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Neyton L, Spottiswoode N. Advancing Sepsis Endotyping Globally: Lessons From a Prospective Study in Uganda. Crit Care Med 2024; 52:515-517. [PMID: 38381016 PMCID: PMC10883597 DOI: 10.1097/ccm.0000000000006063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Affiliation(s)
- Lucile Neyton
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, UCSF Medical Center, San Francisco, CA
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2
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Spottiswoode N, Haston JC, Hanners NW, Gruenberg K, Kim A, DeRisi JL, Wilson MR. Challenges and advances in the medical treatment of granulomatous amebic encephalitis. Ther Adv Infect Dis 2024; 11:20499361241228340. [PMID: 38312848 PMCID: PMC10838035 DOI: 10.1177/20499361241228340] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 01/09/2024] [Indexed: 02/06/2024] Open
Abstract
Granulomatous amebic encephalitis, caused by the free-living amebae Balamuthia mandrillaris or Acanthamoeba species, is a rare and deadly infectious syndrome with a current mortality rate of >90%. Much work remains to define the optimal treatment for these infections. Here, we provide a comprehensive overview of the supporting evidence behind antimicrobials currently recommended by the Centers for Disease Control and Prevention (CDC) with updated statistics on survival rates and medication usage from the CDC Free-Living Ameba Database. We also discuss promising treatments, especially the emerging therapeutic agent nitroxoline, and provide recommendations for the next steps in this area.
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Affiliation(s)
- Natasha Spottiswoode
- Division of Infectious Diseases, University of California San Francisco, San Francisco, CA, USA
| | - Julia C. Haston
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Natasha W. Hanners
- Division of Pediatric Infectious Diseases, University of Texas Southwestern, Dallas, TX, USA
| | - Katherine Gruenberg
- Department of Clinical Pharmacy, University of California San Francisco School of Pharmacy, San Francisco, CA, USA
| | - Annie Kim
- Department of Clinical Pharmacy, Zuckerberg San Francisco General, San Francisco, CA, USA
| | - Joseph L. DeRisi
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub SF, San Francisco, CA, USA
| | - Michael R. Wilson
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA 94143, USA
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3
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Spottiswoode N, Hao S, Sanchez-Guerrero E, Detweiler AM, Mekonen H, Neff N, Macmillan H, Schwartz BS, Engel J, DeRisi JL, Miller SA, Langelier CR. In host evolution of beta lactam resistance during active treatment for Pseudomonas aeruginosa bacteremia. Front Cell Infect Microbiol 2023; 13:1241608. [PMID: 37712060 PMCID: PMC10499174 DOI: 10.3389/fcimb.2023.1241608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 08/14/2023] [Indexed: 09/16/2023] Open
Abstract
Multidrug-resistant (MDR) Pseudomonas aeruginosa has been declared a serious threat by the United States Centers for Disease Control and Prevention. Here, we used whole genome sequencing (WGS) to investigate recurrent P. aeruginosa bloodstream infections in a severely immunocompromised patient. The infections demonstrated unusual, progressive increases in resistance to beta lactam antibiotics in the setting of active treatment with appropriate, guideline-directed agents. WGS followed by comparative genomic analysis of isolates collected over 44 days demonstrated in host evolution of a single P. aeruginosa isolate characterized by stepwise acquisition of two de-novo genetic resistance mechanisms over the course of treatment. We found a novel deletion affecting the ampC repressor ampD and neighboring gene ampE, which associated with initial cefepime treatment failure. This was followed by acquisition of a porin nonsense mutation, OprD, associated with resistance to carbapenems. This study highlights the potential for in-host evolution of P. aeruginosa during bloodstream infections in severely immunocompromised patients despite appropriate antimicrobial therapy. In addition, it demonstrates the utility of WGS for understanding unusual resistance patterns in the clinical context.
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Affiliation(s)
- Natasha Spottiswoode
- Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Samantha Hao
- Johns Hopkins School of Medicine, Baltimore, Maryland, MD, United States
- Chan Zuckerberg Biohub, San Francisco, CA, United States
| | | | | | - Honey Mekonen
- Chan Zuckerberg Biohub, San Francisco, CA, United States
| | - Norma Neff
- Chan Zuckerberg Biohub, San Francisco, CA, United States
| | - Henriette Macmillan
- Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Brian S. Schwartz
- Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Joanne Engel
- Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Joseph L. DeRisi
- Chan Zuckerberg Biohub, San Francisco, CA, United States
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, United States
| | - Steven A. Miller
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, United States
- Delve Bio Inc., San Francisco, CA, United States
| | - Charles R. Langelier
- Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, San Francisco, CA, United States
- Chan Zuckerberg Biohub, San Francisco, CA, United States
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4
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Barth KE, Spottiswoode N, Hurabielle C, Subbaraj L, Calfee CS, Matthay MA, French S, Connolly A, Hewitt SM, Vannella KM, Barnett C, Langelier CR, Patterson S. Clinical and biological heterogeneity of multisystem inflammatory syndrome in adults following SARS-CoV-2 infection: a case series. Front Med (Lausanne) 2023; 10:1187420. [PMID: 37484839 PMCID: PMC10357379 DOI: 10.3389/fmed.2023.1187420] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 06/20/2023] [Indexed: 07/25/2023] Open
Abstract
Importance Multisystem inflammatory syndrome in adults (MIS-A) is a poorly understood complication of SARS-CoV-2 infection with significant morbidity and mortality. Objective Identify clinical, immunological, and histopathologic features of MIS-A to improve understanding of the pathophysiology and approach to treatment. Design Three cases of MIS-A following SARS-CoV-2 infection were clinically identified between October 2021 - March 2022 using the U.S. Centers for Disease Control and Prevention diagnostic criteria. Clinical, laboratory, imaging, and tissue data were assessed. Findings All three patients developed acute onset cardiogenic shock and demonstrated elevated inflammatory biomarkers at the time of hospital admission that resolved over time. One case co-occurred with new onset Type 1 diabetes and sepsis. Retrospective analysis of myocardial tissue from one case identified SARS-CoV-2 RNA. All three patients fully recovered with standard of care interventions plus immunomodulatory therapy that included intravenous immunoglobulin, corticosteroids, and in two cases, anakinra. Conclusion MIS-A is a severe post-acute sequela of COVID-19 characterized by systemic elevation of inflammatory biomarkers. In this series of three cases, we find that although clinical courses and co-existent diseases vary, even severe presentations have potential for full recovery with prompt recognition and treatment. In addition to cardiogenic shock, glucose intolerance, unmasking of autoimmune disease, and sepsis can be features of MIS-A, and SARS-CoV-2 myocarditis can lead to a similar clinical syndrome.
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Affiliation(s)
- Kaia E. Barth
- Department of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Natasha Spottiswoode
- Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, United States
| | - Charlotte Hurabielle
- Division of Rheumatology, University of California, San Francisco, San Francisco, CA, United States
| | - Lakshmi Subbaraj
- Department of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | | | - Carolyn S. Calfee
- Division of Pulmonary, Critical Care, Allergy, and Sleep Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Michael A. Matthay
- Division of Pulmonary, Critical Care, Allergy, and Sleep Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Sarah French
- Division of Rheumatology, University of California, San Francisco, San Francisco, CA, United States
| | - Andrew Connolly
- Department of Pathology, University of California, San Francisco, San Francisco, CA, United States
| | - Stephen M. Hewitt
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Kevin M. Vannella
- Emerging Pathogens Section, Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD, United States
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, Bethesda, MD, United States
| | - Christopher Barnett
- Division of Cardiology, University of California, San Francisco, San Francisco, CA, United States
| | - Charles R. Langelier
- Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, United States
- Chan Zuckerberg Biohub, San Francisco, CA, United States
| | - Sarah Patterson
- Department of Medicine, University of California, San Francisco, San Francisco, CA, United States
- Division of Rheumatology, University of California, San Francisco, San Francisco, CA, United States
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5
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Spottiswoode N, Pet D, Kim A, Gruenberg K, Shah M, Ramachandran A, Laurie MT, Zia M, Fouassier C, Boutros CL, Lu R, Zhang Y, Servellita V, Bollen A, Chiu CY, Wilson MR, Valdivia L, DeRisi JL. Successful Treatment of Balamuthia mandrillaris Granulomatous Amebic Encephalitis with Nitroxoline. Emerg Infect Dis 2023; 29:197-201. [PMID: 36573629 PMCID: PMC9796214 DOI: 10.3201/eid2901.221531] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
A patient in California, USA, with rare and usually fatal Balamuthia mandrillaris granulomatous amebic encephalitis survived after receiving treatment with a regimen that included the repurposed drug nitroxoline. Nitroxoline, which is a quinolone typically used to treat urinary tract infections, was identified in a screen for drugs with amebicidal activity against Balamuthia.
