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Stramer SL, Dodd RY, Chiu CY. Advances in testing technology to ensure transfusion safety - NAT and beyond. ACTA ACUST UNITED AC 2015. [DOI: 10.1111/voxs.12152] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- S. L. Stramer
- American Red Cross Biomedical Services; Gaithersburg MD USA
| | - R. Y. Dodd
- Research and Development; American Red Cross Biomedical Services; Rockville MD USA
| | - C. Y. Chiu
- Laboratory Medicine and Medicine/Infectious Diseases; UCSF School of Medicine; San Francisco CA USA
- UCSF-Abbott Viral Diagnostics and Discovery Center; UCSF School of Medicine; San Francisco CA USA
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302
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Greninger AL, Naccache SN, Messacar K, Clayton A, Yu G, Somasekar S, Federman S, Stryke D, Anderson C, Yagi S, Messenger S, Wadford D, Xia D, Watt JP, Van Haren K, Dominguez SR, Glaser C, Aldrovandi G, Chiu CY. A novel outbreak enterovirus D68 strain associated with acute flaccid myelitis cases in the USA (2012-14): a retrospective cohort study. THE LANCET. INFECTIOUS DISEASES 2015; 15:671-82. [PMID: 25837569 DOI: 10.1016/s1473-3099(15)70093-9] [Citation(s) in RCA: 280] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
BACKGROUND Enterovirus D68 was implicated in a widespread outbreak of severe respiratory illness across the USA in 2014 and has also been reported sporadically in patients with acute flaccid myelitis. We aimed to investigate the association between enterovirus D68 infection and acute flaccid myelitis during the 2014 enterovirus D68 respiratory outbreak in the USA. METHODS Patients with acute flaccid myelitis who presented to two hospitals in Colorado and California, USA, between Nov 24, 2013, and Oct 11, 2014, were included in the study. Additional cases identified from Jan 1, 2012, to Oct 4, 2014, via statewide surveillance were provided by the California Department of Public Health. We investigated the cause of these cases by metagenomic next-generation sequencing, viral genome recovery, and enterovirus D68 phylogenetic analysis. We compared patients with acute flaccid myelitis who were positive for enterovirus D68 with those with acute flaccid myelitis but negative for enterovirus D68 using the two-tailed Fisher's exact test, two-sample unpaired t test, and Mann-Whitney U test. FINDINGS 48 patients were included: 25 with acute flaccid myelitis, two with enterovirus-associated encephalitis, five with enterovirus-D68-associated upper respiratory illness, and 16 with aseptic meningitis or encephalitis who tested positive for enterovirus. Enterovirus D68 was detected in respiratory secretions from seven (64%) of 11 patients comprising two temporally and geographically linked acute flaccid myelitis clusters at the height of the 2014 outbreak, and from 12 (48%) of 25 patients with acute flaccid myelitis overall. Phylogenetic analysis revealed that all enterovirus D68 sequences associated with acute flaccid myelitis grouped into a clade B1 strain that emerged in 2010. Of six coding polymorphisms in the clade B1 enterovirus D68 polyprotein, five were present in neuropathogenic poliovirus or enterovirus D70, or both. One child with acute flaccid myelitis and a sibling with only upper respiratory illness were both infected by identical enterovirus D68 strains. Enterovirus D68 viraemia was identified in a child experiencing acute neurological progression of his paralytic illness. Deep metagenomic sequencing of cerebrospinal fluid from 14 patients with acute flaccid myelitis did not reveal evidence of an alternative infectious cause to enterovirus D68. INTERPRETATION These findings strengthen the putative association between enterovirus D68 and acute flaccid myelitis and the contention that acute flaccid myelitis is a rare yet severe clinical manifestation of enterovirus D68 infection in susceptible hosts. FUNDING National Institutes of Health, University of California, Abbott Laboratories, and the Centers for Disease Control and Prevention.
