1
|
Mwakibete L, Greening SS, Kalantar K, Ahyong V, Anis E, Miller EA, Needle DB, Oglesbee M, Thomas WK, Sevigny JL, Gordon LM, Nemeth NM, Ogbunugafor CB, Ayala AJ, Faith SA, Neff N, Detweiler AM, Baillargeon T, Tanguay S, Simpson SD, Murphy LA, Ellis JC, Tato CM, Gagne RB. Metagenomics for Pathogen Detection During a Mass Mortality Event in Songbirds. J Wildl Dis 2024; 60:362-374. [PMID: 38345467 DOI: 10.7589/jwd-d-23-00109] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 01/02/2024] [Indexed: 04/06/2024]
Abstract
Mass mortality events in wildlife can be indications of an emerging infectious disease. During the spring and summer of 2021, hundreds of dead passerines were reported across the eastern US. Birds exhibited a range of clinical signs including swollen conjunctiva, ocular discharge, ataxia, and nystagmus. As part of the diagnostic investigation, high-throughput metagenomic next-generation sequencing was performed across three molecular laboratories on samples from affected birds. Many potentially pathogenic microbes were detected, with bacteria forming the largest proportion; however, no singular agent was consistently identified, with many of the detected microbes also found in unaffected (control) birds and thus considered to be subclinical infections. Congruent results across laboratories have helped drive further investigation into alternative causes, including environmental contaminants and nutritional deficiencies. This work highlights the utility of metagenomic approaches in investigations of emerging diseases and provides a framework for future wildlife mortality events.
Collapse
Affiliation(s)
| | - Sabrina S Greening
- Department of Pathobiology, Wildlife Futures Program, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, Pennsylvania 19348, USA
| | | | - Vida Ahyong
- Chan Zuckerberg Biohub, San Francisco, California 94158, USA
| | - Eman Anis
- Department of Pathobiology, Wildlife Futures Program, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, Pennsylvania 19348, USA
- Department of Pathobiology, PADLS New Bolton Center, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, Pennsylvania 19348, USA
| | - Erica A Miller
- Department of Pathobiology, Wildlife Futures Program, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, Pennsylvania 19348, USA
| | - David B Needle
- New Hampshire Veterinary Diagnostic Lab, University of New Hampshire, Durham, New Hampshire 03824, USA
| | - Michael Oglesbee
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio 43210, USA
| | - W Kelley Thomas
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire 03824, USA
| | - Joseph L Sevigny
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire 03824, USA
| | - Lawrence M Gordon
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire 03824, USA
| | - Nicole M Nemeth
- Southeastern Cooperative Wildlife Disease Study and Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, Georgia 30602, USA
- Department of Pathology, College of Veterinary Medicine, University of Georgia, Georgia 30602, USA
| | - C Brandon Ogbunugafor
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06511, USA
| | - Andrea J Ayala
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06511, USA
| | - Seth A Faith
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio 43210, USA
| | - Norma Neff
- Chan Zuckerberg Biohub, San Francisco, California 94158, USA
| | | | - Tessa Baillargeon
- New Hampshire Veterinary Diagnostic Lab, University of New Hampshire, Durham, New Hampshire 03824, USA
| | - Stacy Tanguay
- New Hampshire Veterinary Diagnostic Lab, University of New Hampshire, Durham, New Hampshire 03824, USA
| | - Stephen D Simpson
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire 03824, USA
| | - Lisa A Murphy
- Department of Pathobiology, Wildlife Futures Program, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, Pennsylvania 19348, USA
- Department of Pathobiology, PADLS New Bolton Center, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, Pennsylvania 19348, USA
| | - Julie C Ellis
- Department of Pathobiology, Wildlife Futures Program, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, Pennsylvania 19348, USA
| | - Cristina M Tato
- Chan Zuckerberg Biohub, San Francisco, California 94158, USA