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Fung M, DeVoe C, Spottiswoode N, Doernberg SB. Maribavir for Cytomegalovirus Treatment in the Real World-Not a Silver Bullet. Open Forum Infect Dis 2022; 10:ofac686. [PMID: 36632422 PMCID: PMC9830537 DOI: 10.1093/ofid/ofac686] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 12/27/2022] [Indexed: 12/29/2022] Open
Affiliation(s)
- Monica Fung
- Correspondence: Monica Fung, MD, MPH, Division of Infectious Diseases, University of California, San Francisco, 513 Parnassus Ave, S-380, San Francisco, CA 94143, USA ()
| | - Catherine DeVoe
- Division of Infectious Diseases, University of California, San Francisco, California, USA
| | - Natasha Spottiswoode
- Division of Infectious Diseases, University of California, San Francisco, California, USA
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7
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Ghale R, Spottiswoode N, Anderson MS, Mitchell A, Wang G, Calfee CS, DeRisi JL, Langelier CR. Prevalence of type-1 interferon autoantibodies in adults with non-COVID-19 acute respiratory failure. Respir Res 2022; 23:354. [PMID: 36527083 PMCID: PMC9756918 DOI: 10.1186/s12931-022-02283-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022] Open
Abstract
Auto-antibodies (Abs) to type I interferons (IFNs) are found in up to 25% of patients with severe COVID-19, and are implicated in disease pathogenesis. It has remained unknown, however, whether type I IFN auto-Abs are unique to COVID-19, or are also found in other types of severe respiratory illnesses. To address this, we studied a prospective cohort of 284 adults with acute respiratory failure due to causes other than COVID-19. We measured type I IFN auto-Abs by radio ligand binding assay and screened for respiratory viruses using clinical PCR and metagenomic sequencing. Three patients (1.1%) tested positive for type I IFN auto-Abs, and each had a different underlying clinical presentation. Of the 35 patients found to have viral infections, only one patient tested positive for type I IFN auto-Abs. Together, our data suggest that type I IFN auto-Abs are uncommon in critically ill patients with acute respiratory failure due to causes other than COVID-19.
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Affiliation(s)
- Rajani Ghale
- Division of Pulmonary, Critical Care, Allergy, and Sleep Medicine, University of California, San Francisco, CA, USA
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Natasha Spottiswoode
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Mark S Anderson
- Department of Medicine, University of California, San Francisco, CA, USA
- Diabetes Center, University of California, San Francisco, CA, USA
| | - Anthea Mitchell
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - Grace Wang
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - Carolyn S Calfee
- Division of Pulmonary, Critical Care, Allergy, and Sleep Medicine, University of California, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Joseph L DeRisi
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Charles R Langelier
- Division of Infectious Diseases, University of California, San Francisco, CA, USA.
- Department of Medicine, University of California, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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8
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Wick KD, Fang X, Maishan M, Matsumoto S, Spottiswoode N, Sarma A, Simoneau C, Khakoo M, Langelier C, Calfee CS, Gotts JE, Matthay MA. Impact of e-cigarette aerosol on primary human alveolar epithelial type 2 cells. Am J Physiol Lung Cell Mol Physiol 2022; 323:L152-L164. [PMID: 35670478 PMCID: PMC9559034 DOI: 10.1152/ajplung.00503.2021] [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: 12/14/2021] [Revised: 05/03/2022] [Accepted: 06/01/2022] [Indexed: 11/22/2022] Open
Abstract
Electronic cigarettes (e-cigarettes) are designed to simulate combustible cigarette smoking and to aid in smoking cessation. Although the number of e-cigarette users has been increasing, the potential health impacts and biological effects of e-cigarettes are still not fully understood. Previous research has focused on the biological effects of e-cigarettes on lung cancer cell lines and distal airway epithelial cells; however, there have been few published studies on the effect of e-cigarettes on primary lung alveolar epithelial cells. The primary purpose of this study was to investigate the direct effect of e-cigarette aerosol on primary human lung alveolar epithelial type 2 (AT2) cells, both alone and in the presence of viral infection. The Melo-3 atomizer caused direct AT2 cell toxicity, whereas the more popular Juul pod's aerosol did not have a detectable cytotoxic effect on AT2 cells. Juul nicotine aerosol also did not increase short-term susceptibility to viral infection. However, 3 days of exposure upregulated genes central to the generation of reactive oxygen species, lipid peroxidation, and carcinogen metabolism and downregulated key innate immune system genes related to cytokine and chemokine signaling. These findings have implications for the potentially injurious impact of long-term use of popular low-power e-cigarette pods on the human alveolar epithelium. Gene expression data might be an important endpoint for evaluating the potential harmful effects of vaping devices that do not cause overt toxicity.
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Affiliation(s)
- Katherine D Wick
- Cardiovascular Research Institute, University of California, San Francisco, California
| | - Xiaohui Fang
- Cardiovascular Research Institute, University of California, San Francisco, California
| | - Mazharul Maishan
- Cardiovascular Research Institute, University of California, San Francisco, California
| | - Shotaro Matsumoto
- Cardiovascular Research Institute, University of California, San Francisco, California
| | - Natasha Spottiswoode
- Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, California
| | - Aartik Sarma
- Division of Pulmonary and Critical Care, Department of Medicine, University of California, San Francisco, California
| | - Camille Simoneau
- Gladstone Institutes, University of California, San Francisco, California
| | - Manisha Khakoo
- Cardiovascular Research Institute, University of California, San Francisco, California
| | - Chaz Langelier
- Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, California
- Chan Zuckerberg Biohub, San Francisco, California
| | - Carolyn S Calfee
- Cardiovascular Research Institute, University of California, San Francisco, California
- Division of Pulmonary and Critical Care, Department of Medicine, University of California, San Francisco, California
| | - Jeffrey E Gotts
- Cardiovascular Research Institute, University of California, San Francisco, California
| | - Michael A Matthay
- Cardiovascular Research Institute, University of California, San Francisco, California
- Department of Medicine, University of California, San Francisco, California
- Department of Anesthesia, University of California, San Francisco, California
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9
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Mick E, Tsitsiklis A, Spottiswoode N, Caldera S, Serpa PH, Detweiler AM, Neff N, Pisco AO, Li LM, Retallack H, Ratnasiri K, Williamson KM, Soesanto V, Simões EAF, Smith C, Abuogi L, Kistler A, Wagner BD, DeRisi JL, Ambroggio L, Mourani PM, Langelier CR. Upper airway gene expression shows a more robust adaptive immune response to SARS-CoV-2 in children. Nat Commun 2022; 13:3937. [PMID: 35803954 PMCID: PMC9263813 DOI: 10.1038/s41467-022-31600-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 05/31/2022] [Indexed: 12/24/2022] Open
Abstract
Unlike other respiratory viruses, SARS-CoV-2 disproportionately causes severe disease in older adults whereas disease burden in children is lower. To investigate whether differences in the upper airway immune response may contribute to this disparity, we compare nasopharyngeal gene expression in 83 children (<19-years-old; 38 with SARS-CoV-2, 11 with other respiratory viruses, 34 with no virus) and 154 older adults (>40-years-old; 45 with SARS-CoV-2, 28 with other respiratory viruses, 81 with no virus). Expression of interferon-stimulated genes is robustly activated in both children and adults with SARS-CoV-2 infection compared to the respective non-viral groups, with only subtle distinctions. Children, however, demonstrate markedly greater upregulation of pathways related to B cell and T cell activation and proinflammatory cytokine signaling, including response to TNF and production of IFNγ, IL-2 and IL-4. Cell type deconvolution confirms greater recruitment of B cells, and to a lesser degree macrophages, to the upper airway of children. Only children exhibit a decrease in proportions of ciliated cells, among the primary targets of SARS-CoV-2, upon infection. These findings demonstrate that children elicit a more robust innate and especially adaptive immune response to SARS-CoV-2 in the upper airway that likely contributes to their protection from severe disease in the lower airway.
