1
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Beres SB, Olsen RJ, Long SW, Langley R, Williams T, Erlendsdottir H, Smith A, Kristinsson KG, Musser JM. Increase in invasive Streptococcus pyogenes M1 infections with close evolutionary genetic relationship, Iceland and Scotland, 2022 to 2023. Euro Surveill 2024; 29:2400129. [PMID: 38551096 PMCID: PMC10979525 DOI: 10.2807/1560-7917.es.2024.29.13.2400129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 03/27/2024] [Indexed: 04/01/2024] Open
Abstract
Group A Streptococcus isolates of the recently described M1UK clade have emerged to cause human infections in several European countries and elsewhere. Full-genome sequence analysis of M1 isolates discovered a close genomic relationship between some isolates from Scotland and the majority of isolates from Iceland causing serious infections in 2022 and 2023. Phylogenetic analysis strongly suggests that an isolate from or related to Scotland was the precursor to an M1UK variant responsible for almost all recent M1 infections in Iceland.
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Affiliation(s)
- Stephen B Beres
- Laboratory of Molecular and Translational Human Infectious Disease Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, United States
| | - Randall J Olsen
- Laboratory of Molecular and Translational Human Infectious Disease Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, United States
- Departments of Pathology and Laboratory Medicine and Microbiology and Immunology, Weill Cornell Medical College, New York, United States
| | - S Wesley Long
- Laboratory of Molecular and Translational Human Infectious Disease Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, United States
- Departments of Pathology and Laboratory Medicine and Microbiology and Immunology, Weill Cornell Medical College, New York, United States
| | - Ross Langley
- Department of Paediatric Respiratory and Sleep Medicine, Royal Hospital for Children, Glasgow, Scotland
| | - Thomas Williams
- Department of Child Life and Health, University of Edinburgh, Edinburgh, Scotland
| | - Helga Erlendsdottir
- Department of Clinical Microbiology, Landspitali - the National University Hospital of Iceland, Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Andrew Smith
- College of Medical, Veterinary and Life Sciences, Glasgow Dental Hospital and School, University of Glasgow, Glasgow, Scotland
- Scottish Microbiology Reference Laboratory, New Lister Building, Glasgow, Scotland
| | - Karl G Kristinsson
- Department of Clinical Microbiology, Landspitali - the National University Hospital of Iceland, Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - James M Musser
- Laboratory of Molecular and Translational Human Infectious Disease Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, United States
- Departments of Pathology and Laboratory Medicine and Microbiology and Immunology, Weill Cornell Medical College, New York, United States
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2
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Goike J, Hsieh CL, Horton AP, Gardner EC, Zhou L, Bartzoka F, Wang N, Javanmardi K, Herbert A, Abbassi S, Xie X, Xia H, Shi PY, Renberg R, Segall-Shapiro TH, Terrace CI, Wu W, Shroff R, Byrom M, Ellington AD, Marcotte EM, Musser JM, Kuchipudi SV, Kapur V, Georgiou G, Weaver SC, Dye JM, Boutz DR, McLellan JS, Gollihar JD. SARS-COV-2 Omicron variants conformationally escape a rare quaternary antibody binding mode. Commun Biol 2023; 6:1250. [PMID: 38082099 PMCID: PMC10713552 DOI: 10.1038/s42003-023-05649-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
The ongoing evolution of SARS-CoV-2 into more easily transmissible and infectious variants has provided unprecedented insight into mutations enabling immune escape. Understanding how these mutations affect the dynamics of antibody-antigen interactions is crucial to the development of broadly protective antibodies and vaccines. Here we report the characterization of a potent neutralizing antibody (N3-1) identified from a COVID-19 patient during the first disease wave. Cryogenic electron microscopy revealed a quaternary binding mode that enables direct interactions with all three receptor-binding domains of the spike protein trimer, resulting in extraordinary avidity and potent neutralization of all major variants of concern until the emergence of Omicron. Structure-based rational design of N3-1 mutants improved binding to all Omicron variants but only partially restored neutralization of the conformationally distinct Omicron BA.1. This study provides new insights into immune evasion through changes in spike protein dynamics and highlights considerations for future conformationally biased multivalent vaccine designs.
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Affiliation(s)
- Jule Goike
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Ching-Lin Hsieh
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Andrew P Horton
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Antibody Discovery and Accelerated Protein Therapeutics, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, USA
| | - Elizabeth C Gardner
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Ling Zhou
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Foteini Bartzoka
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Nianshuang Wang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Kamyab Javanmardi
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Andrew Herbert
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Shawn Abbassi
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Hongjie Xia
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Rebecca Renberg
- DEVCOM Army Research Laboratory, Biotechnology Branch, Adelphi, MD, USA
| | - Thomas H Segall-Shapiro
- Antibody Discovery and Accelerated Protein Therapeutics, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, USA
- DEVCOM Army Research Laboratory-South, Austin, TX, USA
| | | | - Wesley Wu
- Antibody Discovery and Accelerated Protein Therapeutics, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, USA
| | - Raghav Shroff
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Antibody Discovery and Accelerated Protein Therapeutics, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, USA
- DEVCOM Army Research Laboratory-South, Austin, TX, USA
| | - Michelle Byrom
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Andrew D Ellington
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
| | - Edward M Marcotte
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - James M Musser
- Antibody Discovery and Accelerated Protein Therapeutics, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, USA
| | - Suresh V Kuchipudi
- Department of Veterinary and Biomedical Science and Animal Diagnostic Laboratory, The Pennsylvania State University, University Park, PA, USA
| | - Vivek Kapur
- Department of Animal Science and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - George Georgiou
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
- Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
| | - Scott C Weaver
- University of Texas Medical Branch, World Reference Center for Emerging Viruses and Arboviruses, Galveston, TX, USA
| | - John M Dye
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Daniel R Boutz
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
- Antibody Discovery and Accelerated Protein Therapeutics, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, USA.
- DEVCOM Army Research Laboratory-South, Austin, TX, USA.
| | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
| | - Jimmy D Gollihar
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
- Antibody Discovery and Accelerated Protein Therapeutics, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, USA.
- DEVCOM Army Research Laboratory-South, Austin, TX, USA.
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3
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Kochan TJ, Nozick SH, Valdes A, Mitra SD, Cheung BH, Lebrun-Corbin M, Medernach RL, Vessely MB, Mills JO, Axline CMR, Nelson JA, VanGosen EM, Ward TJ, Ozer EA, van Duin D, Chen L, Kreiswirth BN, Long SW, Musser JM, Bulman ZP, Wunderink RG, Hauser AR. Klebsiella pneumoniae clinical isolates with features of both multidrug-resistance and hypervirulence have unexpectedly low virulence. Nat Commun 2023; 14:7962. [PMID: 38042959 PMCID: PMC10693551 DOI: 10.1038/s41467-023-43802-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 11/21/2023] [Indexed: 12/04/2023] Open
Abstract
Klebsiella pneumoniae has been classified into two types, classical K. pneumoniae (cKP) and hypervirulent K. pneumoniae (hvKP). cKP isolates are highly diverse and important causes of nosocomial infections; they include globally disseminated antibiotic-resistant clones. hvKP isolates are sensitive to most antibiotics but are highly virulent, causing community-acquired infections in healthy individuals. The virulence phenotype of hvKP is associated with pathogenicity loci responsible for siderophore and hypermucoid capsule production. Recently, convergent strains of K. pneumoniae, which possess features of both cKP and hvKP, have emerged and are cause of much concern. Here, we screen the genomes of 2,608 multidrug-resistant K. pneumoniae isolates from the United States and identify 47 convergent isolates. We perform phenotypic and genomic characterization of 12 representative isolates. These 12 convergent isolates contain a variety of antimicrobial resistance plasmids and virulence plasmids. Most convergent isolates contain aerobactin biosynthesis genes and produce more siderophores than cKP isolates but not more capsule. Unexpectedly, only 1 of the 12 tested convergent isolates has a level of virulence consistent with hvKP isolates in a murine pneumonia model. These findings suggest that additional studies should be performed to clarify whether convergent strains are indeed more virulent than cKP in mouse and human infections.
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Affiliation(s)
- Travis J Kochan
- Laboratory of Respiratory and Special Pathogens, Division of Bacterial, Parasitic, and Allergenic Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA.
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
| | - Sophia H Nozick
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Aliki Valdes
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Sumitra D Mitra
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Bettina H Cheung
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Marine Lebrun-Corbin
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Rachel L Medernach
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Madeleine B Vessely
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Jori O Mills
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Christopher M R Axline
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Julia A Nelson
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Ethan M VanGosen
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Timothy J Ward
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Egon A Ozer
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - David van Duin
- Division of Infectious Diseases, University of North Carolina, Chapel Hill, NC, USA
| | - Liang Chen
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
| | - Barry N Kreiswirth
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
| | - S Wesley Long
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital Research Institute, Houston, TX, USA
| | - James M Musser
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital Research Institute, Houston, TX, USA
| | - Zackery P Bulman
- College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Richard G Wunderink
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Simpson Querrey Institute for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Alan R Hauser
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
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4
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Beres SB, Olsen RJ, Long SW, Eraso JM, Boukthir S, Faili A, Kayal S, Musser JM. Analysis of the Genomics and Mouse Virulence of an Emergent Clone of Streptococcus dysgalactiae Subspecies equisimilis. Microbiol Spectr 2023; 11:e0455022. [PMID: 36971562 PMCID: PMC10100674 DOI: 10.1128/spectrum.04550-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 03/04/2023] [Indexed: 03/29/2023] Open
Abstract
Streptococcus dysgalactiae subsp. equisimilis is a bacterial pathogen that is increasingly recognized as a cause of severe human infections. Much less is known about the genomics and infection pathogenesis of S. dysgalactiae subsp. equisimilis strains compared to the closely related bacterium Streptococcus pyogenes. To address these knowledge deficits, we sequenced to closure the genomes of seven S. dysgalactiae subsp. equisimilis human isolates, including six that were emm type stG62647. Recently, for unknown reasons, strains of this emm type have emerged and caused an increasing number of severe human infections in several countries. The genomes of these seven strains vary between 2.15 and 2.21 Mbp. The core chromosomes of these six S. dysgalactiae subsp. equisimilis stG62647 strains are closely related, differing on average by only 495 single-nucleotide polymorphisms, consistent with a recent descent from a common progenitor. The largest source of genetic diversity among these seven isolates is differences in putative mobile genetic elements, both chromosomal and extrachromosomal. Consistent with the epidemiological observations of increased frequency and severity of infections, both stG62647 strains studied were significantly more virulent than a strain of emm type stC74a in a mouse model of necrotizing myositis, as assessed by bacterial CFU burden, lesion size, and survival curves. Taken together, our genomic and pathogenesis data show the strains of emm type stG62647 we studied are closely genetically related and have enhanced virulence in a mouse model of severe invasive disease. Our findings underscore the need for expanded study of the genomics and molecular pathogenesis of S. dysgalactiae subsp. equisimilis strains causing human infections. IMPORTANCE Our studies addressed a critical knowledge gap in understanding the genomics and virulence of the bacterial pathogen Streptococcus dysgalactiae subsp. equisimilis. S. dysgalactiae subsp. equisimilis strains are responsible for a recent increase in severe human infections in some countries. We determined that certain S. dysgalactiae subsp. equisimilis strains are genetically descended from a common ancestor and that these strains can cause severe infections in a mouse model of necrotizing myositis. Our findings highlight the need for expanded studies on the genomics and pathogenic mechanisms of this understudied subspecies of the Streptococcus family.
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Affiliation(s)
- Stephen B. Beres
- Laboratory of Molecular and Translational Human Infectious Disease Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, USA
| | - Randall J. Olsen
- Laboratory of Molecular and Translational Human Infectious Disease Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - S. Wesley Long
- Laboratory of Molecular and Translational Human Infectious Disease Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - Jesus M. Eraso
- Laboratory of Molecular and Translational Human Infectious Disease Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Sarrah Boukthir
- CHU de Rennes, Service de Bacteriologie-Hygiène Hospitalière, Rennes, France
- INSERM, CIC 1414, Rennes, France
- Université Rennes 1, Faculté de Médecine, Rennes, France
| | - Ahmad Faili
- INSERM, CIC 1414, Rennes, France
- Université Rennes 1, Faculté de Pharmacie, Rennes, France
- Chemistry, Oncogenesis, Stress, and Signaling, INSERM 1242, Rennes, France
| | - Samer Kayal
- CHU de Rennes, Service de Bacteriologie-Hygiène Hospitalière, Rennes, France
- INSERM, CIC 1414, Rennes, France
- Université Rennes 1, Faculté de Médecine, Rennes, France
- Chemistry, Oncogenesis, Stress, and Signaling, INSERM 1242, Rennes, France
| | - James M. Musser
- Laboratory of Molecular and Translational Human Infectious Disease Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
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5
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Vandegrift KJ, Yon M, Surendran Nair M, Gontu A, Ramasamy S, Amirthalingam S, Neerukonda S, Nissly RH, Chothe SK, Jakka P, LaBella L, Levine N, Rodriguez S, Chen C, Sheersh Boorla V, Stuber T, Boulanger JR, Kotschwar N, Aucoin SG, Simon R, Toal KL, Olsen RJ, Davis JJ, Bold D, Gaudreault NN, Dinali Perera K, Kim Y, Chang KO, Maranas CD, Richt JA, Musser JM, Hudson PJ, Kapur V, Kuchipudi SV. SARS-CoV-2 Omicron (B.1.1.529) Infection of Wild White-Tailed Deer in New York City. Viruses 2022; 14:v14122770. [PMID: 36560774 PMCID: PMC9785669 DOI: 10.3390/v14122770] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/19/2022] [Accepted: 12/01/2022] [Indexed: 12/15/2022] Open
Abstract
There is mounting evidence of SARS-CoV-2 spillover from humans into many domestic, companion, and wild animal species. Research indicates that humans have infected white-tailed deer, and that deer-to-deer transmission has occurred, indicating that deer could be a wildlife reservoir and a source of novel SARS-CoV-2 variants. We examined the hypothesis that the Omicron variant is actively and asymptomatically infecting the free-ranging deer of New York City. Between December 2021 and February 2022, 155 deer on Staten Island, New York, were anesthetized and examined for gross abnormalities and illnesses. Paired nasopharyngeal swabs and blood samples were collected and analyzed for the presence of SARS-CoV-2 RNA and antibodies. Of 135 serum samples, 19 (14.1%) indicated SARS-CoV-2 exposure, and 11 reacted most strongly to the wild-type B.1 lineage. Of the 71 swabs, 8 were positive for SARS-CoV-2 RNA (4 Omicron and 4 Delta). Two of the animals had active infections and robust neutralizing antibodies, revealing evidence of reinfection or early seroconversion in deer. Variants of concern continue to circulate among and may reinfect US deer populations, and establish enzootic transmission cycles in the wild: this warrants a coordinated One Health response, to proactively surveil, identify, and curtail variants of concern before they can spill back into humans.
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Affiliation(s)
- Kurt J. Vandegrift
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
- The Center for Infectious Disease Dynamics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Correspondence: (K.J.V.); (V.K.); (S.V.K.); Tel.: +1-814-574-9852 (K.J.V.); +1-814-865-9788 (V.K.); +1-814-863-4436 (S.V.K.)
| | - Michele Yon
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Meera Surendran Nair
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Abhinay Gontu
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Santhamani Ramasamy
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Saranya Amirthalingam
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | | | - Ruth H. Nissly
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Shubhada K. Chothe
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Padmaja Jakka
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Lindsey LaBella
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Nicole Levine
- Department of Animal Science, The Pennsylvania State University, University Park, PA 16802, USA
| | - Sophie Rodriguez
- Department of Animal Science, The Pennsylvania State University, University Park, PA 16802, USA
| | - Chen Chen
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Veda Sheersh Boorla
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Tod Stuber
- National Veterinary Services Laboratories, Veterinary Services, U.S. Department of Agriculture, Ames, IA 50010, USA
| | | | | | | | - Richard Simon
- City of New York Parks & Recreation, New York, NY 10029, USA
| | - Katrina L. Toal
- City of New York Parks & Recreation, New York, NY 10029, USA
| | - Randall J. Olsen
- Laboratory of Molecular and Translational Human Infectious Disease Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, TX 77030, USA
- Departments of Pathology and Laboratory Medicine and Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10021, USA
| | - James J. Davis
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60637, USA
- Division of Data Science and Learning, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Dashzeveg Bold
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, USA
| | - Natasha N. Gaudreault
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, USA
| | - Krishani Dinali Perera
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, USA
| | - Yunjeong Kim
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, USA
| | - Kyeong-Ok Chang
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, USA
| | - Costas D. Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Juergen A. Richt
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, USA
| | - James M. Musser
- Laboratory of Molecular and Translational Human Infectious Disease Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, TX 77030, USA
- Departments of Pathology and Laboratory Medicine and Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10021, USA
| | - Peter J. Hudson
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
- The Center for Infectious Disease Dynamics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Vivek Kapur
- The Center for Infectious Disease Dynamics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Animal Science, The Pennsylvania State University, University Park, PA 16802, USA
- Correspondence: (K.J.V.); (V.K.); (S.V.K.); Tel.: +1-814-574-9852 (K.J.V.); +1-814-865-9788 (V.K.); +1-814-863-4436 (S.V.K.)
| | - Suresh V. Kuchipudi
- The Center for Infectious Disease Dynamics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Correspondence: (K.J.V.); (V.K.); (S.V.K.); Tel.: +1-814-574-9852 (K.J.V.); +1-814-865-9788 (V.K.); +1-814-863-4436 (S.V.K.)
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6
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Olsen RJ, Zhu L, Mangham RE, Faili A, Kayal S, Beres SB, Musser JM. A Chimeric Penicillin Binding Protein 2X Significantly Decreases in Vitro Beta-Lactam Susceptibility and Increases in Vivo Fitness of Streptococcus pyogenes. Am J Pathol 2022; 192:1397-1406. [PMID: 35843262 PMCID: PMC9552024 DOI: 10.1016/j.ajpath.2022.06.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 06/27/2022] [Accepted: 06/29/2022] [Indexed: 06/15/2023]
Abstract
All tested strains of Streptococcus pyogenes (group A streptococcus, GAS) remain susceptible to penicillin. However, GAS strains with amino acid substitutions in penicillin-binding proteins that confer decreased susceptibility to beta-lactam antibiotics have been identified recently. This discovery raises concerns about emergence of beta-lactam antibiotic resistance in GAS. Whole genome sequencing recently identified GAS strains with a chimeric penicillin-binding protein 2X (PBP2X) containing a recombinant segment from Streptococcus dysgalactiae subspecies equisimilis (SDSE). To directly test the hypothesis that the chimeric SDSE-like PBP2X alters beta-lactam susceptibility in vitro and fitness in vivo, an isogenic mutant strain was generated and virulence assessed in a mouse model of necrotizing myositis. Compared with naturally occurring and isogenic strains with a wild-type GAS-like PBP2X, strains with the chimeric SDSE-like PBP2X had reduced susceptibility in vitro to nine beta-lactam antibiotics. In a mouse model of necrotizing myositis, the strains had identical fitness in the absence of benzylpenicillin treatment. However, mice treated intermittently with a subtherapeutic dose of benzylpenicillin had significantly more colony-forming units recovered from limbs infected with strains with the chimeric SDSE-like PBP2X. These results show that mutations such as the PBP2X chimera may result in significantly decreased beta-lactam susceptibility and increased fitness and virulence. Expanded diagnostic laboratory surveillance, genome sequencing, and molecular pathogenesis study of potentially emergent beta-lactam antibiotic resistance among GAS are needed.
