1
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de Hoog S, Walsh TJ, Ahmed SA, Alastruey-Izquierdo A, Alexander BD, Arendrup MC, Babady E, Bai FY, Balada-Llasat JM, Borman A, Chowdhary A, Clark A, Colgrove RC, Cornely OA, Dingle TC, Dufresne PJ, Fuller J, Gangneux JP, Gibas C, Glasgow H, Graser Y, Guillot J, Groll AH, Haase G, Hanson K, Harrington A, Hawksworth DL, Hayden RT, Hoenigl M, Hubka V, Johnson K, Kus JV, Li R, Meis JF, Lackner M, Lanternier F, Leal SM, Lee F, Lockhart SR, Luethy P, Martin I, Kwon-Chung KJ, Meyer W, Nguyen MH, Ostrosky-Zeichner L, Palavecino E, Pancholi P, Pappas PG, Procop GW, Redhead SA, Rhoads DD, Riedel S, Stevens B, Sullivan KO, Vergidis P, Roilides E, Seyedmousavi A, Tao L, Vicente VA, Vitale RG, Wang QM, Wengenack NL, Westblade L, Wiederhold N, White L, Wojewoda CM, Zhang SX. Reply to Kidd et al., "Inconsistencies within the proposed framework for stabilizing fungal nomenclature risk further confusion". J Clin Microbiol 2024; 62:e0162523. [PMID: 38441056 PMCID: PMC11005378 DOI: 10.1128/jcm.01625-23] [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] [Indexed: 03/06/2024] Open
Affiliation(s)
- Sybren de Hoog
- Radboudumc-CWZ Centre of Expertise for Mycology, Nijmegen, the Netherlands
- Foundation Atlas of Clinical Fungi, Hilversum, the Netherlands
- Department of Dermatology and Venereology, Peking University First Hospital, Beijing, China
- Department of Basic Pathology, Federal University of Paraná, Curitiba, Brazil
- Research Center for Medical Mycology, Peking University, Beijing, China
- International Society for Human and Animal Mycology (ISHAM), Working Group Nomenclature, ‘s-Hertogenbosch, the Netherlands
| | - Thomas J. Walsh
- International Society for Human and Animal Mycology (ISHAM), Working Group Nomenclature, ‘s-Hertogenbosch, the Netherlands
- Center for Innovative Therapeutics and Diagnostics, Richmond, Virginia, USA
- University of Maryland School of Medicine, Baltimore, Maryland, USA
- Nomenclature Committee for Fungi, International Mycological Association (IMA), Exeter, United Kingdom
- Fungal Diagnostics Laboratory Consortium (FDLC), Baltimore, Maryland, USA
- Mycoses Study Group, Education and Research Consortium (MSG-ERC), Pittsburgh, Pennsylvania, USA
- European Confederation of Medical Mycology (ECMM), ‘s-Hertogenbosch, the Netherlands
- Clinical and Laboratory Standards Institute (CLSI), Pittsburgh, Pennsylvania, USA
- Medical Mycological Society of the Americas (MMSA)
- ISHAM Working Group on Diagnostics, Basel, Switzerland
| | - Sarah A. Ahmed
- Radboudumc-CWZ Centre of Expertise for Mycology, Nijmegen, the Netherlands
- Foundation Atlas of Clinical Fungi, Hilversum, the Netherlands
- International Society for Human and Animal Mycology (ISHAM), Working Group Nomenclature, ‘s-Hertogenbosch, the Netherlands
| | - Ana Alastruey-Izquierdo
- International Society for Human and Animal Mycology (ISHAM), Working Group Nomenclature, ‘s-Hertogenbosch, the Netherlands
- Mycology Reference Laboratory, Spanish National Centre for Microbiology, Madrid, Spain
- Fungal Infection Study Group, European Society of Clinical Microbiology and Infectious Diseases (EFISG/ESCMID), Basel, Switzerland
| | - Barbara D. Alexander
- Fungal Diagnostics Laboratory Consortium (FDLC), Baltimore, Maryland, USA
- Medical Mycological Society of the Americas (MMSA)
- Departments of Medicine and Pathology, Duke University, Durham, North Carolina, USA
| | - Maiken Cavling Arendrup
- Department of Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark
- Department of Clinical Microbiology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Antifungal Susceptibility Testing Subcommittee of European Committee of Antimicrobial Susceptibility Testing (EUCAST-AFST)
| | - Esther Babady
- Fungal Diagnostics Laboratory Consortium (FDLC), Baltimore, Maryland, USA
- Department of Pathology and Laboratory Medicine, Clinical Microbiology Service, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Feng-Yan Bai
- Mycology Committee of Chinese Society for Microbiology, Beijing, China
- Institute of Microbiology, State Key Laboratory of Mycology, Chinese Academy of Sciences, Beijing, China
- Medical Mycology Society of Chinese Medicine and Education Association
- Asia PacificSociety for Medical Mycology
- ISHAM Working Group Veterinary Mycology and One Health, ‘s-Hertogenbosch, the Netherlands
- Mycological Society of China (MSC)
| | - Joan-Miquel Balada-Llasat
- Fungal Diagnostics Laboratory Consortium (FDLC), Baltimore, Maryland, USA
- Clinical Microbiology at The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Andrew Borman
- National Mycology Reference Laboratory, Public Health England, Bristol, United Kingdom
| | - Anuradha Chowdhary
- Fungal Infection Study Group, European Society of Clinical Microbiology and Infectious Diseases (EFISG/ESCMID), Basel, Switzerland
- Department of Microbiology, National Reference Laboratory for Antimicrobial Resistance in Fungal Pathogens, Medical Mycology Unit, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Andrew Clark
- Fungal Diagnostics Laboratory Consortium (FDLC), Baltimore, Maryland, USA
- University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Robert C. Colgrove
- Division of Infectious Diseases, Mount Auburn Hospital, Cambridge, Massachusetts, USA
- Infectious Diseases Society of America (ISDA), Arlington, Virginia, USA
| | - Oliver A. Cornely
- European Confederation of Medical Mycology (ECMM), ‘s-Hertogenbosch, the Netherlands
- Fungal Infection Study Group, European Society of Clinical Microbiology and Infectious Diseases (EFISG/ESCMID), Basel, Switzerland
- University of Cologne, Faculty of Medicine, Institute of Translational Research, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, Cologne, Germany
- Department I of Internal Medicine, University of Cologne, Excellence Center for Medical Mycology, Cologne, Germany
| | - Tanis C. Dingle
- Fungal Diagnostics Laboratory Consortium (FDLC), Baltimore, Maryland, USA
- Clinical and Laboratory Standards Institute (CLSI), Pittsburgh, Pennsylvania, USA
- Alberta Precision Laboratories, Public Health Laboratory, Calgary, Alberta, Canada
| | - Philippe J. Dufresne
- Fungal Diagnostics Laboratory Consortium (FDLC), Baltimore, Maryland, USA
- Clinical and Laboratory Standards Institute (CLSI), Pittsburgh, Pennsylvania, USA
- Department of Mycology, Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec (INSPQ), Sainte-Anne-de-Bellevue, Québec, Canada
| | - Jeff Fuller
- Fungal Diagnostics Laboratory Consortium (FDLC), Baltimore, Maryland, USA
- Department of Pathology and Laboratory Medicine, London Health Sciences Center, London, Ontario, Canada
| | - Jean-Pierre Gangneux
- European Confederation of Medical Mycology (ECMM), ‘s-Hertogenbosch, the Netherlands
- Department of Mycology, Centre Hospitalier Universitaire de Rennes, Rennes, France
| | - Connie Gibas
- University of Texas Health Science Center, San Antonio, Texas, USA
| | - Heather Glasgow
- Fungal Diagnostics Laboratory Consortium (FDLC), Baltimore, Maryland, USA
- Clinical and Laboratory Standards Institute (CLSI), Pittsburgh, Pennsylvania, USA
- Department of Pathology, Clinical and Molecular Microbiology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Yvonne Graser
- Department of Parasitology (Charité), Institute of Microbiology and Hygiene, Humboldt University, Berlin, Germany
| | - Jacques Guillot
- ISHAM Working Group Veterinary Mycology and One Health, ‘s-Hertogenbosch, the Netherlands
- Onoris, École Nationale Vétérinaire, Agroalimentaire et de l'Alimentation Nantes-Atlantique, Nantes, France
| | - Andreas H. Groll
- Fungal Infection Study Group, European Society of Clinical Microbiology and Infectious Diseases (EFISG/ESCMID), Basel, Switzerland
- Department of Pediatric Hematology and Oncology, Infectious Disease Research Program, Center for Bone Marrow Transplantation, University Children’s Hospital, Münster, Germany
| | - Gerhard Haase
- Laboratory Diagnostic Center, RWTH Aachen University Hospital, Aachen, Germany
| | - Kimberly Hanson
- Fungal Diagnostics Laboratory Consortium (FDLC), Baltimore, Maryland, USA
- University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Amanda Harrington
- Fungal Diagnostics Laboratory Consortium (FDLC), Baltimore, Maryland, USA
- Loyola University Health System, Loyola University Chicago, Maywood, Illinois, USA
| | - David L. Hawksworth
- Royal Botanic Gardens, Kew, Richmond, Surrey, United Kingdom
- Natural History Museum, London, United Kingdom
- University of Southampton, Southampton, United Kingdom
- Jilin Agricultural University, Chanchung, China
- General Committee for Nomenclature, International Botanical Congress (IBC)
- Advisory Board of International Commission on the Taxonomy of Fungi (ICTF)
| | - Randall T. Hayden
- Fungal Diagnostics Laboratory Consortium (FDLC), Baltimore, Maryland, USA
- Clinical and Laboratory Standards Institute (CLSI), Pittsburgh, Pennsylvania, USA
- Department of Pathology, Clinical and Molecular Microbiology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Martin Hoenigl
- Mycoses Study Group, Education and Research Consortium (MSG-ERC), Pittsburgh, Pennsylvania, USA
