1
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Shao J, Xu Y, Olsen RJ, Kasparian S, Sun K, Mathur S, Zhang J, He C, Chen SH, Bernicker EH, Li Z. 5-Hydroxymethylcytosine in Cell-Free DNA Predicts Immunotherapy Response in Lung Cancer. Cells 2024; 13:715. [PMID: 38667328 PMCID: PMC11049556 DOI: 10.3390/cells13080715] [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: 02/21/2024] [Revised: 04/04/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
Immune checkpoint inhibitors (ICIs) drastically improve therapeutic outcomes for lung cancer, but accurately predicting individual patient responses to ICIs remains a challenge. We performed the genome-wide profiling of 5-hydroxymethylcytosine (5hmC) in 85 plasma cell-free DNA (cfDNA) samples from lung cancer patients and developed a 5hmC signature that was significantly associated with progression-free survival (PFS). We built a 5hmC predictive model to quantify the 5hmC level and validated the model in the validation, test, and control sets. Low weighted predictive scores (wp-scores) were significantly associated with a longer PFS compared to high wp-scores in the validation [median 7.6 versus 1.8 months; p = 0.0012; hazard ratio (HR) 0.12; 95% confidence interval (CI), 0.03-0.54] and test (median 14.9 versus 3.3 months; p = 0.00074; HR 0.10; 95% CI, 0.02-0.50) sets. Objective response rates in patients with a low or high wp-score were 75.0% (95% CI, 42.8-94.5%) versus 0.0% (95% CI, 0.0-60.2%) in the validation set (p = 0.019) and 80.0% (95% CI, 44.4-97.5%) versus 0.0% (95% CI, 0.0-36.9%) in the test set (p = 0.0011). The wp-scores were also significantly associated with PFS in patients receiving single-agent ICI treatment (p < 0.05). In addition, the 5hmC predictive signature demonstrated superior predictive capability to tumor programmed death-ligand 1 and specificity to ICI treatment response prediction. Moreover, we identified novel 5hmC-associated genes and signaling pathways integral to ICI treatment response in lung cancer. This study provides proof-of-concept evidence that the cfDNA 5hmC signature is a robust biomarker for predicting ICI treatment response in lung cancer.
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Affiliation(s)
- Jianming Shao
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA (R.J.O.)
- Houston Methodist Research Institute, Houston, TX 77030, USA (S.M.); (S.-H.C.)
| | - Yitian Xu
- Houston Methodist Research Institute, Houston, TX 77030, USA (S.M.); (S.-H.C.)
| | - Randall J. Olsen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA (R.J.O.)
- Houston Methodist Research Institute, Houston, TX 77030, USA (S.M.); (S.-H.C.)
- Weill Cornell Medical College, New York, NY 10065, USA
| | - Saro Kasparian
- Neal Cancer Center, Houston Methodist Hospital, Houston, TX 77030, USA (E.H.B.)
- Department of Medical Oncology, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Kai Sun
- Weill Cornell Medical College, New York, NY 10065, USA
- Neal Cancer Center, Houston Methodist Hospital, Houston, TX 77030, USA (E.H.B.)
| | - Sunil Mathur
- Houston Methodist Research Institute, Houston, TX 77030, USA (S.M.); (S.-H.C.)
- Neal Cancer Center, Houston Methodist Hospital, Houston, TX 77030, USA (E.H.B.)
| | - Jun Zhang
- Weill Cornell Medical College, New York, NY 10065, USA
- Neal Cancer Center, Houston Methodist Hospital, Houston, TX 77030, USA (E.H.B.)
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Shu-Hsia Chen
- Houston Methodist Research Institute, Houston, TX 77030, USA (S.M.); (S.-H.C.)
- Neal Cancer Center, Houston Methodist Hospital, Houston, TX 77030, USA (E.H.B.)
| | - Eric H. Bernicker
- Neal Cancer Center, Houston Methodist Hospital, Houston, TX 77030, USA (E.H.B.)
| | - Zejuan Li
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA (R.J.O.)
- Houston Methodist Research Institute, Houston, TX 77030, USA (S.M.); (S.-H.C.)
- Weill Cornell Medical College, New York, NY 10065, USA
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2
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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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3
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Shao J, Olsen RJ, Kasparian S, He C, Bernicker EH, Li Z. Cell-Free DNA 5-Hydroxymethylcytosine Signatures for Lung Cancer Prognosis. Cells 2024; 13:298. [PMID: 38391911 PMCID: PMC10886903 DOI: 10.3390/cells13040298] [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: 12/11/2023] [Revised: 02/01/2024] [Accepted: 02/04/2024] [Indexed: 02/24/2024] Open
Abstract
Accurate prognostic markers are essential for guiding effective lung cancer treatment strategies. The level of 5-hydroxymethylcytosine (5hmC) in tissue is independently associated with overall survival (OS) in lung cancer patients. We explored the prognostic value of cell-free DNA (cfDNA) 5hmC through genome-wide analysis of 5hmC in plasma samples from 97 lung cancer patients. In both training and validation sets, we discovered a cfDNA 5hmC signature significantly associated with OS in lung cancer patients. We built a 5hmC prognostic model and calculated the weighted predictive scores (wp-score) for each sample. Low wp-scores were significantly associated with longer OS compared to high wp-scores in the training [median 22.9 versus 8.2 months; p = 1.30 × 10-10; hazard ratio (HR) 0.04; 95% confidence interval (CI), 0.00-0.16] and validation (median 18.8 versus 5.2 months; p = 0.00059; HR 0.22; 95% CI: 0.09-0.57) sets. The 5hmC signature independently predicted prognosis and outperformed age, sex, smoking, and TNM stage for predicting lung cancer outcomes. Our findings reveal critical genes and signaling pathways with aberrant 5hmC levels, enhancing our understanding of lung cancer pathophysiology. The study underscores the potential of cfDNA 5hmC as a superior prognostic tool for guiding more personalized therapeutic strategies for lung cancer patients.