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Affiliation(s)
- Alexander L Greninger
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Samia N Naccache
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Kevin Messacar
- Department of Pediatrics, Children's Hospital Colorado and University of Colorado School of Medicine, Aurora, CO, USA
| | - Anna Clayton
- California Department of Public Health, Richmond, CA, USA
| | - Guixia Yu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Sneha Somasekar
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Scot Federman
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Doug Stryke
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | | | - Shigeo Yagi
- California Department of Public Health, Richmond, CA, USA
| | | | - Debra Wadford
- California Department of Public Health, Richmond, CA, USA
| | - Dongxiang Xia
- California Department of Public Health, Richmond, CA, USA
| | - James P Watt
- California Department of Public Health, Richmond, CA, USA
| | - Keith Van Haren
- Department of Neurology, Lucile Packard Children's Hospital at Stanford University, Palo Alto, CA, USA
| | - Samuel R Dominguez
- Department of Pediatrics, Children's Hospital Colorado and University of Colorado School of Medicine, Aurora, CO, USA
| | - Carol Glaser
- California Department of Public Health, Richmond, CA, USA
| | - Grace Aldrovandi
- Department of Pediatrics, Children's Hospital Los Angeles and University of Southern California, Los Angeles, CA, USA
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA.
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303
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Kilianski A, Haas JL, Corriveau EJ, Liem AT, Willis KL, Kadavy DR, Rosenzweig CN, Minot SS. Bacterial and viral identification and differentiation by amplicon sequencing on the MinION nanopore sequencer. Gigascience 2015; 4:12. [PMID: 25815165 PMCID: PMC4374364 DOI: 10.1186/s13742-015-0051-z] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 02/27/2015] [Indexed: 11/22/2022] Open
Abstract
Background The MinION™ nanopore sequencer was recently released to a community of alpha-testers for evaluation using a variety of sequencing applications. Recent reports have tested the ability of the MinION™ to act as a whole genome sequencer and have demonstrated that nanopore sequencing has tremendous potential utility. However, the current nanopore technology still has limitations with respect to error-rate, and this is problematic when attempting to assemble whole genomes without secondary rounds of sequencing to correct errors. In this study, we tested the ability of the MinION™ nanopore sequencer to accurately identify and differentiate bacterial and viral samples via directed sequencing of characteristic genes shared broadly across a target clade. Results Using a 6 hour sequencing run time, sufficient data were generated to identify an E. coli sample down to the species level from 16S rDNA amplicons. Three poxviruses (cowpox, vaccinia-MVA, and vaccinia-Lister) were identified and differentiated down to the strain level, despite over 98% identity between the vaccinia strains. The ability to differentiate strains by amplicon sequencing on the MinION™ was accomplished despite an observed per-base error rate of approximately 30%. Conclusions While nanopore sequencing, using the MinION™ platform from Oxford Nanopore in particular, continues to mature into a commercially available technology, practical uses are sought for the current versions of the technology. This study offers evidence of the utility of amplicon sequencing by demonstrating that the current versions of MinION™ technology can accurately identify and differentiate both viral and bacterial species present within biological samples via amplicon sequencing. Electronic supplementary material The online version of this article (doi:10.1186/s13742-015-0051-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andy Kilianski
- Edgewood Chemical Biological Center, 5183 Black Hawk Rd Bldg E3150 Rm 324, Aberdeen Proving Ground, MD 21010 USA
| | - Jamie L Haas
- Signature Science, LLC, 8329 N. MoPac Expressway, Austin, TX 78759 USA
| | - Elizabeth J Corriveau
- Edgewood Chemical Biological Center, 5183 Black Hawk Rd Bldg E3150 Rm 324, Aberdeen Proving Ground, MD 21010 USA
| | - Alvin T Liem
- Edgewood Chemical Biological Center, 5183 Black Hawk Rd Bldg E3150 Rm 324, Aberdeen Proving Ground, MD 21010 USA
| | - Kristen L Willis
- Edgewood Chemical Biological Center, 5183 Black Hawk Rd Bldg E3150 Rm 324, Aberdeen Proving Ground, MD 21010 USA ; Defense Threat Reduction Agency, 8725 John J Kingman Rd Stop 6201, Ft. Belvoir, VA 22060-6201 USA