- European Confederation of Medical Mycology (ECMM), ‘s-Hertogenbosch, the Netherlands
- Division of Infectious Diseases, Medical University of Graz, Graz, Austria
- Translational Medical Mycology Research Unit, ECMM Excellence Center for Medical Mycology, Medical University of Graz, Graz, Austria
- European Hematology Association, Specialized Working Group for Infections in Hematology, The Hague, the Netherlands
| | - Vit Hubka
- Department of Botany, Charles University, Prague, Czechia
| | - Kristie Johnson
- Fungal Diagnostics Laboratory Consortium (FDLC), Baltimore, Maryland, USA
- Clinical Microbiology Laboratory, UMMC Laboratories of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Julianne V. Kus
- Fungal Diagnostics Laboratory Consortium (FDLC), Baltimore, Maryland, USA
- Public Health Ontario, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, Canada and University of Toronto, Toronto, Ontario, Canada
| | - Ruoyu Li
- Department of Dermatology and Venereology, Peking University First Hospital, Beijing, China
- Research Center for Medical Mycology, Peking University, Beijing, China
- ISHAM Working Group on Diagnostics, Basel, Switzerland
- Fungal Infection Study Group, European Society of Clinical Microbiology and Infectious Diseases (EFISG/ESCMID), Basel, Switzerland
- Antifungal Susceptibility Testing Subcommittee of European Committee of Antimicrobial Susceptibility Testing (EUCAST-AFST)
- Medical Mycology Society of Chinese Medicine and Education Association
| | - Jacques F. Meis
- Radboudumc-CWZ Centre of Expertise for Mycology, Nijmegen, the Netherlands
- ISHAM Working Group on Diagnostics, Basel, Switzerland
- University of Cologne, Faculty of Medicine, Institute of Translational Research, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, Cologne, Germany
- Department I of Internal Medicine, University of Cologne, Excellence Center for Medical Mycology, Cologne, Germany
| | - Michaela Lackner
- International Society for Human and Animal Mycology (ISHAM), Working Group Nomenclature, ‘s-Hertogenbosch, the Netherlands
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Sixto M. Leal
- Fungal Diagnostics Laboratory Consortium (FDLC), Baltimore, Maryland, USA
- Mycoses Study Group, Education and Research Consortium (MSG-ERC), Pittsburgh, Pennsylvania, USA
- Clinical and Laboratory Standards Institute (CLSI), Pittsburgh, Pennsylvania, USA
- University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Francesca Lee
- Fungal Diagnostics Laboratory Consortium (FDLC), Baltimore, Maryland, USA
- University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Shawn R. Lockhart
- Radboudumc-CWZ Centre of Expertise for Mycology, Nijmegen, the Netherlands
- Fungal Diagnostics Laboratory Consortium (FDLC), Baltimore, Maryland, USA
- European Hematology Association, Specialized Working Group for Infections in Hematology, The Hague, the Netherlands
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Paul Luethy
- Fungal Diagnostics Laboratory Consortium (FDLC), Baltimore, Maryland, USA
- Clinical Microbiology Laboratory, UMMC Laboratories of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Isabella Martin
- Fungal Diagnostics Laboratory Consortium (FDLC), Baltimore, Maryland, USA
- Dartmouth Health, Lebanon, New Hampshire, USA
| | - Kyung J. Kwon-Chung
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Wieland Meyer
- Nomenclature Committee for Fungi, International Mycological Association (IMA), Exeter, United Kingdom
- Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands
| | - M. Hong Nguyen
- Fungal Diagnostics Laboratory Consortium (FDLC), Baltimore, Maryland, USA
- Mycoses Study Group, Education and Research Consortium (MSG-ERC), Pittsburgh, Pennsylvania, USA
- Medical Mycological Society of the Americas (MMSA)
- University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Luis Ostrosky-Zeichner
- Mycoses Study Group, Education and Research Consortium (MSG-ERC), Pittsburgh, Pennsylvania, USA
- University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Elizabeth Palavecino
- Fungal Diagnostics Laboratory Consortium (FDLC), Baltimore, Maryland, USA
- Clinical Microbiology Laboratory, Wake Forest Baptist Medical Center, Winston-Salem, North Carolina, USA
| | - Preeti Pancholi
- Fungal Diagnostics Laboratory Consortium (FDLC), Baltimore, Maryland, USA
- Clinical Microbiology at The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Peter G. Pappas
- Fungal Diagnostics Laboratory Consortium (FDLC), Baltimore, Maryland, USA
- Mycoses Study Group, Education and Research Consortium (MSG-ERC), Pittsburgh, Pennsylvania, USA
- University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Gary W. Procop
- Fungal Diagnostics Laboratory Consortium (FDLC), Baltimore, Maryland, USA
- Clinical and Laboratory Standards Institute (CLSI), Pittsburgh, Pennsylvania, USA
- The American Board of Pathology, Tampa, Florida, USA
- American Board of Pathology (ABP), Chicago, Illinois, USA
| | - Scott A. Redhead
- Nomenclature Committee for Fungi, International Mycological Association (IMA), Exeter, United Kingdom
- National Mycological Herbarium, Ottawa Research and Development Centre, Science and Technology Branch, Agriculture & Agri-Food Canada, Ottawa, Ontario, Canada
| | - Daniel D. Rhoads
- Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio, USA
- Infection Biology Program, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Stefan Riedel
- Fungal Diagnostics Laboratory Consortium (FDLC), Baltimore, Maryland, USA
- Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Bryan Stevens
- Fungal Diagnostics Laboratory Consortium (FDLC), Baltimore, Maryland, USA
- University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Kaede Ota Sullivan
- Fungal Diagnostics Laboratory Consortium (FDLC), Baltimore, Maryland, USA
- Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania, USA
| | - Paschalis Vergidis
- Fungal Diagnostics Laboratory Consortium (FDLC), Baltimore, Maryland, USA
- Mayo Clinic, Rochester, Minnesota, USA
| | - Emmanuel Roilides
- International Society for Human and Animal Mycology (ISHAM), Working Group Nomenclature, ‘s-Hertogenbosch, the Netherlands
- European Confederation of Medical Mycology (ECMM), ‘s-Hertogenbosch, the Netherlands
- Fungal Infection Study Group, European Society of Clinical Microbiology and Infectious Diseases (EFISG/ESCMID), Basel, Switzerland
- Hippokration Hospital, Thessaloniki, Greece
| | - Amir Seyedmousavi
- Fungal Diagnostics Laboratory Consortium (FDLC), Baltimore, Maryland, USA
- Fungal Infection Study Group, European Society of Clinical Microbiology and Infectious Diseases (EFISG/ESCMID), Basel, Switzerland
- ISHAM Working Group Veterinary Mycology and One Health, ‘s-Hertogenbosch, the Netherlands
- Department of Laboratory Medicine, Microbiology Service, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Lili Tao
- Fungal Diagnostics Laboratory Consortium (FDLC), Baltimore, Maryland, USA
- Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Vania A. Vicente
- Department of Basic Pathology, Federal University of Paraná, Curitiba, Brazil
| | - Roxana G. Vitale
- Consejo Nacional de Investigaciones Científicasy Tecnológicas (CONICET), Buenos Aires, Argentina
- Unidad de Parasitología, Sector Micología, Hospital J.M. Ramos Mejía, Buenos Aires, Argentina
| | - Qi-Ming Wang
- Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Nancy L. Wengenack
- Fungal Diagnostics Laboratory Consortium (FDLC), Baltimore, Maryland, USA
- Mayo Clinic, Rochester, Minnesota, USA
| | - Lars Westblade
- Fungal Diagnostics Laboratory Consortium (FDLC), Baltimore, Maryland, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Nathan Wiederhold
- Fungal Diagnostics Laboratory Consortium (FDLC), Baltimore, Maryland, USA
- Mycoses Study Group, Education and Research Consortium (MSG-ERC), Pittsburgh, Pennsylvania, USA
- Clinical and Laboratory Standards Institute (CLSI), Pittsburgh, Pennsylvania, USA
- Medical Mycological Society of the Americas (MMSA)
- University of Texas Health Science Center, San Antonio, Texas, USA
| | - Lewis White
- Public Health Wales Microbiology, Cardiff, United Kingdom
| | - Christina M. Wojewoda
- Department of Pathology and Laboratory Medicine, University of Vermont Medical Center, Burlington, Vermont, USA
| | - Sean X. Zhang
- International Society for Human and Animal Mycology (ISHAM), Working Group Nomenclature, ‘s-Hertogenbosch, the Netherlands
- Fungal Diagnostics Laboratory Consortium (FDLC), Baltimore, Maryland, USA
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Mettler SK, Charoenngam N, Jaroenlapnopparat A, Ramon HG, Alhariri H, Okoli U, Philips BB, Behlau I, Colgrove RC. Authors' Reply: Trend Analysis Shows There May Be Other Drivers Of The Endocarditis Epidemic in Addition to Intravenous Drug Use. Am J Cardiol 2024; 211:380. [PMID: 38008346 DOI: 10.1016/j.amjcard.2023.11.047] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 11/16/2023] [Indexed: 11/28/2023]
Affiliation(s)
- Sofia K Mettler
- Faculty of Medicine, University of Zurich, Zurich, Switzerland; Department of Medicine, Mount Auburn Hospital, Harvard Medical School, Cambridge, Massachusetts.
