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Ehrenzeller S, Zaffini R, Pecora ND, Kanjilal S, Rhee C, Klompas M. Cycle threshold dynamics of non-severe acute respiratory coronavirus virus 2 (SARS-CoV-2) respiratory viruses. Infect Control Hosp Epidemiol 2024; 45:630-634. [PMID: 38234188 DOI: 10.1017/ice.2023.286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
OBJECTIVE Many providers use severe acute respiratory coronavirus virus 2 (SARS-CoV-2) cycle thresholds (Ct values) as approximate measures of viral burden in association with other clinical data to inform decisions about treatment and isolation. We characterized temporal changes in Ct values for non-SARS-CoV-2 respiratory viruses as a first step to determine whether cycle thresholds could play a similar role in the management of non-SARS-CoV-2 respiratory viruses. DESIGN Retrospective cohort study. SETTING Brigham and Women's Hospital, Boston. METHODS We retrospectively identified all adult patients with positive nasopharyngeal PCRs for influenza, respiratory syncytial virus (RSV), parainfluenza, human metapneumovirus (HMPV), rhinovirus, or adenovirus between January 2022 and March 2023. We plotted Ct distributions relative to days since symptom onset, and we assessed whether distributions varied by immunosuppression and other comorbidities. RESULTS We analyzed 1,863 positive samples: 506 influenza, 502 rhinovirus, 430 RSV, 219 HMPV, 180 parainfluenza, 26 adenovirus. Ct values were generally 25-30 on the day of symptom onset, lower over the ensuing 1-3 days, and progressively higher thereafter with Ct values ≥30 after 1 week for most viruses. Ct values were generally higher and more stable over time for rhinovirus. There was no association between immunocompromised status and median intervals from symptom onset until Ct values were ≥30. CONCLUSIONS Ct values relative to symptom onset for influenza, RSV, and other non-SARS-CoV-2 respiratory viruses generally mirror patterns seen with SARS-CoV-2. Further data on associations between Ct values and viral viability, transmissibility, host characteristics, and response to treatment for non-SARS-CoV-2 respiratory viruses are needed to determine how clinicians and infection preventionists might integrate Ct values into treatment and isolation decisions.
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Affiliation(s)
- Selina Ehrenzeller
- Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, Massachusetts, United States
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Basel, Switzerland
- Department of Medicine, Limmattal Hospital Zurich, Schlieren, Switzerland
| | - Rebecca Zaffini
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, United States
| | - Nicole D Pecora
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, United States
| | - Sanjat Kanjilal
- Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, Massachusetts, United States
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States
| | - Chanu Rhee
- Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, Massachusetts, United States
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States
| | - Michael Klompas
- Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, Massachusetts, United States
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States
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Jhaveri TA, Weiss ZF, Winkler ML, Pyden AD, Basu SS, Pecora ND. A decade of clinical microbiology: top 10 advances in 10 years: what every infection preventionist and antimicrobial steward should know. Antimicrob Steward Healthc Epidemiol 2024; 4:e8. [PMID: 38415089 PMCID: PMC10897726 DOI: 10.1017/ash.2024.10] [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] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/22/2023] [Accepted: 12/28/2023] [Indexed: 02/29/2024]
Abstract
The past 10 years have brought paradigm-shifting changes to clinical microbiology. This paper explores the top 10 transformative innovations across the diagnostic spectrum, including not only state of the art technologies but also preanalytic and post-analytic advances. Clinical decision support tools have reshaped testing practices, curbing unnecessary tests. Innovations like broad-range polymerase chain reaction and metagenomic sequencing, whole genome sequencing, multiplex molecular panels, rapid phenotypic susceptibility testing, and matrix-assisted laser desorption ionization time-of-flight mass spectrometry have all expanded our diagnostic armamentarium. Rapid home-based testing has made diagnostic testing more accessible than ever. Enhancements to clinician-laboratory interfaces allow for automated stewardship interventions and education. Laboratory restructuring and consolidation efforts are reshaping the field of microbiology, presenting both opportunities and challenges for the future of clinical microbiology laboratories. Here, we review key innovations of the last decade.
