the timely diagnosis of several viral infections, such as influenza, respiratory syncytial virus, and COVID-19. Despite the ability of point-of-care tests to provide rapid results (i.e., <30 min), there are issues to consider prior to their routine use, including test performance and specific regulatory requirements. This review will provide a summary of the regulatory landscape of point-of-care tests for viral infections in the United States, and address important considerations such as site certification, training and inspection readiness.
Collapse
Affiliation(s)
- Joshua D Shirley
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, United States
| | - Shannon A Bennett
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, United States
| | - Matthew J Binnicker
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, United States.
| |
Collapse
|
5
|
Blommel JH, Jenkinson G, Binnicker MJ, Karon BS, Boccuto L, Ivankovic DS, Sarasua SM, Kipp BR. Authorized SARS-CoV-2 molecular methods show wide variability in the limit of detection. Diagn Microbiol Infect Dis 2023; 105:115880. [PMID: 36669396 PMCID: PMC9751006 DOI: 10.1016/j.diagmicrobio.2022.115880] [Citation(s) in RCA: 2] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 11/25/2022] [Accepted: 12/09/2022] [Indexed: 12/16/2022]
Abstract
On February 29th, 2020, the U.S. Food and Drug Administration issued the first Emergency Use Authorization (EUA) for a SARS-CoV-2 assay outside of the U.S. Centers for Disease Control and Prevention. As of May 3rd, 2021, 289 total EUAs have been granted. Like influenza, there is no standard for defining limit of detection (LoD), but rather guidance that analytical sensitivity/LoD be established as the level that gives a 95% detection rate in at least 20 replicates. Here we compare the performance characteristics of SARS-CoV-2 tests receiving EUA by standardizing sensitivity to a common unit of measure and assess the variability in LoD between tests. Additionally, we looked at factors that may impact sensitivities due to lack of standardization of the test development process and compare results for a standardized reference panel for comparative analysis within a subset of EUA tests offered by the U.S. Food and Drug Administration.
Collapse
Affiliation(s)
- Joseph H Blommel
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA; Department of Biological Sciences, School of Nursing, Clemson University, Clemson, SC, USA
| | - Garrett Jenkinson
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Matthew J Binnicker
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Brad S Karon
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Luigi Boccuto
- Department of Biological Sciences, School of Nursing, Clemson University, Clemson, SC, USA
| | - Diana S Ivankovic
- Department of Biological Sciences, School of Nursing, Clemson University, Clemson, SC, USA
| | - Sara M Sarasua
- Department of Biological Sciences, School of Nursing, Clemson University, Clemson, SC, USA
| | - Benjamin R Kipp
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.
| |
Collapse
|
6
|
Rodino KG, Babady NE, Bearman G, Binnicker MJ, Isaacs SN, Pinsky BA, Weber DJ. Laboratory Preparedness for the Current Monkeypox Outbreak. Clin Chem 2023; 69:118-124. [PMID: 36544358 DOI: 10.1093/clinchem/hvac198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 11/09/2022] [Indexed: 12/24/2022]
Affiliation(s)
- Kyle G Rodino
- Assistant Director of Clinical Microbiology, Director of the Rittenhouse Molecular Laboratory, and Assistant Professor of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - N Esther Babady
- Chief of Clinical Microbiology Service and Member, Department of Pathology and Laboratory Medicine and Department of Medicine (Infectious Disease Service), Memorial Sloan Kettering Cancer Center, New York, USA
| | - Gonzalo Bearman
- Chief of Infectious Diseases, Department of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Matthew J Binnicker
- Director of Clinical Virology and Professor of Laboratory Medicine and Pathology, Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Stuart N Isaacs
- Associate Professor of Medicine, Division of Infectious Diseases, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Benjamin A Pinsky
- Director of Clinical Virology at Stanford Health Care and Stanford Childrens Health and Professor, Departments of Pathology and Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - David J Weber
- Director of Infection Prevention, University of North Carolina Medical Center and Professor, Division of Infectious Diseases, Department of Medicine, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| |
Collapse
|
7
|
Juhn YJ, Wi CI, Takahashi PY, Ryu E, King KS, Hickman JA, Yao JD, Binnicker MJ, Natoli TL, Evans TK, Sampathkumar P, Patten C, Luyts D, Pirçon JY, Damaso S, Pignolo RJ. Incidence of Respiratory Syncytial Virus Infection in Older Adults Before and During the COVID-19 Pandemic. JAMA Netw Open 2023; 6:e2250634. [PMID: 36662530 PMCID: PMC9860520 DOI: 10.1001/jamanetworkopen.2022.50634] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 11/20/2022] [Indexed: 01/21/2023] Open
Abstract
Importance Little is known about the burden and outcomes of respiratory syncytial virus (RSV)-positive acute respiratory infection (ARI) in community-dwelling older adults. Objective To assess the incidence of RSV-positive ARI before and during the COVID-19 pandemic, and to assess outcomes for RSV-positive ARI in older adults. Design, Setting, and Participants This was a community-based cohort study of adults residing in southeast Minnesota that followed up with 2325 adults aged 50 years or older for 2 RSV seasons (2019-2021) to assess the incidence of RSV-positive ARI. The study assessed outcomes at 2 to 4 weeks, 6 to 7 months, and 12 to 13 months after RSV-positive ARI. Exposure RSV-positive and -negative ARI. Main Outcomes and Measures RSV status was the main study outcome. Incidence and attack rates of RSV-positive ARI were calculated during each RSV season, including before (October 2019 to April 2020) and during (October 2020 to April 2021) COVID-19 pandemic, and further calculated during non-RSV season (May to September 2021) for assessing impact of COVID-19. The self-reported quality of life (QOL) by Short-Form Health Survey-36 (SF-36) and physical functional measures (eg, 6-minute walk and spirometry) at each time point was assessed. Results In this study of 2325 participants, the median (range) age of study participants was 67 (50-98) years, 1380 (59%) were female, and 2240 (96%) were non-Hispanic White individuals. The prepandemic incidence rate of RSV-positive ARI was 48.6 (95% CI, 36.9-62.9) per 1000 person-years with a 2.50% (95% CI, 1.90%-3.21%) attack rate. No RSV-positive ARI case was identified during the COVID-19 pandemic RSV season. Incidence of 10.2 (95% CI, 4.1-21.1) per 1000 person-years and attack rate of 0.42%; (95% CI, 0.17%-0.86%) were observed during the summer of 2021. Based on prepandemic RSV season results, participants with RSV-positive ARI (vs matched RSV-negative ARI) reported significantly lower QOL adjusted mean difference (limitations due to physical health, -16.7 [95% CI, -31.8 to -1.8]; fatigue, -8.4 [95% CI, -14.3 to -2.4]; and difficulty in social functioning, -11.9 [95% CI, -19.8 to -4.0] within 2 to 4 weeks after RSV-positive ARI [ie, short-term outcome]). Compared with participants with RSV-negative ARI, those with RSV-positive ARI also had lower QOL (fatigue: -4.0 [95% CI, -8.5 to -1.3]; difficulty in social functioning, -5.8 [95% CI, -10.3 to -1.3]; and limitation due to emotional problem, -7.0 [95% CI, -12.7 to -1.3] at 6 to 7 months after RSV-positive ARI [intermediate-term outcome]; fatigue, -4.4 [95% CI, -7.3 to -1.5]; difficulty in social functioning, -5.2 [95% CI, -8.7 to -1.7] and limitation due to emotional problem, -5.7 [95% CI, -10.7 to -0.6] at 12-13 months after RSV-positive ARI [ie, long-term outcomes]) independent of age, sex, race and/or ethnicity, socioeconomic status, and high-risk comorbidities. Conclusions and Relevance In this cohort study, the burden of RSV-positive ARI in older adults during the pre-COVID-19 period was substantial. After a reduction of RSV-positive ARI incidence from October 2020 to April 2021, RSV-positive ARI re-emerged during the summer of 2021. RSV-positive ARI was associated with significant long-term lower QOL beyond the short-term lower QOL in older adults.
Collapse
Affiliation(s)
- Young J. Juhn
- Department of Pediatric and Adolescent Medicine and Internal Medicine, Mayo Clinic, Rochester, Minnesota
| | - Chung-Il Wi
- Department of Pediatric and Adolescent Medicine and Internal Medicine, Mayo Clinic, Rochester, Minnesota
| | - Paul Y. Takahashi
- Division of Community Internal Medicine, Mayo Clinic, Rochester, Minnesota
| | - Euijung Ryu
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Katherine S. King
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Joel A. Hickman
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Joseph D. Yao
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Matthew J. Binnicker
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Traci L. Natoli
- Department of Pediatric and Adolescent Medicine and Internal Medicine, Mayo Clinic, Rochester, Minnesota
| | - Tamara K. Evans
- Department of Medicine Research, Mayo Clinic, Rochester, Minnesota
| | | | - Christi Patten
- Behavioral Health Research Program, Department of Psychiatry and Psychology, Mayo Clinic, Rochester, Minnesota
| | | | | | | | - Robert J. Pignolo
- Divisions of Hospital Internal Medicine, Endocrinology, and Geriatric Medicine and Gerontology, Department of Medicine, Mayo Clinic, Rochester, Minnesota
| |
Collapse
|
8
|
Ranganath N, Tosh PK, O'Horo J, Sampathkumar P, Binnicker MJ, Shah AS. Monkeypox 2022: Gearing Up for Another Potential Public Health Crisis. Mayo Clin Proc 2022; 97:1694-1699. [PMID: 35985857 DOI: 10.1016/j.mayocp.2022.07.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/09/2022] [Accepted: 07/19/2022] [Indexed: 11/23/2022]
Abstract
Monkeypox virus, a member of the Orthopoxvirus genus, was first identified as the etiology of monkeypox in 1970 in the Democratic Republic of Congo and remains endemic in regions of Central and West Africa. Following the most recent outbreak of monkeypox in multiple countries throughout Europe and North America, the infection has been declared a public health emergency by the Centers for Disease Control and Prevention. Within this report, we aim to provide clinicians with a focused overview of the epidemiology, clinical manifestation, diagnosis, and approaches to treat and prevent monkeypox infection amidst the global outbreak.