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Affiliation(s)
- Jianming Shao
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA
- Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Randall J. Olsen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA
- Houston Methodist Research Institute, Houston, TX 77030, USA
- Weill Cornell Medical College, New York, NY 10065, USA
| | - Saro Kasparian
- Cancer Center, Houston Methodist Hospital, Houston, TX 77030, USA
- Department of Medical Oncology, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | | | - Zejuan Li
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA
- Houston Methodist Research Institute, Houston, TX 77030, USA
- Weill Cornell Medical College, New York, NY 10065, USA
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4
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Do H, Li ZR, Tripathi PK, Mitra S, Guerra S, Dash A, Weerasekera D, Makthal N, Shams S, Aggarwal S, Singh BB, Gu D, Du Y, Olsen RJ, LaRock C, Zhang W, Kumaraswami M. Engineered probiotic overcomes pathogen defences using signal interference and antibiotic production to treat infection in mice. Nat Microbiol 2024; 9:502-513. [PMID: 38228859 PMCID: PMC10847043 DOI: 10.1038/s41564-023-01583-9] [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: 04/21/2023] [Accepted: 12/11/2023] [Indexed: 01/18/2024]
Abstract
Probiotic supplements are suggested to promote human health by preventing pathogen colonization. However, the mechanistic bases for their efficacy in vivo are largely uncharacterized. Here using metabolomics and bacterial genetics, we show that the human oral probiotic Streptococcus salivarius K12 (SAL) produces salivabactin, an antibiotic that effectively inhibits pathogenic Streptococcus pyogenes (GAS) in vitro and in mice. However, prophylactic dosing with SAL enhanced GAS colonization in mice and ex vivo in human saliva. We showed that, on co-colonization, GAS responds to a SAL intercellular peptide signal that controls SAL salivabactin production. GAS produces a secreted protease, SpeB, that targets SAL-derived salivaricins and enhances GAS survival. Using this knowledge, we re-engineered probiotic SAL to prevent signal eavesdropping by GAS and potentiate SAL antimicrobials. This engineered probiotic demonstrated superior efficacy in preventing GAS colonization in vivo. Our findings show that knowledge of interspecies interactions can identify antibiotic- and probiotic-based strategies to combat infection.
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Affiliation(s)
- Hackwon Do
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, TX, USA
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
- Research unit of cryogenic novel material, Korea Polar Research Institute, Incheon, South Korea
| | - Zhong-Rui Li
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - Praveen Kumar Tripathi
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, TX, USA
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
| | - Sonali Mitra
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, TX, USA
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
| | - Stephanie Guerra
- Department of Microbiology and Immunology, Emory School of Medicine, Atlanta, GA, USA
| | - Ananya Dash
- Department of Microbiology and Immunology, Emory School of Medicine, Atlanta, GA, USA
| | - Dulanthi Weerasekera
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, TX, USA
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
| | - Nishanth Makthal
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, TX, USA
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
| | - Syed Shams
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, TX, USA
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
| | - Shifu Aggarwal
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, TX, USA
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
| | - Bharat Bhushan Singh
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, TX, USA
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
| | - Di Gu
- Department of Chemistry, University of California, Berkeley, CA, USA
| | - Yongle Du
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - Randall J Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, TX, USA
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, NY, USA
| | - Christopher LaRock
- Department of Microbiology and Immunology, Emory School of Medicine, Atlanta, GA, USA
- Department of Medicine, Division of Infectious Diseases, Emory School of Medicine, Atlanta, GA, USA
- Emory Antibiotic Resistance Center, Emory School of Medicine, Atlanta, GA, USA
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
| | - Muthiah Kumaraswami
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, TX, USA.
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA.
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5
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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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6
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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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7
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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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8
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Mushegian AA, Long SW, Olsen RJ, Christensen PA, Subedi S, Chung M, Davis J, Musser J, Ghedin E. Within-host genetic diversity of SARS-CoV-2 in the context of large-scale hospital-associated genomic surveillance. medRxiv 2022:2022.08.17.22278898. [PMID: 36032964 PMCID: PMC9413716 DOI: 10.1101/2022.08.17.22278898] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 11/25/2022]
Abstract
The COVID-19 pandemic has resulted in extensive surveillance of the genomic diversity of SARS-CoV-2. Sequencing data generated as part of these efforts can also capture the diversity of the SARS-CoV-2 virus populations replicating within infected individuals. To assess this within-host diversity of SARS-CoV-2 we quantified low frequency (minor) variants from deep sequence data of thousands of clinical samples collected by a large urban hospital system over the course of a year. Using a robust analytical pipeline to control for technical artefacts, we observe that at comparable viral loads, specimens from patients hospitalized due to COVID-19 had a greater number of minor variants than samples from outpatients. Since individuals with highly diverse viral populations could be disproportionate drivers of new viral lineages in the patient population, these results suggest that transmission control should pay special attention to patients with severe or protracted disease to prevent the spread of novel variants.