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Affiliation(s)
- Tulip A. Jhaveri
- Division of Infectious Diseases, University of Mississippi Medical Center, Jackson, MS, USA
| | - Zoe Freeman Weiss
- Division of Pathology and Laboratory Medicine, Tufts Medical Center, Boston, MA, USA
- Division of Geographic Medicine & Infectious Disease, Tufts Medical Center, Boston, MA, USA
| | - Marisa L. Winkler
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA, USA
| | - Alexander D. Pyden
- Division of Pathology and Laboratory Medicine, Lahey Hospital and Medical Center, Burlington, MA, USA
- Department of Anatomic and Clinical Pathology, Tufts University School of Medicine, Boston, MA, USA
| | - Sankha S. Basu
- Division of Pathology and Laboratory Medicine, Tufts Medical Center, Boston, MA, USA
| | - Nicole D. Pecora
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
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3
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Cameron A, Bohrhunter JL, Porterfield CA, Mangat R, Karasick MH, Pearson Z, Angeloni S, Pecora ND. Simultaneous Measurement of IgM and IgG Antibodies to SARS-CoV-2 Spike, RBD, and Nucleocapsid Multiplexed in a Single Assay on the xMAP INTELLIFLEX DR-SE Flow Analyzer. Microbiol Spectr 2022; 10:e0250721. [PMID: 35389244 PMCID: PMC9045264 DOI: 10.1128/spectrum.02507-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 12/03/2021] [Accepted: 03/13/2022] [Indexed: 11/20/2022] Open
Abstract
The multiplex capabilities of the new xMAP INTELLIFLEX DR-SE flow analyzer were explored by modifying a serological assay previously used to characterize the IgG antibody to infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The goal was to examine the instrument's performance and to simultaneously measure IgM and IgG antibody responses against multiple SARS-CoV-2 antigens in a single assay. Specific antibodies against the SARS-CoV-2 spike (S), receptor binding domain (RBD), and nucleocapsid (N) proteins were investigated in 310 symptomatic case patients using a fluorescent microsphere immunoassay and simultaneous detection of IgM and IgG. Neutralization potential was studied using the addition of soluble angiotensin-converting enzyme 2 (ACE2) to block antibody binding. A profile extending to 180 days from symptom onset (DFSO) was described for antibodies specific to each viral antigen. Generally, IgM levels peaked and declined rapidly ∼3-4 weeks following infection, whereas S- and RBD-specific IgG plateaued at 80 DFSO. ACE2 more effectively prevented IgM and IgG binding in convalescent cases > 30 DFSO, suggesting those antibodies had greater neutralization potential. This work highlighted the multiplex and multi-analyte potential of the xMAP INTELLIFLEX DR-SE, and provided further evidence for antigen-specific IgM and IgG trajectories in acute and convalescent cases. IMPORTANCE The xMAP INTELLIFLEX DR-SE enabled simultaneous and semi-quantitative detection of both IgM and IgG to three different SARS-CoV-2 antigens in a single assay. The assay format is advantageous for rapid and medium-throughput profiling using a small volume of specimen. The xMAP INTELLIFLEX DR-SE technology demonstrated the potential to include numerous SARS-CoV-2 antigens; future work could incorporate multiple spike protein variants in a single assay. This could be an important feature for assessing the serological response to emerging variants of SARS-CoV-2.
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Affiliation(s)
- Andrew Cameron
- Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, New York, USA
| | - Jessica L. Bohrhunter
- Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, New York, USA
| | - Claire A. Porterfield
- Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, New York, USA
| | - Rupinder Mangat
- Division of Infectious Diseases, Department of Medicine, University of Rochester Medical Center, Rochester, New York, USA
| | - Michael H. Karasick
- Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, New York, USA
| | - Zachary Pearson
- Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, New York, USA
| | | | - Nicole D. Pecora
- Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, New York, USA
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
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Abstract
BACKGROUND A protective antibody response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is crucial to decrease morbidity and mortality from severe coronavirus disease 2019 (COVID-19) disease. The effects of preexisting anti-human coronavirus (HCoV) antibodies on the SARS-CoV-2-specific immunoglobulin G (IgG) responses and severity of disease are currently unclear. METHODS We profiled anti-spike (S), S1, S2, and receptor-binding domain IgG antibodies against SARS-CoV-2 and 6 HCoVs using a multiplex assay (mPLEX-CoV) with serum samples from SARS-CoV-2 infected (n = 155) and pre-COVID-19 (n = 188) cohorts. RESULTS COVID-19 subjects showed significantly increased anti-S SARS-CoV-2 IgG levels that were highly correlated with IgG antibodies against OC43 and HKU1 S proteins. However, OC43 and HKU1 anti-S antibodies in pre-COVID-19 era sera did not cross-react with SARS-CoV-2. Unidirectional cross-reactive antibodies elicited by SARS-CoV-2 infection were distinct from the bidirectional cross-reactive antibodies recognizing homologous strains RaTG13 and SARS-CoV-1. High anti-OC43 and anti-S2 antibody levels were associated with both a rapid anti-SARS-CoV-2 antibody response and increased disease severity. Subjects with increased sequential organ failure assessment (SOFA) scores developed a higher ratio of S2- to S1-reactive antibodies. CONCLUSIONS Early and rapid emergence of OC43 S- and S2-reactive IgG after SARS-CoV-2 infection correlates with COVID-19 disease severity.