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Affiliation(s)
- Eran Mick
- Division of Infectious Diseases, University of California, San Francisco, CA, USA.,Division of Pulmonary and Critical Care Medicine, University of California, San Francisco, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Alexandra Tsitsiklis
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
| | - Natasha Spottiswoode
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
| | - Saharai Caldera
- Division of Infectious Diseases, University of California, San Francisco, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Paula Hayakawa Serpa
- Division of Infectious Diseases, University of California, San Francisco, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | - Norma Neff
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | - Lucy M Li
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Hanna Retallack
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | | | - Kayla M Williamson
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado, Aurora, CO, USA
| | - Victoria Soesanto
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado, Aurora, CO, USA
| | - Eric A F Simões
- Department of Pediatrics, University of Colorado and Children's Hospital Colorado, Aurora, CO, USA
| | - Christiana Smith
- Department of Pediatrics, University of Colorado and Children's Hospital Colorado, Aurora, CO, USA
| | - Lisa Abuogi
- Department of Pediatrics, University of Colorado and Children's Hospital Colorado, Aurora, CO, USA
| | - Amy Kistler
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Brandie D Wagner
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado, Aurora, CO, USA.,Department of Pediatrics, University of Colorado and Children's Hospital Colorado, Aurora, CO, USA
| | - Joseph L DeRisi
- Chan Zuckerberg Biohub, San Francisco, CA, USA.,Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - Lilliam Ambroggio
- Department of Pediatrics, University of Colorado and Children's Hospital Colorado, Aurora, CO, USA
| | - Peter M Mourani
- Department of Pediatrics, University of Colorado and Children's Hospital Colorado, Aurora, CO, USA.,Arkansas Children's Research Institute, Arkansas Children's Hospital, Little Rock, AR, USA
| | - Charles R Langelier
- Division of Infectious Diseases, University of California, San Francisco, CA, USA. .,Chan Zuckerberg Biohub, San Francisco, CA, USA.
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10
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Spottiswoode N, Bloomstein JD, Caldera S, Sessolo A, McCauley K, Byanyima P, Zawedde J, Kalantar K, Kaswabuli S, Rutishauser RL, Lieng MK, Davis JL, Moore J, Jan A, Iwai S, Shenoy M, Sanyu I, DeRisi JL, Lynch SV, Worodria W, Huang L, Langelier CR. Pneumonia surveillance with culture-independent metatranscriptomics in HIV-positive adults in Uganda: a cross-sectional study. Lancet Microbe 2022; 3:e357-e365. [PMID: 35544096 DOI: 10.1016/s2666-5247(21)00357-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 12/01/2021] [Accepted: 12/14/2021] [Indexed: 11/29/2022]
Abstract
BACKGROUND Pneumonia is a leading cause of death worldwide and is a major health-care challenge in people living with HIV. Despite this, the causes of pneumonia in this population remain poorly understood. We aimed to assess the feasibility of metatranscriptomics for epidemiological surveillance of pneumonia in patients with HIV in Uganda. METHODS We performed a retrospective observational study in patients with HIV who were admitted to Mulago Hospital, Kampala, Uganda between Oct 1, 2009, and Dec 31, 2011. Inclusion criteria were age 18 years or older, HIV-positivity, and clinically diagnosed pneumonia. Exclusion criteria were contraindication to bronchoscopy or an existing diagnosis of tuberculosis. Bronchoalveolar lavage fluid was collected within 72 h of admission and a combination of RNA sequencing and Mycobacterium tuberculosis culture plus PCR were performed. The primary outcome was detection of an established or possible respiratory pathogen in the total study population. FINDINGS We consecutively enrolled 217 patients during the study period. A potential microbial cause for pneumonia was identified in 211 (97%) patients. At least one microorganism of established respiratory pathogenicity was identified in 113 (52%) patients, and a microbe of possible pathogenicity was identified in an additional 98 (45%). M tuberculosis was the most commonly identified established pathogen (35 [16%] patients; in whom bacterial or viral co-infections were identified in 13 [37%]). Streptococcus mitis, although not previously reported as a cause of pneumonia in patients with HIV, was the most commonly identified bacterial organism (37 [17%] patients). Haemophilus influenzae was the most commonly identified established bacterial pathogen (20 [9%] patients). Pneumocystis jirovecii was only identified in patients with a CD4 count of less than 200 cells per mL. INTERPRETATION We show the feasibility of using metatranscriptomics for epidemiologic surveillance of pneumonia by describing the spectrum of respiratory pathogens in adults with HIV in Uganda. Applying these methods to a contemporary cohort could enable broad assessment of changes in pneumonia aetiology following the emergence of SARS-CoV-2. FUNDING US National Institutes of Health, Chan Zuckerberg Biohub.
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Affiliation(s)
- Natasha Spottiswoode
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA
| | - Joshua D Bloomstein
- Department of Medicine, University of California Davis School of Medicine, Sacramento, CA, USA
| | - Saharai Caldera
- Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Abdul Sessolo
- Infectious Disease Platform, Makerere University, Kampala, Uganda
| | - Kathryn McCauley
- Division of Gastroenterology, University of California, San Francisco, San Francisco, CA, USA
| | - Patrick Byanyima
- Infectious Disease Platform, Makerere University, Kampala, Uganda
| | | | | | - Sylvia Kaswabuli
- Infectious Disease Platform, Makerere University, Kampala, Uganda
| | - Rachel L Rutishauser
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Division of Experimental Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Monica K Lieng
- Department of Medicine, University of California Davis School of Medicine, Sacramento, CA, USA
| | - J Lucian Davis
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health and Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Julia Moore
- Division of Pulmonary and Critical Care Medicine, University of California, San Francisco, San Francisco, CA, USA; Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Amanda Jan
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health and Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Shoko Iwai
- Division of Gastroenterology, University of California, San Francisco, San Francisco, CA, USA
| | - Meera Shenoy
- Division of Gastroenterology, University of California, San Francisco, San Francisco, CA, USA
| | - Ingvar Sanyu
- Infectious Disease Platform, Makerere University, Kampala, Uganda
| | - Joseph L DeRisi
- Department of Biochemistry, University of California, San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Susan V Lynch
- Division of Gastroenterology, University of California, San Francisco, San Francisco, CA, USA
| | - William Worodria
- Infectious Disease Platform, Makerere University, Kampala, Uganda
| | - Laurence Huang
- Division of Pulmonary and Critical Care Medicine, University of California, San Francisco, San Francisco, CA, USA; Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Charles R Langelier
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA.
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11
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Mick E, Tsitsiklis A, Spottiswoode N, Caldera S, Serpa PH, Detweiler AM, Neff N, Pisco AO, Li LM, Retallack H, Ratnasiri K, Williamson KM, Soesanto V, Simões EAF, Kistler A, Wagner BD, DeRisi JL, Ambroggio L, Mourani PM, Langelier CR. Upper airway gene expression reveals a more robust innate and adaptive immune response to SARS-CoV-2 in children compared with older adults. Res Sq 2021:rs.3.rs-784784. [PMID: 34462739 PMCID: PMC8404906 DOI: 10.21203/rs.3.rs-784784/v1] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2023]
Abstract
Unlike other respiratory viruses, SARS-CoV-2 disproportionately causes severe disease in older adults and only rarely in children. To investigate whether differences in the upper airway immune response could contribute to this disparity, we compared nasopharyngeal gene expression in 83 children (<19-years-old; 38 with SARS-CoV-2, 11 with other respiratory viruses, 34 with no virus) and 154 adults (>40-years-old; 45 with SARS-CoV-2, 28 with other respiratory viruses, 81 with no virus). Expression of interferon-stimulated genes (ISGs) was robustly activated in both children and adults with SARS-CoV-2 compared to the respective non-viral groups, with only relatively subtle distinctions. Children, however, demonstrated markedly greater upregulation of pathways related to B cell and T cell activation and proinflammatory cytokine signaling, including TNF, IFNγ, IL-2 and IL-4 production. Cell type deconvolution confirmed greater recruitment of B cells, and to a lesser degree macrophages, to the upper airway of children. Only children exhibited a decrease in proportions of ciliated cells, the primary target of SARS-CoV-2, upon infection with the virus. These findings demonstrate that children elicit a more robust innate and adaptive immune response to SARS-CoV-2 infection in the upper airway that likely contributes to their protection from severe disease in the lower airway.