| | - Dana R Kadavy
- Signature Science, LLC, 8329 N. MoPac Expressway, Austin, TX 78759 USA
| | - C Nicole Rosenzweig
- Edgewood Chemical Biological Center, 5183 Black Hawk Rd Bldg E3150 Rm 324, Aberdeen Proving Ground, MD 21010 USA
| | - Samuel S Minot
- Signature Science, LLC, 8329 N. MoPac Expressway, Austin, TX 78759 USA
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304
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Scheuch M, Höper D, Beer M. RIEMS: a software pipeline for sensitive and comprehensive taxonomic classification of reads from metagenomics datasets. BMC Bioinformatics 2015; 16:69. [PMID: 25886935 PMCID: PMC4351923 DOI: 10.1186/s12859-015-0503-6] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 02/20/2015] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Fuelled by the advent and subsequent development of next generation sequencing technologies, metagenomics became a powerful tool for the analysis of microbial communities both scientifically and diagnostically. The biggest challenge is the extraction of relevant information from the huge sequence datasets generated for metagenomics studies. Although a plethora of tools are available, data analysis is still a bottleneck. RESULTS To overcome the bottleneck of data analysis, we developed an automated computational workflow called RIEMS - Reliable Information Extraction from Metagenomic Sequence datasets. RIEMS assigns every individual read sequence within a dataset taxonomically by cascading different sequence analyses with decreasing stringency of the assignments using various software applications. After completion of the analyses, the results are summarised in a clearly structured result protocol organised taxonomically. The high accuracy and performance of RIEMS analyses were proven in comparison with other tools for metagenomics data analysis using simulated sequencing read datasets. CONCLUSIONS RIEMS has the potential to fill the gap that still exists with regard to data analysis for metagenomics studies. The usefulness and power of RIEMS for the analysis of genuine sequencing datasets was demonstrated with an early version of RIEMS in 2011 when it was used to detect the orthobunyavirus sequences leading to the discovery of Schmallenberg virus.
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Affiliation(s)
- Matthias Scheuch
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald - Insel Riems, Germany.
| | - Dirk Höper
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald - Insel Riems, Germany.
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald - Insel Riems, Germany.
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305
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Afshinnekoo E, Meydan C, Chowdhury S, Jaroudi D, Boyer C, Bernstein N, Maritz JM, Reeves D, Gandara J, Chhangawala S, Ahsanuddin S, Simmons A, Nessel T, Sundaresh B, Pereira E, Jorgensen E, Kolokotronis SO, Kirchberger N, Garcia I, Gandara D, Dhanraj S, Nawrin T, Saletore Y, Alexander N, Vijay P, Hénaff EM, Zumbo P, Walsh M, O'Mullan GD, Tighe S, Dudley JT, Dunaif A, Ennis S, O'Halloran E, Magalhaes TR, Boone B, Jones AL, Muth TR, Paolantonio KS, Alter E, Schadt EE, Garbarino J, Prill RJ, Carlton JM, Levy S, Mason CE. Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics. Cell Syst 2015; 1:72-87. [PMID: 26594662 PMCID: PMC4651444 DOI: 10.1016/j.cels.2015.01.001] [Citation(s) in RCA: 173] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The panoply of microorganisms and other species present in our environment influence human health and disease, especially in cities, but have not been profiled with metagenomics at a city-wide scale. We sequenced DNA from surfaces across the entire New York City (NYC) subway system, the Gowanus Canal, and public parks. Nearly half of the DNA (48%) does not match any known organism; identified organisms spanned 1,688 bacterial, viral, archaeal, and eukaryotic taxa, which were enriched for harmless genera associated with skin (e.g., Acinetobacter). Predicted ancestry of human DNA left on subway surfaces can recapitulate U.S. Census demographic data, and bacterial signatures can reveal a station’s history, such as marine-associated bacteria in a hurricane-flooded station. Some evidence of pathogens was found (Bacillus anthracis), but a lack of reported cases in NYC suggests that the pathogens represent a normal, urban microbiome. This baseline metagenomic map of NYC could help long-term disease surveillance, bioterrorism threat mitigation, and health management in the built environment of cities.