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Affiliation(s)
- Jiong Wang
- Department of Medicine, Division of Nephrology, University of Rochester, Rochester, New York, USA
| | - Dongmei Li
- Clinical and Translational Science Institute, University of Rochester, Rochester, New York, USA
| | - Andrew Cameron
- Clinical Microbiology, Department of Pathology and Laboratory Medicine, University of Rochester, Rochester, New York, USA
| | - Qian Zhou
- Department of Medicine, Division of Nephrology, University of Rochester, Rochester, New York, USA
| | - Alexander Wiltse
- Present affiliation: University of Maryland Medical Center, Baltimore, MD
| | - Jennifer Nayak
- Department of Pediatrics, Division of Infectious Diseases, University of Rochester, Rochester, New York, USA
| | - Nicole D Pecora
- Present affiliation: Brigham and Women’s Hospital, Harvard University, Boston, MA
| | - Martin S Zand
- Correspondence: Martin S. Zand, MD, PhD, University of Rochester Medical Center, Clinical and Translational Science Institute, Room 1.207, 265 Crittendon Boulevard, Rochester, NY 14642 ()
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Pecora ND, Pettengill M. The Role of Laboratory-Based Viral Testing in the COVID-19 Pandemic. Clin Chem 2021; 68:33-35. [PMID: 34662380 DOI: 10.1093/clinchem/hvab227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 10/01/2021] [Indexed: 11/12/2022]
Affiliation(s)
- Nicole D Pecora
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Matthew Pettengill
- Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
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Pecora ND, Pettengill MA. 2020: A Year for Clinical Microbiology. Clin Lab Med 2021; 40:xiii-xiv. [PMID: 33121626 DOI: 10.1016/j.cll.2020.09.001] [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: 11/28/2022]
Affiliation(s)
- Nicole D Pecora
- UR Medicine Central Laboratories, 211 Bailey Road, West Henrietta, NY 14586, USA.
| | - Matthew A Pettengill
- Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, 117 South 11th Street, Pavilion Building, Suite 207, Philadelphia, PA 19107-4998, USA.
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Angeloni S, Cameron A, Pecora ND, Dunbar S. A Rapid, Multiplex Dual Reporter IgG and IgM SARS-CoV-2 Neutralization Assay for a Multiplexed Bead-Based Flow Analysis System. J Vis Exp 2021. [PMID: 33900295 DOI: 10.3791/62487] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The COVID-19 pandemic has underscored the need for rapid high-throughput methods for sensitive and specific serological detection of infection with novel pathogens, such as SARS-CoV-2. Multiplex serological testing can be particularly useful because it can simultaneously analyze antibodies to multiple antigens that optimizes pathogen coverage, and controls for variability in the organism and the individual host response. Here we describe a SARS-CoV-2 IgG 3-plex fluorescent microsphere-based assay that can detect both IgM and IgG antibodies to three major SARS-CoV-2 antigens-the spike (S) protein, spike angiotensin-converting enzyme-2 (ACE2) receptor-binding domain (RBD), and nucleocapsid (Nc). The assay was shown to have comparable performance to a SARS-CoV-2 reference assay for IgG in serum obtained at ≥21 days from symptom onset but had higher sensitivity with samples collected at ≤5 days from symptom onset. Further, using soluble ACE2 in a neutralization assay format, inhibition of antibody binding was demonstrated for S and RBD.