| | - Nipith Charoenngam
- Department of Medicine, Mount Auburn Hospital, Harvard Medical School, Cambridge, Massachusetts; Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | | | - Hendrik G Ramon
- Department of Medicine, Mount Auburn Hospital, Harvard Medical School, Cambridge, Massachusetts
| | - Housam Alhariri
- Department of Medicine, Mount Auburn Hospital, Harvard Medical School, Cambridge, Massachusetts
| | - Unoma Okoli
- Department of Medicine, Mount Auburn Hospital, Harvard Medical School, Cambridge, Massachusetts
| | - Binu B Philips
- Department of Medicine, Mount Auburn Hospital, Harvard Medical School, Cambridge, Massachusetts
| | - Irmgard Behlau
- Department of Medicine, Mount Auburn Hospital, Harvard Medical School, Cambridge, Massachusetts
| | - Robert C Colgrove
- Department of Medicine, Mount Auburn Hospital, Harvard Medical School, Cambridge, Massachusetts
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de Hoog S, Walsh TJ, Ahmed SA, Alastruey-Izquierdo A, Alexander BD, Arendrup MC, Babady E, Bai FY, Balada-Llasat JM, Borman A, Chowdhary A, Clark A, Colgrove RC, Cornely OA, Dingle TC, Dufresne PJ, Fuller J, Gangneux JP, Gibas C, Glasgow H, Gräser Y, Guillot J, Groll AH, Haase G, Hanson K, Harrington A, Hawksworth DL, Hayden RT, Hoenigl M, Hubka V, Johnson K, Kus JV, Li R, Meis JF, Lackner M, Lanternier F, Leal Jr. SM, Lee F, Lockhart SR, Luethy P, Martin I, Kwon-Chung KJ, Meyer W, Nguyen MH, Ostrosky-Zeichner L, Palavecino E, Pancholi P, Pappas PG, Procop GW, Redhead SA, Rhoads DD, Riedel S, Stevens B, Sullivan KO, Vergidis P, Roilides E, Seyedmousavi A, Tao L, Vicente VA, Vitale RG, Wang QM, Wengenack NL, Westblade L, Wiederhold N, White L, Wojewoda CM, Zhang SX. A conceptual framework for nomenclatural stability and validity of medically important fungi: a proposed global consensus guideline for fungal name changes supported by ABP, ASM, CLSI, ECMM, ESCMID-EFISG, EUCAST-AFST, FDLC, IDSA, ISHAM, MMSA, and MSGERC. J Clin Microbiol 2023; 61:e0087323. [PMID: 37882528 PMCID: PMC10662369 DOI: 10.1128/jcm.00873-23] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2023] Open
Abstract
The rapid pace of name changes of medically important fungi is creating challenges for clinical laboratories and clinicians involved in patient care. We describe two sources of name change which have different drivers, at the species versus the genus level. Some suggestions are made here to reduce the number of name changes. We urge taxonomists to provide diagnostic markers of taxonomic novelties. Given the instability of phylogenetic trees due to variable taxon sampling, we advocate to maintain genera at the largest possible size. Reporting of identified species in complexes or series should where possible comprise both the name of the overarching species and that of the molecular sibling, often cryptic species. Because the use of different names for the same species will be unavoidable for many years to come, an open access online database of the names of all medically important fungi, with proper nomenclatural designation and synonymy, is essential. We further recommend that while taxonomic discovery continues, the adaptation of new name changes by clinical laboratories and clinicians be reviewed routinely by a standing committee for validation and stability over time, with reference to an open access database, wherein reasons for changes are listed in a transparent way.
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Affiliation(s)
- Sybren de Hoog
- Radboudumc-CWZ Centre of Expertise for Mycology, Nijmegen, the Netherlands
- Foundation Atlas of Clinical Fungi, Hilversum, the Netherlands
- Department of Dermatology and Venereology, Peking University First Hospital, Beijing, China
- Department of Basic Pathology, Federal University of Paraná, Curitiba, Brazil
- Research Center for Medical Mycology, Peking University, Beijing, China
- International Society for Human and Animal Mycology (ISHAM), Working Group Nomenclature
| | - Thomas J. Walsh
- International Society for Human and Animal Mycology (ISHAM), Working Group Nomenclature
- Center for Innovative Therapeutics and Diagnostics, Richmond, Virginia, USA
- University of Maryland School of Medicine, Baltimore, Maryland, USA
- Nomenclature Committee for Fungi, International Mycological Association (IMA)
- Fungal Diagnostics Laboratory Consortium (FDLC)
- Mycoses Study Group, Education and Research Consortium (MSG-ERC)
- European Confederation of Medical Mycology (ECMM)
- Clinical and Laboratory Standards Institute (CLSI)
- Medical Mycological Society of the Americas (MMSA)
- ISHAM Working Group on Diagnostics
| | - Sarah A. Ahmed
- Radboudumc-CWZ Centre of Expertise for Mycology, Nijmegen, the Netherlands
- Foundation Atlas of Clinical Fungi, Hilversum, the Netherlands
- International Society for Human and Animal Mycology (ISHAM), Working Group Nomenclature
| | - Ana Alastruey-Izquierdo
- International Society for Human and Animal Mycology (ISHAM), Working Group Nomenclature
- Mycology Reference Laboratory, Spanish National Centre for Microbiology, Madrid, Spain
- Fungal Infection Study Group, European Society of Clinical Microbiology and Infectious Diseases (EFISG/ESCMID), Basel, Switzerland
| | - Barbara D. Alexander
- Fungal Diagnostics Laboratory Consortium (FDLC)
- Departments of Medicine and Pathology, Duke University, Durham, North Carolina, USA
| | - Maiken Cavling Arendrup
- Department of Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark; Department of Clinical Microbiology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Antifungal Susceptibility Testing Subcommittee of European Committee of Antimicrobial Susceptibility Testing (EUCAST-AFST)
| | - Esther Babady
- Fungal Diagnostics Laboratory Consortium (FDLC)
- Clinical Microbiology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Feng-Yan Bai
- Mycology Committee of Chinese Society for Microbiology
- Institute of Microbiology, State Key Laboratory of Mycology, Chinese Academy of Sciences, Beijing, China
- Medical Mycology Society of Chinese Medicine and Education Association
- Asia Pacific Society for Medical Mycology
- ISHAM Working Group Veterinary Mycology and One Health
- Mycological Society of China (MSC)
| | - Joan-Miquel Balada-Llasat
- Fungal Diagnostics Laboratory Consortium (FDLC)
- Clinical Microbiology at The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Andrew Borman
- National Mycology Reference Laboratory, Public Health England, Bristol, United Kingdom
| | - Anuradha Chowdhary
- Fungal Infection Study Group, European Society of Clinical Microbiology and Infectious Diseases (EFISG/ESCMID), Basel, Switzerland
- Department of Microbiology, National Reference Laboratory for Antimicrobial Resistance in Fungal Pathogens, Medical Mycology Unit, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Andrew Clark
- Fungal Diagnostics Laboratory Consortium (FDLC)
- University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Robert C. Colgrove
- Division of Infectious Diseases, Mount Auburn Hospital, Cambridge, Massachusetts, USA
- Infectious Diseases Society of America (ISDA)
| | - Oliver A. Cornely
- European Confederation of Medical Mycology (ECMM)
- Fungal Infection Study Group, European Society of Clinical Microbiology and Infectious Diseases (EFISG/ESCMID), Basel, Switzerland
- University of Cologne, Faculty of Medicine, Institute of Translational Research, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, Cologne, Germany
- Department I of Internal Medicine, University of Cologne, Excellence Center for Medical Mycology, Cologne, Germany
| | - Tanis C. Dingle
- Fungal Diagnostics Laboratory Consortium (FDLC)
- Clinical and Laboratory Standards Institute (CLSI)
- Alberta Precision Laboratories, Public Health Laboratory, Calgary, Alberta, Canada
| | - Philippe J. Dufresne
- Fungal Diagnostics Laboratory Consortium (FDLC)
- Clinical and Laboratory Standards Institute (CLSI)
- Mycology Department, Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec (INSPQ), Sainte-Anne-de-Bellevue, Québec, Canada
| | - Jeff Fuller
- Fungal Diagnostics Laboratory Consortium (FDLC)
- Department of Pathology and Laboratory Medicine, London Health Sciences Center, London, Ontario, Canada
| | - Jean-Pierre Gangneux
- European Confederation of Medical Mycology (ECMM)
- Department of Mycology, Centre Hospitalier Universitaire de Rennes, Rennes, France
| | - Connie Gibas
- University of Texas Health Science Center, San Antonio, Texas, USA
| | - Heather Glasgow
- Fungal Diagnostics Laboratory Consortium (FDLC)
- Clinical and Molecular Microbiology, Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Yvonne Gräser
- Department of Parasitology (Charité), Institute of Microbiology and Hygiene, Humboldt University, Berlin, Germany
| | - Jacques Guillot
- ISHAM Working Group Veterinary Mycology and One Health
- Onoris, École Nationale Vétérinaire, Agroalimentaire et de l'Alimentation Nantes-Atlantique, Nantes, France
| | - Andreas H. Groll
- Fungal Infection Study Group, European Society of Clinical Microbiology and Infectious Diseases (EFISG/ESCMID), Basel, Switzerland
- Infectious Disease Research Program, Department of Pediatric Hematology and Oncology and Center for Bone Marrow Transplantation, University Children’s Hospital, Münster, Germany
| | - Gerhard Haase
- Laboratory Diagnostic Center, RWTH Aachen University Hospital, Aachen, Germany
| | - Kimberly Hanson
- Fungal Diagnostics Laboratory Consortium (FDLC)
- University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Amanda Harrington
- Fungal Diagnostics Laboratory Consortium (FDLC)
- Loyola University Health System, Loyola University Chicago, Maywood, Illinois, USA
| | - David L. Hawksworth
- Royal Botanic Gardens, Kew, Richmond, Surrey, United Kingdom
- Natural History Museum, London, United Kingdom