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Affiliation(s)
- Alexandra A. Mushegian
- Systems Genomics Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD USA
| | - Scott W. Long
- Laboratory of Molecular and Translational Human Infectious Diseases Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital Houston, Texas, 77030
| | - Randall J. Olsen
- Laboratory of Molecular and Translational Human Infectious Diseases Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital Houston, Texas, 77030
| | - Paul A. Christensen
- Laboratory of Molecular and Translational Human Infectious Diseases Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital Houston, Texas, 77030
| | - Sishir Subedi
- Laboratory of Molecular and Translational Human Infectious Diseases Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital Houston, Texas, 77030
| | - Matthew Chung
- Systems Genomics Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD USA
| | - James Davis
- Division of Data Science and Learning, Argonne National Laboratory, 9700 S. Cass Ave., Lemont, Illinois, 60439
- University of Chicago Consortium for Advanced Science and Engineering, 5801 South Ellis Avenue, Chicago, Illinois, 60637
| | - James Musser
- Laboratory of Molecular and Translational Human Infectious Diseases Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital Houston, Texas, 77030
| | - Elodie Ghedin
- Systems Genomics Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD USA
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9
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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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10
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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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11
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Smith JA, Gaikwad AA, Mathew L, Rech B, Faro JP, Lucci JA, Bai Y, Olsen RJ, Byrd TT. AHCC® Supplementation to Support Immune Function to Clear Persistent Human Papillomavirus Infections. Front Oncol 2022; 12:881902. [PMID: 35814366 PMCID: PMC9256908 DOI: 10.3389/fonc.2022.881902] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 05/25/2022] [Indexed: 11/13/2022] Open
Abstract
Objective To determine the efficacy, safety, and durability of the use of AHCC supplementation for 6 months to support the host immune system to clear high-risk human papillomavirus (HPV) infections. The AHCC supplement is a proprietary, standardized extract of cultured lentinula edodes mycelia (AHCC®, Amino Up, Ltd., Sapporo, Japan) that has been shown to have unique immune modulatory benefits. Study Design This was a randomized, double-blind, placebo-controlled study (CTN: NCT02405533) in 50 women over 30 years of age with confirmed persistent high-risk HPV infections for greater than 2 years. Patients were randomized to placebo once daily for 12 months (N = 25) or AHCC 3-g supplementation by mouth once daily on empty stomach for 6 months followed by 6 months of placebo (N = 25). Every 3 months, patients were evaluated with HPV DNA and HPV RNA testing as well as a blood sample collected to evaluate a panel of immune markers including interferon-alpha, interferon-beta (IFN-β), interferon-gamma (IFN-γ), IgG1, T lymphocytes, and natural killer (NK) cell levels. At the completion of the 12-month study period, patients on the placebo arm were given the option to continue on the study to receive AHCC supplementation unblinded for 6 months with the same follow-up appointments and testing as the intervention arm. Results Fifty women with high-risk HPV were enrolled, and 41 completed the study. Fourteen (63.6%) of the 22 patients in the AHCC supplementation arm were HPV RNA/HPV DNA negative after 6 months, with 64.3% (9/14) achieving a durable response defined as being HPV RNA/HPV DNA negative 6 months off supplementation. On the placebo arm, two (10.5%) of 19 patients were HPV negative at 12 months. In the twelve placebo arm patients who elected to continue on the unblinded study, 50% (n = 6) were HPV RNA/HPV DNA negative after 6 months of AHCC supplementation. At the time of completion of the study, there were a total of 34 patients (22 blinded and 12 unblinded) who had received AHCC supplementation with an overall response rate of 58.8% that cleared HPV persistent infections. At the time of enrollment, the mean IFN-β level was 60.5 ± 37.6 pg/ml in women with confirmed persistent HPV infections. Suppression of IFN-β to less than 20 pg/ml correlated with an increase in T lymphocytes and IFN-γ and durable clearance of HPV infections in women who received AHCC supplementation. Conclusion Results from this phase II study demonstrated that AHCC 3 g once daily was effective to support the host immune system to eliminate persistent HPV infections and was well tolerated with no significant adverse side effects reported. The duration of AHCC supplementation required beyond the first negative result needs more evaluation to optimize success for durable outcomes. The suppression of the IFN-β level to less than 20 pg/ml correlated with clearance of HPV infections and merits further evaluation as a clinical tool for monitoring patients with HPV infections. Clinical Trial Registration clinicaltrials.gov/ct2/, identifier NCT02405533
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Affiliation(s)
- Judith A. Smith
- Department of Obstetrics, Gynecology and Reproductive Sciences, UT Health McGovern Medical School, Houston, TX, United States
- Department of Pharmacy, UT Heath-Memorial Hermann Cancer Center, Houston, TX, United States
- *Correspondence: Judith A. Smith,
| | - Anjali A. Gaikwad
- Department of Obstetrics, Gynecology and Reproductive Sciences, UT Health McGovern Medical School, Houston, TX, United States
| | - Lata Mathew
- Department of Obstetrics, Gynecology and Reproductive Sciences, UT Health McGovern Medical School, Houston, TX, United States
| | - Barbara Rech
- UT Physicians Women’s Center, Houston, TX, United States
| | - Jonathan P. Faro
- Specialists in Obstetrics & Gynecology, Houston, TX, United States
| | - Joseph A. Lucci
- Department of Obstetrics, Gynecology and Reproductive Sciences, UT Health McGovern Medical School, Houston, TX, United States
- Department of Pharmacy, UT Heath-Memorial Hermann Cancer Center, Houston, TX, United States
| | - Yu Bai
- Department of Pathology, UT Health McGovern Medical School, Houston, TX, United States
| | - Randall J. Olsen
- Department of Molecular Pathology, Houston Methodist Research Institute, Houston, TX, United States