Collapse
Affiliation(s)
- Nischal Ranganath
- Division of Public Health, Infectious Diseases and Occupational Medicine, Mayo Clinic, Rochester, MN.
| | - Pritish K Tosh
- Division of Public Health, Infectious Diseases and Occupational Medicine, Mayo Clinic, Rochester, MN
| | - John O'Horo
- Division of Public Health, Infectious Diseases and Occupational Medicine, Mayo Clinic, Rochester, MN; Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN
| | - Priya Sampathkumar
- Division of Public Health, Infectious Diseases and Occupational Medicine, Mayo Clinic, Rochester, MN
| | | | - Aditya S Shah
- Division of Public Health, Infectious Diseases and Occupational Medicine, Mayo Clinic, Rochester, MN
| |
Collapse
|
9
|
Cullinan SM, Heaton HA, Mullan A, O'Horo J, Binnicker MJ, Tande AJ, Post JA, Campbell RL, Raukar NP. Impact of the COVID-19 Pandemic on Respiratory Infection Rates. Mayo Clin Proc 2022; 97:1023-1025. [PMID: 35512874 PMCID: PMC8942707 DOI: 10.1016/j.mayocp.2022.03.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 03/15/2022] [Indexed: 11/23/2022]
Affiliation(s)
- Susan M Cullinan
- Department of Emergency Medicine, Mayo Clinic Health System, Eau Claire, WI
| | | | | | | | | | | | | | | | | |
Collapse
|
10
|
Tande AJ, Swift MD, Challener DW, Berbari EF, Tommaso CP, Christopherson DR, Binnicker MJ, Breeher LE. Utility of Follow-up COVID-19 Antigen Tests After Acute SARS-CoV-2 Infection Among Healthcare Personnel. Clin Infect Dis 2022; 75:e347-e349. [PMID: 35352091 PMCID: PMC9129106 DOI: 10.1093/cid/ciac235] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Indexed: 12/14/2022] Open
Abstract
We report the utility of rapid antigen tests (RAgT) in a cohort of US healthcare personnel with coronavirus disease 2019 (COVID-19) infection who met symptom criteria to return to work at day 5 or later of isolation. In total, 11.9% of initial RAgT were negative. RAgT can be helpful to guide return to work decisions.
Collapse
Affiliation(s)
- Aaron J Tande
- Division of Public Health, Infectious Diseases and Occupational Medicine, Mayo Clinic, Rochester, MN USA
| | - Melanie D Swift
- Division of Public Health, Infectious Diseases and Occupational Medicine, Mayo Clinic, Rochester, MN USA.,Occupational Health Services, Mayo Clinic, Rochester, MN USA
| | - Douglas W Challener
- Division of Public Health, Infectious Diseases and Occupational Medicine, Mayo Clinic, Rochester, MN USA
| | - Elie F Berbari
- Division of Public Health, Infectious Diseases and Occupational Medicine, Mayo Clinic, Rochester, MN USA
| | | | - Darrin R Christopherson
- Division of Public Health, Infectious Diseases and Occupational Medicine, Mayo Clinic, Rochester, MN USA
| | | | - Laura E Breeher
- Division of Public Health, Infectious Diseases and Occupational Medicine, Mayo Clinic, Rochester, MN USA.,Occupational Health Services, Mayo Clinic, Rochester, MN USA
| |
Collapse
|
11
|
Campbell MR, Binnicker MJ. Analytic and clinical performance of major commercial SARS-CoV-2 molecular assays in the United States. Clin Lab Med 2022; 42:129-145. [PMID: 35636818 PMCID: PMC8858713 DOI: 10.1016/j.cll.2022.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
12
|
Tande AJ, Binnicker MJ, Ting HH, Del Rio C, Jalil L, Brawner M, Carter PW, Toomey K, Shah ND, Berbari EF. SARS-CoV-2 Testing Before International Airline Travel, December 2020 to May 2021. Mayo Clin Proc 2021; 96:2856-2860. [PMID: 34736612 PMCID: PMC8410576 DOI: 10.1016/j.mayocp.2021.08.019] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 08/13/2021] [Accepted: 08/26/2021] [Indexed: 11/29/2022]
Abstract
Although there have been several case reports and simulation models of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission associated with air travel, there are limited data to guide testing strategy to minimize the risk of SARS-CoV-2 exposure and transmission onboard commercial aircraft. Among 9853 passengers with a negative SARS-CoV-2 polymerase chain reaction test performed within 72 hours of departure from December 2020 through May 2021, five (0.05%) passengers with active SARS-CoV-2 infection were identified with rapid antigen tests and confirmed with rapid molecular test performed before and after an international flight from the United States to Italy. This translates to a case detection rate of 1 per 1970 travelers during a time of high prevalence of active infection in the United States. A negative molecular test for SARS-CoV-2 within 72 hours of international airline departure results in a low probability of active infection identified on antigen testing during commercial airline flight.
Collapse
Affiliation(s)
- Aaron J Tande
- Division of Infectious Diseases, Mayo Clinic, Rochester, MN, USA.
| | - Matthew J Binnicker
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | | | - Carlos Del Rio
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | | | | | | | | | - Nilay D Shah
- Division of Health Care Delivery Research, Robert D. and Patricia E, Kern Center for the Science of Health Care Delivery, Mayo Clinic, Rochester, MN, USA
| | - Elie F Berbari
- Division of Infectious Diseases, Mayo Clinic, Rochester, MN, USA
| |
Collapse
|
13
|
Shah VP, Farah WH, Hill JC, Hassett LC, Binnicker MJ, Yao JD, Murad MH. Association Between SARS-CoV-2 Cycle Threshold Values and Clinical Outcomes in Patients With COVID-19: A Systematic Review and Meta-analysis. Open Forum Infect Dis 2021; 8:ofab453. [PMID: 34584900 PMCID: PMC8465328 DOI: 10.1093/ofid/ofab453] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/30/2021] [Indexed: 12/13/2022] Open
Abstract
Cycle threshold (CT) values are correlated with the amount of viral nucleic acid in a sample and may be obtained from some qualitative real-time polymerase chain reaction tests used for diagnosis of most patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, CT values cannot be directly compared across assays, and they must be interpreted with caution as they are influenced by sample type, timing of sample collection, and assay design. Presently, the correlation between CT values and clinical outcomes is not well understood. We conducted a systematic review and meta-analysis of published studies through April 19, 2021, that reported an association between CT values and hospitalization, disease severity, and mortality in patients ≥18 years old with SARS-CoV-2. A meta-analysis of 7 studies showed no significant difference in mean CT values between hospitalized and nonhospitalized patients. Among hospitalized patients, those with CT values <25 had a high risk of more severe disease and mortality than patients with CT values >30 (odds ratio [OR], 2.31; 95% CI, 1.70 to 3.13; and OR, 2.95; 95% CI, 2.19 to 3.96; respectively). The odds of increased disease severity and mortality were less pronounced in patients with CT values of 25–30 compared with >30.
Collapse
Affiliation(s)
- Vishal P Shah
- Division of Preventive, Occupational and Aerospace Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Wigdan H Farah
- Division of Preventive, Occupational and Aerospace Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - James C Hill
- Division of Preventive, Occupational and Aerospace Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | | | | | - Joseph D Yao
- Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
| | - M Hassan Murad
- Division of Preventive, Occupational and Aerospace Medicine, Mayo Clinic, Rochester, Minnesota, USA
| |
Collapse
|
14
|
Boerger AC, Buckwalter S, Fernholz EC, Jannetto PJ, Binnicker MJ, Reed K, Walchak R, Woodliff E, Johnson M, Pritt BS. Evaluation of Self-Collected Midturbinate Nasal Swabs and Saliva for Detection of SARS-CoV-2 RNA. J Clin Microbiol 2021; 59:e0084821. [PMID: 34132579 PMCID: PMC8373001 DOI: 10.1128/jcm.00848-21] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 06/07/2021] [Indexed: 11/20/2022] Open
Abstract
Rapid and accurate diagnostic testing is essential to bring the ongoing COVID-19 pandemic to an end. As the demand for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing continues to increase amid supply shortages, many laboratories have investigated the use of sources other than nasopharyngeal (NP) swabs. Saliva and midturbinate (MT) nasal swabs are attractive alternatives, as they allow for self-collection and are well accepted by patients. Saliva also requires limited consumables. We compared the performance of health care provider-collected NP swabs, patient-collected MT swabs, and patient-collected saliva specimens for SARS-CoV-2 detection using a laboratory-developed PCR assay that had received Emergency Use Authorization by the FDA. Of 281 total evaluable samples, 33 (11.7%) NP swabs, 33 (11.7%) MT swabs, and 32 (11.4%) saliva specimens were positive for SARS-CoV-2 following resolution of discordant results. Compared to NP swabs, saliva exhibited a sensitivity of 90.9% (30/33) and specificity of 99.2% (246/248), while patient-collected MT swabs exhibited a sensitivity of 93.9% (31/33) and specificity of 99.2% (246/248). When comparing to the consensus standard, the sensitivity was found to be 100% (31/31) for both NP and MT swabs and 96.8% (30/31) for saliva specimens, while specificity was the same in both NP swabs and saliva specimens (98.8% [247/250]) and 99.2% (248/250) for MT swabs. Pretreatment of saliva with proteinase K and heating for 15 min prior to extraction reduced the invalid rate from 26.7% (52/195) to 0% (0/195). These data show that midturbinate nasal swabs and saliva are suitable sources for self-collection in individuals who require routine monitoring for SARS-CoV-2 infection.
Collapse
Affiliation(s)
- Aimee C. Boerger
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Seanne Buckwalter
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Emily C. Fernholz
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Paul J. Jannetto
- Division of Clinical Biochemistry, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Matthew J. Binnicker
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Katelyn Reed
- Research and Innovation Office, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Robert Walchak
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Ethan Woodliff
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Michael Johnson
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Bobbi S. Pritt
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| |
Collapse
|
15
|
Swanson AA, Hartley C, Long ME, Chantigian PDM, Casey PM, Jenkins SM, Boerger AC, Binnicker MJ, Henry MR. Evaluation of high-risk human papillomavirus testing and anal cytology to detect high-grade anal intraepithelial neoplasia. J Am Soc Cytopathol 2021; 10:406-413. [PMID: 33896747 DOI: 10.1016/j.jasc.2021.03.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 03/15/2021] [Accepted: 03/31/2021] [Indexed: 01/01/2023]
Abstract
INTRODUCTION Optimal screening for detection of anal precancer has not been established, and most studies involve very high-risk populations. We evaluated high-risk human papillomavirus (HPV) testing and anal cytology to detect high-grade anal intraepithelial neoplasia (≥AIN2) in a cohort with mostly moderate risk factors for AIN. METHODS Patients ≥35 years old undergoing anal biopsy for various lesions received HPV testing by Roche cobas and a subset by Hologic APTIMA HPV assays with concurrent anal ThinPrep cytology. Biopsies were blindly reviewed by 3 authors, and consensus diagnosis was compared with HPV and cytology results. Sensitivity and specificity for ≥AIN2 detection by HPV testing and cytology (≥ASC-US) were calculated. RESULTS Among 64 patients, 19 (29.7%) showed ≥AIN2 on biopsy. All patients were tested by cobas, and 35 (54.7%) were positive. A subset of 39 patients were also tested by APTIMA, and 18 (46.2%) were positive. Positive cytology (≥ASC-US) was present in 37 (57.8%) patients, with 27 (73.0%) of these positive by cobas. HPV testing alone yielded 75.0% and 84.2% sensitivity for APTIMA and cobas, respectively; specificity was 66.7% and 57.8%. Sensitivity and specificity of cytology alone was 78.9% and 51.1%. Combined HPV testing and cytology had a sensitivity and specificity of 91.7% and 37.0% for APTIMA and 94.7% and 40.0% for cobas. CONCLUSIONS Combined HPV testing and cytology had the highest sensitivity for ≥AIN2 detection, with a performance comparable to cervical cancer screening tests, suggesting this strategy may represent a viable screening option in a population with moderate risk factors for AIN.