- University of Southampton, Southampton, United Kingdom
- Jilin Agricultural University, Chanchung, China
- General Committee for Nomenclature, International Botanical Congress (IBC)
- Advisory Board of International Commission on the Taxonomy of Fungi (ICTF)
| | - Randall T. Hayden
- Fungal Diagnostics Laboratory Consortium (FDLC)
- Clinical and Laboratory Standards Institute (CLSI)
- Clinical and Molecular Microbiology, Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Martin Hoenigl
- Mycoses Study Group, Education and Research Consortium (MSG-ERC)
- European Confederation of Medical Mycology (ECMM)
- Division of Infectious Diseases, Medical University of Graz, Graz, Austria
- Translational Medical Mycology Research Unit, ECMM Excellence Center for Medical Mycology, Medical University of Graz, Graz, Austria
- European Hematology Association, Specialized Working Group for Infections in Hematology, The Hague, the Netherlands
| | - Vit Hubka
- Department of Botany, Charles University, Prague, Czechia
| | - Kristie Johnson
- Fungal Diagnostics Laboratory Consortium (FDLC)
- Clinical Microbiology Laboratory, UMMC Laboratories of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Julianne V. Kus
- Fungal Diagnostics Laboratory Consortium (FDLC)
- Public Health Ontario, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, Canada and University of Toronto, Toronto, Ontario, Canada
| | - Ruoyu Li
- Department of Dermatology and Venereology, Peking University First Hospital, Beijing, China
- Research Center for Medical Mycology, Peking University, Beijing, China
- ISHAM Working Group on Diagnostics
- Fungal Infection Study Group, European Society of Clinical Microbiology and Infectious Diseases (EFISG/ESCMID), Basel, Switzerland
- Antifungal Susceptibility Testing Subcommittee of European Committee of Antimicrobial Susceptibility Testing (EUCAST-AFST)
- Medical Mycology Society of Chinese Medicine and Education Association
| | - Jacques F. Meis
- Radboudumc-CWZ Centre of Expertise for Mycology, Nijmegen, the Netherlands
- ISHAM Working Group on Diagnostics
- University of Cologne, Faculty of Medicine, Institute of Translational Research, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, Cologne, Germany
- Department I of Internal Medicine, University of Cologne, Excellence Center for Medical Mycology, Cologne, Germany
| | - Michaela Lackner
- International Society for Human and Animal Mycology (ISHAM), Working Group Nomenclature
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Sixto M. Leal Jr.
- Fungal Diagnostics Laboratory Consortium (FDLC)
- Mycoses Study Group, Education and Research Consortium (MSG-ERC)
- Clinical and Laboratory Standards Institute (CLSI)
- University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Francesca Lee
- Fungal Diagnostics Laboratory Consortium (FDLC)
- University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Shawn R. Lockhart
- Fungal Diagnostics Laboratory Consortium (FDLC)
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Paul Luethy
- Fungal Diagnostics Laboratory Consortium (FDLC)
- Clinical Microbiology Laboratory, UMMC Laboratories of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Isabella Martin
- Fungal Diagnostics Laboratory Consortium (FDLC)
- Dartmouth Health, Lebanon, New Hampshire, USA
| | - Kyung J. Kwon-Chung
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Wieland Meyer
- Nomenclature Committee for Fungi, International Mycological Association (IMA)
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - M. Hong Nguyen
- Fungal Diagnostics Laboratory Consortium (FDLC)
- Mycoses Study Group, Education and Research Consortium (MSG-ERC)
- Medical Mycological Society of the Americas (MMSA)
- University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Luis Ostrosky-Zeichner
- Mycoses Study Group, Education and Research Consortium (MSG-ERC)
- University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Elizabeth Palavecino
- Fungal Diagnostics Laboratory Consortium (FDLC)
- Clinical Microbiology Laboratory, Wake Forest Baptist Medical Center, Winston-Salem, North Carolina, USA
| | - Preeti Pancholi
- Fungal Diagnostics Laboratory Consortium (FDLC)
- Clinical Microbiology at The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Peter G. Pappas
- Mycoses Study Group, Education and Research Consortium (MSG-ERC)
- University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Gary W. Procop
- Fungal Diagnostics Laboratory Consortium (FDLC)
- Clinical and Laboratory Standards Institute (CLSI)
- The American Board of Pathology, Tampa, Florida, USA
- American Board of Pathology (ABP)
| | - Scott A. Redhead
- Nomenclature Committee for Fungi, International Mycological Association (IMA)
- National Mycological Herbarium, Ottawa Research and Development Centre, Science and Technology Branch, Agriculture & Agri-Food Canada, Ottawa, Ontario, Canada
| | - Daniel D. Rhoads
- Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio, USA
- Infection Biology Program, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Stefan Riedel
- Fungal Diagnostics Laboratory Consortium (FDLC)
- Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Bryan Stevens
- Fungal Diagnostics Laboratory Consortium (FDLC)
- University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Kaede Ota Sullivan
- Fungal Diagnostics Laboratory Consortium (FDLC)
- Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania, USA
| | - Paschalis Vergidis
- Fungal Diagnostics Laboratory Consortium (FDLC)
- Mayo Clinic, Rochester, Minnesota, USA
| | - Emmanuel Roilides
- International Society for Human and Animal Mycology (ISHAM), Working Group Nomenclature
- European Confederation of Medical Mycology (ECMM)
- Fungal Infection Study Group, European Society of Clinical Microbiology and Infectious Diseases (EFISG/ESCMID), Basel, Switzerland
- Hippokration Hospital, Thessaloniki, Greece
| | - Amir Seyedmousavi
- Fungal Diagnostics Laboratory Consortium (FDLC)
- Fungal Infection Study Group, European Society of Clinical Microbiology and Infectious Diseases (EFISG/ESCMID), Basel, Switzerland
- ISHAM Working Group Veterinary Mycology and One Health
- Microbiology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Lili Tao
- Fungal Diagnostics Laboratory Consortium (FDLC)
- Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Vania A. Vicente
- Department of Basic Pathology, Federal University of Paraná, Curitiba, Brazil
| | - Roxana G. Vitale
- Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina
- Unidad de Parasitología, Sector Micología, Hospital J.M. Ramos Mejía, Buenos Aires, Argentina
| | - Qi-Ming Wang
- Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Nancy L. Wengenack
- Fungal Diagnostics Laboratory Consortium (FDLC)
- Mayo Clinic, Rochester, Minnesota, USA
| | - Lars Westblade
- Fungal Diagnostics Laboratory Consortium (FDLC)
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, USA
| | - Nathan Wiederhold
- Fungal Diagnostics Laboratory Consortium (FDLC)
- Mycoses Study Group, Education and Research Consortium (MSG-ERC)
- Clinical and Laboratory Standards Institute (CLSI)
- Medical Mycological Society of the Americas (MMSA)
- University of Texas Health Science Center, San Antonio, Texas, USA
| | - Lewis White
- Public Health Wales Microbiology, Cardiff, United Kingdom
| | - Christina M. Wojewoda
- Department of Pathology and Laboratory Medicine, University of Vermont Medical Center, Burlington, Vermont, USA
| | - Sean X. Zhang
- International Society for Human and Animal Mycology (ISHAM), Working Group Nomenclature
- Fungal Diagnostics Laboratory Consortium (FDLC)
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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4
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Mettler SK, Alhariri H, Okoli U, Charoenngam N, Guillen RH, Jaroenlapnopparat A, Philips BB, Behlau I, Colgrove RC. Gender, Age, and Regional Disparities in the Incidence and Mortality Trends of Infective Endocarditis in the United States Between 1990 and 2019. Am J Cardiol 2023; 203:128-135. [PMID: 37494864 DOI: 10.1016/j.amjcard.2023.07.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 02/26/2023] [Revised: 07/01/2023] [Accepted: 07/06/2023] [Indexed: 07/28/2023]
Abstract
The incidence of infective endocarditis (IE) has increased globally in the past decades, including in the United States. However, little is known about the differences in trends across states, gender, and age groups within the United States. Using the Global Burden of Disease database, we analyzed the incidence and mortality trends of IE in the United States between 1990 and 2019 using Joinpoint regression analyses, and compared between states, gender, and age groups. The age-standardized incidence rate (ASIR) of IE in the United States increased from 10.2/100,000 population in 1990 to 14.4 in 2019. The increase in ASIR was greater among men than women (45.8% vs 34.1%). The incidence increase was driven by 55+ year-olds (112.7% increase), with rapid increases in the 1990s and early 2000s, followed by a plateau around the mid-2000s. In contrast, the incidence among 5-to-19-year-olds decreased by -36.6% over the 30-year period. The incidence increased among all age groups in the last 5 years of observation (2015 to 2019), with the largest increase in 5-to-19-year-olds (3.3% yearly). The 30-year increase in ASIR was greatest in Utah (66.2%) and smallest in California (30.2%). The overall age-standardized mortality attributable to IE increased in the United States by 126% between 1990 and 2019 versus 19.6% globally. In conclusion, although the overall incidence and mortality of IE increased over the past 30 years in the United States, there are significant differences between regions, gender, and age groups. These findings indicate unevenly distributed disease burden of IE across the nation.