| | - Teresa T. Byrd
- Department of Obstetrics, Gynecology and Reproductive Sciences, UT Health McGovern Medical School, Houston, TX, United States
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12
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Velu PD, Cushman-Vokoun A, Ewalt MD, Feilotter H, Gastier-Foster JM, Goswami RS, Laudadio J, Olsen RJ, Johnson R, Schlinsog A, Douglas A, Sandersfeld T, Kaul KL. Alignment of Fellowship Training with Practice Patterns for Molecular Pathologists: A Report of the Association for Molecular Pathology Training and Education Committee. J Mol Diagn 2022; 24:825-840. [PMID: 35690309 DOI: 10.1016/j.jmoldx.2022.04.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 04/12/2022] [Accepted: 04/26/2022] [Indexed: 12/19/2022] Open
Abstract
In the two decades since Accreditation Council for Graduate Medical Education-accredited Molecular Genetic Pathology fellowships began, the field of clinical molecular pathology has evolved considerably. The American Board of Pathology gathered data from board-certified molecular genetic pathologists assessing the alignment of skills and knowledge gained during fellowship with current needs on the job. The Association of Molecular Pathology conducted a parallel survey of program directors, and included questions on how various topics were taught during fellowship, as well as ranking their importance. Both surveys showed that most training aligned well with the practice needs of former trainees. Genomic profiling of tumors by next-generation sequencing, bioinformatics, laboratory management, and regulatory issues were topics thought to require increased emphasis in training. Topics related to clinical genetics and microbiology were deemed less important by those in practice, perhaps reflecting the increasing subspecialization of molecular pathologists. Program directors still viewed these topics as important to provide foundational knowledge. Parentage, identity, and human leukocyte antigen testing were less important to both survey audiences. These data may be helpful in guiding future adjustments to the Molecular Genetic Pathology curriculum and Accreditation Council for Graduate Medical Education program requirements.
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Affiliation(s)
- Priya D Velu
- Molecular Genetic Pathology Curriculum Update Working Group of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Allison Cushman-Vokoun
- Molecular Genetic Pathology Curriculum Update Working Group of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska
| | - Mark D Ewalt
- Molecular Genetic Pathology Curriculum Update Working Group of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Harriet Feilotter
- Molecular Genetic Pathology Curriculum Update Working Group of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
| | - Julie M Gastier-Foster
- Molecular Genetic Pathology Curriculum Update Working Group of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Departments of Pediatrics and Pathology and Immunology, Baylor College of Medicine, Houston, Texas; Department of Pathology, Ohio State University College of Medicine, Columbus, Ohio
| | - Rashmi S Goswami
- Molecular Genetic Pathology Curriculum Update Working Group of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Laboratory Medicine and Molecular Diagnostics/Department of Laboratory Medicine and Pathobiology, Sunnybrook Health Sciences Centre/University of Toronto, Toronto, Ontario, Canada
| | - Jennifer Laudadio
- Molecular Genetic Pathology Curriculum Update Working Group of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Randall J Olsen
- Molecular Genetic Pathology Curriculum Update Working Group of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York; Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | | | | | | | | | - Karen L Kaul
- Molecular Genetic Pathology Curriculum Update Working Group of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; NorthShore University HealthSystem, University of Chicago Pritzker School of Medicine, Evanston, Illinois.
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13
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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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14
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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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15
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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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16
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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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17
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Eskandari G, Subedi S, Christensen P, Olsen RJ, Zu Y, Long SW. Implementing flowDensity for Automated Analysis of Bone Marrow Lymphocyte Population. J Pathol Inform 2022; 12:49. [PMID: 35070478 PMCID: PMC8721865 DOI: 10.4103/jopi.jopi_12_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 09/27/2021] [Indexed: 11/04/2022] Open
Abstract
Introduction Manual gating of flow cytometry (FCM) data for marrow cell analysis is a standard approach in current practice, although it is time- and labor-consuming. Recent advances in cytometry technology have led to significant efforts in developing partially or fully automated analysis methods. Although multiple supervised and unsupervised FCM data analysis algorithms have been developed, they have not been widely adopted by the clinical and research laboratories. In this study, we evaluated flowDensity, an open source freely available algorithm, as an automated analysis tool for classification of lymphocyte subsets in the bone marrow biopsy specimens. Materials and Methods FlowDensity-based gating was applied to 102 normal bone marrow samples and compared with the manual analysis. Independent expression of each cell marker was assessed for comprehensive expression analysis and visualization. Results Our findings showed a correlation between the manual and flowDensity-based gating in the lymphocyte subsets. However, flowDensity-based gating in the populations with a small number of cells in each cluster showed a low degree of correlation. Comprehensive expression analysis successfully identified and visualized the lymphocyte subsets. Discussion Our study found that although flowDensity might be a promising method for FCM data analysis, more optimization is required before implementing this algorithm into day-to-day workflow.