Collapse
Affiliation(s)
- Amy A Swanson
- Division of Anatomic Pathology, Mayo Clinic Rochester, Rochester, Minnesota
| | | | - Margaret E Long
- Department of Obstetrics and Gynecology, Mayo Clinic Rochester, Rochester, Minnesota
| | - Paula D M Chantigian
- Department of Obstetrics and Gynecology, Mayo Clinic Rochester, Rochester, Minnesota
| | - Petra M Casey
- Department of Obstetrics and Gynecology, Mayo Clinic Rochester, Rochester, Minnesota
| | - Sarah M Jenkins
- Department of Quantitative Health Sciences, Mayo Clinic Rochester, Rochester, Minnesota
| | - Aimee C Boerger
- Division of Clinical Microbiology, Mayo Clinic Rochester, Rochester, Minnesota
| | - Matthew J Binnicker
- Division of Clinical Microbiology, Mayo Clinic Rochester, Rochester, Minnesota
| | - Michael R Henry
- Division of Anatomic Pathology, Mayo Clinic Rochester, Rochester, Minnesota.
| |
Collapse
|
16
|
Juhn YJ, Wi CI, Ryu E, Sampathkumar P, Takahashi PY, Yao JD, Binnicker MJ, Natoli TL, Evans TK, King KS, Volpe S, Pirçon JY, Silvia Damaso, Pignolo RJ. Adherence to Public Health Measures Mitigates the Risk of COVID-19 Infection in Older Adults: A Community-Based Study. Mayo Clin Proc 2021; 96:912-920. [PMID: 33714601 PMCID: PMC7768210 DOI: 10.1016/j.mayocp.2020.12.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 12/21/2020] [Indexed: 11/29/2022]
Abstract
OBJECTIVE To assess the prevalence and characteristics of coronavirus disease 2019 (COVID-19) cases during the reopening period in older adults, given that little is known about the prevalence of COVID-19 after the stay-at-home order was lifted in the United States, nor the actual effects of adherence to recommended public health measures (RPHM) on the risk of COVID-19. PATIENTS AND METHODS This was a cross-sectional study nested in a parent prospective cohort study, which followed a population-based sample of 2325 adults 50 years and older residing in southeast Minnesota to assess the incidence of viral infections. Participants were instructed to self-collect both nasal and oropharyngeal swabs, which were tested by reverse transcription polymerase chain reaction-based severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) assay between May 8, 2020, and June, 30, 2020. We assessed the prevalence of COVID-19 cases and characteristics of study subjects. RESULTS A total of 1505 eligible subjects participated in the study whose mean age was 68 years, with 885 (59%) women, 32 (2%) racial/ethnic minorities, and 906 (60%) with high-risk conditions for influenza. The prevalence of other Coronaviridae (human coronavirus [HCoV]-229E, HCoV-NL63, and HCoV-OC43) during the 2019 to 2020 flu season was 109 (7%), and none tested positive for SARS-CoV-2. Almost all participants reported adhering to the RPHM (1,488 [99%] for social distancing, 1,438 [96%] for wearing mask in a public space, 1,476 [98%] for hand hygiene, and 1,441 (96%) for staying home mostly). Eighty-six percent of participants resided in a single-family home. CONCLUSION We did not identify SARS-COV-2 infection in our study cohort. The combination of participants' behavior in following the RPHM and their living environment may considerably mitigate the risk of COVID-19.
Collapse
Affiliation(s)
- Young J Juhn
- Department of Pediatric and Internal Medicine, Mayo Clinic, Rochester, MN.
| | - Chung-Il Wi
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN
| | - Euijung Ryu
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN
| | | | - Paul Y Takahashi
- Division of Community Internal Medicine, Mayo Clinic, Rochester, MN
| | - Joseph D Yao
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | | | - Traci L Natoli
- Department of Medicine Research, Mayo Clinic, Rochester, MN
| | - Tamara K Evans
- Department of Medicine Research, Mayo Clinic, Rochester, MN
| | - Katherine S King
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN
| | | | | | | | - Robert J Pignolo
- Division of Geriatric Medicine and Gerontology, Mayo Clinic, Rochester, MN.
| |
Collapse
|
17
|
Binnicker MJ. Can the Severe Acute Respiratory Syndrome Coronavirus 2 Polymerase Chain Reaction Cycle Threshold Value and Time From Symptom Onset to Testing Predict Infectivity? Clin Infect Dis 2021; 71:2667-2668. [PMID: 32504529 PMCID: PMC7314221 DOI: 10.1093/cid/ciaa735] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [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: 05/28/2020] [Accepted: 06/04/2020] [Indexed: 12/23/2022] Open
Affiliation(s)
- Matthew J Binnicker
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| |
Collapse
|
18
|
Donato LJ, Trivedi VA, Stransky AM, Misra A, Pritt BS, Binnicker MJ, Karon BS. Evaluation of the Cue Health point-of-care COVID-19 (SARS-CoV-2 nucleic acid amplification) test at a community drive through collection center. Diagn Microbiol Infect Dis 2021; 100:115307. [PMID: 33571863 PMCID: PMC7785428 DOI: 10.1016/j.diagmicrobio.2020.115307] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [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: 10/29/2020] [Revised: 12/02/2020] [Accepted: 12/28/2020] [Indexed: 01/16/2023]
Abstract
Point-of-care (POC) tests are in high demand in order to facilitate rapid care decisions for patients suspected of SARS-CoV-2. We conducted a clinical validation study of the Cue Health POC nucleic acid amplification test (NAAT) using the Cue lower nasal swab, compared to a reference NAAT using standard nasopharyngeal swab, in 292 symptomatic and asymptomatic outpatients for SARS-CoV-2 detection in a community drive through collection setting. Positive percent agreement between Cue COVID-19 and reference SARS-CoV-2 test was 91.7% (22 of 24); or 95.7% (22 of 23) when one patient with no tie-breaker method was excluded. Negative percent agreement was 98.4% (239 of 243), and there were 25 (8.6%) invalid or canceled results. The Cue COVID-19 test demonstrated very good positive and negative percent agreement with central laboratory tests and will be useful in settings where accurate POC testing is needed to facilitate management of patients suspected of COVID-19.
Collapse
Affiliation(s)
- Leslie J Donato
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Vipul A Trivedi
- Division of Community Laboratory Medicine and Pathology, Mayo Clinic Health System, Eau Claire, WI
| | - Angie M Stransky
- Department of Family Medicine, Mayo Clinic Health System, Mankato MN
| | - Artika Misra
- Department of Family Medicine, Mayo Clinic Health System, Mankato MN
| | - Bobbi S Pritt
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | | | - Brad S Karon
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN.
| |
Collapse
|
19
|
Kies KD, Thomas AS, Binnicker MJ, Bashynski KL, Patel R. Decrease in Enteroviral Meningitis - An Unexpected Benefit of COVID-19 Mitigation? Clin Infect Dis 2020; 73:e2807-e2809. [PMID: 33354704 PMCID: PMC7799197 DOI: 10.1093/cid/ciaa1881] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Indexed: 12/21/2022] Open
Abstract
Enteroviral meningitis is seasonal, typically exhibiting a rise in prevalence in late summer/early fall. Based on clinical microbiology laboratory testing data of cerebrospinal fluid, the expected August/September/October peak in enteroviral meningitis did not occur in 2020, possibly related to COVID-19 mitigation strategies.
Collapse
Affiliation(s)
- Kami D Kies
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Amber S Thomas
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Matthew J Binnicker
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Kelli L Bashynski
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN.,Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, MN
| |
Collapse
|
20
|
Jose T, Warner DO, O'Horo JC, Peters SG, Chaudhry R, Binnicker MJ, Burger CD. Digital Health Surveillance Strategies for Management of Coronavirus Disease 2019. Mayo Clin Proc Innov Qual Outcomes 2020; 5:109-117. [PMID: 33521582 PMCID: PMC7831529 DOI: 10.1016/j.mayocpiqo.2020.12.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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] [Indexed: 12/13/2022] Open
Abstract
Objective To describe the design, implementation, and utilization of electronic health record (EHR)-based digital health surveillance strategies used to manage the coronavirus disease 2019 (COVID-19) pandemic and to ensure delivery of high-quality clinical care, such as case identification, remote monitoring, telemedicine services, and recruitment to clinical trials at Mayo Clinic. Methods The design and implementation work described in this report was performed at Mayo Clinic, a large multistate integrated health care system with more than 1.5 million annual patient visits that uses the Epic EHR system. Rule-based live registries were designed in the EHR system to classify patients who currently test positive for COVID-19, patients who test positive but have recovered from COVID-19, patients who are thought to have COVID-19 but do not yet meet clinical diagnostic criteria, patients who test negative for COVID-19, and patients who exceed a risk score for serious complications from COVID-19. Results By use of registries, custom dashboards and operational reports were developed to provide a daily high-level summary for clinical practice use and up-to-date information to manage individual patients affected by COVID-19, including support of case identification, contact isolation, and other care management tasks. Conclusion We developed and implemented a systematic approach to the use of EHR patient registries to manage the COVID-19 pandemic that proved feasible and useful in a large multistate group clinical practice. The key to harnessing the potential of digital surveillance tools to promote patient-centered care during the COVID-19 pandemic was to use the registry data, reports, and dashboards as informatics tools to inform decision-making.