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Affiliation(s)
- Sofia K Mettler
- Faculty of Medicine, University of Zurich, Zurich, Switzerland; Department of Medicine, Mount Auburn Hospital, Harvard Medical School, Cambridge, Massachusetts.
| | - Housam Alhariri
- Department of Medicine, Mount Auburn Hospital, Harvard Medical School, Cambridge, Massachusetts
| | - Unoma Okoli
- Department of Medicine, Mount Auburn Hospital, Harvard Medical School, Cambridge, Massachusetts
| | - Nipith Charoenngam
- Department of Medicine, Mount Auburn Hospital, Harvard Medical School, Cambridge, Massachusetts; Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Ramon H Guillen
- Department of Medicine, Mount Auburn Hospital, Harvard Medical School, Cambridge, Massachusetts
| | | | - Binu B Philips
- Department of Medicine, Mount Auburn Hospital, Harvard Medical School, Cambridge, Massachusetts
| | - Irmgard Behlau
- Department of Medicine, Mount Auburn Hospital, Harvard Medical School, Cambridge, Massachusetts
| | - Robert C Colgrove
- Department of Medicine, Mount Auburn Hospital, Harvard Medical School, Cambridge, Massachusetts
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5
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Huete-Pérez JA, Colgrove RC, Cabezas-Robelo C, Páiz-Medina L, Hunsajarupan B, Silva S, Quant C, Huete A. SARS-CoV-2 prevalence at eight urban health clinics in Nicaragua: possible implications for the COVID-19 pandemic. IJID Regions 2022; 2:110-117. [PMID: 35721440 PMCID: PMC8730803 DOI: 10.1016/j.ijregi.2021.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 12/22/2021] [Accepted: 12/26/2021] [Indexed: 11/23/2022]
Abstract
In Nicaragua, data regarding coronavirus disease 2019 testing and mortality are severely limited. This study assessed the prevalence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in selected urban health clinics. The prevalence rates of current SARS-CoV-2 infection and seropositivity were fairly high. More than half of the sample population had evidence of current or past infection. This previously unknown infection data is increasingly important for policy makers.
Objective To assess the prevalence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in selected health clinics in the three largest urban areas in Nicaragua, where data regarding coronavirus disease 2019 (COVID-19) testing, morbidity and mortality is severely limited. Methods In this cross-sectional study, participants were tested for SARS-CoV-2 RNA by loop-mediated isothermal amplification (LAMP), and were tested for antibodies using immunoassays. A questionnaire recorded subjects’ COVID-19-associated symptoms and risk factors. Data were collected from 22 February to 19 March 2021, 1 year after the first confirmed cases of SARS-CoV-2 in Nicaragua. Study participants were enrolled while attending routine check-ups or seeking care unrelated to COVID-19. Study participation was random and voluntary. All patients were eligible to participate. Symptom history was not part of the eligibility criteria. Results The prevalence of current SARS-CoV-2 infection was high (14%, LAMP-positive/seronegative). Antibody testing showed higher overall seroprevalence (38%). Cough was the symptom most strongly associated with being LAMP-positive (odds ratio 3.57, 95% confidence interval 2.65–4.81). Loss of smell had the highest positive predictive value, and was significantly associated with being LAMP-positive. Conclusion The prevalence of current SARS-CoV-2 infection and seropositivity were fairly high. More than half of the sample population had evidence of current or past infection. Knowledge of this previously unknown elevated level of infection is crucial for healthcare providers and policy makers.
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Affiliation(s)
- Jorge A. Huete-Pérez
- Molecular Biology Center, University of Central America, Managua, Nicaragua
- Corresponding author. Address: Molecular Biology Center, University of Central America, UCA, Rotonda R. Darío 150 mts Oeste, Managua, Nicaragua.
| | - Robert C. Colgrove
- Division of Infectious Diseases, Mount Auburn Hospital, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | | | - Lucía Páiz-Medina
- Molecular Biology Center, University of Central America, Managua, Nicaragua
| | - Bhanasut Hunsajarupan
- Department of Global Health and Population, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | | | | | - Alejandra Huete
- Division of Infectious Diseases, Mount Auburn Hospital, Cambridge, MA, USA
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6
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Greninger AL, Dien Bard J, Colgrove RC, Graf EH, Hanson KE, Hayden MK, Humphries RM, Lowe CF, Miller MB, Pillai DR, Rhoads DD, Yao JD, Lee FM. Clinical and Infection Prevention Applications of SARS-CoV-2 Genotyping: An IDSA/ASM Consensus Review Document. Clin Infect Dis 2021; 74:1496-1502. [PMID: 34731234 PMCID: PMC8689887 DOI: 10.1093/cid/ciab761] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Indexed: 11/12/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged into a world of maturing pathogen genomics, with >2 million genomes sequenced at this writing. The rise of more transmissible variants of concern that affect vaccine and therapeutic effectiveness has led to widespread interest in SARS-CoV-2 evolution. Clinicians are also eager to take advantage of the information provided by SARS-CoV-2 genotyping beyond surveillance purposes. Here, we review the potential role of SARS-CoV-2 genotyping in clinical care. The review covers clinical use cases for SARS-CoV-2 genotyping, methods of SARS-CoV-2 genotyping, assay validation and regulatory requirements, clinical reporting for laboratories, and emerging issues in clinical SARS-CoV-2 sequencing. While clinical uses of SARS-CoV-2 genotyping are currently limited, rapid technological change along with a growing ability to interpret variants in real time foretell a growing role for SARS-CoV-2 genotyping in clinical care as continuing data emerge on vaccine and therapeutic efficacy.