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Affiliation(s)
- Randall J Olsen
- Laboratory of Molecular and Translational Human Infectious Disease Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas; Departments of Pathology and Laboratory Medicine and Microbiology and Immunology, Weill Cornell Medical College, New York, New York.
| | - Luchang Zhu
- Laboratory of Molecular and Translational Human Infectious Disease Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas; Departments of Pathology and Laboratory Medicine and Microbiology and Immunology, Weill Cornell Medical College, New York, New York
| | - Regan E Mangham
- Laboratory of Molecular and Translational Human Infectious Disease Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Ahmad Faili
- Inserm, CIC 1414, Rennes, France; Faculty of Pharmacy, Université Rennes 1, Rennes, France; CHU de Rennes, Rennes, France
| | - Samer Kayal
- Inserm, CIC 1414, Rennes, France; CHU de Rennes, Rennes, France; Faculty of Medicine, Université Rennes 1, Rennes, France
| | - Stephen B Beres
- Laboratory of Molecular and Translational Human Infectious Disease Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - James M Musser
- Laboratory of Molecular and Translational Human Infectious Disease Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas; Departments of Pathology and Laboratory Medicine and Microbiology and Immunology, Weill Cornell Medical College, New York, New York
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7
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Javanmardi K, Segall-Shapiro TH, Chou CW, Boutz DR, Olsen RJ, Xie X, Xia H, Shi PY, Johnson CD, Annapareddy A, Weaver S, Musser JM, Ellington AD, Finkelstein IJ, Gollihar JD. Antibody escape and cryptic cross-domain stabilization in the SARS-CoV-2 Omicron spike protein. Cell Host Microbe 2022; 30:1242-1254.e6. [PMID: 35988543 PMCID: PMC9350683 DOI: 10.1016/j.chom.2022.07.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 06/17/2022] [Accepted: 07/27/2022] [Indexed: 12/03/2022]
Abstract
The worldwide spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to the repeated emergence of variants of concern. For the Omicron variant, sub-lineages BA.1 and BA.2, respectively, contain 33 and 29 nonsynonymous and indel spike protein mutations. These amino acid substitutions and indels are implicated in increased transmissibility and enhanced immune evasion. By reverting individual spike mutations of BA.1 or BA.2, we characterize the molecular effects of the Omicron spike mutations on expression, ACE2 receptor affinity, and neutralizing antibody recognition. We identified key mutations enabling escape from neutralizing antibodies at a variety of epitopes. Stabilizing mutations in the N-terminal and S2 domains of the spike protein can compensate for destabilizing mutations in the receptor binding domain, enabling the record number of mutations in Omicron. Our results provide a comprehensive account of the mutational effects in the Omicron spike protein and illustrate previously uncharacterized mechanisms of host evasion.
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Affiliation(s)
- Kamyab Javanmardi
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
| | - Thomas H Segall-Shapiro
- Laboratory of Antibody Discovery and Accelerated Protein Therapeutics, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
| | - Chia-Wei Chou
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Daniel R Boutz
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA; Laboratory of Antibody Discovery and Accelerated Protein Therapeutics, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
| | - Randall J Olsen
- Laboratory of Antibody Discovery and Accelerated Protein Therapeutics, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA; Laboratory of Molecular and Translational Human Infectious Diseases Research, Center for Infectious Diseases, HMRI and Department of Pathology and Genomic Medicine, HMH, Houston, TX, USA; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Hongjie Xia
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Charlie D Johnson
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Ankur Annapareddy
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Scott Weaver
- University of Texas Medical Branch, World Reference Center for Emerging Viruses and Arboviruses, Galveston, TX, USA
| | - James M Musser
- Laboratory of Molecular and Translational Human Infectious Diseases Research, Center for Infectious Diseases, HMRI and Department of Pathology and Genomic Medicine, HMH, Houston, TX, USA; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Andrew D Ellington
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, USA.
| | - Jimmy D Gollihar
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA; Laboratory of Antibody Discovery and Accelerated Protein Therapeutics, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA.
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8
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Willgert K, Didelot X, Surendran-Nair M, Kuchipudi SV, Ruden RM, Yon M, Nissly RH, Vandegrift KJ, Nelli RK, Li L, Jayarao BM, Levine N, Olsen RJ, Davis JJ, Musser JM, Hudson PJ, Kapur V, Conlan AJK. Transmission history of SARS-CoV-2 in humans and white-tailed deer. Sci Rep 2022; 12:12094. [PMID: 35840592 PMCID: PMC9284484 DOI: 10.1038/s41598-022-16071-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 07/04/2022] [Indexed: 11/30/2022] Open
Abstract
The emergence of a novel pathogen in a susceptible population can cause rapid spread of infection. High prevalence of SARS-CoV-2 infection in white-tailed deer (Odocoileus virginianus) has been reported in multiple locations, likely resulting from several human-to-deer spillover events followed by deer-to-deer transmission. Knowledge of the risk and direction of SARS-CoV-2 transmission between humans and potential reservoir hosts is essential for effective disease control and prioritisation of interventions. Using genomic data, we reconstruct the transmission history of SARS-CoV-2 in humans and deer, estimate the case finding rate and attempt to infer relative rates of transmission between species. We found no evidence of direct or indirect transmission from deer to human. However, with an estimated case finding rate of only 4.2%, spillback to humans cannot be ruled out. The extensive transmission of SARS-CoV-2 within deer populations and the large number of unsampled cases highlights the need for active surveillance at the human–animal interface.
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Affiliation(s)
- Katriina Willgert
- Disease Dynamics Unit (DDU), Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.
| | - Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, Coventry, UK
| | - Meera Surendran-Nair
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, 16802, USA.,Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Suresh V Kuchipudi
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, 16802, USA.,Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Rachel M Ruden
- Wildlife Bureau, Iowa Department of Natural Resources, Des Moines, IA, USA.,Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Michele Yon
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Ruth H Nissly
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, 16802, USA.,Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Kurt J Vandegrift
- The Center for Infectious Disease Dynamics, Department of Biology and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Rahul K Nelli
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Lingling Li
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Bhushan M Jayarao
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Nicole Levine
- Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA.,Department of Animal Science, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Randall J Olsen
- Laboratory of Molecular and Translational Human Infectious Disease Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, 77030, USA.,Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY, 10021, USA.,Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, 10021, USA
| | - James J Davis
- University of Chicago Consortium for Advanced Science and Engineering, University of Chicago, Chicago, USA.,Division of Data Science and Learning, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - James M Musser
- Laboratory of Molecular and Translational Human Infectious Disease Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, 77030, USA.,Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY, 10021, USA.,Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, 10021, USA
| | - Peter J Hudson
- The Center for Infectious Disease Dynamics, Department of Biology and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Vivek Kapur
- Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA.,Department of Animal Science, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Andrew J K Conlan
- Disease Dynamics Unit (DDU), Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
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9
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Khan A, Zhang K, Singh VK, Mishra A, Kachroo P, Bing T, Won JH, Mani A, Papanna R, Mann LK, Ledezma-Campos E, Aguillon-Duran G, Canaday DH, David SA, Restrepo BI, Viet NN, Phan H, Graviss EA, Musser JM, Kaushal D, Gauduin MC, Jagannath C. Human M1 macrophages express unique innate immune response genes after mycobacterial infection to defend against tuberculosis. Commun Biol 2022; 5:480. [PMID: 35590096 PMCID: PMC9119986 DOI: 10.1038/s42003-022-03387-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [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: 01/07/2021] [Accepted: 04/21/2022] [Indexed: 12/23/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) is responsible for approximately 1.5 million deaths each year. Though 10% of patients develop tuberculosis (TB) after infection, 90% of these infections are latent. Further, mice are nearly uniformly susceptible to Mtb but their M1-polarized macrophages (M1-MΦs) can inhibit Mtb in vitro, suggesting that M1-MΦs may be able to regulate anti-TB immunity. We sought to determine whether human MΦ heterogeneity contributes to TB immunity. Here we show that IFN-γ-programmed M1-MΦs degrade Mtb through increased expression of innate immunity regulatory genes (Inregs). In contrast, IL-4-programmed M2-polarized MΦs (M2-MΦs) are permissive for Mtb proliferation and exhibit reduced Inregs expression. M1-MΦs and M2-MΦs express pro- and anti-inflammatory cytokine-chemokines, respectively, and M1-MΦs show nitric oxide and autophagy-dependent degradation of Mtb, leading to increased antigen presentation to T cells through an ATG-RAB7-cathepsin pathway. Despite Mtb infection, M1-MΦs show increased histone acetylation at the ATG5 promoter and pro-autophagy phenotypes, while increased histone deacetylases lead to decreased autophagy in M2-MΦs. Finally, Mtb-infected neonatal macaques express human Inregs in their lymph nodes and macrophages, suggesting that M1 and M2 phenotypes can mediate immunity to TB in both humans and macaques. We conclude that human MФ subsets show unique patterns of gene expression that enable differential control of TB after infection. These genes could serve as targets for diagnosis and immunotherapy of TB.
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Affiliation(s)
- Arshad Khan
- Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Weill-Cornell Medicine, Houston, TX, USA
| | - Kangling Zhang
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, USA
| | - Vipul K Singh
- Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Weill-Cornell Medicine, Houston, TX, USA
| | - Abhishek Mishra
- Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Weill-Cornell Medicine, Houston, TX, USA
| | - Priyanka Kachroo
- Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Weill-Cornell Medicine, Houston, TX, USA
| | - Tian Bing
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, USA
| | - Jong Hak Won
- Department of Obstetrics, Gynecology and Reproductive Sciences, UTHSC, Houston, TX, USA
| | - Arunmani Mani
- Department of Obstetrics, Gynecology and Reproductive Sciences, UTHSC, Houston, TX, USA
| | - Ramesha Papanna
- Department of Obstetrics, Gynecology and Reproductive Sciences, UTHSC, Houston, TX, USA
| | - Lovepreet K Mann
- Department of Obstetrics, Gynecology and Reproductive Sciences, UTHSC, Houston, TX, USA
| | | | | | - David H Canaday
- Division of Infectious Disease, Case Western Reserve University Cleveland VA, Cleveland, OH, USA
| | - Sunil A David
- Virovax, LLC, Adjuvant Division, Lawrence, Kansas, USA
| | - Blanca I Restrepo
- UT School of Public Health, Brownsville, and STDOI, UT Rio Grande Valley, Brownsville, TX, USA
| | | | - Ha Phan
- Center for Promotion of Advancement of Society, Ha Noi, Vietnam
| | - Edward A Graviss
- Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Weill-Cornell Medicine, Houston, TX, USA
| | - James M Musser
- Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Weill-Cornell Medicine, Houston, TX, USA
| | - Deepak Kaushal
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Marie Claire Gauduin
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Chinnaswamy Jagannath
- Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Weill-Cornell Medicine, Houston, TX, USA.
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10
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Christensen PA, Olsen RJ, Long SW, Snehal R, Davis JJ, Ojeda Saavedra M, Reppond K, Shyer MN, Cambric J, Gadd R, Thakur RM, Batajoo A, Mangham R, Pena S, Trinh T, Kinskey JC, Williams G, Olson R, Gollihar J, Musser JM. Signals of Significantly Increased Vaccine Breakthrough, Decreased Hospitalization Rates, and Less Severe Disease in Patients with Coronavirus Disease 2019 Caused by the Omicron Variant of Severe Acute Respiratory Syndrome Coronavirus 2 in Houston, Texas. Am J Pathol 2022; 192:642-652. [PMID: 35123975 PMCID: PMC8812084 DOI: 10.1016/j.ajpath.2022.01.007] [Citation(s) in RCA: 114] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 01/18/2022] [Accepted: 01/20/2022] [Indexed: 12/19/2022]
Abstract
Genetic variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continue to dramatically alter the landscape of the coronavirus disease 2019 (COVID-19) pandemic. The recently described variant of concern designated Omicron (B.1.1.529) has rapidly spread worldwide and is now responsible for the majority of COVID-19 cases in many countries. Because Omicron was recognized recently, many knowledge gaps exist about its epidemiology, clinical severity, and disease course. A genome sequencing study of SARS-CoV-2 in the Houston Methodist health care system identified 4468 symptomatic patients with infections caused by Omicron from late November 2021 through January 5, 2022. Omicron rapidly increased in only 3 weeks to cause 90% of all new COVID-19 cases, and at the end of the study period caused 98% of new cases. Compared with patients infected with either Alpha or Delta variants in our health care system, Omicron patients were significantly younger, had significantly increased vaccine breakthrough rates, and were significantly less likely to be hospitalized. Omicron patients required less intense respiratory support and had a shorter length of hospital stay, consistent with on average decreased disease severity. Two patients with Omicron stealth sublineage BA.2 also were identified. The data document the unusually rapid spread and increased occurrence of COVID-19 caused by the Omicron variant in metropolitan Houston, Texas, and address the lack of information about disease character among US patients.
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Affiliation(s)
- Paul A Christensen
- Laboratory of Molecular and Translational Human Infectious Diseases Research, Houston Methodist Hospital, Houston, Texas; Laboratory of Antibody Discovery and Accelerated Protein Therapeutics, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Randall J Olsen
- Laboratory of Molecular and Translational Human Infectious Diseases Research, Houston Methodist Hospital, Houston, Texas; Laboratory of Antibody Discovery and Accelerated Protein Therapeutics, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - S Wesley Long
- Laboratory of Molecular and Translational Human Infectious Diseases Research, Houston Methodist Hospital, Houston, Texas; Laboratory of Antibody Discovery and Accelerated Protein Therapeutics, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Richard Snehal
- Laboratory of Molecular and Translational Human Infectious Diseases Research, Houston Methodist Hospital, Houston, Texas
| | - James J Davis
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois; Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, Illinois
| | - Matthew Ojeda Saavedra
- Laboratory of Molecular and Translational Human Infectious Diseases Research, Houston Methodist Hospital, Houston, Texas
| | - Kristina Reppond
- Laboratory of Molecular and Translational Human Infectious Diseases Research, Houston Methodist Hospital, Houston, Texas
| | - Madison N Shyer
- Laboratory of Molecular and Translational Human Infectious Diseases Research, Houston Methodist Hospital, Houston, Texas
| | - Jessica Cambric
- Laboratory of Molecular and Translational Human Infectious Diseases Research, Houston Methodist Hospital, Houston, Texas
| | - Ryan Gadd
- Laboratory of Molecular and Translational Human Infectious Diseases Research, Houston Methodist Hospital, Houston, Texas
| | - Rashi M Thakur
- Laboratory of Molecular and Translational Human Infectious Diseases Research, Houston Methodist Hospital, Houston, Texas
| | - Akanksha Batajoo
- Laboratory of Molecular and Translational Human Infectious Diseases Research, Houston Methodist Hospital, Houston, Texas
| | - Regan Mangham
- Laboratory of Molecular and Translational Human Infectious Diseases Research, Houston Methodist Hospital, Houston, Texas
| | - Sindy Pena
- Laboratory of Molecular and Translational Human Infectious Diseases Research, Houston Methodist Hospital, Houston, Texas
| | - Trina Trinh
- Laboratory of Molecular and Translational Human Infectious Diseases Research, Houston Methodist Hospital, Houston, Texas
| | - Jacob C Kinskey
- Laboratory of Molecular and Translational Human Infectious Diseases Research, Houston Methodist Hospital, Houston, Texas
| | - Guy Williams
- Laboratory of Molecular and Translational Human Infectious Diseases Research, Houston Methodist Hospital, Houston, Texas
| | - Robert Olson
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois; Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, Illinois
| | - Jimmy Gollihar
- Laboratory of Antibody Discovery and Accelerated Protein Therapeutics, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - James M Musser
- Laboratory of Molecular and Translational Human Infectious Diseases Research, Houston Methodist Hospital, Houston, Texas; Laboratory of Antibody Discovery and Accelerated Protein Therapeutics, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York.
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11
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Vandegrift KJ, Yon M, Surendran-Nair M, Gontu A, Amirthalingam S, Nissly RH, Levine N, Stuber T, DeNicola AJ, Boulanger JR, Kotschwar N, Aucoin SG, Simon R, Toal K, Olsen RJ, Davis JJ, Bold D, Gaudreault NN, Richt JA, Musser JM, Hudson PJ, Kapur V, Kuchipudi SV. Detection of SARS-CoV-2 Omicron variant (B.1.1.529) infection of white-tailed deer. bioRxiv 2022:2022.02.04.479189. [PMID: 35169802 PMCID: PMC8845426 DOI: 10.1101/2022.02.04.479189] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
White-tailed deer ( Odocoileus virginianus ) are highly susceptible to infection by SARS-CoV-2, with multiple reports of widespread spillover of virus from humans to free-living deer. While the recently emerged SARS-CoV-2 B.1.1.529 Omicron variant of concern (VoC) has been shown to be notably more transmissible amongst humans, its ability to cause infection and spillover to non-human animals remains a challenge of concern. We found that 19 of the 131 (14.5%; 95% CI: 0.10-0.22) white-tailed deer opportunistically sampled on Staten Island, New York, between December 12, 2021, and January 31, 2022, were positive for SARS-CoV-2 specific serum antibodies using a surrogate virus neutralization assay, indicating prior exposure. The results also revealed strong evidence of age-dependence in antibody prevalence. A significantly (χ 2 , p < 0.001) greater proportion of yearling deer possessed neutralizing antibodies as compared with fawns (OR=12.7; 95% CI 4-37.5). Importantly, SARS-CoV-2 nucleic acid was detected in nasal swabs from seven of 68 (10.29%; 95% CI: 0.0-0.20) of the sampled deer, and whole-genome sequencing identified the SARS-CoV-2 Omicron VoC (B.1.1.529) is circulating amongst the white-tailed deer on Staten Island. Phylogenetic analyses revealed the deer Omicron sequences clustered closely with other, recently reported Omicron sequences recovered from infected humans in New York City and elsewhere, consistent with human to deer spillover. Interestingly, one individual deer was positive for viral RNA and had a high level of neutralizing antibodies, suggesting either rapid serological conversion during an ongoing infection or a "breakthrough" infection in a previously exposed animal. Together, our findings show that the SARS-CoV-2 B.1.1.529 Omicron VoC can infect white-tailed deer and highlights an urgent need for comprehensive surveillance of susceptible animal species to identify ecological transmission networks and better assess the potential risks of spillback to humans. KEY FINDINGS These studies provide strong evidence of infection of free-living white-tailed deer with the SARS-CoV-2 B.1.1.529 Omicron variant of concern on Staten Island, New York, and highlight an urgent need for investigations on human-to-animal-to-human spillovers/spillbacks as well as on better defining the expanding host-range of SARS-CoV-2 in non-human animals and the environment.