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Affiliation(s)
- Ghazaleh Eskandari
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
| | - Sishir Subedi
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
| | - Paul Christensen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
| | - Randall J Olsen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
| | - Youli Zu
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
| | - Scott W Long
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
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18
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Hsu J, Annunziata JF, Burns E, Bernicker EH, Olsen RJ, Thomas JS. Molecular Signatures of KRAS-Mutated Lung Adenocarcinoma: Analysis of Concomitant EGFR, ALK, STK11, and PD-L1 Status. Clin Pathol 2022; 15:2632010X221102054. [PMID: 35634237 PMCID: PMC9134433 DOI: 10.1177/2632010x221102054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 04/22/2022] [Indexed: 12/12/2022]
Abstract
Background KRAS mutations are the most common oncogenic driver mutations of non-small cell lung cancer (NSCLC) in the Western world. Mutations of the KRAS gene are most prevalent in the patient population of current and former cigarette smokers. With the recent pivotal approval of a targeted inhibitor therapy for patients with KRAS p.G12C mutated and pretreated NSCLC, analysis of the heterogeneity of KRAS mutations and concomitant molecular alterations in patients with these tumors at all clinical stages is indicated. Methods In this retrospective analysis, patient pathology records were reviewed for all cases receiving a pathologic diagnosis of NSCLC within our hospital system. All data were collected with IRB approval. Cases of indeterminate tumor type favoring a non-lung primary, as well as non-adenocarcinoma NSCLC (eg, squamous) were excluded from the cohort. In this hospital system, molecular testing for KRAS mutations is part of a molecular biomarker panel that is reflex ordered at initial diagnosis by the pathologist and may be performed as a single gene test or as a solid organ cancer hotspot panel by next generation sequencing. For each patient, KRAS mutational status and specific KRAS mutations, if present, were collated. Additional information assessed for this study included patient demographics (age, gender, and smoking history), tumor staging if available, PD-L1 expression levels by immunohistochemistry (IHC), and the presence of other genetic alterations (EGFR, ALK, and STK11). Results Between January 1, 2017 and January 1, 2019, there were 276 patients diagnosed with NSCLC of all stages who had KRAS mutational analysis performed in our hospital system and who met the criteria for inclusion into the study cohort. A KRAS driver mutation was detected in 29% of these patients. The most frequently identified KRAS mutation was p.G12C (38%), followed by p.G12D (21%) and p.G12V (13%). KRAS-mutated lung adenocarcinoma was significantly associated with current or former patient smoking status in this cohort (29/202 (14%) smokers and 1/74 (1%) non-smokers; P = .0006). PD-L1 expression of at least 1% by IHC was present in 43% of KRAS-mutated lung adenocarcinomas and 45% of non-KRAS-mutated adenocarcinomas. In this study, KRAS mutations were not found to co-occur with gene alterations in EGFR, ALK, or STK11. In 48% of cases, at least one genetic alteration (KRAS, ALK, EGFR, or STK11) was identified. Conclusions In this study cohort, KRAS-mutated lung adenocarcinoma demonstrated significant mutational heterogeneity, which is consistent with previously published studies. KRAS mutational status was also significantly associated with a current or former smoking history. Notably, p.G12C was the most frequently identified KRAS mutation in this cohort, with a frequency of 38%. This finding is particularly relevant given the recent approval of a KRAS p.G12C-specific targeted inhibitor therapy and the continued development of additional KRAS targeted therapies that may prove effective in treating NSCLC. These findings also highlight the necessity of considering molecular testing for KRAS mutations in patients with NSCLC and a smoking history, as this population most frequently harbors KRAS mutations and may benefit from these emerging targeted therapies.
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Affiliation(s)
- Jim Hsu
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
| | | | - Ethan Burns
- Houston Methodist Cancer Center, Houston Methodist Hospital, Houston, TX, USA
| | - Eric H Bernicker
- Houston Methodist Cancer Center, Houston Methodist Hospital, Houston, TX, USA
| | - Randall J Olsen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
| | - Jessica S Thomas
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
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19
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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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20
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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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21
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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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22
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Burns EA, Ensor JE, Hsu J, Thomas JS, Olsen RJ, Bernicker EH. Outcomes and prognostic contributors in patients with KRAS mutated non-small cell pulmonary adenocarcinomas: a single institution experience. J Thorac Dis 2021; 13:4785-4796. [PMID: 34527319 PMCID: PMC8411128 DOI: 10.21037/jtd-21-432] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 06/10/2021] [Indexed: 01/02/2023]
Abstract
Background KRAS is the most frequently encountered driver mutation in advanced non-small cell lung cancer (NSCLC). With targeted therapy for the most common KRAS mutation p.G12C on the horizon, the aim of this study is to retrospectively report outcomes in patients with KRAS mutated NSCLC. Methods This was a retrospective chart review of 7 hospitals in Texas with reflex biomarker testing in all lung adenocarcinomas. Patients were included if they had pathologically diagnosed adenocarcinoma of any stage originating in the lung with molecularly confirmed KRAS driver mutation of any genotypic subtype. Twelve-month survival was assessed and compared between KRAS p.G12C and all other detected KRAS mutations. Other outcomes including impact of age, sex, smoking status, and pack years smoked were assessed to determine if they had prognostic significance on mortality in KRAS mutated patients. Results There were 58 patients diagnosed with KRAS mutated NSCLC, 63.8% were at an advanced stage at diagnosis, 55.8% of patients were female, and 82.8% were white. The median age was 72 [52–88] years, and 93.1% were either current or prior smokers. KRAS p.G12C was the most common KRAS mutation (44.8%). At diagnosis, patients with KRAS p.G12C had poorer performance statuses compared to other KRAS mutations. A total of 32 (55.2%) patients died, 26 with advanced disease. In this study, current smoking status (P=0.1652), pack years smoked (P=0.6597), age (P=0.5092), sex (P=0.4309), and underlying KRAS codon mutation controlling for stage (P=0.2287) did not impact survival. However, KRAS p.G12C had a numerically lower 12 months overall survival (OS) compared to all other KRAS mutations in both early stage (56.3% vs. 90.9%) and advanced stage (25.0% vs. 47.6%) disease. Of note, 16 (27.6%) patients had prior, concurrent, or second malignancies, but these did not significantly impact OS (P=0.7696). Conclusions This study did not find a prognostic difference with sex, smoking history, age, or p.G12C mutation. The patients in this cohort with KRAS p.G12C had a numerically lower 12-month overall survival in both early and advanced stage disease compared to other mutations, and over one-quarter had a notable history of previous and second primary malignancies.