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Affiliation(s)
- Alexander L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Jennifer Dien Bard
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA; Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Robert C Colgrove
- Division of Infectious Diseases, Mount Auburn Hospital, Harvard School of Medicine
| | - Erin H Graf
- Department of Laboratory Medicine and Pathology, Mayo Clinic Arizona, USA
| | - Kimberly E Hanson
- Department of Internal Medicine and Pathology, University of Utah, Salt Lake City, UT, USA
| | - Mary K Hayden
- Division of Infectious Diseases, Department of Medicine and Division of Laboratory Medicine, Department of Pathology, Rush University Medical Center, Chicago, Illinois, USA
| | - Romney M Humphries
- Division of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Christopher F Lowe
- Division of Medical Microbiology and Virology, Providence Health Care, Vancouver, BC, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Melissa B Miller
- Clinical Microbiology Laboratory, University of North Carolina Hospitals and Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Dylan R Pillai
- Department of Pathology and Laboratory Medicine and Microbiology & Infectious Diseases, University of Calgary, Alberta, Canada
| | - Daniel D Rhoads
- Department of Laboratory Medicine, Cleveland Clinic, Cleveland, OH, USA
| | - Joseph D Yao
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Francesca M Lee
- Division of Infectious Diseases and Geographic Medicine, Department of Pathology and Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
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7
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Humphries RM, Azar MM, Caliendo AM, Chou A, Colgrove RC, Fabre V, Ginocchio CC, Hanson KE, Hayden MK, Pillai DR, Pollock NR, Lee FM. To Test, Perchance to Diagnose: Practical Strategies for Severe Acute Respiratory Syndrome Coronavirus 2 Testing. Open Forum Infect Dis 2021; 8:ofab095. [PMID: 33880392 PMCID: PMC7989172 DOI: 10.1093/ofid/ofab095] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 02/26/2021] [Indexed: 01/08/2023] Open
Abstract
Testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in symptomatic and asymptomatic patients is an important component of the multifaceted approach of managing the coronavirus disease 2019 pandemic. Determining how to best define testing strategies for different populations and incorporating these into broader infection prevention programs can be complex. Many circumstances are not addressed by federal, local, or professional guidelines. This commentary describes various scenarios in which testing of symptomatic or asymptomatic individuals for SARS-CoV-2 virus (antigen or ribonucleic acid) can be of potential benefit. Consideration to pretest probability, risks of testing (impact of false-positive or false-negative results), testing strategy, as well as action based on test results are explored. Testing, regardless of setting, must be incorporated into overarching infection control plans, which include use of personal protective equipment (eg, masks), physically distancing, and isolation when exposure is suspected.
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Affiliation(s)
| | - Marwan M Azar
- Section of Infectious Diseases, Yale School of Medicine, New Haven, Connecticut, USA
| | - Angela M Caliendo
- Department of Medicine, Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
| | - Andrew Chou
- Michael E. DeBakey VA Medical Center, Baylor College of Medicine, Houston, Texas, USA
| | - Robert C Colgrove
- Division of Infectious Diseases, Mount Auburn Hospital, Harvard School of Medicine, Boston, Massachusetts, USA
| | - Valeria Fabre
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Kimberly E Hanson
- Division of Infectious Diseases, Department of Medicine, University of Utah School of Medicine, Salt Lake City, Utah, USA.,Section of Clinical Microbiology, Department of Pathology, University of Utah and ARUP Laboratories, Salt Lake City, Utah, USA
| | - Mary K Hayden
- Division of Infectious Diseases, Department of Medicine, Rush University Medical Center, Chicago, Illinois, USA.,Department of Pathology, Rush University Medical Center, Chicago, Illinois, USA
| | - Dylan R Pillai
- Departments of Pathology, Medicine, and Microbiology, Immunology, and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Nira R Pollock
- Department of Laboratory Medicine, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Francesca M Lee
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Division of Infectious Diseases and Geographic Medicine, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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8
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Hanson KE, Azar MM, Banerjee R, Chou A, Colgrove RC, Ginocchio CC, Hayden MK, Holodiny M, Jain S, Koo S, Levy J, Timbrook TT, Caliendo AM. Molecular Testing for Acute Respiratory Tract Infections: Clinical and Diagnostic Recommendations From the IDSA's Diagnostics Committee. Clin Infect Dis 2020; 71:2744-2751. [PMID: 32369578 PMCID: PMC7454374 DOI: 10.1093/cid/ciaa508] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 04/30/2020] [Indexed: 01/08/2023] Open
Abstract
The clinical signs and symptoms of acute respiratory tract infections (RTIs) are not pathogen specific. Highly sensitive and specific nucleic acid amplification tests have become the diagnostic reference standard for viruses, and translation of bacterial assays from basic research to routine clinical practice represents an exciting advance in respiratory medicine. Most recently, molecular diagnostics have played an essential role in the global health response to the novel coronavirus pandemic. How best to use newer molecular tests for RTI in combination with clinical judgment and traditional methods can be bewildering given the plethora of available assays and rapidly evolving technologies. Here, we summarize the current state of the art with respect to the diagnosis of viral and bacterial RTIs, provide a practical framework for diagnostic decision making using selected patient-centered vignettes, and make recommendations for future studies to advance the field.
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Affiliation(s)
- Kimberly E Hanson
- Division of Infectious Diseases, Department of Medicine, University of Utah School of Medicine, Salt Lake City, Utah, USA
- Section of Clinical Microbiology, Department of Pathology, University of Utah and ARUP Laboratories, Salt Lake City, Utah, USA
| | - Marwan M Azar
- Department of Medicine, Section of Infectious Diseases, AIDS Program, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Ritu Banerjee
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Andrew Chou
- Michael E. DeBakey VA Medical Center, Baylor College of Medicine, Houston, Texas, USA
| | - Robert C Colgrove
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Christine C Ginocchio
- Global Medical Affairs, bioMérieux/BioFire Diagnostics, Salt Lake City, Utah, USA
- Department of Pathology and Laboratory Medicine, Hofstra North Shore–Long Island Jewish School of Medicine, Hempstead, New York, USA
| | - Mary K Hayden
- Division of Infectious Diseases, Department of Medicine, Rush University Medical Center, Chicago, Illinois, USA
- Division of Laboratory Medicine, Department of Pathology, Rush University Medical Center, Chicago, Illinois, USA
| | - Mark Holodiny
- VA Palo Alto Health Care System, Palo Alto, California, USA
- Stanford University, Palo Alto, California, USA
| | - Seema Jain
- Disease Investigations Section, Infectious Diseases Branch, California Department of Public Health, Richmond, California, USA
| | - Sophia Koo
- Division of Infectious Diseases, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Jaclyn Levy
- Infectious Diseases Society of America, Arlington, Virginia, USA
| | - Tristan T Timbrook
- Division of Epidemiology, Department of Medicine, University of Utah School of Medicine, Salt Lake City, Utah USA
- Department of Pharmacy, University of Utah Health, Salt Lake City, Utah, USA
| | - Angela M Caliendo
- Division of Infectious Diseases, Department of Medicine, Brown University Warren Alpert School of Medicine, Providence, Rhode Island, USA
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9
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Khosravi H, Hou A, Colgrove RC, Behlau I. Group C streptococcal cellulitis, looking deeper than the skin. JAAD Case Rep 2018; 4:818-821. [PMID: 30238045 PMCID: PMC6143700 DOI: 10.1016/j.jdcr.2018.04.008] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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10
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Taylor TJ, Diaz F, Colgrove RC, Bernard KA, DeLuca NA, Whelan SPJ, Knipe DM. Production of immunogenic West Nile virus-like particles using a herpes simplex virus 1 recombinant vector. Virology 2016; 496:186-193. [PMID: 27336950 DOI: 10.1016/j.virol.2016.06.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 06/09/2016] [Accepted: 06/10/2016] [Indexed: 11/18/2022]
Abstract
West Nile virus (WNV) is a flavivirus that swept rapidly across North America in 1999, declined in prevalence, and then resurged in 2012. To date, no vaccine is available to prevent infection in the human population. Herpes simplex virus (HSV) replication-defective vaccine vectors induce a durable immunity characterized by strong antibody and CD8(+) T cell responses even in HSV-immune animals. In this study, a WNV protein expression cassette was optimized for virus-like particle (VLP) production in transfection studies, and the cassette was recombined into an HSV-1 d106-WNV virus vector, which produced extracellular VLPs, as confirmed by immunoelectron microscopy. Immunization of mice with the d106-WNV recombinant vector elicited a specific anti-WNV IgG response. This study highlights the flavivirus coding sequences needed for efficient assembly of virus-like particles. This information will facilitate generation of additional vaccine vectors against other flaviviruses including the recently emerged Zika virus.
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Affiliation(s)
- Travis J Taylor
- Department of Microbiology and Immunobiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, United States
| | - Fernando Diaz
- Department of Microbiology and Immunobiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, United States
| | - Robert C Colgrove
- Department of Microbiology and Immunobiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, United States
| | - Kristen A Bernard
- Wadsworth Center, New York State Department of Health, P.O Box 509, Albany, NY 12201, United States
| | - Neal A DeLuca
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 523 Bridgeside Point II, 450 Technology Drive, Pittsburgh, PA 15261, United States
| | - Sean P J Whelan
- Department of Microbiology and Immunobiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, United States
| | - David M Knipe
- Department of Microbiology and Immunobiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, United States.