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Affiliation(s)
- Kurt J. Vandegrift
- The Center for Infectious Disease Dynamics, Department of Biology and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Michele Yon
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences and Huck Institutes of the Life Sciences, The Pennsylvania State University, PA,16802, USA
| | - Meera Surendran-Nair
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences and Huck Institutes of the Life Sciences, The Pennsylvania State University, PA,16802, USA
| | - Abhinay Gontu
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences and Huck Institutes of the Life Sciences, The Pennsylvania State University, PA,16802, USA
| | - Saranya Amirthalingam
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences and Huck Institutes of the Life Sciences, The Pennsylvania State University, PA,16802, USA
| | - Ruth H. Nissly
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences and Huck Institutes of the Life Sciences, The Pennsylvania State University, PA,16802, USA
| | - Nicole Levine
- Department of Animal Science and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Tod Stuber
- National Veterinary Services Laboratories, Veterinary Services, U.S. Department of Agriculture, Ames, Iowa, USA
| | | | | | | | - Sarah Grimké Aucoin
- City of New York Parks & Recreation, 1234 5 Avenue, 5 Floor, New York, NY 10029, USA
| | - Richard Simon
- City of New York Parks & Recreation, 1234 5 Avenue, 5 Floor, New York, NY 10029, USA
| | - Katrina Toal
- City of New York Parks & Recreation, 1234 5 Avenue, 5 Floor, New York, NY 10029, USA
| | - Randall J. Olsen
- Laboratory of Molecular and Translational Human Infectious Disease Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, TX 77030, USA
- Departments of Pathology and Laboratory Medicine and Microbiology and Immunology, Weill Cornell Medical College, NY 10021, USA
| | - James J. Davis
- University of Chicago Consortium for Advanced Science and Engineering, University of Chicago and Division of Data Science and Learning, Argonne National Laboratory, Argonne, Illinois, USA
| | - Dashzeveg Bold
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS, USA
| | - Natasha N. Gaudreault
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS, USA
| | - Juergen A. Richt
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS, USA
| | - James M. Musser
- Laboratory of Molecular and Translational Human Infectious Disease Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, TX 77030, USA
- Departments of Pathology and Laboratory Medicine and Microbiology and Immunology, Weill Cornell Medical College, NY 10021, USA
| | - Peter J. Hudson
- The Center for Infectious Disease Dynamics, Department of Biology and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Vivek Kapur
- Department of Animal Science and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Suresh V. Kuchipudi
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences and Huck Institutes of the Life Sciences, The Pennsylvania State University, PA,16802, USA
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12
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Christensen PA, Olsen RJ, Long SW, Subedi S, Davis JJ, Hodjat P, Walley DR, Kinskey JC, Ojeda Saavedra M, Pruitt L, Reppond K, Shyer MN, Cambric J, Gadd R, Thakur RM, Batajoo A, Mangham R, Pena S, Trinh T, Yerramilli P, Nguyen M, Olson R, Snehal R, Gollihar J, Musser JM. Delta Variants of SARS-CoV-2 Cause Significantly Increased Vaccine Breakthrough COVID-19 Cases in Houston, Texas. Am J Pathol 2022. [PMID: 34774517 DOI: 10.1101/2021.07.19.21260808] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Genetic variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have repeatedly altered the course of the coronavirus disease 2019 (COVID-19) pandemic. Delta variants are now the focus of intense international attention because they are causing widespread COVID-19 globally and are associated with vaccine breakthrough cases. We sequenced 16,965 SARS-CoV-2 genomes from samples acquired March 15, 2021, through September 20, 2021, in the Houston Methodist hospital system. This sample represents 91% of all Methodist system COVID-19 patients during the study period. Delta variants increased rapidly from late April onward to cause 99.9% of all COVID-19 cases and spread throughout the Houston metroplex. Compared with all other variants combined, Delta caused a significantly higher rate of vaccine breakthrough cases (23.7% for Delta compared with 6.6% for all other variants combined). Importantly, significantly fewer fully vaccinated individuals required hospitalization. Vaccine breakthrough cases caused by Delta had a low median PCR cycle threshold value (a proxy for high virus load). This value was similar to the median cycle threshold value for unvaccinated patients with COVID-19 caused by Delta variants, suggesting that fully vaccinated individuals can transmit SARS-CoV-2 to others. Patients infected with Alpha and Delta variants had several significant differences. The integrated analysis indicates that vaccines used in the United States are highly effective in decreasing severe COVID-19, hospitalizations, and deaths.
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Affiliation(s)
- Paul A Christensen
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Randall J Olsen
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - S Wesley Long
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Sishir Subedi
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - James J Davis
- Consortium for Advanced Science and Engineering, The University of Chicago, Chicago, Illinois; Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, Illinois
| | - Parsa Hodjat
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Debbie R Walley
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Jacob C Kinskey
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Matthew Ojeda Saavedra
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Layne Pruitt
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Kristina Reppond
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Madison N Shyer
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Jessica Cambric
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Ryan Gadd
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Rashi M Thakur
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Akanksha Batajoo
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Regan Mangham
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Sindy Pena
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Trina Trinh
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Prasanti Yerramilli
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Marcus Nguyen
- Consortium for Advanced Science and Engineering, The University of Chicago, Chicago, Illinois; Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, Illinois
| | - Robert Olson
- Consortium for Advanced Science and Engineering, The University of Chicago, Chicago, Illinois; Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, Illinois
| | - Richard Snehal
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Jimmy Gollihar
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; DEVCOM Army Research Laboratory-South, Austin, Texas
| | - James M Musser
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York.
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13
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Christensen PA, Olsen RJ, Long SW, Subedi S, Davis JJ, Hodjat P, Walley DR, Kinskey JC, Ojeda Saavedra M, Pruitt L, Reppond K, Shyer MN, Cambric J, Gadd R, Thakur RM, Batajoo A, Mangham R, Pena S, Trinh T, Yerramilli P, Nguyen M, Olson R, Snehal R, Gollihar J, Musser JM. Delta Variants of SARS-CoV-2 Cause Significantly Increased Vaccine Breakthrough COVID-19 Cases in Houston, Texas. Am J Pathol 2022; 192:320-331. [PMID: 34774517 PMCID: PMC8580569 DOI: 10.1016/j.ajpath.2021.10.019] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 10/21/2021] [Accepted: 10/26/2021] [Indexed: 11/18/2022]
Abstract
Genetic variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have repeatedly altered the course of the coronavirus disease 2019 (COVID-19) pandemic. Delta variants are now the focus of intense international attention because they are causing widespread COVID-19 globally and are associated with vaccine breakthrough cases. We sequenced 16,965 SARS-CoV-2 genomes from samples acquired March 15, 2021, through September 20, 2021, in the Houston Methodist hospital system. This sample represents 91% of all Methodist system COVID-19 patients during the study period. Delta variants increased rapidly from late April onward to cause 99.9% of all COVID-19 cases and spread throughout the Houston metroplex. Compared with all other variants combined, Delta caused a significantly higher rate of vaccine breakthrough cases (23.7% for Delta compared with 6.6% for all other variants combined). Importantly, significantly fewer fully vaccinated individuals required hospitalization. Vaccine breakthrough cases caused by Delta had a low median PCR cycle threshold value (a proxy for high virus load). This value was similar to the median cycle threshold value for unvaccinated patients with COVID-19 caused by Delta variants, suggesting that fully vaccinated individuals can transmit SARS-CoV-2 to others. Patients infected with Alpha and Delta variants had several significant differences. The integrated analysis indicates that vaccines used in the United States are highly effective in decreasing severe COVID-19, hospitalizations, and deaths.
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Affiliation(s)
- Paul A Christensen
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Randall J Olsen
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - S Wesley Long
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Sishir Subedi
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - James J Davis
- Consortium for Advanced Science and Engineering, The University of Chicago, Chicago, Illinois; Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, Illinois
| | - Parsa Hodjat
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Debbie R Walley
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Jacob C Kinskey
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Matthew Ojeda Saavedra
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Layne Pruitt
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Kristina Reppond
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Madison N Shyer
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Jessica Cambric
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Ryan Gadd
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Rashi M Thakur
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Akanksha Batajoo
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Regan Mangham
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Sindy Pena
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Trina Trinh
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Prasanti Yerramilli
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Marcus Nguyen
- Consortium for Advanced Science and Engineering, The University of Chicago, Chicago, Illinois; Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, Illinois
| | - Robert Olson
- Consortium for Advanced Science and Engineering, The University of Chicago, Chicago, Illinois; Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, Illinois
| | - Richard Snehal
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Jimmy Gollihar
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; DEVCOM Army Research Laboratory-South, Austin, Texas
| | - James M Musser
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York.
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14
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Davis JJ, Long SW, Christensen PA, Olsen RJ, Olson R, Shukla M, Subedi S, Stevens R, Musser JM. Analysis of the ARTIC Version 3 and Version 4 SARS-CoV-2 Primers and Their Impact on the Detection of the G142D Amino Acid Substitution in the Spike Protein. Microbiol Spectr 2021; 9:e0180321. [PMID: 34878296 DOI: 10.1101/2021.09.27.461949] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023] Open
Abstract
The ARTIC Network provides a common resource of PCR primer sequences and recommendations for amplifying SARS-CoV-2 genomes. The initial tiling strategy was developed with the reference genome Wuhan-01, and subsequent iterations have addressed areas of low amplification and sequence drop out. Recently, a new version (V4) was released, based on new variant genome sequences, in response to the realization that some V3 primers were located in regions with key mutations. Herein, we compare the performance of the ARTIC V3 and V4 primer sets with a matched set of 663 SARS-CoV-2 clinical samples sequenced with an Illumina NovaSeq 6000 instrument. We observe general improvements in sequencing depth and quality, and improved resolution of the SNP causing the D950N variation in the spike protein. Importantly, we also find nearly universal presence of spike protein substitution G142D in Delta-lineage samples. Due to the prior release and widespread use of the ARTIC V3 primers during the initial surge of the Delta variant, it is likely that the G142D amino acid substitution is substantially underrepresented among early Delta variant genomes deposited in public repositories. In addition to the improved performance of the ARTIC V4 primer set, this study also illustrates the importance of the primer scheme in downstream analyses. IMPORTANCE ARTIC Network primers are commonly used by laboratories worldwide to amplify and sequence SARS-CoV-2 present in clinical samples. As new variants have evolved and spread, it was found that the V3 primer set poorly amplified several key mutations. In this report, we compare the results of sequencing a matched set of samples with the V3 and V4 primer sets. We find that adoption of the ARTIC V4 primer set is critical for accurate sequencing of the SARS-CoV-2 spike region. The absence of metadata describing the primer scheme used will negatively impact the downstream use of publicly available SARS-Cov-2 sequencing reads and assembled genomes.
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Affiliation(s)
- James J Davis
- Division of Data Science and Learning, Argonne National Laboratorygrid.187073.a, Lemont, Illinois, USA
- University of Chicago Consortium for Advanced Science and Engineering, Chicago, Illinois, USA
| | - S Wesley Long
- Center for Infectious Diseases, Laboratory of Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, USA
- Departments of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Departments of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - Paul A Christensen
- Center for Infectious Diseases, Laboratory of Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, USA
- Departments of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Departments of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - Randall J Olsen
- Center for Infectious Diseases, Laboratory of Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, USA
- Departments of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Departments of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - Robert Olson
- Division of Data Science and Learning, Argonne National Laboratorygrid.187073.a, Lemont, Illinois, USA
- University of Chicago Consortium for Advanced Science and Engineering, Chicago, Illinois, USA
| | - Maulik Shukla
- Division of Data Science and Learning, Argonne National Laboratorygrid.187073.a, Lemont, Illinois, USA
- University of Chicago Consortium for Advanced Science and Engineering, Chicago, Illinois, USA
| | - Sishir Subedi
- Center for Infectious Diseases, Laboratory of Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, USA
- Departments of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Departments of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - Rick Stevens
- Computing, Environment and Life Sciences Directorate, Argonne National Laboratorygrid.187073.a, Argonne, Illinois, USA
- Department of Computer Science, University of Chicago, Chicago, Illinois, USA
| | - James M Musser
- Center for Infectious Diseases, Laboratory of Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, USA
- Departments of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Departments of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
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15
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Davis JJ, Long SW, Christensen PA, Olsen RJ, Olson R, Shukla M, Subedi S, Stevens R, Musser JM. Analysis of the ARTIC Version 3 and Version 4 SARS-CoV-2 Primers and Their Impact on the Detection of the G142D Amino Acid Substitution in the Spike Protein. Microbiol Spectr 2021; 9:e0180321. [PMID: 34878296 PMCID: PMC8653831 DOI: 10.1128/spectrum.01803-21] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 11/05/2021] [Indexed: 12/21/2022] Open
Abstract
The ARTIC Network provides a common resource of PCR primer sequences and recommendations for amplifying SARS-CoV-2 genomes. The initial tiling strategy was developed with the reference genome Wuhan-01, and subsequent iterations have addressed areas of low amplification and sequence drop out. Recently, a new version (V4) was released, based on new variant genome sequences, in response to the realization that some V3 primers were located in regions with key mutations. Herein, we compare the performance of the ARTIC V3 and V4 primer sets with a matched set of 663 SARS-CoV-2 clinical samples sequenced with an Illumina NovaSeq 6000 instrument. We observe general improvements in sequencing depth and quality, and improved resolution of the SNP causing the D950N variation in the spike protein. Importantly, we also find nearly universal presence of spike protein substitution G142D in Delta-lineage samples. Due to the prior release and widespread use of the ARTIC V3 primers during the initial surge of the Delta variant, it is likely that the G142D amino acid substitution is substantially underrepresented among early Delta variant genomes deposited in public repositories. In addition to the improved performance of the ARTIC V4 primer set, this study also illustrates the importance of the primer scheme in downstream analyses. IMPORTANCE ARTIC Network primers are commonly used by laboratories worldwide to amplify and sequence SARS-CoV-2 present in clinical samples. As new variants have evolved and spread, it was found that the V3 primer set poorly amplified several key mutations. In this report, we compare the results of sequencing a matched set of samples with the V3 and V4 primer sets. We find that adoption of the ARTIC V4 primer set is critical for accurate sequencing of the SARS-CoV-2 spike region. The absence of metadata describing the primer scheme used will negatively impact the downstream use of publicly available SARS-Cov-2 sequencing reads and assembled genomes.
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Affiliation(s)
- James J. Davis
- Division of Data Science and Learning, Argonne National Laboratory, Lemont, Illinois, USA
- University of Chicago Consortium for Advanced Science and Engineering, Chicago, Illinois, USA
| | - S. Wesley Long
- Center for Infectious Diseases, Laboratory of Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, USA
- Departments of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Departments of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - Paul A. Christensen
- Center for Infectious Diseases, Laboratory of Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, USA
- Departments of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Departments of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - Randall J. Olsen
- Center for Infectious Diseases, Laboratory of Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, USA
- Departments of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Departments of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - Robert Olson
- Division of Data Science and Learning, Argonne National Laboratory, Lemont, Illinois, USA
- University of Chicago Consortium for Advanced Science and Engineering, Chicago, Illinois, USA
| | - Maulik Shukla
- Division of Data Science and Learning, Argonne National Laboratory, Lemont, Illinois, USA
- University of Chicago Consortium for Advanced Science and Engineering, Chicago, Illinois, USA
| | - Sishir Subedi
- Center for Infectious Diseases, Laboratory of Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, USA
- Departments of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Departments of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - Rick Stevens
- Computing, Environment and Life Sciences Directorate, Argonne National Laboratory, Argonne, Illinois, USA
- Department of Computer Science, University of Chicago, Chicago, Illinois, USA
| | - James M. Musser
- Center for Infectious Diseases, Laboratory of Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, USA
- Departments of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Departments of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
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16
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Cooper MH, Christensen PA, Salazar E, Perez KK, Graviss EA, Nguyen D, Musser JM, Huang HJ, Liebl MG. Real-world Assessment of 2879 COVID-19 Patients Treated With Monoclonal Antibody Therapy: A Propensity Score-Matched Cohort Study. Open Forum Infect Dis 2021; 8:ofab512. [PMID: 35559124 PMCID: PMC9088516 DOI: 10.1093/ofid/ofab512] [Citation(s) in RCA: 6] [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: 08/05/2021] [Accepted: 10/07/2021] [Indexed: 11/16/2022] Open
Abstract
Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to spread globally and cause significant morbidity and mortality. Antispike protein monoclonal antibody (mAb) therapy has been shown to prevent progression to severe coronavirus disease 2019 (COVID-19). The objective of this study was to report the outcomes of high-risk, SARS-CoV-2-positive patients infused with 1 of the 3 mAb therapies available through Food and Drug Administration Emergency Use Authorization (EUA). Methods A total of 4328 SARS-CoV-2-positive patients who satisfied EUA criteria for eligibility for receiving mAb therapy were infused with bamlanivimab or the combination therapies bamlanivimab-etesevimab or casirivimab-imdevimab from November 22, 2020, to May 31, 2021, at 6 infusion clinics and multiple emergency departments within the 8 Houston Methodist Hospitals in Houston, Texas. The primary outcome of hospital admission within 14 and 28 days postinfusion was assessed relative to a propensity score-matched cohort, matched based on age, race/ethnicity, median income by zip code, body mass index, comorbidities, and positive polymerase chain reaction date. Secondary outcomes included intensive care unit admission and mortality. Results A total of 2879 infused patients and matched controls were included in the analysis, including 1718 patients infused with bamlanivimab, 346 patients infused with bamlanivimab-etesevimab, and 815 patients infused with casirivimab-imdevimab. Hospital admission and mortality rates were significantly decreased overall in mAb-infused patients relative to matched controls. Among the infused cohort, those who received casirivimab-imdevimab had a significantly decreased rate of admission relative to the other 2 mAb therapy groups (adjusted risk ratio,0.51; P=.001). Conclusions Treatment with bamlanivimab, bamlanivimab-etesevimab, or casirivimab-imdevimab significantly decreased the number of patients who progressed to severe COVID-19 disease and required hospitalization.