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Affiliation(s)
- Eran Mick
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
- Division of Pulmonary and Critical Care Medicine, University of California, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Alexandra Tsitsiklis
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
| | - Natasha Spottiswoode
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
| | - Saharai Caldera
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Paula Hayakawa Serpa
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | - Norma Neff
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | - Lucy M. Li
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Hanna Retallack
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | | | - Kayla M. Williamson
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado, Aurora, CO, USA
| | - Victoria Soesanto
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado, Aurora, CO, USA
| | - Eric A. F. Simões
- Department of Pediatrics, Children’s Hospital Colorado and University of Colorado, Aurora, CO, USA
| | - Amy Kistler
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Brandie D. Wagner
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado, Aurora, CO, USA
- Department of Pediatrics, Children’s Hospital Colorado and University of Colorado, Aurora, CO, USA
| | - Joseph L. DeRisi
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - Lilliam Ambroggio
- Department of Pediatrics, Children’s Hospital Colorado and University of Colorado, Aurora, CO, USA
| | - Peter M. Mourani
- Department of Pediatrics, Children’s Hospital Colorado and University of Colorado, Aurora, CO, USA
| | - Charles R. Langelier
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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12
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Sarma A, Christenson SA, Byrne A, Mick E, Pisco AO, DeVoe C, Deiss T, Ghale R, Zha BS, Tsitsiklis A, Jauregui A, Moazed F, Detweiler AM, Spottiswoode N, Sinha P, Neff N, Tan M, Serpa PH, Willmore A, Ansel KM, Wilson JG, Leligdowicz A, Siegel ER, Sirota M, DeRisi JL, Matthay MA, Hendrickson CM, Kangelaris KN, Krummel MF, Woodruff PG, Erle DJ, Calfee CS, Langelier CR. Tracheal aspirate RNA sequencing identifies distinct immunological features of COVID-19 ARDS. Nat Commun 2021; 12:5152. [PMID: 34446707 PMCID: PMC8390461 DOI: 10.1038/s41467-021-25040-5] [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: 01/05/2021] [Accepted: 07/13/2021] [Indexed: 12/15/2022] Open
Abstract
The immunological features that distinguish COVID-19-associated acute respiratory distress syndrome (ARDS) from other causes of ARDS are incompletely understood. Here, we report the results of comparative lower respiratory tract transcriptional profiling of tracheal aspirate from 52 critically ill patients with ARDS from COVID-19 or from other etiologies, as well as controls without ARDS. In contrast to a "cytokine storm," we observe reduced proinflammatory gene expression in COVID-19 ARDS when compared to ARDS due to other causes. COVID-19 ARDS is characterized by a dysregulated host response with increased PTEN signaling and elevated expression of genes with non-canonical roles in inflammation and immunity. In silico analysis of gene expression identifies several candidate drugs that may modulate gene expression in COVID-19 ARDS, including dexamethasone and granulocyte colony stimulating factor. Compared to ARDS due to other types of viral pneumonia, COVID-19 is characterized by impaired interferon-stimulated gene (ISG) expression. The relationship between SARS-CoV-2 viral load and expression of ISGs is decoupled in patients with COVID-19 ARDS when compared to patients with mild COVID-19. In summary, assessment of host gene expression in the lower airways of patients reveals distinct immunological features of COVID-19 ARDS.
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Affiliation(s)
- Aartik Sarma
- grid.266102.10000 0001 2297 6811Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, CA USA
| | - Stephanie A. Christenson
- grid.266102.10000 0001 2297 6811Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, CA USA
| | - Ashley Byrne
- grid.499295.aChan Zuckerberg Biohub, San Francisco, CA USA
| | - Eran Mick
- grid.266102.10000 0001 2297 6811Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, CA USA ,grid.499295.aChan Zuckerberg Biohub, San Francisco, CA USA ,grid.266102.10000 0001 2297 6811Division of Infectious Diseases, University of California, San Francisco, CA USA
| | | | - Catherine DeVoe
- grid.266102.10000 0001 2297 6811Division of Infectious Diseases, University of California, San Francisco, CA USA
| | - Thomas Deiss
- grid.499295.aChan Zuckerberg Biohub, San Francisco, CA USA
| | - Rajani Ghale
- grid.266102.10000 0001 2297 6811Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, CA USA ,grid.266102.10000 0001 2297 6811Division of Infectious Diseases, University of California, San Francisco, CA USA
| | - Beth Shoshana Zha
- grid.266102.10000 0001 2297 6811Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, CA USA
| | - Alexandra Tsitsiklis
- grid.266102.10000 0001 2297 6811Division of Infectious Diseases, University of California, San Francisco, CA USA
| | - Alejandra Jauregui
- grid.266102.10000 0001 2297 6811Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, CA USA
| | - Farzad Moazed
- grid.266102.10000 0001 2297 6811Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, CA USA
| | - Angela M. Detweiler
- grid.266102.10000 0001 2297 6811Division of Infectious Diseases, University of California, San Francisco, CA USA
| | - Natasha Spottiswoode
- grid.266102.10000 0001 2297 6811Department of Medicine, University of California, San Francisco, CA USA
| | - Pratik Sinha
- grid.4367.60000 0001 2355 7002Department of Anesthesia, Washington University, Saint Louis, MO USA
| | - Norma Neff
- grid.499295.aChan Zuckerberg Biohub, San Francisco, CA USA
| | - Michelle Tan
- grid.499295.aChan Zuckerberg Biohub, San Francisco, CA USA
| | - Paula Hayakawa Serpa
- grid.266102.10000 0001 2297 6811Division of Infectious Diseases, University of California, San Francisco, CA USA
| | - Andrew Willmore
- grid.266102.10000 0001 2297 6811Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, CA USA
| | - K. Mark Ansel
- grid.266102.10000 0001 2297 6811Department of Microbiology and Immunology, University of California, San Francisco, CA USA ,grid.266102.10000 0001 2297 6811Sandler Asthma Basic Research Center, University of California, San Francisco, CA USA
| | - Jennifer G. Wilson
- grid.168010.e0000000419368956Department of Emergency Medicine, Stanford University, Palo Alto, CA USA
| | - Aleksandra Leligdowicz
- grid.266102.10000 0001 2297 6811Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, CA USA ,grid.17063.330000 0001 2157 2938Interdepartmental Division of Critical Care Medicine, University of Toronto, Toronto, Ontario Canada ,grid.266102.10000 0001 2297 6811Cardiovascular Research Institute, University of California, San Francisco, CA USA
| | - Emily R. Siegel
- grid.266102.10000 0001 2297 6811School of Medicine, University of California, San Francisco, CA USA
| | - Marina Sirota
- grid.266102.10000 0001 2297 6811Division of Rheumatology, University of California, San Francisco, CA USA
| | - Joseph L. DeRisi
- grid.499295.aChan Zuckerberg Biohub, San Francisco, CA USA ,grid.266102.10000 0001 2297 6811Department of Biochemistry and Biophysics, University of California, San Francisco, CA USA
| | - Michael A. Matthay
- grid.266102.10000 0001 2297 6811Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, CA USA ,grid.266102.10000 0001 2297 6811Cardiovascular Research Institute, University of California, San Francisco, CA USA ,grid.266102.10000 0001 2297 6811Department of Anesthesia, University of California, San Francisco, CA USA
| | | | - Carolyn M. Hendrickson
- grid.266102.10000 0001 2297 6811Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, CA USA
| | - Kirsten N. Kangelaris
- grid.266102.10000 0001 2297 6811Department of Medicine, University of California, San Francisco, CA USA
| | - Matthew F. Krummel
- grid.266102.10000 0001 2297 6811Department of Pathology, University of California, San Francisco, CA USA
| | - Prescott G. Woodruff
- grid.266102.10000 0001 2297 6811Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, CA USA ,grid.266102.10000 0001 2297 6811Sandler Asthma Basic Research Center, University of California, San Francisco, CA USA
| | - David J. Erle
- grid.266102.10000 0001 2297 6811Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, CA USA ,grid.266102.10000 0001 2297 6811Department of Medicine, University of California, San Francisco, CA USA ,grid.266102.10000 0001 2297 6811Lung Biology Center, University of California, San Francisco, CA USA ,grid.266102.10000 0001 2297 6811UCSF CoLabs, University of California, San Francisco, CA USA
| | - Carolyn S. Calfee
- grid.266102.10000 0001 2297 6811Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, CA USA ,grid.266102.10000 0001 2297 6811Cardiovascular Research Institute, University of California, San Francisco, CA USA ,grid.266102.10000 0001 2297 6811Department of Anesthesia, University of California, San Francisco, CA USA
| | - Charles R. Langelier
- grid.499295.aChan Zuckerberg Biohub, San Francisco, CA USA ,grid.266102.10000 0001 2297 6811Division of Infectious Diseases, University of California, San Francisco, CA USA
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13
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Sarma A, Christenson SA, Mick E, DeVoe C, Deiss T, Pisco AO, Ghale R, Jauregui A, Byrne A, Moazed F, Spottiswoode N, Sinha P, Zha BS, Neff N, Tan M, Serpa PH, Ansel KM, Wilson JG, Leligdowicz A, Siegel ER, Sirota M, DeRisi JL, Matthay MA, Hendrickson CM, Kangelaris KN, Krummel MF, Woodruff PG, Erle DJ, Calfee CS, Langelier CR. COVID-19 ARDS is characterized by a dysregulated host response that differs from cytokine storm and is modified by dexamethasone. Res Sq 2021:rs.3.rs-141578. [PMID: 33469573 PMCID: PMC7814832 DOI: 10.21203/rs.3.rs-141578/v1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 12/15/2022]
Abstract
We performed comparative lower respiratory tract transcriptional profiling of 52 critically ill patients with the acute respiratory distress syndrome (ARDS) from COVID-19 or from other etiologies, as well as controls without ARDS. In contrast to a cytokine storm, we observed reduced proinflammatory gene expression in COVID-19 ARDS when compared to ARDS due to other causes. COVID-19 ARDS was characterized by a dysregulated host response with increased PTEN signaling and elevated expression of genes with non-canonical roles in inflammation and immunity that were predicted to be modulated by dexamethasone and granulocyte colony stimulating factor. Compared to ARDS due to other types of viral pneumonia, COVID-19 was characterized by impaired interferon-stimulated gene expression (ISG). We found that the relationship between SARS-CoV-2 viral load and expression of ISGs was decoupled in patients with COVID-19 ARDS when compared to patients with mild COVID-19. In summary, assessment of host gene expression in the lower airways of patients with COVID-19 ARDS did not demonstrate cytokine storm but instead revealed a unique and dysregulated host response predicted to be modified by dexamethasone.