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Affiliation(s)
- Ethan A Burns
- Houston Methodist Cancer Center, 6445 Main St. Outpatient Center, Houston, TX, USA
| | - Joe E Ensor
- Houston Methodist Cancer Center, 6445 Main St. Outpatient Center, Houston, TX, USA
| | - Jim Hsu
- Department of Pathology and Genomic Medicine, Houston Methodist hospital and Weill Cornell Medicine, Houston, TX, USA
| | - Jessica S Thomas
- Department of Pathology and Genomic Medicine, Houston Methodist hospital and Weill Cornell Medicine, Houston, TX, USA
| | - Randall J Olsen
- Department of Pathology and Genomic Medicine, Houston Methodist hospital and Weill Cornell Medicine, Houston, TX, USA
| | - Eric H Bernicker
- Houston Methodist Cancer Center, 6445 Main St. Outpatient Center, Houston, TX, USA.,Thoracic and Uveal Melanoma Oncology, Houston Methodist Institute of Academic Medicine, Houston Methodist Cancer Center, 6445 Main St. Outpatient Center, Houston, TX, USA
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23
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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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24
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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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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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26
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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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27
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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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28
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Shao J, Subedi S, Pepper K, Badgett S, Christensen PA, Hendrickson HL, Thomas JS, Olsen RJ, Li Z. Identifying possible germline variants from tumor-only sequencing of hematological malignancies. Leuk Lymphoma 2020; 62:482-485. [PMID: 33054462 DOI: 10.1080/10428194.2020.1832665] [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: 10/23/2022]
Affiliation(s)
- Jianming Shao
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Sishir Subedi
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Kristi Pepper
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Sabrina Badgett
- 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
| | - Heather L Hendrickson
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Jessica S Thomas
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas.,Weill Cornell Medical College, Cornell University, Houston, Texas
| | - Randall J Olsen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas.,Weill Cornell Medical College, Cornell University, Houston, Texas
| | - Zejuan Li
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas.,Weill Cornell Medical College, Cornell University, Houston, Texas
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29
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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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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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31
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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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32
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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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33
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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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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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35
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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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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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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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38
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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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Christensen PA, Subedi S, Pepper K, Hendrickson HL, Li Z, Thomas JS, Long SW, Olsen RJ. Development and validation of Houston Methodist Variant Viewer version 3: updates to our application for interpretation of next-generation sequencing data. JAMIA Open 2020; 3:299-305. [PMID: 32734171 PMCID: PMC7382636 DOI: 10.1093/jamiaopen/ooaa004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 01/21/2020] [Accepted: 02/14/2020] [Indexed: 11/13/2022] Open
Abstract
Objectives Informatics tools that support next-generation sequencing workflows are essential to deliver timely interpretation of somatic variants in cancer. Here, we describe significant updates to our laboratory developed bioinformatics pipelines and data management application termed Houston Methodist Variant Viewer (HMVV). Materials and Methods We collected feature requests and workflow improvement suggestions from the end-users of HMVV version 1. Over 1.5 years, we iteratively implemented these features in five sequential updates to HMVV version 3. Results We improved the performance and data throughput of the application while reducing the opportunity for manual data entry errors. We enabled end-user workflows for pipeline monitoring, variant interpretation and annotation, and integration with our laboratory information system. System maintenance was improved through enhanced defect reporting, heightened data security, and improved modularity in the code and system environments. Discussion and Conclusion Validation of each HMVV update was performed according to expert guidelines. We enabled an 8× reduction in the bioinformatics pipeline computation time for our longest running assay. Our molecular pathologists can interpret the assay results at least 2 days sooner than was previously possible. The application and pipeline code are publicly available at https://github.com/hmvv.