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Affiliation(s)
- Megan H Cooper
- Department of Pharmacy, Houston Methodist Hospital, Houston, Texas, USA
| | - Paul A Christensen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Eric Salazar
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Katherine K Perez
- Department of Pharmacy, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Edward A Graviss
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, Texas, USA
| | - Duc Nguyen
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, Texas, USA
| | - James M Musser
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, Texas, USA
| | - Howard J Huang
- Division of Pulmonology, Pulmonary, Critical Care & Sleep Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Michael G Liebl
- Department of Pharmacy, Houston Methodist Hospital, Houston, Texas, USA
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17
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Olsen RJ, Christensen PA, Long SW, Subedi S, Hodjat P, Olson R, Nguyen M, Davis JJ, Yerramilli P, Saavedra MO, Pruitt L, Reppond K, Shyer MN, Cambric J, Gadd R, Thakur RM, Batajoo A, Finkelstein IJ, Gollihar J, Musser JM. Trajectory of Growth of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants in Houston, Texas, January through May 2021, Based on 12,476 Genome Sequences. Am J Pathol 2021; 191:1754-1773. [PMID: 34303698 PMCID: PMC8299152 DOI: 10.1016/j.ajpath.2021.07.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 06/30/2021] [Accepted: 07/02/2021] [Indexed: 12/13/2022]
Abstract
Certain genetic variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are of substantial concern because they may be more transmissible or detrimentally alter the pandemic course and disease features in individual patients. SARS-CoV-2 genome sequences from 12,476 patients in the Houston Methodist health care system diagnosed from January 1 through May 31, 2021 are reported here. Prevalence of the B.1.1.7 (Alpha) variant increased rapidly and caused 63% to 90% of new cases in the latter half of May. Eleven B.1.1.7 genomes had an E484K replacement in spike protein, a change also identified in other SARS-CoV-2 lineages. Compared with non-B.1.1.7-infected patients, individuals with B.1.1.7 had a significantly lower cycle threshold (a proxy for higher virus load) and significantly higher hospitalization rate. Other variants [eg, B.1.429 and B.1.427 (Epsilon), P.1 (Gamma), P.2 (Zeta), and R.1] also increased rapidly, although the magnitude was less than that in B.1.1.7. Twenty-two patients infected with B.1.617.1 (Kappa) or B.1.617.2 (Delta) variants had a high rate of hospitalization. Breakthrough cases (n = 207) in fully vaccinated patients were caused by a heterogeneous array of virus genotypes, including many not currently designated variants of interest or concern. In the aggregate, this study delineates the trajectory of SARS-CoV-2 variants circulating in a major metropolitan area, documents B.1.1.7 as the major cause of new cases in Houston, TX, and heralds the arrival of B.1.617 variants in the metroplex.
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Affiliation(s)
- Randall J Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas; Departments of Pathology and Laboratory Medicine, and Microbiology and Immunology, Weill Cornell Medical College, New York, New York
| | - Paul A Christensen
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - S Wesley Long
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas; Departments of Pathology and Laboratory Medicine, and Microbiology and Immunology, Weill Cornell Medical College, New York, New York
| | - Sishir Subedi
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Parsa Hodjat
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Robert Olson
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois; Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, Illinois
| | - Marcus Nguyen
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois; Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, Illinois
| | - James J Davis
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois; Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, Illinois
| | - Prasanti Yerramilli
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Matthew O Saavedra
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Layne Pruitt
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Kristina Reppond
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Madison N Shyer
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Jessica Cambric
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Ryan Gadd
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Rashi M Thakur
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Akanksha Batajoo
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Ilya J Finkelstein
- Department of Molecular Biosciences and Institute of Molecular Biosciences, The University of Texas at Austin, Austin, Texas
| | - Jimmy Gollihar
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas; Combat Capabilities Development Command (CCDC) Army Research Laboratory-South, University of Texas, Austin, Texas
| | - James M Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas; Departments of Pathology and Laboratory Medicine, and Microbiology and Immunology, Weill Cornell Medical College, New York, New York.
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18
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Long SW, Olsen RJ, Christensen PA, Subedi S, Olson R, Davis JJ, Saavedra MO, Yerramilli P, Pruitt L, Reppond K, Shyer MN, Cambric J, Finkelstein IJ, Gollihar J, Musser JM. Sequence Analysis of 20,453 Severe Acute Respiratory Syndrome Coronavirus 2 Genomes from the Houston Metropolitan Area Identifies the Emergence and Widespread Distribution of Multiple Isolates of All Major Variants of Concern. Am J Pathol 2021; 191:983-992. [PMID: 33741335 PMCID: PMC7962948 DOI: 10.1016/j.ajpath.2021.03.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/07/2021] [Accepted: 03/08/2021] [Indexed: 12/13/2022]
Abstract
Since the beginning of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, there has been international concern about the emergence of virus variants with mutations that increase transmissibility, enhance escape from the human immune response, or otherwise alter biologically important phenotypes. In late 2020, several variants of concern emerged globally, including the UK variant (B.1.1.7), the South Africa variant (B.1.351), Brazil variants (P.1 and P.2), and two related California variants of interest (B.1.429 and B.1.427). These variants are believed to have enhanced transmissibility. For the South Africa and Brazil variants, there is evidence that mutations in spike protein permit it to escape from some vaccines and therapeutic monoclonal antibodies. On the basis of our extensive genome sequencing program involving 20,453 coronavirus disease 2019 patient samples collected from March 2020 to February 2021, we report identification of all six of these SARS-CoV-2 variants among Houston Methodist Hospital (Houston, TX) patients residing in the greater metropolitan area. Although these variants are currently at relatively low frequency (aggregate of 1.1%) in the population, they are geographically widespread. Houston is the first city in the United States in which active circulation of all six current variants of concern has been documented by genome sequencing. As vaccine deployment accelerates, increased genomic surveillance of SARS-CoV-2 is essential to understanding the presence, frequency, and medical impact of consequential variants and their patterns and trajectory of dissemination.
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Affiliation(s)
- S Wesley Long
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas; Departments of Pathology and Laboratory Medicine, and Microbiology and Immunology, Weill Cornell Medical College, New York, New York
| | - Randall J Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas; Departments of Pathology and Laboratory Medicine, and Microbiology and Immunology, Weill Cornell Medical College, New York, New York
| | - Paul A Christensen
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Sishir Subedi
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Robert Olson
- Consortium for Advanced Science and Engineering, 22 University of Chicago, Chicago, Illinois; Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, Illinois
| | - James J Davis
- Consortium for Advanced Science and Engineering, 22 University of Chicago, Chicago, Illinois; Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, Illinois
| | - Matthew Ojeda Saavedra
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Prasanti Yerramilli
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Layne Pruitt
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Kristina Reppond
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Madison N Shyer
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Jessica Cambric
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Ilya J Finkelstein
- Department of Molecular Biosciences and Institute of Molecular Biosciences, The University of Texas at Austin, Austin, Texas
| | - Jimmy Gollihar
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas; CCDC Army Research Laboratory-South, University of Texas, Austin, Texas
| | - James M Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas; Departments of Pathology and Laboratory Medicine, and Microbiology and Immunology, Weill Cornell Medical College, New York, New York.
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19
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Goike J, Hsieh CL, Horton A, Gardner EC, Bartzoka F, Wang N, Javanmardi K, Herbert A, Abbassi S, Renberg R, Johanson MJ, Cardona JA, Segall-Shapiro T, Zhou L, Nissly RH, Gontu A, Byrom M, Maranhao AC, Battenhouse AM, Gejji V, Soto-Sierra L, Foster ER, Woodard SL, Nikolov ZL, Lavinder J, Voss WN, Annapareddy A, Ippolito GC, Ellington AD, Marcotte EM, Finkelstein IJ, Hughes RA, Musser JM, Kuchipudi SV, Kapur V, Georgiou G, Dye JM, Boutz DR, McLellan JS, Gollihar JD. Synthetic repertoires derived from convalescent COVID-19 patients enable discovery of SARS-CoV-2 neutralizing antibodies and a novel quaternary binding modality. bioRxiv 2021:2021.04.07.438849. [PMID: 33851158 PMCID: PMC8043448 DOI: 10.1101/2021.04.07.438849] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The ongoing evolution of SARS-CoV-2 into more easily transmissible and infectious variants has sparked concern over the continued effectiveness of existing therapeutic antibodies and vaccines. Hence, together with increased genomic surveillance, methods to rapidly develop and assess effective interventions are critically needed. Here we report the discovery of SARS-CoV-2 neutralizing antibodies isolated from COVID-19 patients using a high-throughput platform. Antibodies were identified from unpaired donor B-cell and serum repertoires using yeast surface display, proteomics, and public light chain screening. Cryo-EM and functional characterization of the antibodies identified N3-1, an antibody that binds avidly (Kd,app = 68 pM) to the receptor binding domain (RBD) of the spike protein and robustly neutralizes the virus in vitro. This antibody likely binds all three RBDs of the trimeric spike protein with a single IgG. Importantly, N3-1 equivalently binds spike proteins from emerging SARS-CoV-2 variants of concern, neutralizes UK variant B.1.1.7, and binds SARS-CoV spike with nanomolar affinity. Taken together, the strategies described herein will prove broadly applicable in interrogating adaptive immunity and developing rapid response biological countermeasures to emerging pathogens.
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Affiliation(s)
- Jule Goike
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Ching-Lin Hsieh
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Andrew Horton
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Elizabeth C. Gardner
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Foteini Bartzoka
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Nianshuang Wang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Kamyab Javanmardi
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Andrew Herbert
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Shawn Abbassi
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Rebecca Renberg
- CCDC Army Research Laboratory, Biotechnology Branch, Adelphi, MD, USA
| | - Michael J. Johanson
- National Center for Therapeutics Manufacturing, Texas A&M University, College Station, TX, USA
| | - Jose A. Cardona
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | | | - Ling Zhou
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Ruth H. Nissly
- Department of Veterinary and Biomedical Science and Animal Diagnostic Laboratory, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Abhinay Gontu
- Department of Veterinary and Biomedical Science and Animal Diagnostic Laboratory, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Michelle Byrom
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Andre C. Maranhao
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Anna M. Battenhouse
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Varun Gejji
- National Center for Therapeutics Manufacturing, Texas A&M University, College Station, TX, USA
| | - Laura Soto-Sierra
- National Center for Therapeutics Manufacturing, Texas A&M University, College Station, TX, USA
- Department of Agricultural and Biological Engineering, Texas A&M University, College Station, TX, USA
| | - Emma R. Foster
- National Center for Therapeutics Manufacturing, Texas A&M University, College Station, TX, USA
- Department of Agricultural and Biological Engineering, Texas A&M University, College Station, TX, USA
| | - Susan L. Woodard
- National Center for Therapeutics Manufacturing, Texas A&M University, College Station, TX, USA
| | - Zivko L. Nikolov
- National Center for Therapeutics Manufacturing, Texas A&M University, College Station, TX, USA
- Department of Agricultural and Biological Engineering, Texas A&M University, College Station, TX, USA
| | - Jason Lavinder
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Will N. Voss
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Ankur Annapareddy
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- CCDC Army Research Laboratory-South, Austin, TX, USA
| | - Gregory C. Ippolito
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
| | - Andrew D. Ellington
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
| | - Edward M. Marcotte
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Ilya J. Finkelstein
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Randall A. Hughes
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- CCDC Army Research Laboratory-South, Austin, TX, USA
| | - James M. Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, USA
| | - Suresh V. Kuchipudi
- Department of Veterinary and Biomedical Science and Animal Diagnostic Laboratory, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Vivek Kapur
- Department of Animal Science and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - George Georgiou
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
- Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
| | - John M. Dye
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Daniel R. Boutz
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- CCDC Army Research Laboratory-South, Austin, TX, USA
| | - Jason S. McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Jimmy D. Gollihar
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- CCDC Army Research Laboratory-South, Austin, TX, USA
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, USA
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20
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Klassen SA, Senefeld J, Johnson PW, Carter RE, Wiggins CC, Shoham S, Grossman BJ, Henderson JP, Musser JM, Salazar E, Hartman WR, Bouvier NM, Liu STH, Pirofski LA, Baker SE, Van Helmond N, Wright RS, Fairweather D, Bruno KA, Paneth NS, Casadevall A, Joyner MJ. The Effect of Convalescent Plasma Therapy on COVID-19 Patient Mortality: Systematic Review and Meta-analysis. medRxiv 2021. [PMID: 33140056 DOI: 10.1101/2020.07.29.20162917] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
To determine the effect of COVID-19 convalescent plasma on mortality, we aggregated patient outcome data from 10 randomized clinical trials (RCT), 20 matched-control studies, two dose-response studies, and 96 case-reports or case series. Studies published between January 1, 2020 to January 16, 2021 were identified through a systematic search of online PubMed and MEDLINE databases. Random effects analyses of RCT and matched-control data demonstrated that COVID-19 patients transfused with convalescent plasma exhibited a lower mortality rate compared to patients receiving standard treatments. Additional analyses showed that early transfusion (within 3 days of hospital admission) of higher titer plasma is associated with lower patient mortality. These data provide evidence favoring the efficacy of human convalescent plasma as a therapeutic agent in hospitalized COVID-19 patients.
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21
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Salazar E, Christensen PA, Graviss EA, Nguyen DT, Castillo B, Chen J, Lopez BV, Eagar TN, Yi X, Zhao P, Rogers J, Shehabeldin A, Joseph D, Masud F, Leveque C, Olsen RJ, Bernard DW, Gollihar J, Musser JM. Significantly Decreased Mortality in a Large Cohort of Coronavirus Disease 2019 (COVID-19) Patients Transfused Early with Convalescent Plasma Containing High-Titer Anti-Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Spike Protein IgG. Am J Pathol 2021; 191:90-107. [PMID: 33157066 PMCID: PMC7609241 DOI: 10.1016/j.ajpath.2020.10.008] [Citation(s) in RCA: 108] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 10/23/2020] [Accepted: 10/28/2020] [Indexed: 01/29/2023]
Abstract
Coronavirus disease 2019 (COVID-19) convalescent plasma has emerged as a promising therapy and has been granted Emergency Use Authorization by the US Food and Drug Administration for hospitalized COVID-19 patients. We recently reported results from interim analysis of a propensity score-matched study suggesting that early treatment of COVID-19 patients with convalescent plasma containing high-titer anti-spike protein receptor binding domain (RBD) IgG significantly decreases mortality. We herein present results from a 60-day follow-up of a cohort of 351 transfused hospitalized patients. Prospective determination of enzyme-linked immunosorbent assay anti-RBD IgG titer facilitated selection and transfusion of the highest titer units available. Retrospective analysis by the Ortho VITROS IgG assay revealed a median signal/cutoff ratio of 24.0 for transfused units, a value far exceeding the recent US Food and Drug Administration-required cutoff of 12.0 for designation of high-titer convalescent plasma. With respect to altering mortality, our analysis identified an optimal window of 44 hours after hospitalization for transfusing COVID-19 patients with high-titer convalescent plasma. In the aggregate, the analysis confirms and extends our previous preliminary finding that transfusion of COVID-19 patients soon after hospitalization with high-titer anti-spike protein RBD IgG present in convalescent plasma significantly reduces mortality.
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Affiliation(s)
- Eric Salazar
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Paul A Christensen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Edward A Graviss
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute, Houston, Texas
| | - Duc T Nguyen
- Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute, Houston, Texas
| | - Brian Castillo
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Jian Chen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Bevin V Lopez
- Academic Office of Clinical Trials, Houston Methodist Research Institute, Houston, Texas
| | - Todd N Eagar
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Xin Yi
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Picheng Zhao
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - John Rogers
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Ahmed Shehabeldin
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - David Joseph
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Faisal Masud
- Department of Anesthesiology and Critical Care, Houston Methodist Hospital, Houston, Texas
| | - Christopher Leveque
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Randall J Olsen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York; Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute, Houston, Texas
| | - David W Bernard
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Jimmy Gollihar
- The Combat Capabilities Development Command Army Research Laboratory-South, University of Texas at Austin, Austin, Texas
| | - James M Musser
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York; Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute, Houston, Texas.
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22
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Salazar E, Kuchipudi SV, Christensen PA, Eagar T, Yi X, Zhao P, Jin Z, Long SW, Olsen RJ, Chen J, Castillo B, Leveque C, Towers D, Lavinder J, Gollihar J, Cardona J, Ippolito G, Nissly R, Bird I, Greenawalt D, Rossi RM, Gontu A, Srinivasan S, Poojary I, Cattadori IM, Hudson PJ, Josleyn NM, Prugar L, Huie K, Herbert A, Bernard DW, Dye JM, Kapur V, Musser JM. Convalescent plasma anti-SARS-CoV-2 spike protein ectodomain and receptor-binding domain IgG correlate with virus neutralization. J Clin Invest 2020; 130:6728-6738. [PMID: 32910806 PMCID: PMC7685744 DOI: 10.1172/jci141206] [Citation(s) in RCA: 134] [Impact Index Per Article: 33.5] [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: 06/09/2020] [Accepted: 09/02/2020] [Indexed: 12/13/2022] Open
Abstract
The newly emerged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) highlights the urgent need for assays that detect protective levels of neutralizing antibodies. We studied the relationship among anti-spike ectodomain (anti-ECD), anti-receptor-binding domain (anti-RBD) IgG titers, and SARS-CoV-2 virus neutralization (VN) titers generated by 2 in vitro assays using convalescent plasma samples from 68 patients with COVID-19. We report a strong positive correlation between both plasma anti-RBD and anti-ECD IgG titers and in vitro VN titers. The probability of a VN titer of ≥160, the FDA-recommended level for convalescent plasma used for COVID-19 treatment, was ≥80% when anti-RBD or anti-ECD titers were ≥1:1350. Of all donors, 37% lacked VN titers of ≥160. Dyspnea, hospitalization, and disease severity were significantly associated with higher VN titer. Frequent donation of convalescent plasma did not significantly decrease VN or IgG titers. Analysis of 2814 asymptomatic adults found 73 individuals with anti-ECD IgG titers of ≥1:50 and strong positive correlation with anti-RBD and VN titers. Fourteen of these individuals had VN titers of ≥1:160, and all of them had anti-RBD titers of ≥1:1350. We conclude that anti-RBD or anti-ECD IgG titers can serve as a surrogate for VN titers to identify suitable plasma donors. Plasma anti-RBD or anti-ECD titers of ≥1:1350 may provide critical information about protection against COVID-19 disease.