Collapse
Affiliation(s)
- Thulasee Jose
- Department of Anesthesiology and Perioperative Medicine, Mayo Clinic, Rochester, MN
| | - David O Warner
- Department of Anesthesiology and Perioperative Medicine, Mayo Clinic, Rochester, MN
| | - John C O'Horo
- Department of Internal Medicine, Mayo Clinic, Rochester, MN
| | - Steve G Peters
- Department of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN
| | | | | | - Charles D Burger
- Division of Pulmonary, Allergy and Sleep Medicine, Department of Internal Medicine, Mayo Clinic, Jacksonville, FL
| |
Collapse
|
21
|
Agarwal V, Venkatakrishnan AJ, Puranik A, Kirkup C, Lopez-Marquez A, Challener DW, Theel ES, O'Horo JC, Binnicker MJ, Kremers WK, Faubion WA, Badley AD, Williams AW, Gores GJ, Halamka JD, Morice WG, Soundararajan V. Long-term SARS-CoV-2 RNA shedding and its temporal association to IgG seropositivity. Cell Death Discov 2020; 6:138. [PMID: 33298894 PMCID: PMC7709096 DOI: 10.1038/s41420-020-00375-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [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: 09/04/2020] [Revised: 11/05/2020] [Accepted: 11/13/2020] [Indexed: 12/13/2022] Open
Abstract
Longitudinal characterization of SARS-CoV-2 PCR testing from COVID-19 patient's nasopharynx and its juxtaposition with blood-based IgG-seroconversion diagnostic assays is critical to understanding SARS-CoV-2 infection durations. Here, we retrospectively analyze 851 SARS-CoV-2-positive patients with at least two positive PCR tests and find that 99 of these patients remain SARS-CoV-2-positive after 4 weeks from their initial diagnosis date. For the 851-patient cohort, the mean lower bound of viral RNA shedding was 17.3 days (SD: 7.8), and the mean upper bound of viral RNA shedding from 668 patients transitioning to confirmed PCR-negative status was 22.7 days (SD: 11.8). Among 104 patients with an IgG test result, 90 patients were seropositive to date, with mean upper bound of time to seropositivity from initial diagnosis being 37.8 days (95% CI: 34.3-41.3). Our findings from juxtaposing IgG and PCR tests thus reveal that some SARS-CoV-2-positive patients are non-hospitalized and seropositive, yet actively shed viral RNA (14 of 90 patients). This study emphasizes the need for monitoring viral loads and neutralizing antibody titers in long-term non-hospitalized shedders as a means of characterizing the SARS-CoV-2 infection lifecycle.
Collapse
Affiliation(s)
- Vineet Agarwal
- nference, inc., One Main Street, Suite 400, East Arcade, Cambridge, MA, 02142, USA
| | - A J Venkatakrishnan
- nference, inc., One Main Street, Suite 400, East Arcade, Cambridge, MA, 02142, USA
| | - Arjun Puranik
- nference, inc., One Main Street, Suite 400, East Arcade, Cambridge, MA, 02142, USA
| | - Christian Kirkup
- nference, inc., One Main Street, Suite 400, East Arcade, Cambridge, MA, 02142, USA
| | | | | | | | | | | | | | | | | | | | | | | | - William G Morice
- Mayo Clinic, Rochester, MN, USA
- Mayo Clinic Laboratories, Rochester, MN, USA
| | - Venky Soundararajan
- nference, inc., One Main Street, Suite 400, East Arcade, Cambridge, MA, 02142, USA.
| |
Collapse
|
22
|
Firestone MJ, Wienkes H, Garfin J, Wang X, Vilen K, Smith KE, Holzbauer S, Plumb M, Pung K, Medus C, Yao JD, Binnicker MJ, Nelson AC, Yohe S, Como-Sabetti K, Ehresmann K, Lynfield R, Danila R. COVID-19 Outbreak Associated with a 10-Day Motorcycle Rally in a Neighboring State - Minnesota, August-September 2020. MMWR Morb Mortal Wkly Rep 2020; 69:1771-1776. [PMID: 33237891 PMCID: PMC8022865 DOI: 10.15585/mmwr.mm6947e1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
|
23
|
Abstract
The coronavirus disease (COVID-19) pandemic has placed the clinical laboratory and testing for SARS-CoV-2 front and center in the worldwide discussion of how to end the outbreak. Clinical laboratories have responded by developing, validating, and implementing a variety of molecular and serologic assays to test for SARS-CoV-2 infection. This has played an essential role in identifying cases, informing isolation decisions, and helping to curb the spread of disease. However, as the demand for COVID-19 testing has increased, laboratory professionals have faced a growing list of challenges, uncertainties, and, in some situations, controversy, as they have attempted to balance the need for increasing test capacity with maintaining a high-quality laboratory operation. The emergence of this new viral pathogen has raised unique diagnostic questions for which there have not always been straightforward answers. In this commentary, the author addresses several areas of current debate, including (i) the role of molecular assays in defining the duration of isolation/quarantine, (ii) whether the PCR cycle threshold value should be included on patient reports, (iii) if specimen pooling and testing by research staff represent acceptable solutions to expand screening, and (iv) whether testing a large percentage of the population is feasible and represents a viable strategy to end the pandemic.
Collapse
Affiliation(s)
- Matthew J Binnicker
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Director of Clinical Virology, Mayo Clinic, Rochester, Minnesota, USA
| |
Collapse
|
24
|
Eberly AR, Challener DW, Shweta FNU, Fida M, Boerger AC, Assi M, O'Horo JC, Binnicker MJ. Initial SARS-CoV-2 PCR crossing point does not predict hospitalization and duration of PCR positivity. J Microbiol Immunol Infect 2020; 54:77-80. [PMID: 33069621 PMCID: PMC7546960 DOI: 10.1016/j.jmii.2020.08.020] [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] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/11/2020] [Accepted: 08/25/2020] [Indexed: 11/29/2022]
Abstract
This study aimed to determine if the crossing point of the initial positive SARS-CoV-2 PCR test correlated with patient demographics, subsequent hospitalization, or duration of positivity. Seventy-three patients with two or more positive PCR tests had a median time of 23 days to two consecutive negative results.
Collapse
Affiliation(s)
- Allison R Eberly
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Douglas W Challener
- Division of Infectious Diseases, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - F N U Shweta
- Division of Infectious Diseases, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Madiha Fida
- Division of Infectious Diseases, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Aimee C Boerger
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Mariam Assi
- Division of Infectious Diseases, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - John C O'Horo
- Division of Infectious Diseases, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA; Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Matthew J Binnicker
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.
| |
Collapse
|
25
|
Shah A, O'Horo JC, Berbari EF, Tande A, Challener D, Binnicker MJ. In Reply-Repeated Testing in SARS-CoV-2 Infection. Mayo Clin Proc 2020; 95:2284-2285. [PMID: 33012358 PMCID: PMC7416686 DOI: 10.1016/j.mayocp.2020.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 08/06/2020] [Indexed: 11/20/2022]
Affiliation(s)
- Aditya Shah
- Division of Infectious Diseases, Mayo Clinic, Rochester, MN
| | - John C O'Horo
- Division of Infectious Diseases, Mayo Clinic, Rochester, MN
| | - Elie F Berbari
- Division of Infectious Diseases, Mayo Clinic, Rochester, MN
| | - Aaron Tande
- Division of Infectious Diseases, Mayo Clinic, Rochester, MN
| | | | | |
Collapse
|
26
|
Shah AS, Tande AJ, Challener DW, O'Horo JC, Binnicker MJ, Berbari EF. Diagnostic Stewardship: An Essential Element in a Rapidly Evolving COVID-19 Pandemic. Mayo Clin Proc 2020; 95:S17-S19. [PMID: 32807516 PMCID: PMC7309714 DOI: 10.1016/j.mayocp.2020.05.039] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 05/29/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Aditya S Shah
- Division of Infectious Diseases, Mayo Clinic, Rochester, MN.
| | - Aaron J Tande
- Division of Infectious Diseases, Mayo Clinic, Rochester, MN
| | | | - John C O'Horo
- Division of Infectious Diseases, Mayo Clinic, Rochester, MN; Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN
| | | | - Elie F Berbari
- Division of Infectious Diseases, Mayo Clinic, Rochester, MN
| |
Collapse
|
27
|
Challener DW, Shah A, O'Horo JC, Berbari E, Binnicker MJ, Tande AJ. Low Utility of Repeat Real-Time PCR Testing for SARS-CoV-2 in Clinical Specimens. Mayo Clin Proc 2020; 95:1942-1945. [PMID: 32861337 PMCID: PMC7334934 DOI: 10.1016/j.mayocp.2020.06.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/25/2020] [Accepted: 06/15/2020] [Indexed: 11/21/2022]
Abstract
In a multicenter cohort of 22,315 patients tested for COVID-19, 1676 (7.5%) had repeat testing via real-time polymerase chain reaction following an initial negative test. Of those retested within 7 days of their first negative test, only 2.0% had a positive result. This suggests that repeat testing from the same source is unlikely to provide additional information.
Collapse
Affiliation(s)
| | - Aditya Shah
- Division of Infectious Disease, Mayo Clinic, Rochester, MN
| | - John C O'Horo
- Division of Infectious Disease, Mayo Clinic, Rochester, MN; Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN
| | - Elie Berbari
- Division of Infectious Disease, Mayo Clinic, Rochester, MN
| | - Matthew J Binnicker
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Aaron J Tande
- Division of Infectious Disease, Mayo Clinic, Rochester, MN
| |
Collapse
|
28
|
Corsini Campioli C, Cano Cevallos E, Assi M, Patel R, Binnicker MJ, O'Horo JC. Clinical predictors and timing of cessation of viral RNA shedding in patients with COVID-19. J Clin Virol 2020; 130:104577. [PMID: 32777762 PMCID: PMC7405830 DOI: 10.1016/j.jcv.2020.104577] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 07/30/2020] [Accepted: 08/03/2020] [Indexed: 01/12/2023]
Abstract
BACKGROUND Molecular detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is key in the diagnosis of coronavirus disease 2019 (COVID-19) and has been widely used for followup of cases as a proxy for contagiousness. The persistence of SARS-CoV-2 RNA shedding in the context of clinical features and comorbidities is understudied. METHODS We retrospectively reviewed laboratory-confirmed COVID-19 adult symptomatic cases at Mayo Clinic, eventually achieving cessation of viral RNA shedding (CVS), defined as two consecutive negative SARS-CoV-2 PCR results on nasopharyngeal swabs collected at least 24 h apart. RESULTS A total of 251 patients were included, median age was 53 years and 59 % female. The most common symptoms at diagnosis were cough, myalgia, dyspnea, fever and chills. Myalgia, cough, anosmia, ageusia and sore throat were common at CVS, but fever and dyspnea were not observed. The median time from symptom onset to CVS was 23 days, and did not differ by symptoms. The weekly cumulative CVS rate was 2, 14, 44, 73, 91 and 95 % at 1-6 weeks from symptom onset, respectively. Cough and fever were associated with a positive PCR test if tested within 2 weeks of symptoms (P < 0.05). Patients with asthma or immunosuppression were less likely to achieve CVS if tested 3 weeks into symptoms (P < 0.04). CONCLUSIONS The cumulative CVS rate at 3 weeks from symptom-onset is 44 % in our entire cohort. The findings of our study highlight the low yield of repeating a SARS-CoV-2 NP PCR test within 21 days of a laboratoryconfirmed COVID-19 diagnosis.