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Affiliation(s)
| | - Andrew Cameron
- Departments of Pathology and Laboratory Medicine, Clinical Microbiology, University of Rochester Medical Center
| | - Nicole D Pecora
- Departments of Pathology and Laboratory Medicine, Clinical Microbiology, University of Rochester Medical Center; Department of Microbiology and Immunology, University of Rochester Medical Center
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Zhang YV, Wiencek J, Meng QH, Theel ES, Babic N, Sepiashvili L, Pecora ND, Slev P, Cameron A, Konforte D. AACC Practical Recommendations for Implementing and Interpreting SARS-CoV-2 EUA and LDT Serologic Testing in Clinical Laboratories. Clin Chem 2021; 67:1188-1200. [PMID: 34470034 PMCID: PMC8083777 DOI: 10.1093/clinchem/hvab051] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 01/14/2021] [Accepted: 03/12/2021] [Indexed: 12/24/2022]
Abstract
BACKGROUND The clinical laboratory continues to play a critical role in managing the coronavirus pandemic. Numerous FDA emergency use authorization (EUA) and laboratory developed test (LDT) serologic assays have become available. The performance characteristics of these assays and their clinical utility continue to be defined in real-time during this pandemic. The American Association for Clinical Chemistry (AACC) convened a panel of experts from clinical chemistry, microbiology, and immunology laboratories, the in vitro diagnostics (IVD) industry, and regulatory agencies to provide practical recommendations for implementation and interpretation of these serologic tests in clinical laboratories. CONTENT The currently available EUA serologic tests and platforms, information on assay design, antibody classes including neutralizing antibodies, and the humoral immune responses to SARS-CoV-2 are discussed. Verification and validation of EUA and LDTs are described along with quality management approach. Four indications for serologic testing are outlined. Result interpretation, reporting comments, and the role of orthogonal testing are also recommended. SUMMARY This document aims to provide a comprehensive reference for laboratory professionals and healthcare workers to appropriately implement SARS-CoV-2 serologic assays in the clinical laboratory and interpret test results during this pandemic. Given the more frequent occurrence of outbreaks associated with either vector-borne or respiratory pathogens, this document will be a useful resource in planning for similar scenarios in the future.
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Affiliation(s)
- Y Victoria Zhang
- Department of Pathology and Lab Medicine, University of Rochester Medical Center
| | - Joesph Wiencek
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center
| | - Qing H Meng
- Department of Laboratory Medicine, Division of Pathology and Laboratory Medicine, The University of Texas/MD Anderson Cancer Center
| | - Elitza S Theel
- Department of Laboratory Medicine and Pathology, Mayo Clinic
| | - Nikolina Babic
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina
| | - Lusia Sepiashvili
- Departments of Biochemistry and Laboratory Medicine & Pathobiology The Hospital for Sick Children/University of Toronto
| | - Nicole D Pecora
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center
| | - Patricia Slev
- Department of Pathology, University of Utah, ARUP Laboratories
| | - Andrew Cameron
- Department of Clinical Microbiology, University of Rochester Medical Center
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Crawford JM, Aguero-Rosenfeld ME, Aifantis I, Cadoff EM, Cangiarella JF, Cordon-Cardo C, Cushing M, Firpo-Betancourt A, Fox AS, Furuya Y, Hacking S, Jhang J, Leonard DGB, Libien J, Loda M, Mendu DR, Mulligan MJ, Nasr MR, Pecora ND, Pessin MS, Prystowsky MB, Ramanathan LV, Rauch KR, Riddell S, Roach K, Roth KA, Shroyer KR, Smoller BR, Spitalnik SL, Spitzer ED, Tomaszewski JE, Waltman S, Willis L, Sumer-King Z. The New York State SARS-CoV-2 Testing Consortium: Regional Communication in Response to the COVID-19 Pandemic. Acad Pathol 2021; 8:23742895211006818. [PMID: 34013020 PMCID: PMC8107494 DOI: 10.1177/23742895211006818] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/28/2021] [Accepted: 03/11/2021] [Indexed: 01/22/2023] Open
Abstract
The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2, created an unprecedented need for comprehensive laboratory testing of populations, in order to meet the needs of medical practice and to guide the management and functioning of our society. With the greater New York metropolitan area as an epicenter of this pandemic beginning in March 2020, a consortium of laboratory leaders from the assembled New York academic medical institutions was formed to help identify and solve the challenges of deploying testing. This report brings forward the experience of this consortium, based on the real-world challenges which we encountered in testing patients and in supporting the recovery effort to reestablish the health care workplace. In coordination with the Greater New York Hospital Association and with the public health laboratory of New York State, this consortium communicated with state leadership to help inform public decision-making addressing the crisis. Through the length of the pandemic, the consortium has been a critical mechanism for sharing experience and best practices in dealing with issues including the following: instrument platforms, sample sources, test performance, pre- and post-analytical issues, supply chain, institutional testing capacity, pooled testing, biospecimen science, and research. The consortium also has been a mechanism for staying abreast of state and municipal policies and initiatives, and their impact on institutional and laboratory operations. The experience of this consortium may be of value to current and future laboratory professionals and policy-makers alike, in dealing with major events that impact regional laboratory services.