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Affiliation(s)
- Eric Salazar
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Suresh V. Kuchipudi
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, and
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Paul A. Christensen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Todd Eagar
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Xin Yi
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Picheng Zhao
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Zhicheng Jin
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - S. Wesley Long
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute, Houston, Texas, USA
| | - Randall J. Olsen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute, Houston, Texas, USA
| | - Jian Chen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Brian Castillo
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Christopher Leveque
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Dalton Towers
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
| | - Jason Lavinder
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
| | - Jimmy Gollihar
- Combat Capabilities Development Command Army Research Laboratory — South, University of Texas, Austin, Texas, USA
| | - Jose Cardona
- Combat Capabilities Development Command Army Research Laboratory — South, University of Texas, Austin, Texas, USA
| | - Gregory Ippolito
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
- Department of Oncology, Dell Medical School, University of Texas at Austin, Austin, Texas, USA
| | - Ruth Nissly
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, and
| | - Ian Bird
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, and
| | - Denver Greenawalt
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, and
| | | | - Abhinay Gontu
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, and
| | | | | | - Isabella M. Cattadori
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, Pennsylvania, USA
- Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute, Houston, Texas, USA
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Peter J. Hudson
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, Pennsylvania, USA
- Huck Institutes of the Life Sciences and
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Nicole M. Josleyn
- US Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, USA
| | - Laura Prugar
- US Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, USA
| | - Kathleen Huie
- US Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, USA
| | - Andrew Herbert
- US Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, USA
| | - David W. Bernard
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
| | - John M. Dye
- US Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, USA
| | - Vivek Kapur
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, Pennsylvania, USA
- Huck Institutes of the Life Sciences and
- Department of Animal Science, Pennsylvania State University, University Park, Pennsylvania, USA
| | - James M. Musser
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute, Houston, Texas, USA
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23
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Salazar E, Christensen PA, Graviss EA, Nguyen DT, Castillo B, Chen J, Lopez BV, Eagar TN, Yi X, Zhao P, Rogers J, Shehabeldin A, Joseph D, Leveque C, Olsen RJ, Bernard DW, Gollihar J, Musser JM. Treatment of Coronavirus Disease 2019 Patients with Convalescent Plasma Reveals a Signal of Significantly Decreased Mortality. Am J Pathol 2020; 190:2290-2303. [PMID: 32795424 PMCID: PMC7417901 DOI: 10.1016/j.ajpath.2020.08.001] [Citation(s) in RCA: 157] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/01/2020] [Accepted: 08/03/2020] [Indexed: 12/28/2022]
Abstract
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2, has spread globally, and proven treatments are limited. Transfusion of convalescent plasma collected from donors who have recovered from COVID-19 is among many approaches being studied as potentially efficacious therapy. We are conducting a prospective, propensity score-matched study assessing the efficacy of COVID-19 convalescent plasma transfusion versus standard of care as treatment for severe and/or critical COVID-19. We present herein the results of an interim analysis of 316 patients enrolled at Houston Methodist hospitals from March 28 to July 6, 2020. Of the 316 transfused patients, 136 met a 28-day outcome and were matched to 251 non-transfused control COVID-19 patients. Matching criteria included age, sex, body mass index, comorbidities, and baseline ventilation requirement 48 hours from admission, and in a second matching analysis, ventilation status at day 0. Variability in the timing of transfusion relative to admission and titer of antibodies of plasma transfused allowed for analysis in specific matched cohorts. The analysis showed a significant reduction (P = 0.047) in mortality within 28 days, specifically in patients transfused within 72 hours of admission with plasma with an anti-spike protein receptor binding domain titer of ≥1:1350. These data suggest that treatment of COVID-19 with high anti-receptor binding domain IgG titer convalescent plasma is efficacious in early-disease patients.
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Affiliation(s)
- Eric Salazar
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Paul A Christensen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Edward A Graviss
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute, Houston, Texas
| | - Duc T Nguyen
- Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute, Houston, Texas
| | - Brian Castillo
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Jian Chen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Bevin V Lopez
- Academic Office of Clinical Trials, Houston Methodist Research Institute, Houston, Texas
| | - Todd N Eagar
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Xin Yi
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Picheng Zhao
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - John Rogers
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Ahmed Shehabeldin
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - David Joseph
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Christopher Leveque
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Randall J Olsen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York; Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute, Houston, Texas
| | - David W Bernard
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Jimmy Gollihar
- Combat Capabilities Development Command Army Research Laboratory-South, University of Texas at Austin, Austin, Texas
| | - James M Musser
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York; Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute, Houston, Texas.
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24
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Long SW, Olsen RJ, Christensen PA, Bernard DW, Davis JJ, Shukla M, Nguyen M, Saavedra MO, Yerramilli P, Pruitt L, Subedi S, Kuo HC, Hendrickson H, Eskandari G, Nguyen HAT, Long JH, Kumaraswami M, Goike J, Boutz D, Gollihar J, McLellan JS, Chou CW, Javanmardi K, Finkelstein IJ, Musser JM. Molecular Architecture of Early Dissemination and Massive Second Wave of the SARS-CoV-2 Virus in a Major Metropolitan Area. mBio 2020; 11:e02707-20. [PMID: 33127862 PMCID: PMC7642679 DOI: 10.1128/mbio.02707-20] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [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: 09/25/2020] [Accepted: 10/05/2020] [Indexed: 01/18/2023] Open
Abstract
We sequenced the genomes of 5,085 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains causing two coronavirus disease 2019 (COVID-19) disease waves in metropolitan Houston, TX, an ethnically diverse region with 7 million residents. The genomes were from viruses recovered in the earliest recognized phase of the pandemic in Houston and from viruses recovered in an ongoing massive second wave of infections. The virus was originally introduced into Houston many times independently. Virtually all strains in the second wave have a Gly614 amino acid replacement in the spike protein, a polymorphism that has been linked to increased transmission and infectivity. Patients infected with the Gly614 variant strains had significantly higher virus loads in the nasopharynx on initial diagnosis. We found little evidence of a significant relationship between virus genotype and altered virulence, stressing the linkage between disease severity, underlying medical conditions, and host genetics. Some regions of the spike protein-the primary target of global vaccine efforts-are replete with amino acid replacements, perhaps indicating the action of selection. We exploited the genomic data to generate defined single amino acid replacements in the receptor binding domain of spike protein that, importantly, produced decreased recognition by the neutralizing monoclonal antibody CR3022. Our report represents the first analysis of the molecular architecture of SARS-CoV-2 in two infection waves in a major metropolitan region. The findings will help us to understand the origin, composition, and trajectory of future infection waves and the potential effect of the host immune response and therapeutic maneuvers on SARS-CoV-2 evolution.IMPORTANCE There is concern about second and subsequent waves of COVID-19 caused by the SARS-CoV-2 coronavirus occurring in communities globally that had an initial disease wave. Metropolitan Houston, TX, with a population of 7 million, is experiencing a massive second disease wave that began in late May 2020. To understand SARS-CoV-2 molecular population genomic architecture and evolution and the relationship between virus genotypes and patient features, we sequenced the genomes of 5,085 SARS-CoV-2 strains from these two waves. Our report provides the first molecular characterization of SARS-CoV-2 strains causing two distinct COVID-19 disease waves.
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MESH Headings
- Amino Acid Sequence
- Amino Acid Substitution
- Antibodies, Neutralizing/immunology
- Base Sequence
- Betacoronavirus/genetics
- Betacoronavirus/immunology
- COVID-19
- COVID-19 Testing
- Clinical Laboratory Techniques
- Coronavirus Infections/diagnosis
- Coronavirus Infections/epidemiology
- Coronavirus Infections/immunology
- Coronavirus Infections/virology
- Coronavirus RNA-Dependent RNA Polymerase
- Genome, Viral
- Genotype
- Humans
- Machine Learning
- Models, Molecular
- Molecular Diagnostic Techniques
- Pandemics
- Phylogeny
- Pneumonia, Viral/epidemiology
- Pneumonia, Viral/immunology
- Pneumonia, Viral/virology
- RNA-Dependent RNA Polymerase/chemistry
- RNA-Dependent RNA Polymerase/genetics
- SARS-CoV-2
- Sequence Analysis, Protein
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Texas/epidemiology
- Viral Nonstructural Proteins/chemistry
- Viral Nonstructural Proteins/genetics
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Affiliation(s)
- S Wesley Long
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - Randall J Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - Paul A Christensen
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
| | - David W Bernard
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - James J Davis
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, Illinois, USA
| | - Maulik Shukla
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, Illinois, USA
| | - Marcus Nguyen
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, Illinois, USA
| | - Matthew Ojeda Saavedra
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
| | - Prasanti Yerramilli
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
| | - Layne Pruitt
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
| | - Sishir Subedi
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
| | - Hung-Che Kuo
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
- Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Heather Hendrickson
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
| | - Ghazaleh Eskandari
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
| | - Hoang A T Nguyen
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
| | - J Hunter Long
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
| | - Muthiah Kumaraswami
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
| | - Jule Goike
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
- Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Daniel Boutz
- CCDC Army Research Laboratory-South, University of Texas, Austin, Texas, USA
| | - Jimmy Gollihar
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
- CCDC Army Research Laboratory-South, University of Texas, Austin, Texas, USA
| | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
- Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Chia-Wei Chou
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
- Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Kamyab Javanmardi
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
- Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
- Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas, USA
| | - James M Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
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25
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Long SW, Olsen RJ, Christensen PA, Bernard DW, Davis JJ, Shukla M, Nguyen M, Saavedra MO, Yerramilli P, Pruitt L, Subedi S, Kuo HC, Hendrickson H, Eskandari G, Nguyen HAT, Long JH, Kumaraswami M, Goike J, Boutz D, Gollihar J, McLellan JS, Chou CW, Javanmardi K, Finkelstein IJ, Musser JM. Molecular Architecture of Early Dissemination and Massive Second Wave of the SARS-CoV-2 Virus in a Major Metropolitan Area. medRxiv 2020:2020.09.22.20199125. [PMID: 33024977 PMCID: PMC7536878 DOI: 10.1101/2020.09.22.20199125] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
We sequenced the genomes of 5,085 SARS-CoV-2 strains causing two COVID-19 disease waves in metropolitan Houston, Texas, an ethnically diverse region with seven million residents. The genomes were from viruses recovered in the earliest recognized phase of the pandemic in Houston, and an ongoing massive second wave of infections. The virus was originally introduced into Houston many times independently. Virtually all strains in the second wave have a Gly614 amino acid replacement in the spike protein, a polymorphism that has been linked to increased transmission and infectivity. Patients infected with the Gly614 variant strains had significantly higher virus loads in the nasopharynx on initial diagnosis. We found little evidence of a significant relationship between virus genotypes and altered virulence, stressing the linkage between disease severity, underlying medical conditions, and host genetics. Some regions of the spike protein - the primary target of global vaccine efforts - are replete with amino acid replacements, perhaps indicating the action of selection. We exploited the genomic data to generate defined single amino acid replacements in the receptor binding domain of spike protein that, importantly, produced decreased recognition by the neutralizing monoclonal antibody CR30022. Our study is the first analysis of the molecular architecture of SARS-CoV-2 in two infection waves in a major metropolitan region. The findings will help us to understand the origin, composition, and trajectory of future infection waves, and the potential effect of the host immune response and therapeutic maneuvers on SARS-CoV-2 evolution.
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Affiliation(s)
- S. Wesley Long
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030
- Departments of Pathology and Laboratory Medicine, and Microbiology and Immunology, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10065
| | - Randall J. Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030
- Departments of Pathology and Laboratory Medicine, and Microbiology and Immunology, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10065
| | - Paul A. Christensen
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030
| | - David W. Bernard
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030
- Departments of Pathology and Laboratory Medicine, and Microbiology and Immunology, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10065
| | - James J. Davis
- Consortium for Advanced Science and Engineering, University of Chicago, 5801 South Ellis Avenue, Chicago, Illinois, 60637
- Computing, Environment and Life Sciences, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439
| | - Maulik Shukla
- Consortium for Advanced Science and Engineering, University of Chicago, 5801 South Ellis Avenue, Chicago, Illinois, 60637
- Computing, Environment and Life Sciences, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439
| | - Marcus Nguyen
- Consortium for Advanced Science and Engineering, University of Chicago, 5801 South Ellis Avenue, Chicago, Illinois, 60637
- Computing, Environment and Life Sciences, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439
| | - Matthew Ojeda Saavedra
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030
| | - Prasanti Yerramilli
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030
| | - Layne Pruitt
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030
| | - Sishir Subedi
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030
| | - Hung-Che Kuo
- Department of Molecular Biosciences and Institute of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Heather Hendrickson
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030
| | - Ghazaleh Eskandari
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030
| | - Hoang A. T. Nguyen
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030
| | - J. Hunter Long
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030
| | - Muthiah Kumaraswami
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030
| | - Jule Goike
- Department of Molecular Biosciences and Institute of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Daniel Boutz
- CCDC Army Research Laboratory-South, University of Texas, Austin, Texas 78712
| | - Jimmy Gollihar
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030
- CCDC Army Research Laboratory-South, University of Texas, Austin, Texas 78712
| | - Jason S. McLellan
- Department of Molecular Biosciences and Institute of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Chia-Wei Chou
- Department of Molecular Biosciences and Institute of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Kamyab Javanmardi
- Department of Molecular Biosciences and Institute of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Ilya J. Finkelstein
- Department of Molecular Biosciences and Institute of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas 78712
| | - James M. Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030
- Departments of Pathology and Laboratory Medicine, and Microbiology and Immunology, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10065
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26
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Salazar E, Perez KK, Ashraf M, Chen J, Castillo B, Christensen PA, Eubank T, Bernard DW, Eagar TN, Long SW, Subedi S, Olsen RJ, Leveque C, Schwartz MR, Dey M, Chavez-East C, Rogers J, Shehabeldin A, Joseph D, Williams G, Thomas K, Masud F, Talley C, Dlouhy KG, Lopez BV, Hampton C, Lavinder J, Gollihar JD, Maranhao AC, Ippolito GC, Saavedra MO, Cantu CC, Yerramilli P, Pruitt L, Musser JM. Treatment of Coronavirus Disease 2019 (COVID-19) Patients with Convalescent Plasma. Am J Pathol 2020; 190:1680-1690. [PMID: 32473109 PMCID: PMC7251400 DOI: 10.1016/j.ajpath.2020.05.014] [Citation(s) in RCA: 190] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 05/21/2020] [Accepted: 05/21/2020] [Indexed: 12/13/2022]
Abstract
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2, has spread globally, and no proven treatments are available. Convalescent plasma therapy has been used with varying degrees of success to treat severe microbial infections for >100 years. Patients (n = 25) with severe and/or life-threatening COVID-19 disease were enrolled at the Houston Methodist hospitals from March 28, 2020, to April 14, 2020. Patients were transfused with convalescent plasma, obtained from donors with confirmed severe acute respiratory syndrome coronavirus 2 infection who had recovered. The primary study outcome was safety, and the secondary outcome was clinical status at day 14 after transfusion. Clinical improvement was assessed on the basis of a modified World Health Organization six-point ordinal scale and laboratory parameters. Viral genome sequencing was performed on donor and recipient strains. At day 7 after transfusion with convalescent plasma, nine patients had at least a one-point improvement in clinical scale, and seven of those were discharged. By day 14 after transfusion, 19 (76%) patients had at least a one-point improvement in clinical status, and 11 were discharged. No adverse events as a result of plasma transfusion were observed. Whole genome sequencing data did not identify a strain genotype-disease severity correlation. The data indicate that administration of convalescent plasma is a safe treatment option for those with severe COVID-19 disease.
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Affiliation(s)
- Eric Salazar
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Katherine K Perez
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pharmacy, Houston Methodist Hospital, Houston, Texas
| | - Madiha Ashraf
- Division of Infectious Diseases, Department of Clinical Medicine, Houston Methodist Hospital, Houston, Texas
| | - Jian Chen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Brian Castillo
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Paul A Christensen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Taryn Eubank
- Department of Pharmacy, Houston Methodist Hospital, Houston, Texas
| | - David W Bernard
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Todd N Eagar
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - S Wesley Long
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York; Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute, Houston, Texas
| | - Sishir Subedi
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Randall J Olsen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York; Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute, Houston, Texas
| | - Christopher Leveque
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Mary R Schwartz
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Monisha Dey
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Cheryl Chavez-East
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - John Rogers
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Ahmed Shehabeldin
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - David Joseph
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Guy Williams
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Karen Thomas
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Faisal Masud
- Division of Infectious Diseases, Department of Clinical Medicine, Houston Methodist Hospital, Houston, Texas; Department of Anesthesiology and Critical Care, Houston Methodist Hospital, Houston, Texas
| | - Christina Talley
- Academic Office of Clinical Trials, Houston Methodist Research Institute, Houston, Texas
| | - Katharine G Dlouhy
- Academic Office of Clinical Trials, Houston Methodist Research Institute, Houston, Texas
| | - Bevin V Lopez
- Academic Office of Clinical Trials, Houston Methodist Research Institute, Houston, Texas
| | - Curt Hampton
- Academic Office of Clinical Trials, Houston Methodist Research Institute, Houston, Texas
| | - Jason Lavinder
- Department of Molecular Biosciences, Dell Medical School, University of Texas at Austin, Austin, Texas
| | - Jimmy D Gollihar
- Combat Capabilities Development Command (CCDC) Army Research Laboratory-South, University of Texas at Austin, Austin, Texas
| | - Andre C Maranhao
- Department of Molecular Biosciences, Dell Medical School, University of Texas at Austin, Austin, Texas
| | - Gregory C Ippolito
- Department of Molecular Biosciences, Dell Medical School, University of Texas at Austin, Austin, Texas; Department of Oncology, Dell Medical School, University of Texas at Austin, Austin, Texas
| | - Matthew O Saavedra
- Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute, Houston, Texas
| | - Concepcion C Cantu
- Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute, Houston, Texas
| | - Prasanti Yerramilli
- Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute, Houston, Texas
| | - Layne Pruitt
- Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute, Houston, Texas
| | - James M Musser
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York; Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute, Houston, Texas.
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Hujer AM, Long SW, Olsen RJ, Taracila MA, Rojas LJ, Musser JM, Bonomo RA. Predicting β-lactam resistance using whole genome sequencing in Klebsiella pneumoniae: the challenge of β-lactamase inhibitors. Diagn Microbiol Infect Dis 2020; 98:115149. [PMID: 32858260 DOI: 10.1016/j.diagmicrobio.2020.115149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 06/01/2020] [Accepted: 07/18/2020] [Indexed: 11/25/2022]
Abstract
Although multiple antimicrobial resistance (AMR) determinants can confer the same in vitro antimicrobial susceptibility testing (AST) phenotype, their differing effect on optimal therapeutic choices is uncertain. Using a large population-based collection of clinical strains spanning a 3.5-year period, we applied WGS to detect inhibitor resistant (IR), extended-spectrum β-lactamase (ESBL), and carbapenem resistant (CR) β-lactamase (bla) genes and compared the genotype to the AST phenotype in select isolates. All blaNDM-1 (9/9) and the majority of blaNDM-1/OXA-48 (3/4) containing isolates were resistant to CAZ/AVI as predicted by WGS. The combination of ATM and CAZ/AVI restored susceptibility by disk diffusion assay. Unexpectedly, clinical Kp isolates bearing blaKPC-8 (V240G) and blaKPC-14 (G242 and T243 deletion) did not test fully resistant to CAZ/AVI. Lastly, despite the complexity of the β-lactamase background, CAZ/AVI retained potency. Presumed phenotypes conferred by AMR determinants need to be tested if therapeutic decisions are being guided by their presence or absence.
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Affiliation(s)
- Andrea M Hujer
- Department of Medicine, Case Western Reserve University, Cleveland, OH; Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH
| | - S Wesley Long
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, TX; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
| | - Randall J Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, TX; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
| | - Magdalena A Taracila
- Department of Medicine, Case Western Reserve University, Cleveland, OH; Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH
| | - Laura J Rojas
- Department of Medicine, Case Western Reserve University, Cleveland, OH; Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH
| | - James M Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, TX; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
| | - Robert A Bonomo
- Department of Medicine, Case Western Reserve University, Cleveland, OH; Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH; Department of Molecular Biology and Microbiology, Pharmacology, Biochemistry, and the Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH; CWRU-Cleveland VAMC, Center, for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, OH.