Collapse
Affiliation(s)
| | - Edison Cano Cevallos
- Division of Infectious Diseases, Rochester, MN, USA; Infectious Diseases Research Laboratory, Rochester, MN, USA
| | - Mariam Assi
- Division of Infectious Diseases, Rochester, MN, USA
| | - Robin Patel
- Division of Infectious Diseases, Rochester, MN, USA; Infectious Diseases Research Laboratory, Rochester, MN, USA; Division of Clinical Microbiology, Rochester, MN, USA
| | - Matthew J Binnicker
- Infectious Diseases Research Laboratory, Rochester, MN, USA; Division of Clinical Microbiology, Rochester, MN, USA
| | - John C O'Horo
- Division of Infectious Diseases, Rochester, MN, USA; Division of Pulmonary and Critical Care, Mayo Clinic, Rochester, MN, USA
| |
Collapse
|
29
|
Naddaf E, Laughlin RS, Klein CJ, Toledano M, Theel ES, Binnicker MJ, Nagappan V, Abdulrazzak M, Phelan DM. Guillain-Barré Syndrome in a Patient With Evidence of Recent SARS-CoV-2 Infection. Mayo Clin Proc 2020; 95:1799-1801. [PMID: 32753154 PMCID: PMC7284228 DOI: 10.1016/j.mayocp.2020.05.029] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 05/20/2020] [Accepted: 05/27/2020] [Indexed: 12/22/2022]
Affiliation(s)
- Elie Naddaf
- Department of Neurology, Mayo Clinic, Rochester, Minnesota
| | | | | | | | - Elitza S Theel
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Matthew J Binnicker
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | | | | | - David M Phelan
- Department of Hospital Internal Medicine, Mayo Clinic, Rochester, Minnesota
| |
Collapse
|
30
|
Rucinski SL, Binnicker MJ, Thomas AS, Patel R. Seasonality of Coronavirus 229E, HKU1, NL63, and OC43 From 2014 to 2020. Mayo Clin Proc 2020; 95:1701-1703. [PMID: 32753142 PMCID: PMC7275147 DOI: 10.1016/j.mayocp.2020.05.032] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 05/21/2020] [Accepted: 05/27/2020] [Indexed: 12/05/2022]
Abstract
The possibility of seasonality of COVID-19 is being discussed; we show clinical microbiology laboratory data illustrating seasonality of coronaviruses 229E, HKU1, NL63, and OC43. The data shown are specific to the 4 studied coronaviruses and may or may not generalize to COVID-19.
Collapse
Affiliation(s)
- Stefanea L Rucinski
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Matthew J Binnicker
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Amber S Thomas
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota; Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota.
| |
Collapse
|
31
|
Affiliation(s)
- Nicholas Clements
- Well Living Lab, Rochester, Minnesota; Mayo Clinic, College of Medicine, Rochester, Minnesota
| | - Matthew J Binnicker
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Véronique L Roger
- Well Living Lab, Rochester, Minnesota; Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota; Department of Cardiovascular Diseases, Mayo Clinic, Rochester, Minnesota.
| |
Collapse
|
32
|
Agarwal V, Venkatakrishnan AJ, Puranik A, Kirkup C, Lopez-Marquez A, Challener DW, O’Horo JC, Binnicker MJ, Kremers WK, Faubion WA, Badley AD, Williams AW, Gores GJ, Halamka JD, Morice WG, Soundararajan V. Long-term SARS-CoV-2 RNA Shedding and its Temporal Association to IgG Seropositivity. medRxiv 2020:2020.06.02.20120774. [PMID: 32577666 PMCID: PMC7302207 DOI: 10.1101/2020.06.02.20120774] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Analysis of 851 COVID-19 patients with a SARS-CoV-2-positive PCR at follow-up shows 99 patients remained SARS-CoV-2-positive after four weeks from initial diagnosis. Surprisingly, a majority of these long-term viral RNA shedders were not hospitalized (61 of 99), with variable PCR Crossing point values over the month post diagnosis. For the 851-patient cohort, the mean lower bound of viral RNA shedding was 17.3 days (SD: 7.8), and the mean upper bound of viral RNA shedding from 668 patients transitioning to confirmed PCR-negative status was 22.7 days (SD: 11.8). Among 104 patients with an IgG test result, 90 patients were seropositive to date, with mean upper bound of time to seropositivity from initial diagnosis being 37.8 days (95%CI: 34.3-41.3). Juxtaposing IgG/PCR tests revealed that 14 of 90 patients are non-hospitalized and seropositive yet shed viral RNA. This study emphasizes the need for monitoring viral loads and neutralizing antibody titers in long-term shedders.
Collapse
Affiliation(s)
- Vineet Agarwal
- nference, inc., One Main Street, Suite 400, East Arcade, Cambridge, MA 02142, USA
| | - AJ Venkatakrishnan
- nference, inc., One Main Street, Suite 400, East Arcade, Cambridge, MA 02142, USA
| | - Arjun Puranik
- nference, inc., One Main Street, Suite 400, East Arcade, Cambridge, MA 02142, USA
| | - Christian Kirkup
- nference, inc., One Main Street, Suite 400, East Arcade, Cambridge, MA 02142, USA
| | | | | | | | | | | | | | | | | | | | - John D. Halamka
- Mayo Clinic, Rochester MN, USA
- Mayo Clinic Platform, Rochester MN, USA
| | - William G. Morice
- Mayo Clinic, Rochester MN, USA
- Mayo Clinic Laboratories, Rochester MN, USA
| | - Venky Soundararajan
- nference, inc., One Main Street, Suite 400, East Arcade, Cambridge, MA 02142, USA
| |
Collapse
|
33
|
Binnicker MJ. Emergence of a Novel Coronavirus Disease (COVID-19) and the Importance of Diagnostic Testing: Why Partnership between Clinical Laboratories, Public Health Agencies, and Industry Is Essential to Control the Outbreak. Clin Chem 2020; 66:664-666. [PMID: 32077933 PMCID: PMC7108487 DOI: 10.1093/clinchem/hvaa071] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 02/18/2020] [Indexed: 12/13/2022]
Affiliation(s)
- Matthew J Binnicker
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| |
Collapse
|
34
|
Boerger AC, Binnicker MJ. Comparison of the Panther Fusion respiratory panels to routine methods for detection of viruses in upper and lower respiratory tract specimens. Diagn Microbiol Infect Dis 2020; 97:115014. [PMID: 32192787 DOI: 10.1016/j.diagmicrobio.2020.115014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 11/26/2019] [Revised: 02/05/2020] [Accepted: 02/05/2020] [Indexed: 12/18/2022]
Abstract
Viral respiratory infections remain a significant cause of morbidity and mortality in pediatric, elderly, and immunocompromised patients. The Panther Fusion respiratory panels consist of 3 separate multiplex assays that test for 1) influenza A, influenza B, and RSV; 2) parainfluenza virus types 1-4; or 3) adenovirus, human metapneumovirus, and rhinovirus. This study evaluated the performance of the Fusion assays for both upper and lower respiratory tract specimens in comparison to routine methods, including viral culture and targeted real-time polymerase chain reaction assays. Following discordant resolution, the Fusion assays demonstrated high overall correlation (98.6% [648/657]) with routine methods. In addition, prospective testing of respiratory specimens (n = 146) submitted for viral culture showed a ~10-fold increase in detection by the Fusion panels compared to viral culture (28.1% versus 2.7% positivity). The Fusion respiratory panels offer a flexible, more targeted approach to respiratory virus testing with a turnaround time comparable to other molecular assays.
Collapse
Affiliation(s)
- Aimee C Boerger
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905
| | - Matthew J Binnicker
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905.
| |
Collapse
|
35
|
Miller JM, Binnicker MJ, Campbell S, Carroll KC, Chapin KC, Gilligan PH, Gonzalez MD, Jerris RC, Kehl SC, Patel R, Pritt BS, Richter SS, Robinson-Dunn B, Schwartzman JD, Snyder JW, Telford S, Theel ES, Thomson RB, Weinstein MP, Yao JD. A Guide to Utilization of the Microbiology Laboratory for Diagnosis of Infectious Diseases: 2018 Update by the Infectious Diseases Society of America and the American Society for Microbiology. Clin Infect Dis 2019; 67:813-816. [PMID: 30169655 DOI: 10.1093/cid/ciy584] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Accepted: 04/28/2018] [Indexed: 11/13/2022] Open
Abstract
The critical nature of the microbiology laboratory in infectious disease diagnosis calls for a close, positive working relationship between the physician/advanced practice provider and the microbiologists who provide enormous value to the healthcare team. This document, developed by experts in laboratory and adult and pediatric clinical medicine, provides information on which tests are valuable and in which contexts, and on tests that add little or no value for diagnostic decisions. This document presents a system-based approach rather than specimen-based approach, and includes bloodstream and cardiovascular system infections, central nervous system infections, ocular infections, soft tissue infections of the head and neck, upper and lower respiratory infections, infections of the gastrointestinal tract, intra-abdominal infections, bone and joint infections, urinary tract infections, genital infections, and other skin and soft tissue infections; or into etiologic agent groups, including arthropod-borne infections, viral syndromes, and blood and tissue parasite infections. Each section contains introductory concepts, a summary of key points, and detailed tables that list suspected agents; the most reliable tests to order; the samples (and volumes) to collect in order of preference; specimen transport devices, procedures, times, and temperatures; and detailed notes on specific issues regarding the test methods, such as when tests are likely to require a specialized laboratory or have prolonged turnaround times. In addition, the pediatric needs of specimen management are also emphasized. There is intentional redundancy among the tables and sections, as many agents and assay choices overlap. The document is intended to serve as a guidance for physicians in choosing tests that will aid them to quickly and accurately diagnose infectious diseases in their patients.