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Affiliation(s)
- Ebrahim Afshinnekoo
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA ; School of Earth and Environmental Sciences, City University of New York (CUNY) Queens College, Flushing, NY 11367, USA
| | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Shanin Chowdhury
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA ; CUNY Hunter College, New York, NY 10065, USA
| | - Dyala Jaroudi
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Collin Boyer
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Nick Bernstein
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Julia M Maritz
- Center for Genomics, New York University, New York, NY 10003, USA
| | - Darryl Reeves
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA ; Tri-Institutional Program on Computational Biology and Medicine (CBM), New York, NY 10065, USA
| | - Jorge Gandara
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Sagar Chhangawala
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Sofia Ahsanuddin
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA ; CUNY Brooklyn College, Department of Biology, Brooklyn, NY 11210, USA
| | - Amber Simmons
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | | | | | | | | | | | - Nell Kirchberger
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Isaac Garcia
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - David Gandara
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Sean Dhanraj
- CUNY Brooklyn College, Department of Biology, Brooklyn, NY 11210, USA
| | - Tanzina Nawrin
- CUNY Brooklyn College, Department of Biology, Brooklyn, NY 11210, USA
| | - Yogesh Saletore
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA ; Tri-Institutional Program on Computational Biology and Medicine (CBM), New York, NY 10065, USA
| | - Noah Alexander
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Priyanka Vijay
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA ; Tri-Institutional Program on Computational Biology and Medicine (CBM), New York, NY 10065, USA
| | - Elizabeth M Hénaff
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Paul Zumbo
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Michael Walsh
- State University of New York, Downstate, Brooklyn, NY 11203, USA
| | - Gregory D O'Mullan
- School of Earth and Environmental Sciences, City University of New York (CUNY) Queens College, Flushing, NY 11367, USA
| | - Scott Tighe
- University of Vermont, Burlington, VT 05405, USA
| | - Joel T Dudley
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anya Dunaif
- Rockefeller University, New York, NY 10065, USA
| | - Sean Ennis
- Academic Centre on Rare Diseases, School of Medicine and Medical Science, University College Dublin 4, Ireland ; National Centre for Medical Genetics, Our Lady's Children's Hospital, Dublin 12, Ireland
| | - Eoghan O'Halloran
- Academic Centre on Rare Diseases, School of Medicine and Medical Science, University College Dublin 4, Ireland
| | - Tiago R Magalhaes
- Academic Centre on Rare Diseases, School of Medicine and Medical Science, University College Dublin 4, Ireland ; National Centre for Medical Genetics, Our Lady's Children's Hospital, Dublin 12, Ireland
| | - Braden Boone
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Angela L Jones
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Theodore R Muth
- CUNY Brooklyn College, Department of Biology, Brooklyn, NY 11210, USA
| | | | | | - Eric E Schadt
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Robert J Prill
- Accelerated Discovery Lab, IBM Almaden Research Center, San Jose, CA 95120, USA
| | - Jane M Carlton
- Center for Genomics, New York University, New York, NY 10003, USA
| | - Shawn Levy
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA ; The Feil Family Brain and Mind Research Institute, New York, NY 10065, USA
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306
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Hubbard A, Lewis CM, Yoshida K, Ramirez-Gonzalez RH, de Vallavieille-Pope C, Thomas J, Kamoun S, Bayles R, Uauy C, Saunders DGO. Field pathogenomics reveals the emergence of a diverse wheat yellow rust population. Genome Biol 2015. [PMID: 25723868 DOI: 10.1186/s13059-015-0590-598] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023] Open
Abstract
BACKGROUND Emerging and re-emerging pathogens imperil public health and global food security. Responding to these threats requires improved surveillance and diagnostic systems. Despite their potential, genomic tools have not been readily applied to emerging or re-emerging plant pathogens such as the wheat yellow (stripe) rust pathogen Puccinia striiformis f. sp. tritici (PST). This is due largely to the obligate parasitic nature of PST, as culturing PST isolates for DNA extraction remains slow and tedious. RESULTS To counteract the limitations associated with culturing PST, we developed and applied a field pathogenomics approach by transcriptome sequencing infected wheat leaves collected from the field in 2013. This enabled us to rapidly gain insights into this emerging pathogen population. We found that the PST population across the United Kingdom (UK) underwent a major shift in recent years. Population genetic structure analyses revealed four distinct lineages that correlated to the phenotypic groups determined through traditional pathology-based virulence assays. Furthermore, the genetic diversity between members of a single population cluster for all 2013 PST field samples was much higher than that displayed by historical UK isolates, revealing a more diverse population of PST. CONCLUSIONS Our field pathogenomics approach uncovered a dramatic shift in the PST population in the UK, likely due to a recent introduction of a diverse set of exotic PST lineages. The methodology described herein accelerates genetic analysis of pathogen populations and circumvents the difficulties associated with obligate plant pathogens. In principle, this strategy can be widely applied to a variety of plant pathogens.