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28
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Makthal N, Do H, Wendel BM, Olsen RJ, Helmann JD, Musser JM, Kumaraswami M. Group A Streptococcus AdcR Regulon Participates in Bacterial Defense against Host-Mediated Zinc Sequestration and Contributes to Virulence. Infect Immun 2020; 88:e00097-20. [PMID: 32393509 PMCID: PMC7375770 DOI: 10.1128/iai.00097-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 05/06/2020] [Indexed: 12/11/2022] Open
Abstract
Colonization by pathogenic bacteria depends on their ability to overcome host nutritional defenses and acquire nutrients. The human pathogen group A streptococcus (GAS) encounters the host defense factor calprotectin (CP) during infection. CP inhibits GAS growth in vitro by imposing zinc (Zn) limitation. However, GAS counterstrategies to combat CP-mediated Zn limitation and the in vivo relevance of CP-GAS interactions to bacterial pathogenesis remain unknown. Here, we report that GAS upregulates the AdcR regulon in response to CP-mediated Zn limitation. The AdcR regulon includes genes encoding Zn import (adcABC), Zn sparing (rpsN.2), and Zn scavenging systems (adcAII, phtD, and phtY). Each gene in the AdcR regulon contributes to GAS Zn acquisition and CP resistance. The ΔadcC and ΔrpsN.2 mutant strains were the most susceptible to CP, whereas the ΔadcA, ΔadcAII, and ΔphtD mutant strains displayed less CP sensitivity during growth in vitro However, the ΔphtY mutant strain did not display an increased CP sensitivity. The varied sensitivity of the mutant strains to CP-mediated Zn limitation suggests distinct roles for individual AdcR regulon genes in GAS Zn acquisition. GAS upregulates the AdcR regulon during necrotizing fasciitis infection in WT mice but not in S100a9-/- mice lacking CP. This suggests that CP induces Zn deficiency in the host. Finally, consistent with the in vitro results, several of the AdcR regulon genes are critical for GAS virulence in WT mice, whereas they are dispensable for virulence in S100a9-/- mice, indicating the direct competition for Zn between CP and proteins encoded by the GAS AdcR regulon during infection.
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Affiliation(s)
- Nishanth Makthal
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, Texas, USA
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Hackwon Do
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, Texas, USA
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Brian M Wendel
- Department of Microbiology, Cornell University, Ithaca, New York, USA
| | - Randall J Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, Texas, USA
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, New York, USA
| | - John D Helmann
- Department of Microbiology, Cornell University, Ithaca, New York, USA
| | - James M Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, Texas, USA
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, New York, USA
| | - Muthiah Kumaraswami
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, Texas, USA
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
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29
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Salazar E, Kuchipudi SV, Christensen PA, Eagar TN, Yi X, Zhao P, Jin Z, Long SW, Olsen RJ, Chen J, Castillo B, Leveque C, Towers DM, Lavinder J, Gollihar JD, Cardona J, Ippolito GC, Nissly RH, Bird IM, Greenawalt D, Rossi RM, Gontu A, Srinivasan S, Poojary IB, Cattadori IM, Hudson PJ, Joselyn N, Prugar L, Huie K, Herbert A, Bernard DW, Dye J, Kapur V, Musser JM. Relationship between Anti-Spike Protein Antibody Titers and SARS-CoV-2 In Vitro Virus Neutralization in Convalescent Plasma. bioRxiv 2020:2020.06.08.138990. [PMID: 32577662 PMCID: PMC7302218 DOI: 10.1101/2020.06.08.138990] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Newly emerged pathogens such as SARS-CoV-2 highlight the urgent need for assays that detect levels of neutralizing antibodies that may be protective. We studied the relationship between anti-spike ectodomain (ECD) and anti-receptor binding domain (RBD) IgG titers, and SARS-CoV-2 virus neutralization (VN) titers generated by two different in vitro assays using convalescent plasma samples obtained from 68 COVID-19 patients, including 13 who donated plasma multiple times. Only 23% (16/68) of donors had been hospitalized. We also studied 16 samples from subjects found to have anti-spike protein IgG during surveillance screening of asymptomatic individuals. We report a strong positive correlation between both plasma anti-RBD and anti-ECD IgG titers, and in vitro VN titer. Anti-RBD plasma IgG correlated slightly better than anti-ECD IgG titer with VN titer. The probability of a VN titer ≥160 was 80% or greater with anti-RBD or anti-ECD titers of ≥1:1350. Thirty-seven percent (25/68) of convalescent plasma donors lacked VN titers ≥160, the FDA-recommended level for convalescent plasma used for COVID-19 treatment. Dyspnea, hospitalization, and disease severity were significantly associated with higher VN titer. Frequent donation of convalescent plasma did not significantly decrease either VN or IgG titers. Analysis of 2,814 asymptomatic adults found 27 individuals with anti-RBD or anti-ECD IgG titers of ≥1:1350, and evidence of VN ≥1:160. Taken together, we conclude that anti-RBD or anti-ECD IgG titers can serve as a surrogate for VN titers to identify suitable plasma donors. Plasma anti-RBD or anti-ECD titer of ≥1:1350 may provide critical information about protection against COVID-19 disease.
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Affiliation(s)
- Eric Salazar
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Suresh V. Kuchipudi
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania
- Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, Pennsylvania
| | - Paul A. Christensen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Todd N. Eagar
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Xin Yi
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Picheng Zhao
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Zhicheng Jin
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - S. Wesley Long
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
- Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute, Houston, Texas
| | - Randall J. Olsen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
- Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute, Houston, Texas
| | - Jian Chen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Brian Castillo
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Christopher Leveque
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Dalton M. Towers
- Department of Molecular Biosciences, University of Texas at Austin
| | - Jason Lavinder
- Department of Molecular Biosciences, University of Texas at Austin
| | - Jimmy D. Gollihar
- CCDC Army Research Laboratory-South, University of Texas, Austin, Texas
| | - Jose Cardona
- CCDC Army Research Laboratory-South, University of Texas, Austin, Texas
| | - Gregory C. Ippolito
- Department of Molecular Biosciences, University of Texas at Austin
- Department of Oncology, Dell Medical School, University of Texas at Austin, Austin, Texas
| | - Ruth H. Nissly
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania
| | - Ian M. Bird
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania
| | - Denver Greenawalt
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania
| | - Randall M. Rossi
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania
| | - Abinhay Gontu
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania
| | - Sreenidhi Srinivasan
- Department of Animal Science, Pennsylvania State University, University Park, Pennsylvania
| | - Indira B. Poojary
- Department of Animal Science, Pennsylvania State University, University Park, Pennsylvania
| | - Isabella M. Cattadori
- Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, Pennsylvania
- Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute, Houston, Texas
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania
| | - Peter J. Hudson
- Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, Pennsylvania
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania
| | - Nicole Joselyn
- USAMRIID (United States Army Medical Research Institute of Infectious Diseases), Frederick, Maryland
| | - Laura Prugar
- USAMRIID (United States Army Medical Research Institute of Infectious Diseases), Frederick, Maryland
| | - Kathleen Huie
- USAMRIID (United States Army Medical Research Institute of Infectious Diseases), Frederick, Maryland
| | - Andrew Herbert
- USAMRIID (United States Army Medical Research Institute of Infectious Diseases), Frederick, Maryland
| | - David W. Bernard
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - John Dye
- USAMRIID (United States Army Medical Research Institute of Infectious Diseases), Frederick, Maryland
| | - Vivek Kapur
- Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, Pennsylvania
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania
- Department of Animal Science, Pennsylvania State University, University Park, Pennsylvania
| | - James M. Musser
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
- Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute, Houston, Texas
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30
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Zhu L, Olsen RJ, Beres SB, Saavedra MO, Kubiak SL, Cantu CC, Jenkins L, Waller AS, Sun Z, Palzkill T, Porter AR, DeLeo FR, Musser JM. Streptococcus pyogenes genes that promote pharyngitis in primates. JCI Insight 2020; 5:137686. [PMID: 32493846 DOI: 10.1172/jci.insight.137686] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 04/30/2020] [Indexed: 02/02/2023] Open
Abstract
Streptococcus pyogenes (group A streptococcus; GAS) causes 600 million cases of pharyngitis annually worldwide. There is no licensed human GAS vaccine despite a century of research. Although the human oropharynx is the primary site of GAS infection, the pathogenic genes and molecular processes used to colonize, cause disease, and persist in the upper respiratory tract are poorly understood. Using dense transposon mutant libraries made with serotype M1 and M28 GAS strains and transposon-directed insertion sequencing, we performed genome-wide screens in the nonhuman primate (NHP) oropharynx. We identified many potentially novel GAS fitness genes, including a common set of 115 genes that contribute to fitness in both genetically distinct GAS strains during experimental NHP pharyngitis. Targeted deletion of 4 identified fitness genes/operons confirmed that our newly identified targets are critical for GAS virulence during experimental pharyngitis. Our screens discovered many surface-exposed or secreted proteins - substrates for vaccine research - that potentially contribute to GAS pharyngitis, including lipoprotein HitA. Pooled human immune globulin reacted with purified HitA, suggesting that humans produce antibodies against this lipoprotein. Our findings provide new information about GAS fitness in the upper respiratory tract that may assist in translational research, including developing novel vaccines.
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Affiliation(s)
- Luchang Zhu
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Randall J Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA.,Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, New York, USA
| | - Stephen B Beres
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Matthew Ojeda Saavedra
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Samantha L Kubiak
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Concepcion C Cantu
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Leslie Jenkins
- Department of Comparative Medicine, Houston Methodist Research Institute, Houston, Texas, USA
| | - Andrew S Waller
- Animal Health Trust, Lanwades Park, Newmarket, United Kingdom
| | - Zhizeng Sun
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Timothy Palzkill
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Adeline R Porter
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, Montana, USA
| | - Frank R DeLeo
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, Montana, USA
| | - James M Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA.,Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, New York, USA
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31
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Salazar E, Perez KK, Ashraf M, Chen J, Castillo B, Christensen PA, Eubank T, Bernard DW, Eagar TN, Long SW, Subedi S, Olsen RJ, Leveque C, Schwartz MR, Dey M, Chavez-East C, Rogers J, Shehabeldin A, Joseph D, Williams G, Thomas K, Masud F, Talley C, Dlouhy KG, Lopez BV, Hampton C, Lavinder J, Gollihar JD, Maranhao AC, Ippolito GC, Saavedra MO, Cantu CC, Yerramilli P, Pruitt L, Musser JM. Treatment of COVID-19 Patients with Convalescent Plasma in Houston, Texas. medRxiv 2020:2020.05.08.20095471. [PMID: 32511574 PMCID: PMC7274255 DOI: 10.1101/2020.05.08.20095471] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
BACKGROUND COVID-19 disease, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has spread globally, and no proven treatments are available. Convalescent plasma therapy has been used with varying degrees of success to treat severe microbial infections for more than 100 years. METHODS Patients (n=25) with severe and/or life-threatening COVID-19 disease were enrolled at the Houston Methodist hospitals from March 28 to April 14, 2020. Patients were transfused with convalescent plasma obtained from donors with confirmed SARS-CoV-2 infection and had been symptom free for 14 days. The primary study outcome was safety, and the secondary outcome was clinical status at day 14 post-transfusion. Clinical improvement was assessed based on a modified World Health Organization 6-point ordinal scale and laboratory parameters. Viral genome sequencing was performed on donor and recipient strains. RESULTS At baseline, all patients were receiving supportive care, including anti-inflammatory and anti-viral treatments, and all patients were on oxygen support. At day 7 post-transfusion with convalescent plasma, nine patients had at least a 1-point improvement in clinical scale, and seven of those were discharged. By day 14 post-transfusion, 19 (76%) patients had at least a 1-point improvement in clinical status and 11 were discharged. No adverse events as a result of plasma transfusion were observed. The whole genome sequencing data did not identify a strain genotype-disease severity correlation. CONCLUSIONS The data indicate that administration of convalescent plasma is a safe treatment option for those with severe COVID-19 disease. Randomized, controlled trials are needed to determine its efficacy.
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32
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Olsen RJ, Zhu L, Musser JM. A Single Amino Acid Replacement in Penicillin-Binding Protein 2X in Streptococcus pyogenes Significantly Increases Fitness on Subtherapeutic Benzylpenicillin Treatment in a Mouse Model of Necrotizing Myositis. Am J Pathol 2020; 190:1625-1631. [PMID: 32407732 DOI: 10.1016/j.ajpath.2020.04.014] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/14/2020] [Accepted: 04/21/2020] [Indexed: 12/15/2022]
Abstract
Invasive strains of Streptococcus pyogenes with significantly reduced susceptibility to β-lactam antibiotics have been recently described. These reports have caused considerable concern in the international infectious disease, medical microbiology, and public health communities because S. pyogenes has remained universally susceptible to β-lactam antibiotics for 70 years. Virtually all analyzed strains had single amino acid replacements in penicillin-binding protein 2X (PBP2X), a major target of β-lactam antibiotics in pathogenic bacteria. We used isogenic strains to test the hypothesis that a single amino acid replacement in PBP2X conferred a fitness advantage in a mouse model of necrotizing myositis. We determined that when mice were administered intermittent subtherapeutic dosing of benzylpenicillin, the strain with a Pro601Leu amino acid replacement in PBP2X that confers reduced β-lactam susceptibility in vitro was more fit, as assessed by the magnitude of colony-forming units recovered from disease tissue. These data provide important pathogenesis information that bears on this emerging global infectious disease problem.
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Affiliation(s)
- Randall J Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, Texas; Clinical Microbiology Laboratory, Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Luchang Zhu
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, Texas
| | - James M Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, Texas; Clinical Microbiology Laboratory, Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York.
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33
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Bernard PE, Kachroo P, Eraso JM, Zhu L, Madry JE, Duarte A, Linson SE, Saavedra MO, Cantu C, Musser JM, Olsen RJ. Polymorphisms in RocA contribute to the molecular pathogenesis of serotype M28 group A streptococcus. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.03097] [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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34
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Eraso JM, Kachroo P, Olsen RJ, Beres SB, Zhu L, Badu T, Shannon S, Cantu CC, Saavedra MO, Kubiak SL, Porter AR, DeLeo FR, Musser JM. Genetic heterogeneity of the Spy1336/R28-Spy1337 virulence axis in Streptococcus pyogenes and effect on gene transcript levels and pathogenesis. PLoS One 2020; 15:e0229064. [PMID: 32214338 PMCID: PMC7098570 DOI: 10.1371/journal.pone.0229064] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 01/28/2020] [Indexed: 12/20/2022] Open
Abstract
Streptococcus pyogenes is a strict human pathogen responsible for more than 700 million infections annually worldwide. Strains of serotype M28 S. pyogenes are typically among the five more abundant types causing invasive infections and pharyngitis in adults and children. Type M28 strains also have an unusual propensity to cause puerperal sepsis and neonatal disease. We recently discovered that a one-nucleotide indel in an intergenic homopolymeric tract located between genes Spy1336/R28 and Spy1337 altered virulence in a mouse model of infection. In the present study, we analyzed size variation in this homopolymeric tract and determined the extent of heterogeneity in the number of tandemly-repeated 79-amino acid domains in the coding region of Spy1336/R28 in large samples of strains recovered from humans with invasive infections. Both repeat sequence elements are highly polymorphic in natural populations of M28 strains. Variation in the homopolymeric tract results in (i) changes in transcript levels of Spy1336/R28 and Spy1337 in vitro, (ii) differences in virulence in a mouse model of necrotizing myositis, and (iii) global transcriptome changes as shown by RNAseq analysis of isogenic mutant strains. Variation in the number of tandem repeats in the coding sequence of Spy1336/R28 is responsible for size variation of R28 protein in natural populations. Isogenic mutant strains in which genes encoding R28 or transcriptional regulator Spy1337 are inactivated are significantly less virulent in a nonhuman primate model of necrotizing myositis. Our findings provide impetus for additional studies addressing the role of R28 and Spy1337 variation in pathogen-host interactions.
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Affiliation(s)
- Jesus M. Eraso
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, United States of America
| | - Priyanka Kachroo
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, United States of America
| | - Randall J. Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, United States of America
- Departments of Pathology and Laboratory Medicine and Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America
| | - Stephen B. Beres
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, United States of America
| | - Luchang Zhu
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, United States of America
| | - Traci Badu
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, United States of America
| | - Sydney Shannon
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, United States of America
| | - Concepcion C. Cantu
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, United States of America
| | - Matthew Ojeda Saavedra
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, United States of America
| | - Samantha L. Kubiak
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, United States of America
| | - Adeline R. Porter
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Frank R. DeLeo
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - James M. Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, United States of America
- Departments of Pathology and Laboratory Medicine and Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America
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Kachroo P, Eraso JM, Olsen RJ, Zhu L, Kubiak SL, Pruitt L, Yerramilli P, Cantu CC, Ojeda Saavedra M, Pensar J, Corander J, Jenkins L, Kao L, Granillo A, Porter AR, DeLeo FR, Musser JM. New Pathogenesis Mechanisms and Translational Leads Identified by Multidimensional Analysis of Necrotizing Myositis in Primates. mBio 2020; 11:e03363-19. [PMID: 32071274 PMCID: PMC7029145 DOI: 10.1128/mbio.03363-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 01/06/2020] [Indexed: 01/08/2023] Open
Abstract
A fundamental goal of contemporary biomedical research is to understand the molecular basis of disease pathogenesis and exploit this information to develop targeted and more-effective therapies. Necrotizing myositis caused by the bacterial pathogen Streptococcus pyogenes is a devastating human infection with a high mortality rate and few successful therapeutic options. We used dual transcriptome sequencing (RNA-seq) to analyze the transcriptomes of S. pyogenes and host skeletal muscle recovered contemporaneously from infected nonhuman primates. The in vivo bacterial transcriptome was strikingly remodeled compared to organisms grown in vitro, with significant upregulation of genes contributing to virulence and altered regulation of metabolic genes. The transcriptome of muscle tissue from infected nonhuman primates (NHPs) differed significantly from that of mock-infected animals, due in part to substantial changes in genes contributing to inflammation and host defense processes. We discovered significant positive correlations between group A streptococcus (GAS) virulence factor transcripts and genes involved in the host immune response and inflammation. We also discovered significant correlations between the magnitude of bacterial virulence gene expression in vivo and pathogen fitness, as assessed by previously conducted genome-wide transposon-directed insertion site sequencing (TraDIS). By integrating the bacterial RNA-seq data with the fitness data generated by TraDIS, we discovered five new pathogen genes, namely, S. pyogenes 0281 (Spy0281 [dahA]), ihk-irr, slr, isp, and ciaH, that contribute to necrotizing myositis and confirmed these findings using isogenic deletion-mutant strains. Taken together, our study results provide rich new information about the molecular events occurring in severe invasive infection of primate skeletal muscle that has extensive translational research implications.IMPORTANCE Necrotizing myositis caused by Streptococcus pyogenes has high morbidity and mortality rates and relatively few successful therapeutic options. In addition, there is no licensed human S. pyogenes vaccine. To gain enhanced understanding of the molecular basis of this infection, we employed a multidimensional analysis strategy that included dual RNA-seq and other data derived from experimental infection of nonhuman primates. The data were used to target five streptococcal genes for pathogenesis research, resulting in the unambiguous demonstration that these genes contribute to pathogen-host molecular interactions in necrotizing infections. We exploited fitness data derived from a recently conducted genome-wide transposon mutagenesis study to discover significant correlation between the magnitude of bacterial virulence gene expression in vivo and pathogen fitness. Collectively, our findings have significant implications for translational research, potentially including vaccine efforts.