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Affiliation(s)
- James M. Crawford
- Department of Pathology and Laboratory Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA
| | | | - Ioannis Aifantis
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
| | - Evan M. Cadoff
- Department of Pathology, Montefiore Medical Center, Bronx, NY, USA
| | - Joan F. Cangiarella
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
| | - Carlos Cordon-Cardo
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine, Mount Sinai Health System, New York, NY, USA
| | - Melissa Cushing
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Aldolfo Firpo-Betancourt
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine, Mount Sinai Health System, New York, NY, USA
| | - Amy S. Fox
- Department of Pathology, Montefiore Medical Center, Bronx, NY, USA
| | - Yoko Furuya
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Sean Hacking
- Department of Pathology and Laboratory Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA
| | - Jeffrey Jhang
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine, Mount Sinai Health System, New York, NY, USA
| | - Debra G. B. Leonard
- Department of Pathology and Laboratory Medicine, Robert Larner MD College of Medicine, University of Vermont, Burlington, VT, USA
| | - Jenny Libien
- Department of Pathology, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - Massimo Loda
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Damadora Rao Mendu
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine, Mount Sinai Health System, New York, NY, USA
| | - Mark J. Mulligan
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY, USA
| | - Michel R. Nasr
- Department of Pathology, Upstate Medical University, Syracuse, NY, USA
| | - Nicole D. Pecora
- Department of Pathology and Laboratory Medicine, School of Medicine and Dentistry, University of Rochester Medical Center, Rochester, NY, USA
| | - Melissa S. Pessin
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Lakshmi V. Ramanathan
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Scott Riddell
- Department of Pathology, Upstate Medical University, Syracuse, NY, USA
| | - Karen Roach
- Hospital Association of New York, Renssaeler, NY, USA
| | - Kevin A. Roth
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Kenneth R. Shroyer
- Department of Pathology, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Bruce R. Smoller
- Department of Pathology and Laboratory Medicine, School of Medicine and Dentistry, University of Rochester Medical Center, Rochester, NY, USA
| | - Steven L. Spitalnik
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Eric D. Spitzer
- Department of Pathology, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY, USA
| | - John E. Tomaszewski
- Department of Pathology and Anatomical Sciences, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, in partnership with Kaleida Health Laboratories, Buffalo, NY, USA
| | - Susan Waltman
- Greater New York Hospital Association, New York, NY, USA
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Pecora ND, Pettengill MA. Current Issues in Clinical Microbiology. Clin Lab Med 2020. [DOI: 10.1016/s0272-2712(20)30073-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Abstract
The entire spectrum of diagnostic testing, from reagent supply to test performance, has been a major focus during the coronavirus disease 2019 (COVID-19) pandemic. The hope for serologic testing is that it will provide both epidemiologic information about seroprevalence as well as individual information about previous infection. This information is particularly helpful for high-risk individuals who may be outside of the viral shedding window, such as children with suspected multisystem inflammatory syndrome. It is not yet understood whether serologic testing can be interpreted in terms of protective immunity. These concerns must be addressed using highly sensitive and specific tests.
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Affiliation(s)
| | - Martin S Zand
- Department of Medicine, Nephrology (SMD), Clinical & Translational Science Institute, Clinical Research University of Rochester Medical Center, School of Medicine and Dentistry, 601 Elmwood Avenue, Box 675, Rochester, NY 14642, USA
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Mostafa HH, Cameron A, Taffner SM, Wang J, Malek A, Dumyati G, Hardy DJ, Pecora ND. Genomic Surveillance of Ceftriaxone-Resistant Escherichia coli in Western New York Suggests the Extended-Spectrum β-Lactamase bla CTX-M-27 Is Emerging on Distinct Plasmids in ST38. Front Microbiol 2020; 11:1747. [PMID: 32849376 PMCID: PMC7406970 DOI: 10.3389/fmicb.2020.01747] [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] [Received: 04/24/2020] [Accepted: 07/03/2020] [Indexed: 12/20/2022] Open
Abstract
Extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae pose significant treatment and infection prevention challenges. Escherichia coli sequence type (ST) 131 associated with the blaCTX-M-15 gene has been the dominant lineage of ESBL-producing E. coli in the US and worldwide. In this study, our objective was to determine the β-lactamase profile, means of dissemination, prevalence, and the clonal identity of ESBL-producing E. coli in our region of Western New York. Whole-genome SNP-based phylogenomics was used to assess 89 ceftriaxone-resistant (CTR) E. coli. Isolates were collected from both inpatients and outpatients and from urine and sterile-sites over a 2 month period in 2017 or throughout the year, respectively. ST131 was the predominant ST (46.0%), followed by ST38 (15.7%). The blaCTX-M-15 gene was commonly found in 53.7% of ST131 isolates, whereas the blaCTX-M-27 gene was found in 26.8% of ST131, though was significantly associated with ST38, and was found in 71.4% of those strains. When compared to ST131, ST38 E. coli exhibited increased frequency of resistance to nitrofurantoin and decreased frequency of resistance to ciprofloxacin and ampicillin-sulbactam. Using Nanopore long-read sequencing technology, an analysis of the ESBL genetic context showed that the blaCTX-M-15 gene was chromosomal in 68.2% of ST131, whereas the blaCTX-M-27 gene was plasmid-borne in all ST131 and 90% of ST38 isolates. Notably, the blaCTX-M-27 gene in ST38 resided on highly-related (99.0–100.0% identity and 65.0–98.0% query coverage) conjugative IncF plasmids of distinct plasmid multi-locus sequence types (pMLSTs) from those in ST131. Furthermore, ST131 and ST38 were found to harbor different antibiotic resistance gene and virulence factor profiles. These findings raise the possibility of an emerging ESBL-producing E. coli lineage in our region.