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Affiliation(s)
- Paul A Christensen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Weill Cornell Medical College of Cornell University, Houston, Texas, USA
| | - Sishir Subedi
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Weill Cornell Medical College of Cornell University, Houston, Texas, USA
| | - Kristi Pepper
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Weill Cornell Medical College of Cornell University, Houston, Texas, USA
| | - Heather L Hendrickson
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Weill Cornell Medical College of Cornell University, Houston, Texas, USA
| | - Zejuan Li
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Weill Cornell Medical College of Cornell University, Houston, Texas, USA
| | - Jessica S Thomas
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Weill Cornell Medical College of Cornell University, Houston, Texas, USA
| | - S Wesley Long
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Weill Cornell Medical College of Cornell University, Houston, Texas, USA
| | - Randall J Olsen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Weill Cornell Medical College of Cornell University, Houston, Texas, USA
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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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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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42
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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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43
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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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44
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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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Ge Y, Mody RR, Olsen RJ, Zhou H, Luna E, Armylagos D, Puntachart N, Hendrickson H, Schwartz MR, Mody DR. HPV status in women with high-grade dysplasia on cervical biopsy and preceding negative HPV tests. J Am Soc Cytopathol 2019; 8:149-156. [PMID: 31097291 DOI: 10.1016/j.jasc.2019.01.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 01/06/2019] [Accepted: 01/08/2019] [Indexed: 06/09/2023]
Abstract
INTRODUCTION A considerable number of patients with high-grade cervical lesions have undergone preceding human papillomavirus (HPV) tests with negative results. In the present study, we attempted to elucidate the factors potentially contributing to the findings by testing biopsied samples from these patients. MATERIALS AND METHODS Of the 1654 women with HPV testing and follow-up cervicovaginal biopsies from March 1, 2013 to June 30, 2014, 21 of 252 women (8.3%) with biopsy-confirmed high-grade squamous intraepithelial lesion (HSIL) or worse had had negative results from preceding high-risk (hr)HPV tests. The corresponding paraffin blocks were tested for HPV using the Cobas 4800 system, a DNA microarray against 40 HPV genotypes, and DNA sequencing. RESULTS HPV was detected in 20 (95%) of the 21 biopsies with HSIL or worse, including HPV16/18 in 4, non-16/18 hrHPV in 10, and non-hrHPV in 6. HPV59 and HPV45 were 2.2 times more frequently detected than HPV16/18 in these samples. One sample was negative for all 3 tests (5%). CONCLUSIONS Our study has demonstrated that 8.3% of women with biopsy-confirmed HSIL or worse had preceding test results that were negative for hrHPV. The vast majority of the biopsied samples had detectable HPV, primarily hrHPV genotypes (67%) with HPV59 and HPV45 predominance. This genotypic prevalence pattern was markedly different from those reported in the general population. Non-hrHPV genotypes contributed to 29% of the cases, and HPV-negative cases were rare. In addition to the limited Cobas testing panel and rare possible HPV-negative HSIL or worse, other possible contributing factors to the discrepancy include cytologic sampling, interference material, technical errors, and reduced L1 gene expression in high-grade lesions.
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Affiliation(s)
- Yimin Ge
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Weill Medical College of Cornell University, New York, New York.
| | - Roxanne R Mody
- Department of Obstetrics and Gynecology, St. Joseph's Hospital, Denver, Colorado
| | - Randall J Olsen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Weill Medical College of Cornell University, New York, New York
| | - Haijun Zhou
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Eric Luna
- BioReference Laboratories, Houston, Texas
| | | | - Natu Puntachart
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Heather Hendrickson
- 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
| | - Dina R Mody
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Weill Medical College of Cornell University, New York, New York
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46
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Smith JA, Mathew L, Gaikwad A, Rech B, Burney MN, Faro JP, Lucci JA, Bai Y, Olsen RJ, Byrd TT. From Bench to Bedside: Evaluation of AHCC Supplementation to Modulate the Host Immunity to Clear High-Risk Human Papillomavirus Infections. Front Oncol 2019; 9:173. [PMID: 30949451 PMCID: PMC6435520 DOI: 10.3389/fonc.2019.00173] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [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: 10/11/2018] [Accepted: 02/27/2019] [Indexed: 11/13/2022] Open
Abstract
Objective: There is currently no effective medicine or supplement for clearance of high risk- human papillomavirus (HR-HPV) infections. We have taken a systematic approach evaluating the potential use of AHCC supplementation to support clearance of HR-HPV infections. The primary objective of this research was to evaluate AHCC supplementation to modulation of the host immune system to clear HR-HPV infections from bench to bedside. Methods: Cervical cancer cells, CaSki (HPV16+), HeLa(HPV18+), SiHa(HPV16/18+), and C-33A(HPV−), were treated in vitro with AHCC 0.42 mg/mL daily x7 days then observed x7 days with daily sample collection. A confirmatory study in cervical cancer mouse models, SiHa(HPV16/18+) and C-33A(HPV−), was conducted: mice were divided into three groups per cell line then dosed with AHCC 50 mg/kg/d (N = 10), or vehicle alone (N = 10), or no supplementation (N = 10) for a total of 90 days followed by 30 days of observation. Tumors were measured 3x/week and blood samples collected bi-weekly to evaluate interferon (IFN) alpha(α), beta(β), and gamma(γ) and immunoglobulin G(IgG) by immunoassays. Tumors were evaluated for HR-HPV expression by PCR. Two pilot studies of 10 patients each were conducted in women with confirmed persistent HR-HPV+ infections. The 1st study evaluated AHCC 3g from 5 weeks up to 6 months and 2nd study evaluated AHCC 1g < 8 months. HR-HPV DNA status and the immune panel were monitored at each visit. Results: HR-HPV clearance was observed in vitro and confirmed in the animal studies as a durable response. Four of six (66.7%) patients had confirmed HR-HPV clearance after 3–6 months of AHCC 3g. Similarly, 4 of 9 (44%) patients had confirmed HR-HPV clearance after 7 months of AHCC 1g. Suppression of IFNβ <25 pg/mL was observed in those clearing the HR-HPV infection. Conclusion: Pre-clinical in vitro and in vivo studies demonstrated durable clearance of HR-HPV infections. The preliminary data from the two pilot studies suggested that AHCC supplementation supports the host immune system for successful clearance of HR-HPV infections. A confirmatory phase II randomized, double-blinded, placebo-controlled study is ongoing.