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Affiliation(s)
- Aartik Sarma
- Division of Pulmonary, Critical Care, Allergy, and Sleep Medicine, University of California, San Francisco, CA, USA
| | - Stephanie A. Christenson
- Division of Pulmonary, Critical Care, Allergy, and Sleep Medicine, University of California, San Francisco, CA, USA
| | - Eran Mick
- Division of Pulmonary, Critical Care, Allergy, and Sleep Medicine, University of California, San Francisco, CA, USA
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Catherine DeVoe
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
| | - Thomas Deiss
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
| | | | - Rajani Ghale
- Division of Pulmonary, Critical Care, Allergy, and Sleep Medicine, University of California, San Francisco, CA, USA
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
| | - Alejandra Jauregui
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
| | | | - Farzad Moazed
- Division of Pulmonary, Critical Care, Allergy, and Sleep Medicine, University of California, San Francisco, CA, USA
| | | | - Pratik Sinha
- Department of Anesthesia, Washington University, Saint Louis, Missouri, MO, USA
| | - Beth Shoshana Zha
- Division of Pulmonary, Critical Care, Allergy, and Sleep Medicine, University of California, San Francisco, CA, USA
| | - Norma Neff
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | - Paula Hayakawa Serpa
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - K. Mark Ansel
- Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
- Sandler Asthma Basic Research Center, University of California, San Francisco, CA, USA
| | - Jennifer G. Wilson
- Department of Emergency Medicine, Stanford University, Palo Alto, CA, USA
| | | | - Emily R. Siegel
- School of Medicine, University of California, San Francisco, CA, USA
| | - Marina Sirota
- Division of Rheumatology, University of California, San Francisco, CA, USA
| | - Joseph L. DeRisi
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - Michael A. Matthay
- Division of Pulmonary, Critical Care, Allergy, and Sleep Medicine, University of California, San Francisco, CA, USA
| | | | - Carolyn M. Hendrickson
- Division of Pulmonary, Critical Care, Allergy, and Sleep Medicine, University of California, San Francisco, CA, USA
| | | | - Matthew F. Krummel
- Department of Pathology, University of California, San Francisco, CA, USA
| | - Prescott G. Woodruff
- Division of Pulmonary, Critical Care, Allergy, and Sleep Medicine, University of California, San Francisco, CA, USA
- Sandler Asthma Basic Research Center, University of California, San Francisco, CA, USA
| | - David J. Erle
- Department of Medicine, University of California, San Francisco, CA, USA
- Lung Biology Center, University of California, San Francisco, CA, USA
- UCSF CoLabs, University of California, San Francisco, CA, USA
| | - Carolyn S. Calfee
- Division of Pulmonary, Critical Care, Allergy, and Sleep Medicine, University of California, San Francisco, CA, USA
| | - Charles R. Langelier
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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14
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Jain V, Brown LB, Marquez C, Rubio L, Spottiswoode N, Churnet B, Brooks K, Zhou M, Muldoon T, Hendrickson C, Cattamanchi A, Gomez A, Haas B, Charlebois E, Luetkemeyer A, Luetkemeyer A, Gandhi M, Havlir D, Ranji S, Winston LG. 448. Disproportionate Burden of COVID-19 on Latinx Residents among Hospitalized Patients at San Francisco’s Public Health Hospital. Open Forum Infect Dis 2020. [PMCID: PMC7777674 DOI: 10.1093/ofid/ofaa439.641] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Background San Francisco implemented one of the earliest shelter-in-place public health mandates in the U.S., with flattened curves of diagnoses and deaths. We describe demographics, clinical features and outcomes of COVID-19 patients admitted to a public health hospital in a high population-density city with an early containment response. Methods We analyzed inpatients with COVID-19 admitted to San Francisco General Hospital (SFGH) from 3/5/2020–5/11/2020. SFGH serves a network of >63,000 patients (32% Latinx/24% Asian/19% African American/19% Caucasian). Demographic and clinical data through 5/18/2020 were abstracted from hospital records, along with ICU and ventilator utilization, lengths of stay, and in-hospital deaths. Results Of 157 admitted patients, 105/157 (67%) were male, median age was 49 (range 19-96y), and 127/157 (81%) of patients with COVID-19 were Latinx. Crowded living conditions were common: 60/157 (38%) lived in multi-family shared housing, 12/1578 (8%) with multigenerational families, and 8/157 (5%) were homeless living in shelters. Of 102 patients with ascertained occupations, most had frontline essential jobs: 23% food service, 14% construction/home maintenance, and 10% cleaning. Overall, 86/157 (55%) of patients lived in neighborhoods home to majority Latinx and African-American populations. Overall, 45/157 (29%) of patients needed ICU care, and 26/157 (17%) required mechanical ventilation; 20/26 (77%) of ventilated patients were successfully extubated, and 137/157 (87%) were discharged home. Median hospitalization duration was 4 days (IQR, 2–10), and only 6/157 (4%) patients died in hospital. Conclusion In San Francisco, where early COVID-19 mitigation was enacted, we report a stark, disproportionate COVID-19 burden on Latinx patients, who accounted for 81% of hospitalizations despite making up only 32% of the patient base and 15% of San Francisco’s total population. Latinx inpatients frequently lived in high-density settings, increasing household risk, and frequently worked essential jobs, potentially limiting the opportunity to effectively distance from others. We also report here favorable clinical outcomes and low overall mortality. However, an effective COVID-19 response must urgently address racial and ethnic disparities. Disclosures All Authors: No reported disclosures
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Affiliation(s)
- Vivek Jain
- ZSFG Division of ID/HIV, San Francisco, California
| | - Lillian B Brown
- University of California San Francisco, San Francisco, California
| | | | | | | | | | - Katherine Brooks
- University of California, San Francisco, San Francisco, California
| | - Mengyu Zhou
- University of California, San Francisco, San Francisco, California
| | - Timothy Muldoon
- University of California, San Francisco, San Francisco, California
| | | | | | - Antonio Gomez
- University of California, San Francisco, San Francisco, California
| | - Brian Haas
- University of California, San Francisco, San Francisco, California
| | - Edwin Charlebois
- University of California, San Francisco, San Francisco, California
| | | | | | - Monica Gandhi
- University of California, San Francisco, San Francisco, CA
| | - Diane Havlir
- University of California, San Francisco, San Francisco, California
| | - Sumant Ranji
- University of California, San Francisco, San Francisco, California
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15
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Mick E, Kamm J, Pisco AO, Ratnasiri K, Babik JM, Castañeda G, DeRisi JL, Detweiler AM, Hao SL, Kangelaris KN, Kumar GR, Li LM, Mann SA, Neff N, Prasad PA, Serpa PH, Shah SJ, Spottiswoode N, Tan M, Calfee CS, Christenson SA, Kistler A, Langelier C. Upper airway gene expression reveals suppressed immune responses to SARS-CoV-2 compared with other respiratory viruses. Nat Commun 2020; 11:5854. [PMID: 33203890 PMCID: PMC7673985 DOI: 10.1038/s41467-020-19587-y] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [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: 05/22/2020] [Accepted: 10/16/2020] [Indexed: 12/12/2022] Open
Abstract
SARS-CoV-2 infection is characterized by peak viral load in the upper airway prior to or at the time of symptom onset, an unusual feature that has enabled widespread transmission of the virus and precipitated a global pandemic. How SARS-CoV-2 is able to achieve high titer in the absence of symptoms remains unclear. Here, we examine the upper airway host transcriptional response in patients with COVID-19 (n = 93), other viral (n = 41) or non-viral (n = 100) acute respiratory illnesses (ARIs). Compared with other viral ARIs, COVID-19 is characterized by a pronounced interferon response but attenuated activation of other innate immune pathways, including toll-like receptor, interleukin and chemokine signaling. The IL-1 and NLRP3 inflammasome pathways are markedly less responsive to SARS-CoV-2, commensurate with a signature of diminished neutrophil and macrophage recruitment. This pattern resembles previously described distinctions between symptomatic and asymptomatic viral infections and may partly explain the propensity for pre-symptomatic transmission in COVID-19. We further use machine learning to build 27-, 10- and 3-gene classifiers that differentiate COVID-19 from other ARIs with AUROCs of 0.981, 0.954 and 0.885, respectively. Classifier performance is stable across a wide range of viral load, suggesting utility in mitigating false positive or false negative results of direct SARS-CoV-2 tests.