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Affiliation(s)
- Heba H Mostafa
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY, United States.,Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Andrew Cameron
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY, United States
| | - Samantha M Taffner
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY, United States
| | - Jun Wang
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY, United States
| | - Adel Malek
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY, United States
| | - Ghinwa Dumyati
- Department of Medicine, Infectious Diseases, University of Rochester Medical Center, Rochester, NY, United States
| | - Dwight J Hardy
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY, United States.,Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, United States
| | - Nicole D Pecora
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY, United States.,Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, United States
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Li Q, Ding X, Thomas JJ, Harding CV, Pecora ND, Ziady AG, Shank S, Boom WH, Lancioni CL, Rojas RE. Rv2468c, a novel Mycobacterium tuberculosis protein that costimulates human CD4+ T cells through VLA-5. J Leukoc Biol 2011; 91:311-20. [PMID: 22158781 DOI: 10.1189/jlb.0711364] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Mtb regulates many aspects of the host immune response, including CD4+ T lymphocyte responses that are essential for protective immunity to Mtb, and Mtb effects on the immune system are paradoxical, having the capacity to inhibit (immune evasion) and to activate (adjuvant effect) immune cells. Mtb regulates CD4+ T cells indirectly (e.g., by manipulation of APC function) and directly, via integrins and TLRs expressed on T cells. We now report that previously uncharacterized Mtb protein Rv2468c/MT2543 can directly regulate human CD4+ T cell activation by delivering costimulatory signals. When combined with TCR stimulation (e.g., anti-CD3), Rv2468c functioned as a direct costimulator for CD4+ T cells, inducing IFN-γ secretion and T cell proliferation. Studies with blocking antibodies and soluble RGD motifs demonstrated that Rv2468c engaged integrin VLA-5 (α5β1) on CD4+ T cells through its FN-like RGD motif. Costimulation by Rv2468c induced phosphorylation of FAKs and Pyk2. These results reveal that by expressing molecules that mimic host protein motifs, Mtb can directly engage receptors on CD4+ T cells and regulate their function. Rv2468c-induced costimulation of CD4+ T cells could have implications for TB immune pathogenesis and Mtb adjuvant effect.
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Affiliation(s)
- Qing Li
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
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Drage MG, Tsai HC, Pecora ND, Cheng TY, Arida AR, Shukla S, Rojas RE, Seshadri C, Moody DB, Boom WH, Sacchettini JC, Harding CV. Mycobacterium tuberculosis lipoprotein LprG (Rv1411c) binds triacylated glycolipid agonists of Toll-like receptor 2. Nat Struct Mol Biol 2010; 17:1088-95. [PMID: 20694006 PMCID: PMC2933325 DOI: 10.1038/nsmb.1869] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2010] [Accepted: 06/11/2010] [Indexed: 11/09/2022]
Abstract
Knockout of lprG results in decreased virulence of Mycobacterium tuberculosis (Mtb) in mice. Mtb lipoprotein LprG has TLR2 agonist activity, thought to be dependent on its N-terminal triacylation. Surprisingly, here we find that non-acylated LprG retains TLR2 activity. Moreover, we show LprG association with triacylated glycolipid TLR2 agonists lipoarabinomannan, lipomannan and phosphatidylinositol mannosides (which share core structures). Binding of triacylated species was specific to LprG (not LprA) and increased LprG TLR2 agonist activity; conversely, association of glycolipids with LprG enhanced their recognition by TLR2. The crystal structure of LprG in complex with phosphatidylinositol mannoside revealed a hydrophobic pocket that accommodates the three alkyl chains of the ligand. In conclusion, we demonstrate a glycolipid binding function of LprG that enhances recognition of triacylated Mtb glycolipids by TLR2 and may affect glycolipid assembly or transport for bacterial cell wall biogenesis.