| | - Roderick B Gagne
- Department of Pathobiology, Wildlife Futures Program, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, Pennsylvania 19348, USA
| |
Collapse
|
2
|
Mwakibete L, Takahashi S, Ahyong V, Black A, Rek J, Ssewanyana I, Kamya M, Dorsey G, Jagannathan P, Rodríguez-Barraquer I, Tato CM, Greenhouse B. Metagenomic next-generation sequencing to characterize potential etiologies of non-malarial fever in a cohort living in a high malaria burden area of Uganda. PLOS Glob Public Health 2023; 3:e0001675. [PMID: 37134083 PMCID: PMC10156012 DOI: 10.1371/journal.pgph.0001675] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 04/12/2023] [Indexed: 05/04/2023]
Abstract
Causes of non-malarial fevers in sub-Saharan Africa remain understudied. We hypothesized that metagenomic next-generation sequencing (mNGS), which allows for broad genomic-level detection of infectious agents in a biological sample, can systematically identify potential causes of non-malarial fevers. The 212 participants in this study were of all ages and were enrolled in a longitudinal malaria cohort in eastern Uganda. Between December 2020 and August 2021, respiratory swabs and plasma samples were collected at 313 study visits where participants presented with fever and were negative for malaria by microscopy. Samples were analyzed using CZ ID, a web-based platform for microbial detection in mNGS data. Overall, viral pathogens were detected at 123 of 313 visits (39%). SARS-CoV-2 was detected at 11 visits, from which full viral genomes were recovered from nine. Other prevalent viruses included Influenza A (14 visits), RSV (12 visits), and three of the four strains of seasonal coronaviruses (6 visits). Notably, 11 influenza cases occurred between May and July 2021, coinciding with when the Delta variant of SARS-CoV-2 was circulating in this population. The primary limitation of this study is that we were unable to estimate the contribution of bacterial microbes to non-malarial fevers, due to the difficulty of distinguishing bacterial microbes that were pathogenic from those that were commensal or contaminants. These results revealed the co-circulation of multiple viral pathogens likely associated with fever in the cohort during this time period. This study illustrates the utility of mNGS in elucidating the multiple potential causes of non-malarial febrile illness. A better understanding of the pathogen landscape in different settings and age groups could aid in informing diagnostics, case management, and public health surveillance systems.
Collapse
Affiliation(s)
- Lusajo Mwakibete
- Chan Zuckerberg Biohub, San Francisco, CA, United States of America
| | - Saki Takahashi
- Department of Medicine, Division of HIV, ID, and Global Medicine, EPPIcenter Research Program, University of California San Francisco, San Francisco, CA, United States of America
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States of America
| | - Vida Ahyong
- Chan Zuckerberg Biohub, San Francisco, CA, United States of America
| | - Allison Black
- Chan Zuckerberg Biohub, San Francisco, CA, United States of America
| | - John Rek
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | | | - Moses Kamya
- Infectious Diseases Research Collaboration, Kampala, Uganda
- Department of Medicine, Makerere University, Kampala, Uganda
| | - Grant Dorsey
- Department of Medicine, Division of HIV, ID, and Global Medicine, University of California San Francisco, San Francisco, CA, United States of America
| | - Prasanna Jagannathan
- Department of Medicine, Stanford University, Palo Alto, CA, United States of America
- Department of Microbiology and Immunology, Stanford University, Palo Alto, CA, United States of America
| | - Isabel Rodríguez-Barraquer
- Department of Medicine, Division of HIV, ID, and Global Medicine, EPPIcenter Research Program, University of California San Francisco, San Francisco, CA, United States of America
| | - Cristina M. Tato
- Chan Zuckerberg Biohub, San Francisco, CA, United States of America
| | - Bryan Greenhouse
- Department of Medicine, Division of HIV, ID, and Global Medicine, EPPIcenter Research Program, University of California San Francisco, San Francisco, CA, United States of America
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|