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Affiliation(s)
- Judith A Smith
- Department of Obstetrics, Gynecology and Reproductive Sciences, UTHealth McGovern Medical School, Houston, TX, United States.,Department of Pharmacy, Memorial Hermann Cancer Center, Houston, TX, United States
| | - Lata Mathew
- Department of Obstetrics, Gynecology and Reproductive Sciences, UTHealth McGovern Medical School, Houston, TX, United States
| | - Anjali Gaikwad
- Department of Obstetrics, Gynecology and Reproductive Sciences, UTHealth McGovern Medical School, Houston, TX, United States
| | - Barbara Rech
- UT Physicians Women's Center, Houston, TX, United States
| | - Maryam N Burney
- Department of Obstetrics, Gynecology and Reproductive Sciences, UTHealth McGovern Medical School, Houston, TX, United States
| | - Jonathan P Faro
- Specialists in Obstetrics & Gynecology, Houston, TX, United States
| | - Joseph A Lucci
- Department of Obstetrics, Gynecology and Reproductive Sciences, UTHealth McGovern Medical School, Houston, TX, United States.,Department of Pharmacy, Memorial Hermann Cancer Center, Houston, TX, United States
| | - Yu Bai
- Department of Pathology, UTHealth McGovern Medical School, Houston, TX, United States
| | - Randall J Olsen
- Department of Molecular Pathology, Institute for Academic Medicine, Houston Methodist Research Institute, Houston, TX, United States
| | - Teresa T Byrd
- Department of Obstetrics, Gynecology and Reproductive Sciences, UTHealth McGovern Medical School, Houston, TX, United States
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47
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Nguyen M, Long SW, McDermott PF, Olsen RJ, Olson R, Stevens RL, Tyson GH, Zhao S, Davis JJ. Using Machine Learning To Predict Antimicrobial MICs and Associated Genomic Features for Nontyphoidal Salmonella. J Clin Microbiol 2019; 57:e01260-18. [PMID: 30333126 PMCID: PMC6355527 DOI: 10.1128/jcm.01260-18] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 09/25/2018] [Indexed: 11/20/2022] Open
Abstract
Nontyphoidal Salmonella species are the leading bacterial cause of foodborne disease in the United States. Whole-genome sequences and paired antimicrobial susceptibility data are available for Salmonella strains because of surveillance efforts from public health agencies. In this study, a collection of 5,278 nontyphoidal Salmonella genomes, collected over 15 years in the United States, was used to generate extreme gradient boosting (XGBoost)-based machine learning models for predicting MICs for 15 antibiotics. The MIC prediction models had an overall average accuracy of 95% within ±1 2-fold dilution step (confidence interval, 95% to 95%), an average very major error rate of 2.7% (confidence interval, 2.4% to 3.0%), and an average major error rate of 0.1% (confidence interval, 0.1% to 0.2%). The model predicted MICs with no a priori information about the underlying gene content or resistance phenotypes of the strains. By selecting diverse genomes for the training sets, we show that highly accurate MIC prediction models can be generated with less than 500 genomes. We also show that our approach for predicting MICs is stable over time, despite annual fluctuations in antimicrobial resistance gene content in the sampled genomes. Finally, using feature selection, we explore the important genomic regions identified by the models for predicting MICs. To date, this is one of the largest MIC modeling studies to be published. Our strategy for developing whole-genome sequence-based models for surveillance and clinical diagnostics can be readily applied to other important human pathogens.
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Affiliation(s)
- Marcus Nguyen
- University of Chicago Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne, Illinois, 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, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Patrick F McDermott
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Office of Research, Laurel, Maryland, 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
| | - Robert Olson
- University of Chicago Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne, Illinois, USA
| | - Rick L Stevens
- Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne, Illinois, USA
- Department of Computer Science, University of Chicago, Chicago, Illinois, USA
| | - Gregory H Tyson
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Office of Research, Laurel, Maryland, USA
| | - Shaohua Zhao
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Office of Research, Laurel, Maryland, USA
| | - James J Davis
- University of Chicago Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne, Illinois, USA
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48
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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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49
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Christensen PA, Olsen RJ, Perez KK, Cernoch PL, Long SW. Real-time Communication With Health Care Providers Through an Online Respiratory Pathogen Laboratory Report. Open Forum Infect Dis 2019; 5:ofy322. [PMID: 30619910 PMCID: PMC6306568 DOI: 10.1093/ofid/ofy322] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 11/27/2018] [Indexed: 11/24/2022] Open
Abstract
We implemented a real-time report to distribute respiratory pathogen data for our 8-hospital system to anyone with an Internet connection and a web browser. Real-time access to accurate regional laboratory observation data during an epidemic influenza season can guide diagnostic and therapeutic strategies.
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Affiliation(s)
- Paul A Christensen
- 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
| | - Katherine K Perez
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas.,Department of Pharmacy, Houston Methodist Hospital, Houston, Texas
| | - Patricia L Cernoch
- 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
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50
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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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