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Affiliation(s)
- Priyanka Kachroo
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, USA
| | - Jesus M Eraso
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, USA
| | - Randall J Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - Luchang Zhu
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, USA
| | - Samantha L Kubiak
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, USA
| | - Layne Pruitt
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, USA
| | - Prasanti Yerramilli
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, USA
| | - Concepcion C Cantu
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, USA
| | - Matthew Ojeda Saavedra
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, USA
| | - Johan Pensar
- Department of Mathematics and Statistics, Helsinki Institute of Information Technology, University of Helsinki, Helsinki, Finland
| | - Jukka Corander
- Department of Mathematics and Statistics, Helsinki Institute of Information Technology, University of Helsinki, Helsinki, Finland
- Department of Biostatistics, University of Oslo, Oslo, Norway
| | - Leslie Jenkins
- Comparative Medicine Program, Houston Methodist Research Institute, Houston, Texas, USA
| | - Lillian Kao
- Department of Surgery, University of Texas McGovern Medical School, Houston, Texas, USA
| | - Alejandro Granillo
- Department of Internal Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, USA
| | - Adeline R Porter
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Frank R DeLeo
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - James M Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
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Lu S, Soeung V, Nguyen HAT, Long SW, Musser JM, Palzkill T. Development and Evaluation of a Novel Protein-Based Assay for Specific Detection of KPC β-Lactamases from Klebsiella pneumoniae Clinical Isolates. mSphere 2020; 5:e00918-19. [PMID: 31915233 PMCID: PMC6952207 DOI: 10.1128/msphere.00918-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 12/07/2019] [Accepted: 12/12/2019] [Indexed: 11/20/2022] Open
Abstract
Carbapenemases confer resistance to nearly all β-lactam antibiotics. The extensive spread of carbapenemase-producing multidrug-resistant bacteria contributes significantly to hospital-acquired infections. We have developed a novel protein-based binding assay that identifies KPC β-lactamases from clinical isolates. We used the protein-protein interaction between KPCs and a soluble β-lactamase inhibitory protein (BLIP) variant, BLIPK74T/W112D, which specifically inhibits KPCs but not other β-lactamases. In this assay, BLIPK74T/W112D was allowed to form complexes with KPC-2 in bacterial cell lysates and then extracted using His tag binding resins. We demonstrated the presence of KPC-2 by monitoring the hydrolysis of a colorimetric β-lactam substrate. Also, to further increase the accuracy of the method, a BLIPK74T/W112D-mediated inhibition assay was developed. The binding and inhibition assays were validated by testing 127 Klebsiella pneumoniae clinical isolates with known genome sequences for the presence of KPC. Our assays identified a total of 32 strains as KPC-2 producers, a result in 100% concordance with genome sequencing predictions. To further simplify the assay and decrease the time to obtain results, the BLIPK74T/W112D protein was tested in combination with the widely used Carba-NP assay. For this purpose, the genome-sequenced K. pneumoniae strains were tested for the presence of carbapenemases with the Carba-NP test with and without the addition of BLIPK74T/W122D The test accurately identified carbapenemase-producing strains and the addition of BLIPK74T/W112D allowed a further determination that the strains contain KPC carbapenemase. Thus, the BLIPK74T/W112D protein is an effective sensor to specifically detect KPC β-lactamases produced by clinical isolates.IMPORTANCE Infections caused by carbapenem-resistant Enterobacteriaceae are associated with high therapeutic failure and mortality rates. Thus, it is critical to rapidly identify clinical isolates expressing KPC β-lactamases to facilitate administration of the correct antibiotic treatment and initiate infection control strategies. To address this problem, we developed a protein-based, KPC-specific binding assay in combination with a cell lysate inhibition assay that provided a 100% identification rate of KPC from clinical isolates of known genomic sequence. In addition, this protein sensor was adapted to the Carba-NP assay to provide a rapid strategy to detect KPC-producing isolates that will facilitate informed treatment of critically ill patients.
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Affiliation(s)
- Shuo Lu
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Victoria Soeung
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Hoang A T Nguyen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital Research Institute, Houston, Texas, USA
| | - S Wesley Long
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital Research Institute, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
| | - James M Musser
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital Research Institute, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Timothy Palzkill
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas, USA
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA
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37
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Do H, Makthal N, Chandrangsu P, Olsen RJ, Helmann JD, Musser JM, Kumaraswami M. Metal sensing and regulation of adaptive responses to manganese limitation by MtsR is critical for group A streptococcus virulence. Nucleic Acids Res 2019; 47:7476-7493. [PMID: 31188450 PMCID: PMC6698748 DOI: 10.1093/nar/gkz524] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [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: 03/26/2019] [Revised: 05/29/2019] [Accepted: 06/03/2019] [Indexed: 01/24/2023] Open
Abstract
Pathogenic bacteria encounter host-imposed manganese (Mn) limitation during infection. Herein we report that in the human pathogen Streptococcus pyogenes, the adaptive response to Mn limitation is controlled by a DtxR family metalloregulator, MtsR. Genes upregulated by MtsR during Mn limitation include Mn (mtsABC) and Fe acquisition systems (sia operon), and a metal-independent DNA synthesis enzyme (nrdFEI.2). To elucidate the mechanism of metal sensing and gene regulation by MtsR, we determined the crystal structure of MtsR. MtsR employs two Mn-sensing sites to monitor metal availability, and metal occupancy at each site influences MtsR regulatory activity. The site 1 acts as the primary Mn sensing site, and loss of metal at site 1 causes robust upregulation of mtsABC. The vacant site 2 causes partial induction of mtsABC, indicating that site 2 functions as secondary Mn sensing site. Furthermore, we show that the C-terminal FeoA domains of adjacent dimers participate in the oligomerization of MtsR on DNA, and multimerization is critical for MtsR regulatory activity. Finally, the mtsR mutant strains defective in metal sensing and oligomerization are attenuated for virulence in a mouse model of invasive infection, indicating that Mn sensing and gene regulation by MtsR are critical processes during S. pyogenes infection.
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Affiliation(s)
- Hackwon Do
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA
| | - Nishanth Makthal
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA
| | - Pete Chandrangsu
- Department of Microbiology, Cornell University, Ithaca, NY 14853-8101, USA.,W.M. Keck Science Department, Claremont McKenna, Pitzer and Scripps College, Claremont, CA 91711, USA
| | - Randall J Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA.,Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - John D Helmann
- Department of Microbiology, Cornell University, Ithaca, NY 14853-8101, USA
| | - James M Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA.,Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Muthiah Kumaraswami
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA
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Bernard PE, Kachroo P, Eraso JM, Zhu L, Madry JE, Linson SE, Ojeda Saavedra M, Cantu C, Musser JM, Olsen RJ. Polymorphisms in Regulator of Cov Contribute to the Molecular Pathogenesis of Serotype M28 Group A Streptococcus. Am J Pathol 2019; 189:2002-2018. [PMID: 31369755 DOI: 10.1016/j.ajpath.2019.06.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 06/11/2019] [Accepted: 06/13/2019] [Indexed: 12/12/2022]
Abstract
Two-component systems (TCSs) are signal transduction proteins that enable bacteria to respond to external stimuli by altering the global transcriptome. Accessory proteins interact with TCSs to fine-tune their activity. In group A Streptococcus (GAS), regulator of Cov (RocA) is an accessory protein that functions with the control of virulence regulator/sensor TCS, which regulates approximately 15% of the GAS transcriptome. Whole-genome sequencing analysis of serotype M28 GAS strains collected from invasive infections in humans identified a higher number of missense (amino acid-altering) and nonsense (protein-truncating) polymorphisms in rocA than expected. We hypothesized that polymorphisms in RocA alter the global transcriptome and virulence of serotype M28 GAS. We used naturally occurring clinical isolates with rocA polymorphisms (n = 48), an isogenic rocA deletion mutant strain, and five isogenic rocA polymorphism mutant strains to perform genome-wide transcript analysis (RNA sequencing), in vitro virulence factor assays, and mouse and nonhuman primate pathogenesis studies to test this hypothesis. Results demonstrated that polymorphisms in rocA result in either a subtle transcriptome change, causing a wild-type-like virulence phenotype, or a substantial transcriptome change, leading to a significantly increased virulence phenotype. Each polymorphism had a unique effect on the global GAS transcriptome. Taken together, our data show that naturally occurring polymorphisms in one gene encoding an accessory protein can significantly alter the global transcriptome and virulence phenotype of GAS, an important human pathogen.
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Affiliation(s)
- Paul E Bernard
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas; Texas A&M Health Science Center College of Medicine, Bryan, Texas
| | - Priyanka Kachroo
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Jesus M Eraso
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Luchang Zhu
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Jessica E Madry
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Sarah E Linson
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Matthew Ojeda Saavedra
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Concepcion Cantu
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - James M Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Randall J Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas; Texas A&M Health Science Center College of Medicine, Bryan, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York.
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39
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Do H, Makthal N, Chandrangsu P, Olsen RJ, Helmann JD, Musser JM, Kumaraswami M. Metal sensing and regulation of adaptive responses to manganese limitation by MtsR is critical for group A streptococcus virulence. Nucleic Acids Res 2019; 47:8333-8334. [PMID: 31329935 PMCID: PMC6736032 DOI: 10.1093/nar/gkz641] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Affiliation(s)
- Hackwon Do
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA
| | - Nishanth Makthal
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA
| | - Pete Chandrangsu
- Department of Microbiology, Cornell University, Ithaca, NY 14853-8101, USA.,W.M. Keck Science Department, Claremont McKenna, Pitzer and Scripps College, Claremont, CA 91711, USA
| | - Randall J Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA.,Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - John D Helmann
- Department of Microbiology, Cornell University, Ithaca, NY 14853-8101, USA
| | - James M Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA.,Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Muthiah Kumaraswami
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA
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40
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Do H, Makthal N, VanderWal AR, Saavedra MO, Olsen RJ, Musser JM, Kumaraswami M. Environmental pH and peptide signaling control virulence of Streptococcus pyogenes via a quorum-sensing pathway. Nat Commun 2019; 10:2586. [PMID: 31197146 PMCID: PMC6565748 DOI: 10.1038/s41467-019-10556-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [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: 01/02/2019] [Accepted: 05/14/2019] [Indexed: 12/20/2022] Open
Abstract
Bacteria control gene expression in concert with their population density by a process called quorum sensing, which is modulated by bacterial chemical signals and environmental factors. In the human pathogen Streptococcus pyogenes, production of secreted virulence factor SpeB is controlled by a quorum-sensing pathway and environmental pH. The quorum-sensing pathway consists of a secreted leaderless peptide signal (SIP), and its cognate receptor RopB. Here, we report that the SIP quorum-sensing pathway has a pH-sensing mechanism operative through a pH-sensitive histidine switch located at the base of the SIP-binding pocket of RopB. Environmental acidification induces protonation of His144 and reorganization of hydrogen bonding networks in RopB, which facilitates SIP recognition. The convergence of two disparate signals in the SIP signaling pathway results in induction of SpeB production and increased bacterial virulence. Our findings provide a model for investigating analogous crosstalk in other microorganisms.
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Affiliation(s)
- Hackwon Do
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, TX, 77030, USA
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, 77030, USA
| | - Nishanth Makthal
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, TX, 77030, USA
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, 77030, USA
| | - Arica R VanderWal
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, TX, 77030, USA
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, 77030, USA
| | - Matthew Ojeda Saavedra
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, TX, 77030, USA
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, 77030, USA
| | - Randall J Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, TX, 77030, USA
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, 77030, USA
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, NY, 10021, USA
| | - James M Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, TX, 77030, USA
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, 77030, USA
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, NY, 10021, USA
| | - Muthiah Kumaraswami
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, TX, 77030, USA.
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, 77030, USA.
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41
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Zhu L, Olsen RJ, Beres SB, Eraso JM, Saavedra MO, Kubiak SL, Cantu CC, Jenkins L, Charbonneau ARL, Waller AS, Musser JM. Gene fitness landscape of group A streptococcus during necrotizing myositis. J Clin Invest 2019; 129:887-901. [PMID: 30667377 PMCID: PMC6355216 DOI: 10.1172/jci124994] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 11/27/2018] [Indexed: 12/15/2022] Open
Abstract
Necrotizing fasciitis and myositis are devastating infections characterized by high mortality. Group A streptococcus (GAS) is a common cause of these infections, but the molecular pathogenesis is poorly understood. We report a genome-wide analysis using serotype M1 and M28 strains that identified GAS genes contributing to necrotizing myositis in nonhuman primates (NHP), a clinically relevant model. Using transposon-directed insertion-site sequencing (TraDIS), we identified 126 and 116 GAS genes required for infection by serotype M1 and M28 organisms, respectively. For both M1 and M28 strains, more than 25% of the GAS genes required for necrotizing myositis encode known or putative transporters. Thirteen GAS transporters contributed to both M1 and M28 strain fitness in NHP myositis, including putative importers for amino acids, carbohydrates, and vitamins and exporters for toxins, quorum-sensing peptides, and uncharacterized molecules. Targeted deletion of genes encoding 5 transporters confirmed that each isogenic mutant strain was significantly (P < 0.05) impaired in causing necrotizing myositis in NHPs. Quantitative reverse-transcriptase PCR (qRT-PCR) analysis showed that these 5 genes are expressed in infected NHP and human skeletal muscle. Certain substrate-binding lipoproteins of these transporters, such as Spy0271 and Spy1728, were previously documented to be surface exposed, suggesting that our findings have translational research implications.
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Affiliation(s)
- Luchang Zhu
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Randall J. Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, New York, USA
| | - Stephen B. Beres
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Jesus M. Eraso
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Matthew Ojeda Saavedra
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Samantha L. Kubiak
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Concepcion C. Cantu
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Leslie Jenkins
- Department of Comparative Medicine, Houston Methodist Research Institute, Houston, Texas, USA
| | - Amelia R. L. Charbonneau
- Animal Health Trust, Newmarket, Suffolk, United Kingdom
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | | | - James M. Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, New York, USA
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42
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Alexander AJ, Myers C, Beres SB, Olsen RJ, Musser JM, Mangino JE. Postpartum Group A Streptococcus Case Series: Reach Out to Infection Prevention! Open Forum Infect Dis 2018; 5:ofy159. [PMID: 30038929 PMCID: PMC6051448 DOI: 10.1093/ofid/ofy159] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 06/28/2018] [Indexed: 12/02/2022] Open
Abstract
A series of postpartum Streptococcus pyogenes infections prompted an investigation to rule out potential transmission by a health care worker. None of the hospital staff screened were colonized. All isolates were determined to be unrelated by molecular methods, including whole-genome sequencing. Thus, nosocomial transmission was considered unlikely.
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Affiliation(s)
- Andrew J Alexander
- Division of Infectious Diseases, Ohio State University Wexner Medical Center, Columbus, Ohio
| | - Carol Myers
- Department of Clinical Epidemiology, Ohio State University Wexner Medical Center, Columbus, Ohio
| | - Stephen B Beres
- Department of Pathology and Genomic Medicine, Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Randall J Olsen
- Department of Pathology and Genomic Medicine, Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - James M Musser
- Department of Pathology and Genomic Medicine, Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Julie E Mangino
- Division of Infectious Diseases, Ohio State University Wexner Medical Center, Columbus, Ohio.,Department of Clinical Epidemiology, Ohio State University Wexner Medical Center, Columbus, Ohio
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43
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Makthal N, Do H, VanderWal AR, Olsen RJ, Musser JM, Kumaraswami M. Signaling by a Conserved Quorum Sensing Pathway Contributes to Growth Ex Vivo and Oropharyngeal Colonization of Human Pathogen Group A Streptococcus. Infect Immun 2018; 86:e00169-18. [PMID: 29531135 PMCID: PMC5913841 DOI: 10.1128/iai.00169-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [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: 03/02/2018] [Accepted: 03/04/2018] [Indexed: 02/06/2023] Open
Abstract
Bacterial virulence factor production is a highly coordinated process. The temporal pattern of bacterial gene expression varies in different host anatomic sites to overcome niche-specific challenges. The human pathogen group A streptococcus (GAS) produces a potent secreted protease, SpeB, that is crucial for pathogenesis. Recently, we discovered that a quorum sensing pathway comprised of a leaderless short peptide, SpeB-inducing peptide (SIP), and a cytosolic global regulator, RopB, controls speB expression in concert with bacterial population density. The SIP signaling pathway is active in vivo and contributes significantly to GAS invasive infections. In the current study, we investigated the role of the SIP signaling pathway in GAS-host interactions during oropharyngeal colonization. The SIP signaling pathway is functional during growth ex vivo in human saliva. SIP-mediated speB expression plays a crucial role in GAS colonization of the mouse oropharynx. GAS employs a distinct pattern of SpeB production during growth ex vivo in saliva that includes a transient burst of speB expression during early stages of growth coupled with sustained levels of secreted SpeB protein. SpeB production aids GAS survival by degrading LL37, an abundant human antimicrobial peptide. We found that SIP signaling occurs during growth in human blood ex vivo. Moreover, the SIP signaling pathway is critical for GAS survival in blood. SIP-dependent speB regulation is functional in strains of diverse emm types, indicating that SIP signaling is a conserved virulence regulatory mechanism. Our discoveries have implications for future translational studies.
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Affiliation(s)
- Nishanth Makthal
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Hackwon Do
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Arica R VanderWal
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Randall J Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, New York, USA
| | - James M Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, New York, USA
| | - Muthiah Kumaraswami
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
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44
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Sitkiewicz I, Musser JM. Deletion of from Streptococcus pyogenes. Results in Hypervirulence in a Mouse Model of Sepsis and is LuxS Independent. Pol J Microbiol 2018; 66:17-24. [PMID: 29359701 DOI: 10.5604/17331331.1234989] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Group A Streptococcus (GAS) is a Gram-positive human pathogen that causes a variety of diseases ranging from pharyngitis to life-threatening streptococcal toxic shock syndrome. Recently, several global gene expression analyses have yielded extensive new information regarding the regulation of genes encoding known and putative virulence factors in GAS. A microarray analysis found that transcription of the GAS gene M5005_Spy_1343 was significantly increased in response to interaction with human polymorphonuclear leukocytes. M5005_Spy_1343 is predicted to encode a member of the LysR family of transcriptional regulators and is located upstream of a putative operon containing six genes. Five of these genes have sequence similarity to genes involved in short-chain fatty acid metabolism, whereas the sixth gene (luxS) is found in many bacterial species and is involved in quorum sensing. Unexpectedly, inactivation of the M5005_Spy_1343 gene resulted in hypervirulence in an intraperitoneal mouse model of infection. Increased virulence was not due to changes in luxS gene expression. We postulate that short-chain fatty acid metabolism is involved in GAS pathogenesis.