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Affiliation(s)
- Michael G Drage
- Department of Pathology, Case Western Reserve University/University Hospitals Case Medical Center, Cleveland, Ohio, USA
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15
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Drage MG, Pecora ND, Hise AG, Febbraio M, Silverstein RL, Golenbock DT, Boom WH, Harding CV. TLR2 and its co-receptors determine responses of macrophages and dendritic cells to lipoproteins of Mycobacterium tuberculosis. Cell Immunol 2009; 258:29-37. [PMID: 19362712 DOI: 10.1016/j.cellimm.2009.03.008] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.7] [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] [Received: 02/22/2009] [Accepted: 03/12/2009] [Indexed: 12/20/2022]
Abstract
Mycobacterium tuberculosis (Mtb) signals through Toll-like receptor 2 (TLR2) to regulate antigen presenting cells (APCs). Mtb lipoproteins, including LpqH, LprA, LprG and PhoS1, are TLR2 agonists, but their co-receptor requirements are unknown. We studied Mtb lipoprotein-induced responses in TLR2(-/-), TLR1(-/-), TLR6(-/-), CD14(-/-) and CD36(-/-) macrophages. Responses to LprA, LprG, LpqH and PhoS1 were completely dependent on TLR2. LprG, LpqH, and PhoS1 were dependent on TLR1, but LprA did not require TLR1. None of the lipoproteins required TLR6, although a redundant contribution by TLR6 cannot be excluded. CD14 contributed to detection of LprA, LprG and LpqH, whereas CD36 contributed only to detection of LprA. Studies of lung APC subsets revealed lower TLR2 expression by CD11b(high)/CD11c(low) lung macrophages than CD11b(low)/CD11c(high) alveolar macrophages, which correlated with hyporesponsiveness of lung macrophages to LpqH. Thus, lung APC subsets differ in TLR expression, which may determine differences in responses to Mtb.
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Affiliation(s)
- Michael G Drage
- Department of Pathology, Case Western Reserve University School of Medicine/University Hospitals Case Medical Center, Cleveland, OH 44106, USA
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16
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Pecora ND, Fulton SA, Reba SM, Drage MG, Simmons DP, Urankar-Nagy NJ, Boom WH, Harding CV. Mycobacterium bovis BCG decreases MHC-II expression in vivo on murine lung macrophages and dendritic cells during aerosol infection. Cell Immunol 2008; 254:94-104. [PMID: 18762288 DOI: 10.1016/j.cellimm.2008.07.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2008] [Revised: 07/11/2008] [Accepted: 07/15/2008] [Indexed: 12/20/2022]
Abstract
Mycobacterium tuberculosis and M. bovis BCG infect APCs. In vitro, mycobacteria inhibit IFN-gamma-induced MHC-II expression by macrophages, but the effects of mycobacteria on lung APCs in vivo remain unclear. To assess MHC-II expression on APCs infected in vivo, mice were aerosol-infected with GFP-expressing BCG. At 28 d, approximately 1% of lung APCs were GFP+ by flow cytometry and CFU data. Most GFP+ cells were CD11b(high)/CD11c(neg-mid) lung macrophages (58-68%) or CD11b(high)/CD11c(high) DCs (28-31%). Lung APC MHC-II expression was higher in infected mice than naïve mice. Within infected lungs, however, MHC-II expression was lower in GFP+ cells than GFP- cells for both macrophages and DCs. MHC-II expression was also inhibited on purified lung macrophages and DCs that were infected with BCG in vitro. Thus, lung APCs that harbor mycobacteria in vivo have decreased MHC-II expression relative to uninfected APCs from the same lung, possibly contributing to evasion of T cell responses.
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Affiliation(s)
- Nicole D Pecora
- Department of Pathology, Case Western Reserve University, Wolstein 6534, 10900 Euclid Avenue, Cleveland, OH 44106-7288, USA
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Lancioni CL, Thomas J, Ding X, Pecora ND, Drage M, Harding C, Boom WH, Rojas RE. Direct upregulation of human CD4+ T cell proliferation and cytokine secretion by Mycobacterium tuberculosis (MTB). FASEB J 2008. [DOI: 10.1096/fasebj.22.1_supplement.860.4] [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: 11/11/2022]
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18
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Gerding MA, Ogata Y, Pecora ND, Niki H, de Boer PAJ. The trans-envelope Tol-Pal complex is part of the cell division machinery and required for proper outer-membrane invagination during cell constriction in E. coli. Mol Microbiol 2007; 63:1008-25. [PMID: 17233825 PMCID: PMC4428343 DOI: 10.1111/j.1365-2958.2006.05571.x] [Citation(s) in RCA: 263] [Impact Index Per Article: 15.5] [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: 11/29/2022]
Abstract
Fission of bacterial cells involves the co-ordinated invagination of the envelope layers. Invagination of the cytoplasmic membrane (IM) and peptidoglycan (PG) layer is likely driven by the septal ring organelle. Invagination of the outer membrane (OM) in Gram-negative species is thought to occur passively via its tethering to the underlying PG layer with generally distributed PG-binding OM (lipo)proteins. The Tol-Pal system is energized by proton motive force and is well conserved in Gram-negative bacteria. It consists of five proteins that can connect the OM to both the PG and IM layers via protein-PG and protein-protein interactions. Although the system is needed to maintain full OM integrity, and for class A colicins and filamentous phages to enter cells, its precise role has remained unclear. We show that all five components accumulate at constriction sites in Escherichia coli and that mutants lacking an intact system suffer delayed OM invagination and contain large OM blebs at constriction sites and cell poles. We propose that Tol-Pal constitutes a dynamic subcomplex of the division apparatus in Gram-negative bacteria that consumes energy to establish transient trans-envelope connections at/near the septal ring to draw the OM onto the invaginating PG and IM layers during constriction.