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11
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Colgrove RC, Liu X, Griffiths A, Raja P, Deluca NA, Newman RM, Coen DM, Knipe DM. History and genomic sequence analysis of the herpes simplex virus 1 KOS and KOS1.1 sub-strains. Virology 2015; 487:215-21. [PMID: 26547038 DOI: 10.1016/j.virol.2015.09.026] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [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: 07/23/2015] [Revised: 09/28/2015] [Accepted: 09/30/2015] [Indexed: 10/22/2022]
Abstract
A collection of genomic DNA sequences of herpes simplex virus (HSV) strains has been defined and analyzed, and some information is available about genomic stability upon limited passage of viruses in culture. The nature of genomic change upon extensive laboratory passage remains to be determined. In this report we review the history of the HSV-1 KOS laboratory strain and the related KOS1.1 laboratory sub-strain, also called KOS (M), and determine the complete genomic sequence of an early passage stock of the KOS laboratory sub-strain and a laboratory stock of the KOS1.1 sub-strain. The genomes of the two sub-strains are highly similar with only five coding changes, 20 non-coding changes, and about twenty non-ORF sequence changes. The coding changes could potentially explain the KOS1.1 phenotypic properties of increased replication at high temperature and reduced neuroinvasiveness. The study also provides sequence markers to define the provenance of specific laboratory KOS virus stocks.
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Affiliation(s)
- Robert C Colgrove
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, United States; Mount Auburn Hospital, Cambridge, MA, United States
| | - Xueqiao Liu
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, United States
| | - Anthony Griffiths
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, United States
| | - Priya Raja
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, United States
| | - Neal A Deluca
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, United States
| | - Ruchi M Newman
- Broad Institute of Harvard and MIT, Cambridge, MA, United States
| | - Donald M Coen
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, United States
| | - David M Knipe
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, United States.
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12
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Welles SL, Bauer GR, LaRussa PS, Colgrove RC, Pitt J. Time Trends for HIV-1 Antiretroviral Resistance Among Antiretroviral-Experienced and Naive Pregnant Women in New York City During 1991 to Early 2001. J Acquir Immune Defic Syndr 2007; 44:329-35. [PMID: 17179768 DOI: 10.1097/qai.0b013e31802f1296] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Time trends in the prevalence of drug resistance to antiretroviral therapy (ART) in pregnant women have not been studied. Treatment and prophylactic efficacy could be compromised by drug-resistant HIV strains. We conducted a repeated cross-sectional study of antiretroviral resistance mutations to nucleoside reverse transcriptase inhibitors (NRTIs) and nonnucleoside reverse transcriptase inhibitors (NNRTIs) and of major mutations to protease inhibitors (PIs) in virus isolates from 300 HIV-infected pregnant women in New York City from 1991 to early 2001. The overall prevalence of mutations for NRTIs from 1991 to early 2001 was higher for ART-experienced (25.6% [95% confidence interval (CI): 19.1% to 32.1%]) than ART-naive (8.6% [95% CI: 3.7% to 13.4%]) mothers (P < 0.002). For NNRTIs, the overall prevalence of mutations was somewhat higher among ART-experienced (5.8% [95% CI: 2.3% to 9.3%]) versus ART-naive (1.6% [95% CI: 0% to 3.7%]) women (P = 0.06), and increased over time for ART-naive women (0%-7.4%; P = 0.03) and ART-experienced women (0%-19.4%; P = 0.0002). The prevalence of PI-associated mutations was also higher overall among ART-experienced mothers (5.8% [95% CI: 2.3% to 9.3%] vs. 1.6% [95% CI: 0% to 3.7%]; P = 0.06), with increases over time seen for ART-naive women (0%-7.4%; P = 0.03) and ART-experienced women (0%-16.1%; P = 0.0008). The increasing prevalence of drug resistance in pregnant women, including those who are drug-naive, underscores the necessity for resistance testing to guide treatment to achieve suppression of the mother's virus.
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Affiliation(s)
- Seth L Welles
- Department of Epidemiology, Boston University School of Public Health, 715 Albany Street, Boston, MA 02118, USA.
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13
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Abstract
OBJECTIVE To characterize concordance of resistance mutations to antiretroviral drugs (ART) in mother-infant pairs. DESIGN Case series of HIV-transmitting mothers and infants in the Women and Infants Transmission Study, where delivery occurred between April 1994 and December 1999. METHODS Reverse transcriptase and protease genes were sequenced in stored viral isolates from 32 mother-infant pairs. Mutations were coded as "pure mutants" where only mutant virus was detected or as "mixtures" where a mixed mutant/wild-type population was identified. ART resistance mutations were compared for concordance between mothers and their infants. RESULTS Maternal mutations associated with resistance to nucleoside reverse transcriptase inhibitor (NRTI) and minor protease inhibitor (PI) drugs were typically concordant with that of infant, while those associated with non-nucleoside reverse transcriptase inhibitors (NNRTI) and major PI drugs were not. Of five NRTI-associated maternal mutations observed, three pure mutants corresponded with mutant in the infant, while two wild-type-predominant mixtures corresponded with infant wild type. The only NNRTI-associated mutation observed, K103N, was not transmitted, nor were the two major PI-associated mutations, L90M and V82I/V. Transmission of minor PI-associated mutations was consistent with the sole observed or dominant variant for 20 of 21 mutations. CONCLUSIONS For NRTI- and minor PI-associated mutations, transmission was consistent with relative quantity of variants in maternal virus. However, where NNRTI- and major PI-associated mutations were present in three cases, they were not transmitted, even where only mutant virus was detectable in maternal isolates. This is consistent with evidence of loss of transmission with resistance to NNRTI and PI drugs.
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Affiliation(s)
- Greta R Bauer
- University of New Hampshire, Durham, New Hampshire, USA.
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14
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Simpson-Holley M, Colgrove RC, Nalepa G, Harper JW, Knipe DM. Identification and functional evaluation of cellular and viral factors involved in the alteration of nuclear architecture during herpes simplex virus 1 infection. J Virol 2005; 79:12840-51. [PMID: 16188986 PMCID: PMC1235858 DOI: 10.1128/jvi.79.20.12840-12851.2005] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Herpes simplex virus 1 (HSV-1) replicates in the nucleus of host cells and radically alters nuclear architecture as part of its replication process. Replication compartments (RCs) form, and host chromatin is marginalized. Chromatin is later dispersed, and RCs spread past it to reach the nuclear edge. Using a lamin A-green fluorescent protein fusion, we provide direct evidence that the nuclear lamina is disrupted during HSV-1 infection and that the UL31 and UL34 proteins are required for this. We show nuclear expansion from 8 h to 24 h postinfection and place chromatin rearrangement and disruption of the lamina in the context of this global change in nuclear architecture. We show HSV-1-induced disruption of the localization of Cdc14B, a cellular protein and component of a putative nucleoskeleton. We also show that UL31 and UL34 are required for nuclear expansion. Studies with inhibitors of globular actin (G-actin) indicate that G-actin plays an essential role in nuclear expansion and chromatin dispersal but not in lamina alterations induced by HSV-1 infection. From analyses of HSV infections under various conditions, we conclude that nuclear expansion and chromatin dispersal are dispensable for optimal replication, while lamina rearrangement is associated with efficient replication.
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Affiliation(s)
- Martha Simpson-Holley
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, 02115, USA
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15
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Wang QY, Zhou C, Johnson KE, Colgrove RC, Coen DM, Knipe DM. Herpesviral latency-associated transcript gene promotes assembly of heterochromatin on viral lytic-gene promoters in latent infection. Proc Natl Acad Sci U S A 2005; 102:16055-9. [PMID: 16247011 PMCID: PMC1266038 DOI: 10.1073/pnas.0505850102] [Citation(s) in RCA: 193] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Herpes simplex virus (HSV) persists in its human host and evades the immune response by undergoing a latent infection in sensory neurons, from which it can reactivate periodically. HSV expresses >80 gene products during productive ("lytic") infection, but only the latency-associated transcript (LAT) gene is expressed at abundant levels during latent infection. The LAT gene has been shown to repress lytic-gene expression in sensory neurons. In this study, we use chromatin immunoprecipitation to show that HSV lytic-gene promoters become complexed with modified histones associated with heterochromatin during the course of establishment of latent infection. Experiments comparing LAT-negative and LAT-positive viruses show that a function encoded by the LAT gene increases the amount of dimethyl lysine 9 form of histone H3 or heterochromatin and reduces the amount of dimethyl lysine 4 form of histone H3, a part of active chromatin, on viral lytic-gene promoters. Thus, HSV, and in particular the HSV LAT gene, may manipulate the cellular histone modification machinery to repress its lytic-gene expression and contribute to the persistence of its genome in a quiescent form in sensory neurons.