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307
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Hubbard A, Lewis CM, Yoshida K, Ramirez-Gonzalez RH, de Vallavieille-Pope C, Thomas J, Kamoun S, Bayles R, Uauy C, Saunders DGO. Field pathogenomics reveals the emergence of a diverse wheat yellow rust population. Genome Biol 2015; 16:23. [PMID: 25723868 PMCID: PMC4342793 DOI: 10.1186/s13059-015-0590-8] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 01/20/2015] [Indexed: 11/28/2022] Open
Abstract
Background Emerging and re-emerging pathogens imperil public health and global food security. Responding to these threats requires improved surveillance and diagnostic systems. Despite their potential, genomic tools have not been readily applied to emerging or re-emerging plant pathogens such as the wheat yellow (stripe) rust pathogen Puccinia striiformis f. sp. tritici (PST). This is due largely to the obligate parasitic nature of PST, as culturing PST isolates for DNA extraction remains slow and tedious. Results To counteract the limitations associated with culturing PST, we developed and applied a field pathogenomics approach by transcriptome sequencing infected wheat leaves collected from the field in 2013. This enabled us to rapidly gain insights into this emerging pathogen population. We found that the PST population across the United Kingdom (UK) underwent a major shift in recent years. Population genetic structure analyses revealed four distinct lineages that correlated to the phenotypic groups determined through traditional pathology-based virulence assays. Furthermore, the genetic diversity between members of a single population cluster for all 2013 PST field samples was much higher than that displayed by historical UK isolates, revealing a more diverse population of PST. Conclusions Our field pathogenomics approach uncovered a dramatic shift in the PST population in the UK, likely due to a recent introduction of a diverse set of exotic PST lineages. The methodology described herein accelerates genetic analysis of pathogen populations and circumvents the difficulties associated with obligate plant pathogens. In principle, this strategy can be widely applied to a variety of plant pathogens. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0590-8) contains supplementary material, which is available to authorized users.
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308
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Wang Q, Jia P, Zhao Z. VERSE: a novel approach to detect virus integration in host genomes through reference genome customization. Genome Med 2015; 7:2. [PMID: 25699093 PMCID: PMC4333248 DOI: 10.1186/s13073-015-0126-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 01/05/2015] [Indexed: 12/28/2022] Open
Abstract
Fueled by widespread applications of high-throughput next generation sequencing (NGS) technologies and urgent need to counter threats of pathogenic viruses, large-scale studies were conducted recently to investigate virus integration in host genomes (for example, human tumor genomes) that may cause carcinogenesis or other diseases. A limiting factor in these studies, however, is rapid virus evolution and resulting polymorphisms, which prevent reads from aligning readily to commonly used virus reference genomes, and, accordingly, make virus integration sites difficult to detect. Another confounding factor is host genomic instability as a result of virus insertions. To tackle these challenges and improve our capability to identify cryptic virus-host fusions, we present a new approach that detects Virus intEgration sites through iterative Reference SEquence customization (VERSE). To the best of our knowledge, VERSE is the first approach to improve detection through customizing reference genomes. Using 19 human tumors and cancer cell lines as test data, we demonstrated that VERSE substantially enhanced the sensitivity of virus integration site detection. VERSE is implemented in the open source package VirusFinder 2 that is available at http://bioinfo.mc.vanderbilt.edu/VirusFinder/.