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Affiliation(s)
- Matthew A. Gerding
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Yasuyuki Ogata
- Radioisotope Center, Genetic Strains Research Center, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Nicole D. Pecora
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Hironori Niki
- Radioisotope Center, Genetic Strains Research Center, National Institute of Genetics, Mishima, Shizuoka, Japan
- Microbial Genetics Laboratory, Genetic Strains Research Center, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Piet A. J. de Boer
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- For correspondence. ; Tel. (+1) 216 368 1697; Fax (+1) 216 368 3055
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Pecora ND, Gehring AJ, Canaday DH, Boom WH, Harding CV. Mycobacterium tuberculosis LprA is a lipoprotein agonist of TLR2 that regulates innate immunity and APC function. J Immunol 2006; 177:422-9. [PMID: 16785538 DOI: 10.4049/jimmunol.177.1.422] [Citation(s) in RCA: 160] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
TLR2 recognizes components of Mycobacterium tuberculosis (Mtb) and initiates responses by APCs that influence both innate and adaptive immunity. Mtb lipoproteins are an important class of TLR2 ligand, but only two, LpqH and LprG, have been characterized to date. In this study, we characterize a third Mtb lipoprotein, LprA, and determine its effects on host macrophages and dendritic cells. LprA is a cell wall-associated lipoprotein with no homologs outside the slow-growing mycobacteria. Using Mycobacterium smegmatis as an expression host, we purified 6x His-tagged LprA both with and without its acyl modifications. Acylated LprA had agonist activity for both human and murine TLR2 and induced expression of TNF-alpha, IL-10, and IL-12. LprA also induced dendritic cell maturation as shown by increased expression of CD40, CD80, and class II MHC (MHC-II). In macrophages, prolonged (24 h) incubation with LprA decreased IFN-gamma-induced MHC-II Ag processing and presentation, consistent with an observed decrease in MHC-II expression (macrophage viability was not affected and apoptosis was not induced by LprA). Reduced MHC-II Ag presentation may represent a negative feedback mechanism for control of inflammation that may be subverted by Mtb for immune evasion. Thus, Mtb LprA is a TLR2 agonist that induces cytokine responses and regulates APC function.
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Affiliation(s)
- Nicole D Pecora
- Department of Pathology, Case Western Reserve University, 2103 Cornell Road, Cleveland, OH 44106-7288, USA
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Sturgill GM, Siddiqui S, Ding X, Pecora ND, Rather PN. Isolation of lacZ fusions to Proteus mirabilis genes regulated by intercellular signaling: potential role for the sugar phosphotransferase (Pts) system in regulation. FEMS Microbiol Lett 2002; 217:43-50. [PMID: 12445644 DOI: 10.1111/j.1574-6968.2002.tb11454.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Using a mini-Tn5lacZ1 reporter transposon, lacZ fusions have been identified in Proteus mirabilis that are activated by the accumulation of self-produced extracellular signals. Genes identified by this approach include putative homologs of pgm, nlpA and two genes of unknown function. The extracellular signal(s) involved in activation were resistant to the effects of acid and alkali. The signal required for activation of (nlpA) cma482::lacZ was sensitive to protease, suggesting the signal is a peptide or small protein. The signals behaved as polar molecules and were not extractable with ethyl acetate. A mini-Tn5Cm insertion was identified in a probable ptsI homolog that blocked activation of the cma134::lacZ fusion by an extracellular signal. The ptsI mutation did not alter extracellular signal production and may have a role in signal response.
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Affiliation(s)
- Gwen M Sturgill
- Research Service, Louis Stokes Veterans Affairs Medical Center, Cleveland, OH 44106, USA
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