Collapse
Affiliation(s)
| | - Matthew J Binnicker
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | | | - Karen C Carroll
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | | | - Peter H Gilligan
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill
| | - Mark D Gonzalez
- Department of Pathology, Children's Healthcare of Atlanta, Georgia
| | - Robert C Jerris
- Department of Pathology, Children's Healthcare of Atlanta, Georgia
| | | | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Bobbi S Pritt
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | | | - Barbara Robinson-Dunn
- Department of Pathology and Laboratory Medicine, Beaumont Health, Royal Oak, Michigan
| | | | - James W Snyder
- Department of Pathology and Laboratory Medicine, University of Louisville, Kentucky
| | - Sam Telford
- Department of Infectious Disease and Global Health, Tufts University, North Grafton, Massachusetts
| | - Elitza S Theel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Richard B Thomson
- Department of Pathology and Laboratory Medicine, NorthShore University HealthSystem, Evanston, Illinois
| | - Melvin P Weinstein
- Departments of Medicine and Pathology & Laboratory Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey
| | - Joseph D Yao
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| |
Collapse
|
36
|
Miller JM, Binnicker MJ, Campbell S, Carroll KC, Chapin KC, Gilligan PH, Gonzalez MD, Jerris RC, Kehl SC, Patel R, Pritt BS, Richter SS, Robinson-Dunn B, Schwartzman JD, Snyder JW, Telford S, Theel ES, Thomson RB, Weinstein MP, Yao JD. A Guide to Utilization of the Microbiology Laboratory for Diagnosis of Infectious Diseases: 2018 Update by the Infectious Diseases Society of America and the American Society for Microbiology. Clin Infect Dis 2018; 67:e1-e94. [PMID: 29955859 PMCID: PMC7108105 DOI: 10.1093/cid/ciy381] [Citation(s) in RCA: 264] [Impact Index Per Article: 44.0] [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: 04/22/2018] [Accepted: 04/28/2018] [Indexed: 12/12/2022] Open
Abstract
The critical nature of the microbiology laboratory in infectious disease diagnosis calls for a close, positive working relationship between the physician/advanced practice provider and the microbiologists who provide enormous value to the healthcare team. This document, developed by experts in laboratory and adult and pediatric clinical medicine, provides information on which tests are valuable and in which contexts, and on tests that add little or no value for diagnostic decisions. This document presents a system-based approach rather than specimen-based approach, and includes bloodstream and cardiovascular system infections, central nervous system infections, ocular infections, soft tissue infections of the head and neck, upper and lower respiratory infections, infections of the gastrointestinal tract, intra-abdominal infections, bone and joint infections, urinary tract infections, genital infections, and other skin and soft tissue infections; or into etiologic agent groups, including arthropod-borne infections, viral syndromes, and blood and tissue parasite infections. Each section contains introductory concepts, a summary of key points, and detailed tables that list suspected agents; the most reliable tests to order; the samples (and volumes) to collect in order of preference; specimen transport devices, procedures, times, and temperatures; and detailed notes on specific issues regarding the test methods, such as when tests are likely to require a specialized laboratory or have prolonged turnaround times. In addition, the pediatric needs of specimen management are also emphasized. There is intentional redundancy among the tables and sections, as many agents and assay choices overlap. The document is intended to serve as a guidance for physicians in choosing tests that will aid them to quickly and accurately diagnose infectious diseases in their patients.
Collapse
Affiliation(s)
| | - Matthew J Binnicker
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | | | - Karen C Carroll
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | | | - Peter H Gilligan
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill
| | - Mark D Gonzalez
- Department of Pathology, Children’s Healthcare of Atlanta, Georgia
| | - Robert C Jerris
- Department of Pathology, Children’s Healthcare of Atlanta, Georgia
| | | | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Bobbi S Pritt
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | | | - Barbara Robinson-Dunn
- Department of Pathology and Laboratory Medicine, Beaumont Health, Royal Oak, Michigan
| | | | - James W Snyder
- Department of Pathology and Laboratory Medicine, University of Louisville, Kentucky
| | - Sam Telford
- Department of Infectious Disease and Global Health, Tufts University, North Grafton, Massachusetts
| | - Elitza S Theel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Richard B Thomson
- Department of Pathology and Laboratory Medicine, NorthShore University HealthSystem, Evanston, Illinois
| | - Melvin P Weinstein
- Departments of Medicine and Pathology & Laboratory Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey
| | - Joseph D Yao
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| |
Collapse
|
37
|
Beam E, Germer JJ, Lahr B, Yao JD, Limper AH, Binnicker MJ, Razonable RR. Cytomegalovirus (CMV) DNA quantification in bronchoalveolar lavage fluid of immunocompromised patients with CMV pneumonia. Clin Transplant 2017; 32. [DOI: 10.1111/ctr.13149] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/30/2017] [Indexed: 12/18/2022]
Affiliation(s)
- Elena Beam
- Division of Infectious Diseases; Mayo Clinic; Rochester MN USA
| | - Jeffrey J. Germer
- Department of Laboratory Medicine and Pathology; Mayo Clinic; Rochester MN USA
| | - Brian Lahr
- Department of Health Sciences Research; Mayo Clinic; Rochester MN USA
| | - Joseph D.C. Yao
- Department of Laboratory Medicine and Pathology; Mayo Clinic; Rochester MN USA
| | | | | | - Raymund R. Razonable
- Division of Infectious Diseases; Mayo Clinic; Rochester MN USA
- William J. von Liebig Center for Transplantation and Clinical Regeneration; Mayo Clinic; Rochester MN USA
| |
Collapse
|
38
|
Sacco KA, Pongdee T, Binnicker MJ, Espy M, Pardi D, Khanna S, Joshi AY. Presence of immune deficiency increases the risk of hospitalization in patients with norovirus infection. Diagn Microbiol Infect Dis 2017; 90:300-306. [PMID: 29398461 DOI: 10.1016/j.diagmicrobio.2017.11.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 11/18/2017] [Accepted: 11/25/2017] [Indexed: 12/22/2022]
Abstract
Norovirus is an emerging pathogen causing gastroenteritis. We sought to identify factors associated with clinical outcomes in a cohort of patients with laboratory-confirmed norovirus infection. We performed a retrospective chart review of patients with positive norovirus polymerase chain reaction in stool between October 1, 2015, and May 31, 2016. 128 unique patients were identified during the study period, 64 of whom had immune deficiency, of which only 3 patients had a primary immune deficiency (common variable immune deficiency), while 61 patients had a secondary immune deficiency. 50% of patients with immune deficiency were hospitalized as compared to only 30% of the non-immune-deficient cohort (odds ratio: 2.1 (1.1-4.18, P=0.04). One-third (32.8%) of the patients had a polymicrobial stool infection, and 21.1% had concurrent Clostridium difficile infection. Initial mean total leukocyte count was higher in the hospitalized group at 8.40×109/L versus 6.31×109/L in the nonhospitalized group (P=0.049). All 13 patients presenting with fever had symptomatic resolution (P=0.002). The presence of C. difficile infection was correlated with persistent symptoms (OR 2.30 [0.95-5.58], P=0.067). The overall mortality rate among our cohort was 3.13% (4 patients). All deceased patients had secondary immune deficiency, and none had C. difficile coinfection. Presence of an immune deficiency increases the risk of hospitalization with norovirus infection. Absence of fever is associated with lower resolution and possibly may contribute to a persistent infectious state. Presence of concomitant C. difficile infection is correlated with a lower overall mortality rate.
Collapse
Affiliation(s)
- Keith A Sacco
- Department of Internal Medicine, Mayo Clinic, Jacksonville, FL
| | - Thanai Pongdee
- Division of Allergic Diseases, Mayo Clinic, Rochester, MN
| | | | - Mark Espy
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Darrell Pardi
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Mayo Clinic, Rochester, MN
| | - Sahil Khanna
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Mayo Clinic, Rochester, MN
| | - Avni Y Joshi
- Division of Allergic Diseases, Mayo Clinic, Rochester, MN; Mayo Clinic Children's Center, Division of Pediatric Allergy and Immunology, Mayo Clinic, Rochester, MN.
| |
Collapse
|
39
|
Holtz KK, Townsend KR, Furst JW, Myers JF, Binnicker MJ, Quigg SM, Maxson JA, Espy MJ. An Assessment of the AdenoPlus Point-of-Care Test for Diagnosing Adenoviral Conjunctivitis and Its Effect on Antibiotic Stewardship. Mayo Clin Proc Innov Qual Outcomes 2017; 1:170-175. [PMID: 30225413 PMCID: PMC6135020 DOI: 10.1016/j.mayocpiqo.2017.06.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [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] [Indexed: 06/08/2023] Open
Abstract
OBJECTIVE To determine the sensitivity and specificity of the AdenoPlus test compared with real-time polymerase chain reaction (PCR) and to determine whether there was a reduction in antibiotic prescriptions with the use of AdenoPlus compared with the previous year. PATIENTS AND METHODS A total of 125 patients with suspected infectious conjunctivitis were accrued from June 4, 2015, through September 27, 2015. Forty-six participants from the prospective cohort completed both AdenoPlus and PCR testing. Two hundred fifty age-matched individuals were in the retrospective cohort. RESULTS There was a significant reduction in the percentage of patients who received an antibiotic ophthalmic prescription in the prospective cohort vs the retrospective cohort (32% vs 45%; χ2P=.01). AdenoPlus test sensitivity was 50% (5 of 10) and specificity was 92% (33 of 36) compared with real-time PCR testing. CONCLUSION The AdenoPlus test has high specificity for diagnosing adenoviral conjunctivitis but lower sensitivity than has been previously published. These data suggest that negative AdenoPlus results should be confirmed by real-time PCR owing to the low overall sensitivity of AdenoPlus observed.