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Affiliation(s)
- Qingguo Wang
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37203 USA
| | - Peilin Jia
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37203 USA ; Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 37232 USA
| | - Zhongming Zhao
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37203 USA ; Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 37232 USA ; Department of Psychiatry, Vanderbilt University School of Medicine, Nashville, TN 37232 USA ; Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN 37232 USA
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309
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Deng X, Naccache SN, Ng T, Federman S, Li L, Chiu CY, Delwart EL. An ensemble strategy that significantly improves de novo assembly of microbial genomes from metagenomic next-generation sequencing data. Nucleic Acids Res 2015; 43:e46. [PMID: 25586223 PMCID: PMC4402509 DOI: 10.1093/nar/gkv002] [Citation(s) in RCA: 198] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 01/04/2015] [Indexed: 11/12/2022] Open
Abstract
Next-generation sequencing (NGS) approaches rapidly produce millions to billions of short reads, which allow pathogen detection and discovery in human clinical, animal and environmental samples. A major limitation of sequence homology-based identification for highly divergent microorganisms is the short length of reads generated by most highly parallel sequencing technologies. Short reads require a high level of sequence similarities to annotated genes to confidently predict gene function or homology. Such recognition of highly divergent homologues can be improved by reference-free (de novo) assembly of short overlapping sequence reads into larger contigs. We describe an ensemble strategy that integrates the sequential use of various de Bruijn graph and overlap-layout-consensus assemblers with a novel partitioned sub-assembly approach. We also proposed new quality metrics that are suitable for evaluating metagenome de novo assembly. We demonstrate that this new ensemble strategy tested using in silico spike-in, clinical and environmental NGS datasets achieved significantly better contigs than current approaches.
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Affiliation(s)
- Xutao Deng
- Blood Systems Research Institute, San Francisco, CA 94118, USA Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA 94107, USA
| | - Samia N Naccache
- Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA 94107, USA UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA 94107, USA
| | - Terry Ng
- Blood Systems Research Institute, San Francisco, CA 94118, USA Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA 94107, USA
| | - Scot Federman
- Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA 94107, USA UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA 94107, USA
| | - Linlin Li
- Blood Systems Research Institute, San Francisco, CA 94118, USA Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA 94107, USA
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA 94107, USA UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA 94107, USA Department of Medicine, Division of Infectious Diseases, UCSF, San Francisco, CA 94143, USA
| | - Eric L Delwart
- Blood Systems Research Institute, San Francisco, CA 94118, USA Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA 94107, USA
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310
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Naccache SN, Peggs KS, Mattes FM, Phadke R, Garson JA, Grant P, Samayoa E, Federman S, Miller S, Lunn MP, Gant V, Chiu CY. Diagnosis of neuroinvasive astrovirus infection in an immunocompromised adult with encephalitis by unbiased next-generation sequencing. Clin Infect Dis 2015; 60:919-23. [PMID: 25572898 PMCID: PMC4345816 DOI: 10.1093/cid/ciu912] [Citation(s) in RCA: 213] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Metagenomic next-generation sequencing (NGS) was used to diagnose an unusual and fatal case of progressive encephalitis in an immunocompromised adult presenting at disease onset as bilateral hearing loss. The sequencing and confirmatory studies revealed neuroinvasive infection of the brain by an astrovirus belonging to a recently discovered VA/HMO clade.