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Affiliation(s)
- Eran Mick
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
- Division of Pulmonary and Critical Care Medicine, University of California, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Jack Kamm
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | | | - Jennifer M Babik
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
| | | | - Joseph L DeRisi
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | | | | | | | | | - Lucy M Li
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Sabrina A Mann
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - Norma Neff
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Priya A Prasad
- Division of Hospital Medicine, University of California, San Francisco, CA, USA
| | - Paula Hayakawa Serpa
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Sachin J Shah
- Division of Hospital Medicine, University of California, San Francisco, CA, USA
| | | | | | - Carolyn S Calfee
- Division of Pulmonary and Critical Care Medicine, University of California, San Francisco, CA, USA
| | - Stephanie A Christenson
- Division of Pulmonary and Critical Care Medicine, University of California, San Francisco, CA, USA
| | - Amy Kistler
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Charles Langelier
- Division of Infectious Diseases, University of California, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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16
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Shah SJ, Barish PN, Prasad PA, Kistler A, Neff N, Kamm J, Li LM, Chiu CY, Babik JM, Fang MC, Abe-Jones Y, Alipanah N, Alvarez FN, Botvinnik OB, Castaneda G, Dadasovich RM, Davis J, Deng X, DeRisi JL, Detweiler AM, Federman S, Haliburton J, Hao S, Kerkhoff AD, Kumar GR, Malcolm KB, Mann SA, Martinez S, Mary RK, Mick E, Mwakibete L, Najafi N, Peluso MJ, Phelps M, Pisco AO, Ratnasiri K, Rubio LA, Sellas A, Sherwood KD, Sheu J, Spottiswoode N, Tan M, Yu G, Kangelaris KN, Langelier C. Clinical features, diagnostics, and outcomes of patients presenting with acute respiratory illness: A retrospective cohort study of patients with and without COVID-19. EClinicalMedicine 2020; 27:100518. [PMID: 32864588 PMCID: PMC7447618 DOI: 10.1016/j.eclinm.2020.100518] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/27/2020] [Accepted: 08/05/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Most data on the clinical presentation, diagnostics, and outcomes of patients with COVID-19 have been presented as case series without comparison to patients with other acute respiratory illnesses. METHODS We examined emergency department patients between February 3 and March 31, 2020 with an acute respiratory illness who were tested for SARS-CoV-2. We determined COVID-19 status by PCR and metagenomic next generation sequencing (mNGS). We compared clinical presentation, diagnostics, treatment, and outcomes. FINDINGS Among 316 patients, 33 tested positive for SARS-CoV-2; 31 without COVID-19 tested positive for another respiratory virus. Among patients with additional viral testing (27/33), no SARS-CoV-2 co-infections were identified. Compared to those who tested negative, patients with COVID-19 reported longer symptoms duration (median 7d vs. 3d, p < 0.001). Patients with COVID-19 were more often hospitalized (79% vs. 56%, p = 0.014). When hospitalized, patients with COVID-19 had longer hospitalizations (median 10.7d vs. 4.7d, p < 0.001) and more often developed ARDS (23% vs. 3%, p < 0.001). Most comorbidities, medications, symptoms, vital signs, laboratories, treatments, and outcomes did not differ by COVID-19 status. INTERPRETATION While we found differences in clinical features of COVID-19 compared to other acute respiratory illnesses, there was significant overlap in presentation and comorbidities. Patients with COVID-19 were more likely to be admitted to the hospital, have longer hospitalizations and develop ARDS, and were unlikely to have co-existent viral infections. FUNDING National Center for Advancing Translational Sciences, National Heart Lung Blood Institute, National Institute of Allergy and Infectious Diseases, Chan Zuckerberg Biohub, Chan Zuckerberg Initiative.
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Affiliation(s)
- Sachin J. Shah
- Division of Hospital Medicine, University of California, San Francisco, CA, USA
| | - Peter N. Barish
- Division of Hospital Medicine, University of California, San Francisco, CA, USA
| | - Priya A. Prasad
- Division of Hospital Medicine, University of California, San Francisco, CA, USA
| | - Amy Kistler
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Norma Neff
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Jack Kamm
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Lucy M. Li
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Charles Y. Chiu
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Jennifer M. Babik
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
| | - Margaret C. Fang
- Division of Hospital Medicine, University of California, San Francisco, CA, USA
| | - Yumiko Abe-Jones
- Division of Hospital Medicine, University of California, San Francisco, CA, USA
| | - Narges Alipanah
- Division of Pulmonary and Critical Care Medicine, University of California, San Francisco, CA, USA
| | | | | | | | | | - Rand M. Dadasovich
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Jennifer Davis
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Xianding Deng
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Joseph L. DeRisi
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | | | - Scot Federman
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | | | | | - Andrew D. Kerkhoff
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
| | | | - Katherine B. Malcolm
- Division of Pulmonary and Critical Care Medicine, University of California, San Francisco, CA, USA
| | - Sabrina A. Mann
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - Sandra Martinez
- Division of Hospital Medicine, University of California, San Francisco, CA, USA
| | - Rupa K. Mary
- Division of Hospital Medicine, University of California, San Francisco, CA, USA
| | - Eran Mick
- Division of Pulmonary and Critical Care Medicine, University of California, San Francisco, CA, USA
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | - Nader Najafi
- Division of Hospital Medicine, University of California, San Francisco, CA, USA
| | - Michael J. Peluso
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
| | | | | | - Kalani Ratnasiri
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Program in Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Luis A. Rubio
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
| | - Anna Sellas
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Vitalant Research Institute, San Francisco, CA, USA
| | - Kyla D. Sherwood
- Department of Medicine, University of California, San Francisco, CA, USA
| | | | | | | | - Guixia Yu
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | | | - Charles Langelier
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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17
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Vanaerschot M, Murithi JM, Pasaje CFA, Ghidelli-Disse S, Dwomoh L, Bird M, Spottiswoode N, Mittal N, Arendse LB, Owen ES, Wicht KJ, Siciliano G, Bösche M, Yeo T, Kumar TRS, Mok S, Carpenter EF, Giddins MJ, Sanz O, Ottilie S, Alano P, Chibale K, Llinás M, Uhlemann AC, Delves M, Tobin AB, Doerig C, Winzeler EA, Lee MCS, Niles JC, Fidock DA. Inhibition of Resistance-Refractory P. falciparum Kinase PKG Delivers Prophylactic, Blood Stage, and Transmission-Blocking Antiplasmodial Activity. Cell Chem Biol 2020; 27:806-816.e8. [PMID: 32359426 PMCID: PMC7369637 DOI: 10.1016/j.chembiol.2020.04.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [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: 02/15/2020] [Revised: 03/20/2020] [Accepted: 03/31/2020] [Indexed: 12/28/2022]
Abstract
The search for antimalarial chemotypes with modes of action unrelated to existing drugs has intensified with the recent failure of first-line therapies across Southeast Asia. Here, we show that the trisubstituted imidazole MMV030084 potently inhibits hepatocyte invasion by Plasmodium sporozoites, merozoite egress from asexual blood stage schizonts, and male gamete exflagellation. Metabolomic, phosphoproteomic, and chemoproteomic studies, validated with conditional knockdown parasites, molecular docking, and recombinant kinase assays, identified cGMP-dependent protein kinase (PKG) as the primary target of MMV030084. PKG is known to play essential roles in Plasmodium invasion of and egress from host cells, matching MMV030084's activity profile. Resistance selections and gene editing identified tyrosine kinase-like protein 3 as a low-level resistance mediator for PKG inhibitors, while PKG itself never mutated under pressure. These studies highlight PKG as a resistance-refractory antimalarial target throughout the Plasmodium life cycle and promote MMV030084 as a promising Plasmodium PKG-targeting chemotype.