Collapse
Affiliation(s)
- Kelly K. Holtz
- Department of Family Medicine, Mayo Clinic, Rochester, MN
| | - Kalie R. Townsend
- Department of Family Medicine, Mayo Clinic, Rochester, MN
- Urgent Care and Emergency Medicine Department, Mayo Clinic Health System Red Cedar, Menomonie, WI
| | | | - Jane F. Myers
- Department of Family Medicine, Mayo Clinic, Rochester, MN
| | - Matthew J. Binnicker
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | | | | | - Mark J. Espy
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| |
Collapse
|
40
|
Binnicker MJ, Espy MJ, Duresko B, Irish C, Mandrekar J. Automated processing, extraction and detection of herpes simplex virus types 1 and 2: A comparative evaluation of three commercial platforms using clinical specimens. J Clin Virol 2017; 89:30-33. [PMID: 28226272 DOI: 10.1016/j.jcv.2017.02.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 02/08/2017] [Accepted: 02/12/2017] [Indexed: 01/25/2023]
Abstract
BACKGROUND Recently, automated platforms have been developed that can perform processing, extraction and testing for herpes simplex virus (HSV) nucleic acid on a single instrument. OBJECTIVES In this study, we compared three commercially-available systems; Aptima®/Panther (Hologic, San Diego, CA), ARIES® (Luminex Corporation, Austin, TX), and cobas® 4800 (Roche Molecular Systems Inc, Pleasanton, CA) for the qualitative detection of HSV-1/2 in clinical samples. STUDY DESIGN Two-hundred seventy-seven specimens (genital [n=193], dermal [n=84]) were submitted for routine HSV-1/2 real-time PCR by a laboratory developed test. Following routine testing, samples were also tested by the Aptima, ARIES, and cobas HSV-1/2 assays per the manufacturer's recommendations. Results were compared to a "consensus standard" defined as the result obtained from ≥3 of the 4 assays. RESULTS Following testing of 277 specimens, the cobas and ARIES assays demonstrated a sensitivity of 100% for HSV-1 (61/61) and HSV-2 (55/55). The Aptima assays showed a sensitivity of 91.8% (56/61) for HSV-1 and 90.9% (50/55) for HSV-2. Percent specificities for HSV-1 were 96.2% (202/210) by cobas, 99.5% (209/210) by ARIES and 100% (236/236) by Aptima. For HSV-2, the specificities were 98.1% (211/215) by cobas, 99.5% (215/216) by ARIES and 100% (216/216) by Aptima. The turnaround time for testing 24 samples was 2.5h by the cobas 4800, 3.1h by Aptima/Panther, and 3.9h by ARIES. CONCLUSIONS The three commercial systems can perform all current functions on a single platform, thereby improving workflow and potentially reducing errors associated with manual processing of samples.
Collapse
Affiliation(s)
- Matthew J Binnicker
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, United States.
| | - Mark J Espy
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, United States
| | - Brian Duresko
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, United States
| | - Cole Irish
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, United States
| | - Jay Mandrekar
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, United States; Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN 55905, United States
| |
Collapse
|
41
|
Ramanan P, Espy MJ, Khare R, Binnicker MJ. Detection and differentiation of norovirus genogroups I and II from clinical stool specimens using real-time PCR. Diagn Microbiol Infect Dis 2017; 87:325-327. [PMID: 28159444 DOI: 10.1016/j.diagmicrobio.2017.01.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 01/13/2017] [Accepted: 01/16/2017] [Indexed: 11/29/2022]
Abstract
A real-time RT-PCR assay was designed to detect and differentiate norovirus genogroups I (GI) and II (GII), with primers and probes targeting the nonstructural polyprotein gene. Stool samples (n = 100) submitted for routine testing by the BioFire FilmArray® GI panel were also tested by the norovirus GI/GII real-time PCR assays. When compared to the FilmArray GI panel, the norovirus real-time PCR assay demonstrated a sensitivity of 77.5% (62/80) and specificity of 95% (19/20). Specimens yielding discordant results (n = 19) were tested at two outside laboratories for adjudication. Following discordant resolution, the adjusted sensitivity and specificity of the norovirus real-time PCR assays were 96.9% (63/65) and 100% (35/35), respectively. These results suggest that the real-time PCR assays are able to accurately detect and differentiate norovirus GI/GII from clinical stool specimens. Furthermore, our report highlights a potential issue with the specificity of the BioFire FilmArray® norovirus assay, which warrants additional investigation.
Collapse
Affiliation(s)
- Poornima Ramanan
- Division of Clinical Microbiology, Mayo Clinic, Rochester, MN, USA 55905
| | - M J Espy
- Division of Clinical Microbiology, Mayo Clinic, Rochester, MN, USA 55905
| | - Reeti Khare
- Division of Infectious Disease Diagnostics, Northwell Health, Lake Success, New York, NY, USA 11042
| | - M J Binnicker
- Division of Clinical Microbiology, Mayo Clinic, Rochester, MN, USA 55905.
| |
Collapse
|
42
|
Ramanan P, Timmerman EA, Fidler ME, Amer H, Pritt BS, Schwab DA, Batterman HJ, Binnicker MJ. A kidney transplant recipient with renal medullary viral cytopathic changes. Transpl Infect Dis 2017; 19. [PMID: 27925350 DOI: 10.1111/tid.12646] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 08/11/2016] [Accepted: 09/09/2016] [Indexed: 01/17/2023]
Abstract
We present a case of JC polyomavirus (JCV)-associated nephropathy (PyVAN) in an asymptomatic deceased-donor kidney transplant recipient. Despite the presence of viral cytopathic effect in the kidney biopsy and positive BK polyomavirus (BKV) in situ hybridization (ISH), BKV real-time polymerase chain reaction (PCR) results of plasma and urine were negative. JCV ISH was performed and was found to be positive. JCV real-time PCR on urine, plasma, and the kidney biopsy tissue was positive. Reduction in immunosuppression resulted in resolution of JCV viremia. This case highlights that JC-PyVAN is a distinct clinical entity and is likely to have a better clinical outcome than BK-PyVAN. Concurrent infection with BKV and JCV may occur, but may be difficult to confirm due to the potential for cross-reactivity between BKV and JCV ISH stains.
Collapse
Affiliation(s)
- Poornima Ramanan
- Division of Clinical Microbiology, Mayo Clinic, Rochester, MN, USA
| | - Elizabeth A Timmerman
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA.,The William J von Liebig Center for Transplantation and Clinical Regeneration, Mayo Clinic, Rochester, MN, USA
| | - Mary E Fidler
- Division of Anatomic Pathology, Mayo Clinic, Rochester, MN, USA
| | - Hatem Amer
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA.,The William J von Liebig Center for Transplantation and Clinical Regeneration, Mayo Clinic, Rochester, MN, USA
| | - Bobbi S Pritt
- Division of Clinical Microbiology, Mayo Clinic, Rochester, MN, USA
| | - Dale A Schwab
- Focus Diagnostics Inc. Reference Laboratory, A Quest Subsidiary, San Juan Capistrano, CA, USA
| | - Hollis J Batterman
- Focus Diagnostics Inc. Reference Laboratory, A Quest Subsidiary, San Juan Capistrano, CA, USA
| | | |
Collapse
|
43
|
Cockerill CC, Orvidas LJ, Moore EJ, Binnicker MJ, Duresko BJ, Espy MJ, Cockerill FR, Tombers NM, Pritt BS. Detection of high-risk human papillomavirus infection in tonsillar specimens using 2 commercially available assays. Diagn Microbiol Infect Dis 2016; 86:365-368. [PMID: 27638349 DOI: 10.1016/j.diagmicrobio.2016.08.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [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: 06/30/2016] [Revised: 08/09/2016] [Accepted: 08/16/2016] [Indexed: 01/24/2023]
Abstract
THE OBJECTIVE OF THE STUDY IS TO DETERMINE THE PREVALENCE OF HIGH-RISK HUMAN PAPILLOMAVIRUS (HRHPV) INFECTION IN TONSILLAR SWABS AND TISSUE: Patients undergoing tonsillectomy for nonmalignant causes were enrolled. A flocked swab and fresh tissue were collected from the left and right tonsil of each patient. Specimens were tested for hrHPV DNA using the Roche cobas test and for the presence of E6/E7 messenger RNA using the Hologic Aptima hrHPV test. Of the 193 patients enrolled, 129 were in the pediatric group (ages 1-12years; median, 5years), and 64 were in the adult group (ages 13-55; median, 22years). All swab and tissue specimens were negative for hrHPV by both methods. Positive, negative, and internal controls performed as expected. We found a 0% rate of infection indicating that detectable hrHPV infection in tonsillar tissue appears to be uncommon in the children and adults in the population sampled.
Collapse
MESH Headings
- Adolescent
- Adult
- Aged
- Aged, 80 and over
- Child
- Child, Preschool
- DNA, Viral/analysis
- DNA, Viral/genetics
- DNA, Viral/isolation & purification
- Female
- Genotype
- Humans
- Infant
- Male
- Middle Aged
- Palatine Tonsil/virology
- Papillomaviridae/classification
- Papillomaviridae/genetics
- Papillomaviridae/isolation & purification
- Papillomavirus Infections/epidemiology
- Papillomavirus Infections/virology
- Prevalence
- RNA, Messenger/analysis
- RNA, Messenger/genetics
- RNA, Messenger/isolation & purification
- RNA, Viral/analysis
- RNA, Viral/genetics
- RNA, Viral/isolation & purification
- Young Adult
Collapse
Affiliation(s)
- Cara C Cockerill
- The Department of Otorhinolaryngology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905.
| | - Laura J Orvidas
- The Department of Otorhinolaryngology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905.
| | - Eric J Moore
- The Department of Otorhinolaryngology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905.
| | - Matthew J Binnicker
- The Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905.
| | - Brian J Duresko
- The Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905.
| | - Mark J Espy
- The Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905.
| | - Franklin R Cockerill
- The Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905.
| | - Nicole M Tombers
- The Department of Otorhinolaryngology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905.
| | - Bobbi S Pritt
- The Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905.
| |
Collapse
|
44
|
Anderson NW, Binnicker MJ, Harris DM, Chirila RM, Brumble L, Mandrekar J, Hata DJ. Morbidity and mortality among patients with respiratory syncytial virus infection: a 2-year retrospective review. Diagn Microbiol Infect Dis 2016; 85:367-371. [DOI: 10.1016/j.diagmicrobio.2016.02.025] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 02/12/2016] [Accepted: 02/17/2016] [Indexed: 11/26/2022]
|
45
|
Linnoila JJ, Binnicker MJ, Majed M, Klein CJ, McKeon A. CSF herpes virus and autoantibody profiles in the evaluation of encephalitis. Neurol Neuroimmunol Neuroinflamm 2016; 3:e245. [PMID: 27308306 PMCID: PMC4897981 DOI: 10.1212/nxi.0000000000000245] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 04/17/2016] [Indexed: 12/18/2022]
Abstract
Objective: To report the frequency of coexisting herpes viruses (herpes simplex virus 1 [HSV-1] or HSV-2, varicella zoster virus, Epstein-Barr virus [EBV], cytomegalovirus, or human herpes virus 6 [HHV-6]) and autoantibodies in patients with encephalitis (herpes or autoimmune) in clinical laboratory service. Methods: Three groups were evaluated for herpes viruses and antibodies: group 1—patients whose CSF was positive for a herpes virus by real-time PCR over a period of 6 months; group 2—patients whose CSF was positive for an autoimmune encephalitis–associated antibody over 5 years (e.g., NMDA receptor [NMDA-R] antibody), and the same number of controls without autoimmune/infectious disease; and group 3—incidental autoimmune parainfectious encephalitis cases encountered over 1 year. Results: In group 1, antibodies were detected in 27 of 100 herpes PCR-positive CSF specimens (CSFs), either unclassified neural or nonneural in all but one patient with NMDA-R antibody detected after EBV infection. Antibodies were also detected in 3 of 7 CSFs submitted for repeat PCR testing (unclassified, 2; AMPA receptor, 1). In group 2, herpes viruses were detected in 1 of 77 controls (HHV-6) and 4 of 77 patients with autoimmune encephalitis (EBV, 2; HHV-6, 2); autoantibodies targeted NMDA-R in 3/4 and GABAB-R in 1/4. In group 3, NMDA-R antibody was detected in 7 patients post–HSV-1 encephalitis. Of the remaining 3 patients, 2 had unclassified neural antibodies detected, and one had GABAB-R autoimmunity. Concomitant neoplasms were discovered in 2 patients each from groups 2 and 3. Conclusions: Autoantibodies and herpes virus DNA frequently coexist in encephalitic CSF. Some patients develop parainfectious autoimmunity following viral CNS infection (usually HSV-1 encephalitis). The significance of detecting herpes nucleic acids in others remains unclear.