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Affiliation(s)
- Izabela Sitkiewicz
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
| | - James M Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
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45
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Nguyen M, Brettin T, Long SW, Musser JM, Olsen RJ, Olson R, Shukla M, Stevens RL, Xia F, Yoo H, Davis JJ. Developing an in silico minimum inhibitory concentration panel test for Klebsiella pneumoniae. Sci Rep 2018; 8:421. [PMID: 29323230 PMCID: PMC5765115 DOI: 10.1038/s41598-017-18972-w] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [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: 09/27/2017] [Accepted: 12/12/2017] [Indexed: 12/20/2022] Open
Abstract
Antimicrobial resistant infections are a serious public health threat worldwide. Whole genome sequencing approaches to rapidly identify pathogens and predict antibiotic resistance phenotypes are becoming more feasible and may offer a way to reduce clinical test turnaround times compared to conventional culture-based methods, and in turn, improve patient outcomes. In this study, we use whole genome sequence data from 1668 clinical isolates of Klebsiella pneumoniae to develop a XGBoost-based machine learning model that accurately predicts minimum inhibitory concentrations (MICs) for 20 antibiotics. The overall accuracy of the model, within ±1 two-fold dilution factor, is 92%. Individual accuracies are ≥90% for 15/20 antibiotics. We show that the MICs predicted by the model correlate with known antimicrobial resistance genes. Importantly, the genome-wide approach described in this study offers a way to predict MICs for isolates without knowledge of the underlying gene content. This study shows that machine learning can be used to build a complete in silico MIC prediction panel for K. pneumoniae and provides a framework for building MIC prediction models for other pathogenic bacteria.
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Affiliation(s)
- Marcus Nguyen
- Northern Illinois University, Computation Science, DeKalb, IL, 60115, USA.,University of Chicago, Computation Institute, Chicago, IL, 60637, USA.,Argonne National Laboratory, Computing Environment and Life Sciences, Argonne, IL, 60439, USA
| | - Thomas Brettin
- University of Chicago, Computation Institute, Chicago, IL, 60637, USA.,Argonne National Laboratory, Computing Environment and Life Sciences, Argonne, IL, 60439, USA
| | - S Wesley Long
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, 77030, USA.,Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, 10065, USA
| | - James M Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, 77030, USA.,Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, 10065, USA
| | - Randall J Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, 77030, USA.,Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, 10065, USA
| | - Robert Olson
- University of Chicago, Computation Institute, Chicago, IL, 60637, USA.,Argonne National Laboratory, Computing Environment and Life Sciences, Argonne, IL, 60439, USA
| | - Maulik Shukla
- University of Chicago, Computation Institute, Chicago, IL, 60637, USA.,Argonne National Laboratory, Computing Environment and Life Sciences, Argonne, IL, 60439, USA
| | - Rick L Stevens
- University of Chicago, Computation Institute, Chicago, IL, 60637, USA.,Argonne National Laboratory, Computing Environment and Life Sciences, Argonne, IL, 60439, USA.,University of Chicago, Department of Computer Science, Chicago, IL, 60439, USA
| | - Fangfang Xia
- University of Chicago, Computation Institute, Chicago, IL, 60637, USA.,Argonne National Laboratory, Computing Environment and Life Sciences, Argonne, IL, 60439, USA
| | - Hyunseung Yoo
- University of Chicago, Computation Institute, Chicago, IL, 60637, USA.,Argonne National Laboratory, Computing Environment and Life Sciences, Argonne, IL, 60439, USA
| | - James J Davis
- University of Chicago, Computation Institute, Chicago, IL, 60637, USA. .,Argonne National Laboratory, Computing Environment and Life Sciences, Argonne, IL, 60439, USA.
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46
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Beres SB, Olsen RJ, Ojeda Saavedra M, Ure R, Reynolds A, Lindsay DSJ, Smith AJ, Musser JM. Genome sequence analysis of emm89 Streptococcus pyogenes strains causing infections in Scotland, 2010-2016. J Med Microbiol 2017; 66:1765-1773. [PMID: 29099690 PMCID: PMC5845742 DOI: 10.1099/jmm.0.000622] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Purpose Strains of type emm89 Streptococcus pyogenes have recently increased in frequency as a cause of human infections in several countries in Europe and North America. This increase has been molecular epidemiologically linked with the emergence of a new genetically distinct clone, designated clade 3. We sought to extend our understanding of this epidemic behavior by the genetic characterization of type emm89 strains responsible in recent years for an increased frequency of infections in Scotland. Methodology We sequenced the genomes of a retrospective cohort of 122 emm89 strains recovered from patients with invasive and noninvasive infections throughout Scotland during 2010 to 2016. Results All but one of the 122 emm89 infection isolates are of the recently emerged epidemic clade 3 clonal lineage. The Scotland isolates are closely related to and not genetically distinct from recent emm89 strains from England, they constitute a single genetic population. Conclusions The clade 3 clone causes virtually all-contemporary emm89 infections in Scotland. These findings add Scotland to a growing list of countries of Europe and North America where, by whole genome sequencing, emm89 clade 3 strains have been demonstrated to be the cause of an ongoing epidemic of invasive infections and to be genetically related due to descent from a recent common progenitor.
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Affiliation(s)
- Stephen B Beres
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, and Houston Methodist Hospital, Houston, TX 77030, USA
| | - Randall J Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, and Houston Methodist Hospital, Houston, TX 77030, USA.,Departments of Pathology and Laboratory Medicine and Microbiology and Immunology, Weill Cornell Medical College, NY 10021, USA
| | - Matthew Ojeda Saavedra
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, and Houston Methodist Hospital, Houston, TX 77030, USA
| | - Roisin Ure
- Scottish Haemophilus Legionella Meningococcus Pneumococcus Reference Laboratory, New Lister Building, Glasgow, G31 2ER, Scotland, UK
| | - Arlene Reynolds
- Scottish Haemophilus Legionella Meningococcus Pneumococcus Reference Laboratory, New Lister Building, Glasgow, G31 2ER, Scotland, UK
| | - Diane S J Lindsay
- Scottish Haemophilus Legionella Meningococcus Pneumococcus Reference Laboratory, New Lister Building, Glasgow, G31 2ER, Scotland, UK
| | - Andrew J Smith
- Scottish Haemophilus Legionella Meningococcus Pneumococcus Reference Laboratory, New Lister Building, Glasgow, G31 2ER, Scotland, UK.,College of Medical, Veterinary and Life Sciences, Glasgow Dental Hospital and School, University of Glasgow, 378 Sauchiehall Street, Glasgow, G2 3JZ, Scotland, UK
| | - James M Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, and Houston Methodist Hospital, Houston, TX 77030, USA.,Departments of Pathology and Laboratory Medicine and Microbiology and Immunology, Weill Cornell Medical College, NY 10021, USA
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47
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Do H, Makthal N, VanderWal AR, Rettel M, Savitski MM, Peschek N, Papenfort K, Olsen RJ, Musser JM, Kumaraswami M. Leaderless secreted peptide signaling molecule alters global gene expression and increases virulence of a human bacterial pathogen. Proc Natl Acad Sci U S A 2017; 114:E8498-E8507. [PMID: 28923955 PMCID: PMC5635878 DOI: 10.1073/pnas.1705972114] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [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] [Indexed: 01/09/2023] Open
Abstract
Successful pathogens use complex signaling mechanisms to monitor their environment and reprogram global gene expression during specific stages of infection. Group A Streptococcus (GAS) is a major human pathogen that causes significant disease burden worldwide. A secreted cysteine protease known as streptococcal pyrogenic exotoxin B (SpeB) is a key virulence factor that is produced abundantly during infection and is critical for GAS pathogenesis. Although identified nearly a century ago, the molecular basis for growth phase control of speB gene expression remains unknown. We have discovered that GAS uses a previously unknown peptide-mediated intercellular signaling system to control SpeB production, alter global gene expression, and enhance virulence. GAS produces an eight-amino acid leaderless peptide [SpeB-inducing peptide (SIP)] during high cell density and uses the secreted peptide for cell-to-cell signaling to induce population-wide speB expression. The SIP signaling pathway includes peptide secretion, reimportation into the cytosol, and interaction with the intracellular global gene regulator Regulator of Protease B (RopB), resulting in SIP-dependent modulation of DNA binding and regulatory activity of RopB. Notably, SIP signaling causes differential expression of ∼14% of GAS core genes. Several genes that encode toxins and other virulence genes that enhance pathogen dissemination and infection are significantly up-regulated. Using three mouse infection models, we show that the SIP signaling pathway is active during infection and contributes significantly to GAS pathogenesis at multiple host anatomic sites. Together, our results delineate the molecular mechanisms involved in a previously undescribed virulence regulatory pathway of an important human pathogen and suggest new therapeutic strategies.
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Affiliation(s)
- Hackwon Do
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX 77030
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030
| | - Nishanth Makthal
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX 77030
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030
| | - Arica R VanderWal
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX 77030
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030
| | - Mandy Rettel
- Genome Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Mikhail M Savitski
- Genome Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Nikolai Peschek
- Munich Center for Integrated Protein Science, Department of Microbiology, Ludwig Maximilians University of Munich, 82152 Martinsried, Germany
| | - Kai Papenfort
- Munich Center for Integrated Protein Science, Department of Microbiology, Ludwig Maximilians University of Munich, 82152 Martinsried, Germany
| | - Randall J Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX 77030
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, NY 10021
| | - James M Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX 77030
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, NY 10021
| | - Muthiah Kumaraswami
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX 77030;
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030
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48
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Teatero S, Coleman BL, Beres SB, Olsen RJ, Kandel C, Reynolds O, Athey TBT, Musser JM, McGeer A, Fittipaldi N. Rapid Emergence of a New Clone Impacts the Population at Risk and Increases the Incidence of Type emm89 Group A Streptococcus Invasive Disease. Open Forum Infect Dis 2017; 4:ofx042. [PMID: 28470020 PMCID: PMC5407211 DOI: 10.1093/ofid/ofx042] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 03/02/2017] [Indexed: 12/02/2022] Open
Abstract
Background Invasive group A Streptococcus (iGAS) disease caused by type emm89 strains has been increasing worldwide, driven by the emergence of an epidemic clonal variant (clade 3 emm89). The clinical characteristics of patients with emm89 iGAS disease, and in particular with clade 3 emm89 iGAS disease, are poorly described. Methods We used population-based iGAS surveillance data collected in metropolitan Toronto, Ontario, Canada during the period 2000–2014. We sequenced the genomes of 105 emm89 isolates representing all emm89 iGAS disease cases in the area during the period and 138 temporally matched emm89 iGAS isolates collected elsewhere in Ontario. Results Clades 1 and 2 and clade O, a newly discovered emm89 genetic variant, caused most cases of emm89 iGAS disease in metropolitan Toronto before 2008. After rapid emergence of new clade 3, previously circulating clades were purged from the population and the incidence of emm89 iGAS disease significantly increased from 0.14 per 100000 in 2000–2007 to 0.22 per 100000 in 2008–2014. Overall, emm89 organisms caused significantly more arthritis but less necrotizing fasciitis than strains of the more common type emm1. Other clinical presentations were soft tissue and severe respiratory tract infections. Clinical outcomes did not differ significantly between emm89 clades overall. However, clade 3 emm89 iGAS disease was more common in youth and middle-aged individuals. Conclusions The rapid shift in emm89 iGAS strain genetics in metropolitan Toronto has resulted in a significant increase in the incidence of emm89 iGAS disease, with noticeably higher rates of clade 3 disease in younger patients.
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Affiliation(s)
| | - Brenda L Coleman
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Canada.,Mount Sinai Hospital, Toronto, Canada; and
| | - Stephen B Beres
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Texas
| | - Randall J Olsen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Texas
| | - Christopher Kandel
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Canada.,Mount Sinai Hospital, Toronto, Canada; and
| | | | | | - James M Musser
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Texas
| | - Allison McGeer
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Canada.,Mount Sinai Hospital, Toronto, Canada; and
| | - Nahuel Fittipaldi
- Public Health Ontario, Toronto, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Canada
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49
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Skwark MJ, Croucher NJ, Puranen S, Chewapreecha C, Pesonen M, Xu YY, Turner P, Harris SR, Beres SB, Musser JM, Parkhill J, Bentley SD, Aurell E, Corander J. Interacting networks of resistance, virulence and core machinery genes identified by genome-wide epistasis analysis. PLoS Genet 2017; 13:e1006508. [PMID: 28207813 PMCID: PMC5312804 DOI: 10.1371/journal.pgen.1006508] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [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: 08/03/2016] [Accepted: 11/24/2016] [Indexed: 12/05/2022] Open
Abstract
Recent advances in the scale and diversity of population genomic datasets for bacteria now provide the potential for genome-wide patterns of co-evolution to be studied at the resolution of individual bases. Here we describe a new statistical method, genomeDCA, which uses recent advances in computational structural biology to identify the polymorphic loci under the strongest co-evolutionary pressures. We apply genomeDCA to two large population data sets representing the major human pathogens Streptococcus pneumoniae (pneumococcus) and Streptococcus pyogenes (group A Streptococcus). For pneumococcus we identified 5,199 putative epistatic interactions between 1,936 sites. Over three-quarters of the links were between sites within the pbp2x, pbp1a and pbp2b genes, the sequences of which are critical in determining non-susceptibility to beta-lactam antibiotics. A network-based analysis found these genes were also coupled to that encoding dihydrofolate reductase, changes to which underlie trimethoprim resistance. Distinct from these antibiotic resistance genes, a large network component of 384 protein coding sequences encompassed many genes critical in basic cellular functions, while another distinct component included genes associated with virulence. The group A Streptococcus (GAS) data set population represents a clonal population with relatively little genetic variation and a high level of linkage disequilibrium across the genome. Despite this, we were able to pinpoint two RNA pseudouridine synthases, which were each strongly linked to a separate set of loci across the chromosome, representing biologically plausible targets of co-selection. The population genomic analysis method applied here identifies statistically significantly co-evolving locus pairs, potentially arising from fitness selection interdependence reflecting underlying protein-protein interactions, or genes whose product activities contribute to the same phenotype. This discovery approach greatly enhances the future potential of epistasis analysis for systems biology, and can complement genome-wide association studies as a means of formulating hypotheses for targeted experimental work. Epistatic interactions between polymorphisms in DNA are recognized as important drivers of evolution in numerous organisms. Study of epistasis in bacteria has been hampered by the lack of densely sampled population genomic data, suitable statistical models and inference algorithms sufficiently powered for extremely high-dimensional parameter spaces. We introduce the first model-based method for genome-wide epistasis analysis and use two of the largest available bacterial population genome data sets on Streptococcus pneumoniae (the pneumococcus) and Streptococcus pyogenes (group A Streptococcus) to demonstrate its potential for biological discovery. Our approach reveals interacting networks of resistance, virulence and core machinery genes in the pneumococcus, which highlights putative candidates for novel drug targets. We also discover a number of plausible targets of co-selection in S. pyogenes linked to RNA pseudouridine synthases. Our method significantly enhances the future potential of epistasis analysis for systems biology, and can complement genome-wide association studies as a means of formulating hypotheses for targeted experimental work.
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Affiliation(s)
- Marcin J Skwark
- Department of Chemistry, Vanderbilt University, Nashville, TN, United States of America
| | - Nicholas J Croucher
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Santeri Puranen
- Department of Computer Science, Aalto University, Espoo, Finland
| | | | - Maiju Pesonen
- Department of Computer Science, Aalto University, Espoo, Finland
| | - Ying Ying Xu
- Department of Computer Science, Aalto University, Espoo, Finland
| | - Paul Turner
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand.,Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Simon R Harris
- Pathogen Genomics, Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Stephen B Beres
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, and Houston Methodist Hospital, Houston, Texas, United States of America
| | - James M Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, and Houston Methodist Hospital, Houston, Texas, United States of America.,Departments of Pathology and Laboratory Medicine and Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America
| | - Julian Parkhill
- Pathogen Genomics, Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Stephen D Bentley
- Pathogen Genomics, Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Erik Aurell
- Department of Computational Biology, KTH-Royal Institute of Technology, Stockholm, Sweden.,Departments of Applied Physics and Computer Science, Aalto University, Espoo, Finland.,Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing, China
| | - Jukka Corander
- Pathogen Genomics, Wellcome Trust Sanger Institute, Cambridge, United Kingdom.,Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland.,Department of Biostatistics, University of Oslo, Oslo, Norway.,Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
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Zhu L, Olsen RJ, Lee JD, Porter AR, DeLeo FR, Musser JM. Contribution of Secreted NADase and Streptolysin O to the Pathogenesis of Epidemic Serotype M1 Streptococcus pyogenes Infections. Am J Pathol 2016; 187:605-613. [PMID: 28034602 DOI: 10.1016/j.ajpath.2016.11.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 10/28/2016] [Accepted: 11/03/2016] [Indexed: 12/11/2022]
Abstract
Streptococcus pyogenes secretes many toxins that facilitate human colonization, invasion, and dissemination. NADase (SPN) and streptolysin O (SLO) are two toxins that play important roles in pathogenesis. We previously showed that increased production of SPN and SLO in epidemic serotype M1 and M89 S. pyogenes strains is associated with rapid intercontinental spread and enhanced virulence. The biological functions of SPN and SLO have been extensively studied using eukaryotic cell lines, but the relative contribution of each of these two toxins to pathogenesis of epidemic M1 or M89 strains remains unexplored. Herein, using a genetically representative epidemic M1 strain and a panel of isogenic mutant derivative strains, we evaluated the relative contributions of SPN and SLO toxins to virulence in mouse models of necrotizing myositis, bacteremia, and skin and soft tissue infection. We found that isogenic mutants lacking SPN, SLO, and both toxins are equally impaired in ability to cause necrotizing myositis. In addition, mutants lacking either SPN or SLO are significantly attenuated in the bacteremia and soft tissue infection models, and the mutant strain lacking production of both toxins is further attenuated. The mutant strain lacking both SPN and SLO production is severely attenuated in ability to resist killing by human polymorphonuclear leukocytes. We conclude that both SPN and SLO contribute significantly to S. pyogenes pathogenesis in these virulence assays.
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Affiliation(s)
- Luchang Zhu
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, Texas; Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Randall J Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, Texas; Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Jessica D Lee
- Department of Biosciences, Rice University, Houston, Texas
| | - Adeline R Porter
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana
| | - Frank R DeLeo
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana
| | - James M Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, Texas; Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas.
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