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Affiliation(s)
- Manu Vanaerschot
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - James M Murithi
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Charisse Flerida A Pasaje
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Louis Dwomoh
- Centre for Translational Pharmacology, Institute of Molecular Cell and Systems Biology, University of Glasgow, Glasgow G12 8QQ, UK, Scotland
| | - Megan Bird
- Department of Microbiology, Monash University, Melbourne, VIC 3800, Australia
| | - Natasha Spottiswoode
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Nimisha Mittal
- School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Lauren B Arendse
- Drug Discovery and Development Centre (H3D), South African Medical Research Council Drug Discovery and Development Research Unit, Department of Chemistry & Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch 7701, South Africa
| | - Edward S Owen
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16801, USA; Huck Center for Malaria Research, Pennsylvania State University, University Park, PA 16802, USA
| | - Kathryn J Wicht
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Giulia Siciliano
- Dipartimento di Malattie Infettive, Istituto Superiore di Sanità, Rome, Italy
| | - Markus Bösche
- Cellzome GmbH, GlaxoSmithKline, 69117 Heidelberg, Germany
| | - Tomas Yeo
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - T R Santha Kumar
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Sachel Mok
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Emma F Carpenter
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Marla J Giddins
- Division of Infectious Diseases, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Olalla Sanz
- Diseases of the Developing World Global Health Pharma Unit, GlaxoSmithKline, 28760 Tres Cantos, Spain
| | - Sabine Ottilie
- School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Pietro Alano
- Dipartimento di Malattie Infettive, Istituto Superiore di Sanità, Rome, Italy
| | - Kelly Chibale
- Drug Discovery and Development Centre (H3D), South African Medical Research Council Drug Discovery and Development Research Unit, Department of Chemistry & Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch 7701, South Africa
| | - Manuel Llinás
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16801, USA; Huck Center for Malaria Research, Pennsylvania State University, University Park, PA 16802, USA; Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
| | - Anne-Catrin Uhlemann
- Division of Infectious Diseases, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Michael Delves
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Andrew B Tobin
- Centre for Translational Pharmacology, Institute of Molecular Cell and Systems Biology, University of Glasgow, Glasgow G12 8QQ, UK, Scotland
| | - Christian Doerig
- Department of Microbiology, Monash University, Melbourne, VIC 3800, Australia; School of Health and Biomedical Sciences, RMIT University, Bundoora VIC 3083, Australia
| | | | - Marcus C S Lee
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Jacquin C Niles
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - David A Fidock
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA; Division of Infectious Diseases, Columbia University Irving Medical Center, New York, NY 10032, USA.
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18
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Mick E, Kamm J, Pisco AO, Ratnasiri K, Babik JM, Calfee CS, Castañeda G, DeRisi JL, Detweiler AM, Hao S, Kangelaris KN, Kumar GR, Li LM, Mann SA, Neff N, Prasad PA, Serpa PH, Shah SJ, Spottiswoode N, Tan M, Christenson SA, Kistler A, Langelier C. Upper airway gene expression differentiates COVID-19 from other acute respiratory illnesses and reveals suppression of innate immune responses by SARS-CoV-2. medRxiv 2020:2020.05.18.20105171. [PMID: 32511476 PMCID: PMC7273244 DOI: 10.1101/2020.05.18.20105171] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
We studied the host transcriptional response to SARS-CoV-2 by performing metagenomic sequencing of upper airway samples in 238 patients with COVID-19, other viral or non-viral acute respiratory illnesses (ARIs). Compared to other viral ARIs, COVID-19 was characterized by a diminished innate immune response, with reduced expression of genes involved in toll-like receptor and interleukin signaling, chemokine binding, neutrophil degranulation and interactions with lymphoid cells. Patients with COVID-19 also exhibited significantly reduced proportions of neutrophils and macrophages, and increased proportions of goblet, dendritic and B-cells, compared to other viral ARIs. Using machine learning, we built 26-, 10- and 3-gene classifiers that differentiated COVID-19 from other acute respiratory illnesses with AUCs of 0.980, 0.950 and 0.871, respectively. Classifier performance was stable at low viral loads, suggesting utility in settings where direct detection of viral nucleic acid may be unsuccessful. Taken together, our results illuminate unique aspects of the host transcriptional response to SARS-CoV-2 in comparison to other respiratory viruses and demonstrate the feasibility of COVID-19 diagnostics based on patient gene expression.
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Affiliation(s)
- Eran Mick
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
- Division of Pulmonary and Critical Care Medicine, University of California, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Jack Kamm
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | | | - Jennifer M. Babik
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
| | - Carolyn S. Calfee
- Division of Pulmonary and Critical Care Medicine, University of California, San Francisco, CA, USA
| | | | - Joseph L. DeRisi
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | | | | | | | | | - Lucy M. Li
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Sabrina A. Mann
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - Norma Neff
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Priya A. Prasad
- Division of Hospital Medicine, University of California, San Francisco, CA, USA
| | - Paula Hayakawa Serpa
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Sachin J. Shah
- Division of Hospital Medicine, University of California, San Francisco, CA, USA
| | | | | | - Stephanie A. Christenson
- Division of Pulmonary and Critical Care Medicine, University of California, San Francisco, CA, USA
| | - Amy Kistler
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Charles Langelier
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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19
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Spottiswoode N, Armitage AE, Williams AR, Fyfe AJ, Biswas S, Hodgson SH, Llewellyn D, Choudhary P, Draper SJ, Duffy PE, Drakesmith H. Role of Activins in Hepcidin Regulation during Malaria. Infect Immun 2017; 85:e00191-17. [PMID: 28893916 PMCID: PMC5695100 DOI: 10.1128/iai.00191-17] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 08/23/2017] [Indexed: 12/21/2022] Open
Abstract
Epidemiological observations have linked increased host iron with malaria susceptibility, and perturbed iron handling has been hypothesized to contribute to the potentially life-threatening anemia that may accompany blood-stage malaria infection. To improve our understanding of these relationships, we examined the pathways involved in regulation of the master controller of iron metabolism, the hormone hepcidin, in malaria infection. We show that hepcidin upregulation in Plasmodium berghei murine malaria infection was accompanied by changes in expression of bone morphogenetic protein (BMP)/sons of mothers against decapentaplegic (SMAD) pathway target genes, a key pathway involved in hepcidin regulation. We therefore investigated known agonists of the BMP/SMAD pathway and found that Bmp gene expression was not increased in infection. In contrast, activin B, which can signal through the BMP/SMAD pathway and has been associated with increased hepcidin during inflammation, was upregulated in the livers of Plasmodium berghei-infected mice; hepatic activin B was also upregulated at peak parasitemia during infection with Plasmodium chabaudi Concentrations of the closely related protein activin A increased in parallel with hepcidin in serum from malaria-naive volunteers infected in controlled human malaria infection (CHMI) clinical trials. However, antibody-mediated neutralization of activin activity during murine malaria infection did not affect hepcidin expression, suggesting that these proteins do not stimulate hepcidin upregulation directly. In conclusion, we present evidence that the BMP/SMAD signaling pathway is perturbed in malaria infection but that activins, although raised in malaria infection, may not have a critical role in hepcidin upregulation in this setting.