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Affiliation(s)
- Samia N Naccache
- Department of Laboratory Medicine, University of California, San Francisco UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California
| | | | | | | | - Jeremy A Garson
- Research Department of Infection, Division of Infection and Immunity, University College London, United Kingdom
| | | | - Erik Samayoa
- Department of Laboratory Medicine, University of California, San Francisco UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California
| | - Scot Federman
- Department of Laboratory Medicine, University of California, San Francisco UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California
| | - Steve Miller
- Department of Laboratory Medicine, University of California, San Francisco UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California
| | - Michael P Lunn
- Neurology, University College London Hospitals NHS Foundation Trust
| | | | - Charles Y Chiu
- Department of Laboratory Medicine, University of California, San Francisco UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California Department of Medicine, Division of Infectious Diseases, University of California, San Francisco
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311
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Calistri A, Palu G. Editorial Commentary: Unbiased Next-Generation Sequencing and New Pathogen Discovery: Undeniable Advantages and Still-Existing Drawbacks. Clin Infect Dis 2015; 60:889-91. [DOI: 10.1093/cid/ciu913] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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312
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Pyne S, Vullikanti AKS, Marathe MV. Big Data Applications in Health Sciences and Epidemiology. HANDBOOK OF STATISTICS 2015. [PMCID: PMC7152243 DOI: 10.1016/b978-0-444-63492-4.00008-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Saumyadipta Pyne
- Bioinformatics, CR Rao Advanced Institute of Mathematics, Statistics and Computer Science, University of Hyderabad Campus, Hyderabad, India
- Public Health Foundation of India, New Delhi, India
- Corresponding author:
| | | | - Madhav V. Marathe
- Department of Computer Science, Virginia Tech, Blacksburg, Virginia, USA
- Network Dynamics and Simulation Science Laboratory, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, USA
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313
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Fournier PE, Dubourg G, Raoult D. Clinical detection and characterization of bacterial pathogens in the genomics era. Genome Med 2014; 6:114. [PMID: 25593594 PMCID: PMC4295418 DOI: 10.1186/s13073-014-0114-2] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The availability of genome sequences obtained using next-generation sequencing (NGS) has revolutionized the field of infectious diseases. Indeed, more than 38,000 bacterial and 5,000 viral genomes have been sequenced to date, including representatives of all significant human pathogens. These tremendous amounts of data have not only enabled advances in fundamental biology, helping to understand the pathogenesis of microorganisms and their genomic evolution, but have also had implications for clinical microbiology. Here, we first review the current achievements of genomics in the development of improved diagnostic tools, including those that are now available in the clinic, such as the design of PCR assays for the detection of microbial pathogens, virulence factors or antibiotic-resistance determinants, or the design of optimized culture media for 'unculturable' pathogens. We then review the applications of genomics to the investigation of outbreaks, either through the design of genotyping assays or the direct sequencing of the causative strains. Finally, we discuss how genomics might change clinical microbiology in the future.
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Affiliation(s)
- Pierre-Edouard Fournier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, InsermU1095, Institut hospitalo-universitaire Méditerranée-Infection, Aix-Marseille University, Faculté de Medecine, 27 Blvd Jean Moulin, Marseille, 13385, cedex 5 France
| | - Gregory Dubourg
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, InsermU1095, Institut hospitalo-universitaire Méditerranée-Infection, Aix-Marseille University, Faculté de Medecine, 27 Blvd Jean Moulin, Marseille, 13385, cedex 5 France
| | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, InsermU1095, Institut hospitalo-universitaire Méditerranée-Infection, Aix-Marseille University, Faculté de Medecine, 27 Blvd Jean Moulin, Marseille, 13385, cedex 5 France
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314
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Abstract
Recent technological innovations have ignited an explosion in virus genome sequencing that promises to fundamentally alter our understanding of viral biology and profoundly impact public health policy. Yet, any potential benefits from the billowing cloud of next generation sequence data hinge upon well implemented reference resources that facilitate the identification of sequences, aid in the assembly of sequence reads and provide reference annotation sources. The NCBI Viral Genomes Resource is a reference resource designed to bring order to this sequence shockwave and improve usability of viral sequence data. The resource can be accessed at http://www.ncbi.nlm.nih.gov/genome/viruses/ and catalogs all publicly available virus genome sequences and curates reference genome sequences. As the number of genome sequences has grown, so too have the difficulties in annotating and maintaining reference sequences. The rapid expansion of the viral sequence universe has forced a recalibration of the data model to better provide extant sequence representation and enhanced reference sequence products to serve the needs of the various viral communities. This, in turn, has placed increased emphasis on leveraging the knowledge of individual scientific communities to identify important viral sequences and develop well annotated reference virus genome sets.