Collapse
Affiliation(s)
- Jenny J Linnoila
- Departments of Neurology (J.J.L., C.J.K., A.M.), and Laboratory Medicine and Pathology (M.J.B., M.M., C.J.K., A.M.), College of Medicine, Mayo Clinic, Rochester, MN
| | - Matthew J Binnicker
- Departments of Neurology (J.J.L., C.J.K., A.M.), and Laboratory Medicine and Pathology (M.J.B., M.M., C.J.K., A.M.), College of Medicine, Mayo Clinic, Rochester, MN
| | - Masoud Majed
- Departments of Neurology (J.J.L., C.J.K., A.M.), and Laboratory Medicine and Pathology (M.J.B., M.M., C.J.K., A.M.), College of Medicine, Mayo Clinic, Rochester, MN
| | - Christopher J Klein
- Departments of Neurology (J.J.L., C.J.K., A.M.), and Laboratory Medicine and Pathology (M.J.B., M.M., C.J.K., A.M.), College of Medicine, Mayo Clinic, Rochester, MN
| | - Andrew McKeon
- Departments of Neurology (J.J.L., C.J.K., A.M.), and Laboratory Medicine and Pathology (M.J.B., M.M., C.J.K., A.M.), College of Medicine, Mayo Clinic, Rochester, MN
| |
Collapse
|
46
|
Heaton PR, Espy MJ, Binnicker MJ. Evaluation of 2 multiplex real-time PCR assays for the detection of HSV-1/2 and Varicella zoster virus directly from clinical samples. Diagn Microbiol Infect Dis 2014; 81:169-70. [PMID: 25511233 DOI: 10.1016/j.diagmicrobio.2014.11.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [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: 09/15/2014] [Revised: 11/21/2014] [Accepted: 11/22/2014] [Indexed: 11/29/2022]
Abstract
We compared the performance of 2 multiplex assays (Focus Simplexa and Quidel Lyra) to individual real-time PCR for the detection of herpes simplex virus-1 (HSV-1), HSV-2, and Varicella zoster virus (VZV) from clinical specimens. Results were compared to a consensus standard, defined as the result obtained by at least 2 of the 3 molecular methods. The sensitivity of the Quidel assay ranged from 92.0% for HSV-1 to 97.7% for HSV-2, while the specificity for all targets was 100%. The Focus assay demonstrated 100% sensitivity for all targets, and the percent specificity ranged from 96.8% for HSV-1 to 100% for HSV-2 and VZV.
Collapse
Affiliation(s)
- Phillip R Heaton
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Mark J Espy
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Matthew J Binnicker
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.
| |
Collapse
|
47
|
Bruminhent J, Deziel PJ, Wotton JT, Binnicker MJ, Razonable RR. Prolonged shedding of pandemic influenza A (H1N1) 2009 virus in a pancreas-after-kidney transplant recipient. J Clin Virol 2014; 61:302-4. [PMID: 25081940 DOI: 10.1016/j.jcv.2014.07.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [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: 05/29/2014] [Revised: 07/04/2014] [Accepted: 07/08/2014] [Indexed: 11/17/2022]
Abstract
Prolonged shedding of influenza virus has been reported in immunocompromised patients. Delayed viral clearance may contribute to antiviral resistance and nosocomial transmission. We report a case of a pancreas-after-kidney transplant recipient who had detectable pandemic influenza A virus for 12 months. Pyrosequencing analysis detected the H275Y mutation, which is associated with resistance to oseltamivir.
Collapse
Affiliation(s)
| | - Paul J Deziel
- William J. von Liebig Center for Transplantation and Clinical Regeneration, Mayo Clinic, Rochester, MN 55905, USA.
| | - Jason T Wotton
- Minnesota Department of Health, St. Paul, MN 55164, USA.
| | - Matthew J Binnicker
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA.
| | - Raymund R Razonable
- Division of Infectious Diseases, Mayo Clinic, Rochester, MN 55905, USA; William J. von Liebig Center for Transplantation and Clinical Regeneration, Mayo Clinic, Rochester, MN 55905, USA.
| |
Collapse
|
48
|
Theel ES, Jespersen DJ, Harring J, Mandrekar J, Binnicker MJ. Evaluation of an enzyme immunoassay for detection of Histoplasma capsulatum antigen from urine specimens. J Clin Microbiol 2013; 51:3555-9. [PMID: 23966508 PMCID: PMC3889733 DOI: 10.1128/jcm.01868-13] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 08/09/2013] [Indexed: 12/29/2022] Open
Abstract
Detection of Histoplasma capsulatum urinary antigen (UAg) is important for the initial diagnosis of infection and for monitoring of patient responses to antifungal therapy. This study evaluated an analyte-specific reagent (ASR) enzyme immunoassay (EIA) for the detection of H. capsulatum UAg from Immuno Mycologics, Inc. (IMMY) (Norman, OK) in comparison with routine testing with the MiraVista (MVista) H. capsulatum quantitative EIA (MiraVista Diagnostics, Indianapolis, IN). Using prospectively collected urine specimens (n = 1,003), we observed an overall percent agreement between the two assays of 97.6% (979/1,003 samples). Compared with the MVista EIA, the sensitivity and specificity of the IMMY ASR EIA were 64.5% (40/62 samples) and 99.8% (939/941 samples), respectively, using a cutoff value of 0.5 ng/ml. Based on available clinical histories for 23/24 discordant samples, 5 IMMY assay-negative/MVista assay-positive samples were considered falsely positive. Furthermore, 10/23 discordant samples were positive by the MVista EIA but were below the limit of quantitation (<0.4 ng/ml). The clinical significance of these low positive results in the MVista EIA is unclear. In addition to the prospective study, we tested 11 urine specimens collected from patients with culture-confirmed Histoplasma infections, and 100% (11/11 samples) were positive by the IMMY ASR EIA. In conclusion, the IMMY ASR EIA may offer an alternative approach for the detection of Histoplasma UAg. Additional prospective studies are needed to better characterize the performance of the IMMY ASR EIA in conjunction with clinical and laboratory findings.
Collapse
Affiliation(s)
- Elitza S. Theel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology
| | - Deborah J. Jespersen
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology
| | - Julie Harring
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology
| | - Jay Mandrekar
- Division of Biomedical Statistics and Informatics, Department of Health Sciences and Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Matthew J. Binnicker
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology
| |
Collapse
|
49
|
Binnicker MJ, Theel ES, Pritt BS. Lack of evidence for rapid transmission of Lyme disease following a tick bite. Diagn Microbiol Infect Dis 2012; 73:102-3. [PMID: 22578945 DOI: 10.1016/j.diagmicrobio.2012.02.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Accepted: 02/27/2012] [Indexed: 10/28/2022]
|
50
|
Pritt BS, Sloan LM, Johnson DKH, Munderloh UG, Paskewitz SM, McElroy KM, McFadden JD, Binnicker MJ, Neitzel DF, Liu G, Nicholson WL, Nelson CM, Franson JJ, Martin SA, Cunningham SA, Steward CR, Bogumill K, Bjorgaard ME, Davis JP, McQuiston JH, Warshauer DM, Wilhelm MP, Patel R, Trivedi VA, Eremeeva ME. Emergence of a new pathogenic Ehrlichia species, Wisconsin and Minnesota, 2009. N Engl J Med 2011; 365:422-9. [PMID: 21812671 PMCID: PMC3319926 DOI: 10.1056/nejmoa1010493] [Citation(s) in RCA: 178] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
BACKGROUND Ehrlichiosis is a clinically important, emerging zoonosis. Only Ehrlichia chaffeensis and E. ewingii have been thought to cause ehrlichiosis in humans in the United States. Patients with suspected ehrlichiosis routinely undergo testing to ensure proper diagnosis and to ascertain the cause. METHODS We used molecular methods, culturing, and serologic testing to diagnose and ascertain the cause of cases of ehrlichiosis. RESULTS On testing, four cases of ehrlichiosis in Minnesota or Wisconsin were found not to be from E. chaffeensis or E. ewingii and instead to be caused by a newly discovered ehrlichia species. All patients had fever, malaise, headache, and lymphopenia; three had thrombocytopenia; and two had elevated liver-enzyme levels. All recovered after receiving doxycycline treatment. At least 17 of 697 Ixodes scapularis ticks collected in Minnesota or Wisconsin were positive for the same ehrlichia species on polymerase-chain-reaction testing. Genetic analyses revealed that this new ehrlichia species is closely related to E. muris. CONCLUSIONS We report a new ehrlichia species in Minnesota and Wisconsin and provide supportive clinical, epidemiologic, culture, DNA-sequence, and vector data. Physicians need to be aware of this newly discovered close relative of E. muris to ensure appropriate testing, treatment, and regional surveillance. (Funded by the National Institutes of Health and the Centers for Disease Control and Prevention.).
Collapse
Affiliation(s)
- Bobbi S Pritt
- Mayo Clinic, Division of Clinical Microbiology, Hilton 470-B, 200 1st St. SW, Rochester, MN 55905, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|