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Affiliation(s)
- Qing-Yin Wang
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115, USA
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16
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Abstract
Prevalence and patterns of HIV p6 duplications in HIV-1 mother-to-baby transmission are examined. Resistance genotyping was performed in a multisite U.S. study of antiretroviral resistance in vertical transmission. Sequence data were used in secondary analyses of HIV genetic variation. Two hundred sixty HIV viral RNA samples from HIV-infected pregnant women and their infants were analyzed with a commercial resistance genotyping kit. Chromatograms were examined for variability in the 3' region of gag. From 103 mother-baby sets, 190 samples gave readable p6 sequence. Of 103 mother-baby sets, 20 (19%) showed duplication of between 3 and 12 codons ending at the PTAPP motif of p6. When maternal p6 duplication was present and the p6 sequence was available from both maternal and infant isolates, all (seven of seven) infants had p6 duplications, but two cases showed discordancies between maternal and infant sequences. The prevalence of p6 duplication varied among geographical sites, ranging from 4 of 43 families (9%, Puerto Rico and New York sites) to 16 of 60 families (27%, Massachusetts, Texas, and Illinois). The presence of p6 duplication was not associated with differences in transmission, viral load, or disease progression in the infants, but showed a trend toward association with lower maternal CD4 count. Substantial p6 variation data are generated by resistance genotyping. PTAP duplication is prevalent in this group of HIV-infected women and infants. The duplication is efficiently transmitted from mother to infant, is present at variable prevalence at different geographic sites, and shows no clear association with vertical transmission risks.
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Affiliation(s)
- Robert C Colgrove
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
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17
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Englund JA, Raskino C, Vavro C, Palumbo P, Ross LL, McKinney R, Nikolic-Djokic D, Colgrove RC, Baker CJ. Mutations linked to drug resistance, human immunodeficiency virus type 1 biologic phenotype and their association with disease progression in children receiving nucleoside reverse transcriptase inhibitors. Pediatr Infect Dis J 2004; 23:15-22. [PMID: 14743040 DOI: 10.1097/01.inf.0000105105.80229.ba] [Citation(s) in RCA: 9] [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] [Indexed: 11/26/2022]
Abstract
BACKGROUND Few data are available concerning the impact of antiretroviral resistance in response to antiviral therapy in children. We evaluated the development of antiretroviral genotypic resistance and clinical outcome in a subgroup of children involved in a prospective antiretroviral therapy trial (Pediatric AIDS Clinical Trials Group Protocol 152). DESIGN We studied 26 matched case/control pairs. A case was defined as having clinical disease progression during the study period; controls did not have disease progression. Cases and controls were matched by age and CD4+ cell count at baseline. Matched pairs received treatment with zidovudine (9 pairs), didanosine (12 pairs) or combined therapy (5 pairs). Multiple codons of the reverse transcriptase coding region (41, 67, 70, 74, 151, 184, 210, 215 and 219) were analyzed. Patients were evaluated for CD4+ cell count, HIV-1 viral load and HIV-1 biologic phenotype at baseline and clinical endpoint. RESULTS The presence of mutations associated with resistance after nucleoside antiretroviral therapy (P = 0.039) and syncytium-inducing phenotype (P = 0.031), were significantly associated with increased risk of clinical disease progression. The mean difference in HIV-1 RNA levels between cases and their matched controls after nucleoside antiretroviral therapy was 0.77 log10 copies/ml higher for cases (P = 0.003). The median difference between cases and controls for CD4+ cell count after nucleoside antiretroviral therapy was 349 cells/mm3 lower for cases (P < 0.001). CONCLUSIONS In this small prospective study of HIV-infected children, mutations in the reverse transcriptase coding region, syncytium-inducing viral phenotype, higher HIV-1 RNA load and lower CD4+ cell count were significantly correlated with increased risk of HIV clinical disease progression.
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Affiliation(s)
- Janet A Englund
- University of Chicago, Pritzker School of Medicine, Chicago, IL, USA
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18
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Barth AH, Colgrove RC. Percutaneous K-wire fixation: protection of the exposed end. J Foot Ankle Surg 2002; 41:197-8. [PMID: 12075910 DOI: 10.1016/s1067-2516(02)80072-2] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Alan H Barth
- Orthopedic Department, Kaiser Permanente, San Diego, CA 92120, USA.
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20
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Abstract
This report documents the experience of using combined internal and external fixation in ankle arthrodesis. During the period from 1992 to 2000 a single surgeon used this method of fixation on 26 ankle fusions in 26 consecutive patients without exclusions. There were no nonunions and no delayed unions. The median time to union was 10.3 weeks and the mean time was 11.3 weeks (range, 7.4 to 23.2 weeks). Complications specific to this procedure included 3 (12%) minor pin tract infections which cleared with oral, out-patient antibiotics, 4 (15%) skin irritations from internal fixation pins sufficiently bothersome to require pin removal after union was obtained, and 1 (4%) painful pin tract which cleared spontaneously. Most of these complications occurred early in the series and subsequent changes in technique considerably decreased their incidence. This fixation technique produced excellent results. Combined internal and external fixation is recommended as a useful option in arthrodesis of the ankle.
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Affiliation(s)
- R C Colgrove
- Orthopedic Dept, Kaiser Permanente, San Diego, CA 92119, USA.
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21
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Abstract
This prospective, randomized study compares the treatment of an interdigital neuroma (IDN) by the standard resection operation with a technique in which the IDN is transposed into the inter-muscular space between the adductor hallucis and the interossei muscles after division of the digital nerves distal to the IDN. The resection group contained 22 patients and 22 neuromas and the transposition group contained 22 patients and 23 neuromas. An interviewer, blinded as to the operative technique used, telephoned each patient preoperatively, and at 1 month, 3 months, 6 months, 12 months, and 36-48 months postoperatively. The interviewer recorded the patient's reported pain level on a numerical rating scale of 0 to 100. In the resection group the average pain level was slightly lower through the first 6 month period, but at the 12 month review the resection group had a slightly higher average pain level . At the 36-48 month survey the resection group again reported a greater average pain level and fewer asymptomatic patients. It was concluded that it is unnecessary to excise the IDN to obtain excellent relief of pain. It was also concluded that transposition of the IDN into an intermuscular position between the adductor hallucis and the interossei muscles produced significantly better long term results than did the standard resection operation.
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Affiliation(s)
- R C Colgrove
- Orthopedic Dept., Kaiser Permanente, San Diego, CA 92119, USA.
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22
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Abstract
OBJECTIVE To examine the patterns of vertical transmission of zidovudine (ZDV) resistance mutations. DESIGN HIV-1 reverse transcriptase codons 10-250 were sequenced from 24 pairs of ZDV-exposed women and their HIV-infected infants as part of the Women and Infants Transmission Study. METHODS Viral RNA was extracted from tissue culture supernatants and sequenced using fluorescent dye-primer chemistry and an automated sequencer. RESULTS For 17 of these pairs, maternal and infant sequences were identical to one another and lacking known ZDV resistance mutations. The remaining seven maternal sequences contained known mutations associated with ZDV resistance at reverse transcriptase codons 70, 210, 215 and 219. In each case where the maternal HIV isolate showed a pure mutant species, the infant sequence was identical. When the maternal sequence showed the presence of a sequence mixture at codon 70 or 219, the infant's virus showed only wild-type sequence even when the ZDV-resistant mutant was quantitatively dominant in the mother. The single maternal HIV isolate showing mixed sequence at codon positions 210 and 215 transmitted an unmixed mutant to the infant at both positions. When maternal mixtures were present at sites not associated with ZDV resistance, only the dominant species appeared in the infant. CONCLUSIONS When maternal HIV isolates contained mixed wild-type and ZDV-resistant subpopulations, only a single component of the mixture could be detected in the infected infants. Resistance mutants without the codon 215 mutation were not transmitted from mixtures, even when the mutants formed the majority of circulating maternal virus. In perinatal HIV transmission, specific ZDV-resistant HIV genotypes circulating in the maternal virus pool may influence whether infection in the infant will be established by a wild-type or ZDV-resistant HIV strain.
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Affiliation(s)
- R C Colgrove
- Division of Infectious Diseases, Beth Israel Deaconess Medical Center, Harvard School of Medicine, Boston, Massachusetts 02215, USA
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23
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Peterson DA, Zilberfarb JL, Greene MA, Colgrove RC. Avascular necrosis of the first metatarsal head: incidence in distal osteotomy combined with lateral soft tissue release. Foot Ankle Int 1994; 15:59-63. [PMID: 7981801 DOI: 10.1177/107110079401500201] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.0] [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] [Indexed: 02/01/2023]
Abstract
The incidence of avascular necrosis of the metatarsal head following distal first metatarsal osteotomy combined with adductor tendon release has not been documented in a large series of patients. Of 82 consecutive procedures in 64 patients performed between 1986 and 1988, 42 patients (58 procedures) were available for clinical and radiographic examination. Average follow-up was 2.5 years (range 1.0-4.2 years). There were 35 L-shaped and 23 chevron osteotomies which were combined with a lateral soft tissue release that included adductor tenotomy. Preoperative hallux valgus angle averaged 25 degrees (range 15-40 degrees), and intermetatarsal angle averaged 12 degrees (range 5-24 degrees). Follow-up amount of correction averaged 13 degrees and 5 degrees, respectively. Eighty-four percent of patients were satisfied with their result. There was one case of avascular necrosis. The patient was asymptomatic at 4.2 years' follow-up, and the remaining patients included two with infections, one hallux varus, and no nonunions.
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Affiliation(s)
- D A Peterson
- Department of Orthopedics, Naval Medical Center, San Diego, California 92134-5000
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