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Affiliation(s)
- J Rodney Brister
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Danso Ako-Adjei
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Yiming Bao
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Olga Blinkova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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315
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Rawat A, Engelthaler DM, Driebe EM, Keim P, Foster JT. MetaGeniE: characterizing human clinical samples using deep metagenomic sequencing. PLoS One 2014; 9:e110915. [PMID: 25365329 PMCID: PMC4218713 DOI: 10.1371/journal.pone.0110915] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 09/19/2014] [Indexed: 11/19/2022] Open
Abstract
With the decreasing cost of next-generation sequencing, deep sequencing of clinical samples provides unique opportunities to understand host-associated microbial communities. Among the primary challenges of clinical metagenomic sequencing is the rapid filtering of human reads to survey for pathogens with high specificity and sensitivity. Metagenomes are inherently variable due to different microbes in the samples and their relative abundance, the size and architecture of genomes, and factors such as target DNA amounts in tissue samples (i.e. human DNA versus pathogen DNA concentration). This variation in metagenomes typically manifests in sequencing datasets as low pathogen abundance, a high number of host reads, and the presence of close relatives and complex microbial communities. In addition to these challenges posed by the composition of metagenomes, high numbers of reads generated from high-throughput deep sequencing pose immense computational challenges. Accurate identification of pathogens is confounded by individual reads mapping to multiple different reference genomes due to gene similarity in different taxa present in the community or close relatives in the reference database. Available global and local sequence aligners also vary in sensitivity, specificity, and speed of detection. The efficiency of detection of pathogens in clinical samples is largely dependent on the desired taxonomic resolution of the organisms. We have developed an efficient strategy that identifies “all against all” relationships between sequencing reads and reference genomes. Our approach allows for scaling to large reference databases and then genome reconstruction by aggregating global and local alignments, thus allowing genetic characterization of pathogens at higher taxonomic resolution. These results were consistent with strain level SNP genotyping and bacterial identification from laboratory culture.
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Affiliation(s)
- Arun Rawat
- Pathogen Genomics Division, Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
- * E-mail: (AR); (JTF)
| | - David M. Engelthaler
- Pathogen Genomics Division, Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Elizabeth M. Driebe
- Pathogen Genomics Division, Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Paul Keim
- Pathogen Genomics Division, Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Jeffrey T. Foster
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, United States of America
- * E-mail: (AR); (JTF)
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316
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Wilson MR, Naccache SN, Samayoa E, Biagtan M, Bashir H, Yu G, Salamat SM, Somasekar S, Federman S, Miller S, Sokolic R, Garabedian E, Candotti F, Buckley RH, Reed KD, Meyer TL, Seroogy CM, Galloway R, Henderson SL, Gern JE, DeRisi JL, Chiu CY. Actionable diagnosis of neuroleptospirosis by next-generation sequencing. N Engl J Med 2014; 370:2408-17. [PMID: 24896819 PMCID: PMC4134948 DOI: 10.1056/nejmoa1401268] [Citation(s) in RCA: 595] [Impact Index Per Article: 59.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A 14-year-old boy with severe combined immunodeficiency presented three times to a medical facility over a period of 4 months with fever and headache that progressed to hydrocephalus and status epilepticus necessitating a medically induced coma. Diagnostic workup including brain biopsy was unrevealing. Unbiased next-generation sequencing of the cerebrospinal fluid identified 475 of 3,063,784 sequence reads (0.016%) corresponding to leptospira infection. Clinical assays for leptospirosis were negative. Targeted antimicrobial agents were administered, and the patient was discharged home 32 days later with a status close to his premorbid condition. Polymerase-chain-reaction (PCR) and serologic testing at the Centers for Disease Control and Prevention (CDC) subsequently confirmed evidence of Leptospira santarosai infection.
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Affiliation(s)
- Michael R Wilson
- From the Departments of Biochemistry and Biophysics (M.R.W., J.L.D.), Neurology (M.R.W.), and Laboratory Medicine (S.N.N., E.S., G.Y., S.S., S.F., S.M., C.Y.C.), and the Department of Medicine, Division of Infectious Diseases (C.Y.C.), University of California, San Francisco (UCSF), and UCSF-Abbott Viral Diagnostics and Discovery Center (S.N.N., E.S., G.Y., S.S., S.F., S.M., C.Y.C.) - both in San Francisco; the Department of Medicine, Division of Allergy and Immunology (M.B., H.B., J.E.G.), and the Departments of Pathology and Laboratory Medicine (S.M.S., K.D.R.) and Pediatrics (T.L.M., C.M.S., S.L.H., J.E.G.), University of Wisconsin, Madison; the Experimental Transplantation and Immunology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD (R.S., E.G., F.C.); the Departments of Pediatrics and Immunology, Division of Allergy and Immunology, Duke University, Durham, NC (R.H.B.); and the Centers for Disease Control and Prevention, Atlanta (R.G.)
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