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Affiliation(s)
- Natasha Spottiswoode
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- Laboratory of Malaria Immunology & Vaccinology, NIAID, NIH, Bethesda, Maryland, USA
| | - Andrew E Armitage
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Andrew R Williams
- Department of Veterinary Disease Biology, University of Copenhagen, Frederiksberg, Denmark
- The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Alex J Fyfe
- The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Sumi Biswas
- The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | | | - David Llewellyn
- The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | | | - Simon J Draper
- The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Patrick E Duffy
- Laboratory of Malaria Immunology & Vaccinology, NIAID, NIH, Bethesda, Maryland, USA
| | - Hal Drakesmith
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
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20
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Brickley EB, Spottiswoode N, Kabyemela E, Morrison R, Kurtis JD, Wood AM, Drakesmith H, Fried M, Duffy PE. Cord Blood Hepcidin: Cross-Sectional Correlates and Associations with Anemia, Malaria, and Mortality in a Tanzanian Birth Cohort Study. Am J Trop Med Hyg 2016; 95:817-826. [PMID: 27352871 DOI: 10.4269/ajtmh.16-0218] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 05/06/2016] [Indexed: 12/21/2022] Open
Abstract
Hepcidin, the master regulator of bioavailable iron, is a key mediator of anemia and also plays a central role in host defense against infection. We hypothesized that measuring hepcidin levels in cord blood could provide an early indication of interindividual differences in iron regulation with quantifiable implications for anemia, malaria, and mortality-related risk. Hepcidin concentrations were measured in cord plasma from a birth cohort (N = 710), which was followed for up to 4 years in a region of perennial malaria transmission in Muheza, Tanzania (2002-2006). At the time of delivery, cord hepcidin levels were correlated with inflammatory mediators, iron markers, and maternal health conditions. Hepcidin levels were 30% (95% confidence interval [CI]: 12%, 44%) lower in children born to anemic mothers and 48% (95% CI: 11%, 97%) higher in placental malaria-exposed children. Relative to children in the lowest third, children in the highest third of cord hepcidin had on average 2.5 g/L (95% CI: 0.1, 4.8) lower hemoglobin levels over the duration of follow-up, increased risk of anemia and severe anemia (adjusted hazard ratio [HR] [95% CI]: 1.18 [1.03, 1.36] and 1.34 [1.08, 1.66], respectively), and decreased risk of malaria and all-cause mortality (adjusted HR [95% CI]: 0.78 [0.67, 0.91] and 0.34 [0.14, 0.84], respectively). Although longitudinal measurements of hepcidin and iron stores are required to strengthen causal inference, these results suggest that hepcidin may have utility as a biomarker indicating children's susceptibility to anemia and infection in early life.
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Affiliation(s)
- Elizabeth B Brickley
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland. Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom. Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire
| | - Natasha Spottiswoode
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland. Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom. Department of Microbiology and Immunology, Columbia University College of Physicians and Surgeons, New York, New York
| | | | - Robert Morrison
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland
| | - Jonathan D Kurtis
- Rhode Island Hospital, Department of Pathology and Laboratory Medicine, Brown University Medical School, Providence, Rhode Island
| | - Angela M Wood
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Hal Drakesmith
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Michal Fried
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland
| | - Patrick E Duffy
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland.
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21
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Abstract
Malaria and iron have a complex but important relationship. Plasmodium proliferation requires iron, both during the clinically silent liver stage of growth and in the disease-associated phase of erythrocyte infection. Precisely how the protozoan acquires its iron from its mammalian host remains unclear, but iron chelators can inhibit pathogen growth in vitro and in animal models. In humans, iron deficiency appears to protect against severe malaria, while iron supplementation increases risks of infection and disease. Malaria itself causes profound disturbances in physiological iron distribution and utilization, through mechanisms that include hemolysis, release of heme, dyserythropoiesis, anemia, deposition of iron in macrophages, and inhibition of dietary iron absorption. These effects have significant consequences. Malarial anemia is a major global health problem, especially in children, that remains incompletely understood and is not straightforward to treat. Furthermore, the changes in iron metabolism during a malaria infection may modulate susceptibility to co-infections. The release of heme and accumulation of iron in granulocytes may explain increased vulnerability to non-typhoidal Salmonella during malaria. The redistribution of iron away from hepatocytes and into macrophages may confer host resistance to superinfection, whereby blood-stage parasitemia prevents the development of a second liver-stage Plasmodium infection in the same organism. Key to understanding the pathophysiology of iron metabolism in malaria is the activity of the iron regulatory hormone hepcidin. Hepcidin is upregulated during blood-stage parasitemia and likely mediates much of the iron redistribution that accompanies disease. Understanding the regulation and role of hepcidin may offer new opportunities to combat malaria and formulate better approaches to treat anemia in the developing world.
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Affiliation(s)
- Natasha Spottiswoode
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of HealthBethesda, MD, USA
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of OxfordOxford, UK
| | - Patrick E. Duffy
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of HealthBethesda, MD, USA
| | - Hal Drakesmith
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of OxfordOxford, UK
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22
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Abstract
The populations in greatest need of iron supplementation are also those at greatest risk of malaria: pregnant women and young children. Iron supplementation has been shown to increase malaria risk in these groups in numerous studies, although this effect is likely diminished by factors such as host immunity, host iron status, and effective malaria surveillance and control. Conversely, the risk of anemia is increased by malaria infections and preventive measures against malaria decrease anemia prevalence in susceptible populations without iron supplementation. Studies have shown that subjects with malaria experience diminished absorption of orally administered iron, so that as a consequence, iron supplementation may have generally reduced efficacy in malarious populations. A possible mechanistic link between malaria, poor absorption of iron, and anemia is provided by recent research on hepcidin, the human iron control hormone. Our improved understanding of iron metabolism may contribute to the control of malaria and the treatment of anemia. Malaria surveillance and control are necessary components of programs to control iron deficiency and may enhance the efficacy of iron supplementation.
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Affiliation(s)
- Natasha Spottiswoode
- Laboratory of Malaria Immunology and Vaccinology, NIAID, National Institutes of Health, Bethesda, MD; and,Molecular Immunology Group, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, UK
| | - Michal Fried
- Laboratory of Malaria Immunology and Vaccinology, NIAID, National Institutes of Health, Bethesda, MD; and
| | - Hal Drakesmith
- Molecular Immunology Group, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, UK
| | - Patrick E. Duffy
- Laboratory of Malaria Immunology and Vaccinology, NIAID, National Institutes of Health, Bethesda, MD; and
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23
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Armitage AE, Eddowes LA, Gileadi U, Cole S, Spottiswoode N, Selvakumar TA, Ho LP, Townsend ARM, Drakesmith H. Hepcidin regulation by innate immune and infectious stimuli. Blood 2011; 118:4129-39. [PMID: 21873546 DOI: 10.1182/blood-2011-04-351957] [Citation(s) in RCA: 218] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Hepcidin controls the levels and distribution of iron, an element whose availability can influence the outcome of infections. We investigated hepcidin regulation by infection-associated cytokines, pathogen-derived molecules, and whole pathogens in vitro and in vivo. We found that IL-22, an effector cytokine implicated in responses to extracellular infections, caused IL-6-independent hepcidin up-regulation in human hepatoma cells, suggesting it might represent an additional inflammatory hepcidin agonist. Like IL-6, IL-22 caused phosphorylation of STAT3 and synergized with BMP6 potentiating hepcidin induction. In human leukocytes, IL-6 caused potent, transient hepcidin up-regulation that was augmented by TGF-β1. Pathogen-derived TLR agonists also stimulated hepcidin, most notably the TLR5 agonist flagellin in an IL-6-dependent manner. In contrast, leukocyte hepcidin induction by heat-killed Candida albicans hyphae was IL-6-independent, but partially TGF-β-dependent. In a murine acute systemic candidiasis model, C albicans strongly stimulated hepcidin, accompanied by a major reduction in transferrin saturation. Similarly, hepcidin was up-regulated with concomitant lowering of serum iron during acute murine Influenza A/PR/8/34 virus (H1N1) infection. This intracellular pathogen also stimulated hepcidin expression in leukocytes and hepatoma cells. Together, these results indicate that hepcidin induction represents a component of the innate immune response to acute infection, with the potential to affect disease pathogenesis.
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Affiliation(s)
- Andrew E Armitage
- Molecular Immunology Group, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
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