Clinical features, diagnostics, and outcomes of patients presenting with acute respiratory illness: A retrospective cohort study of patients with and without COVID-19

Autor: Sachin J. Shah, Peter N. Barish, Priya A. Prasad, Amy Kistler, Norma Neff, Jack Kamm, Lucy M. Li, Charles Y. Chiu, Jennifer M. Babik, Margaret C. Fang, Yumiko Abe-Jones, Narges Alipanah, Francisco N. Alvarez, Olga Borisovna Botvinnik, Gloria Castaneda, Rand M. Dadasovich, Jennifer Davis, Xianding Deng, Joseph L. DeRisi, Angela M. Detweiler, Scot Federman, John Haliburton, Samantha Hao, Andrew D. Kerkhoff, G. Renuka Kumar, Katherine B. Malcolm, Sabrina A. Mann, Sandra Martinez, Rupa K. Mary, Eran Mick, Lusajo Mwakibete, Nader Najafi, Michael J. Peluso, Maira Phelps, Angela Oliveira Pisco, Kalani Ratnasiri, Luis A. Rubio, Anna Sellas, Kyla D. Sherwood, Jonathan Sheu, Natasha Spottiswoode, Michelle Tan, Guixia Yu, Kirsten Neudoerffer Kangelaris, Charles Langelier

Publikováno v: EClinicalMedicine, Vol 27, Iss , Pp 100518- (2020)

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 departmen

Externí odkaz: https://doaj.org/article/2d343b2b38d34defb7023809f69ef7d7

Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections

Autor: Paula Hayakawa, Serpa, Xianding, Deng, Mazin, Abdelghany, Emily, Crawford, Katherine, Malcolm, Saharai, Caldera, Monica, Fung, Aaron, McGeever, Katrina L, Kalantar, Amy, Lyden, Rajani, Ghale, Thomas, Deiss, Norma, Neff, Steven A, Miller, Sarah B, Doernberg, Charles Y, Chiu, Joseph L, DeRisi, Carolyn S, Calfee, Charles R, Langelier

Publikováno v: Genome medicine, vol 14, iss 1

Background Antimicrobial resistance (AMR) is rising at an alarming rate and complicating the management of infectious diseases including lower respiratory tract infections (LRTI). Metagenomic next-generation sequencing (mNGS) is a recently establishe

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::9a50c7fe92464144b030a381faa3893f
https://escholarship.org/uc/item/2nx6b55c

Fatal Case of Chronic Jamestown Canyon Virus Encephalitis Diagnosed by Metagenomic Sequencing in Patient Receiving Rituximab

Autor: Anne Piantadosi, Steve Miller, Darlene Morse, J. Erin Staples, Xianding Deng, Jana M. Ritter, Michael R. Wilson, Isaac H. Solomon, Vijay S. Ganesh, Shibani S. Mukerji, Guixia Yu, Charles Y. Chiu, Justin Linxweiler, Holly R. Hughes, Tracey A. Milligan, Pardis C. Sabeti, Carolyn V. Gould, Abigail A Mathewson

Publikováno v: Emerging infectious diseases, vol 27, iss 1
Emerging Infectious Diseases
Emerging Infectious Diseases, Vol 27, Iss 1, Pp 238-242 (2021)

A 56-year-old man receiving rituximab who had months of neurologic symptoms was found to have Jamestown Canyon virus in cerebrospinal fluid by clinical metagenomic sequencing. The patient died, and postmortem examination revealed extensive neuropatho

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::690a9ac579f948cead2449571328ca3d
https://doi.org/10.3201/eid2701.203448

Rapid pathogen detection by metagenomic next-generation sequencing of infected body fluids

Autor: Guixia Yu, Joseph L. DeRisi, Elaine Hsu, Charles Y. Chiu, Doug Stryke, Yasemin D. Sucu, Eric D. Chow, Benjamin Briggs, Marco Lee, Allan Gopez, Wei Gu, Xianding Deng, Shaun Arevalo, Hannah A. Sample, Amy C. Berger, Gurpreet Ishpuniani, Michael R. Wilson, Scot Federman, Kevin Reyes, Steve Miller, Kelsey C. Zorn, Candace Wang

Publikováno v: Nature medicine, vol 27, iss 1
Nat Med

We developed a metagenomic next-generation sequencing (mNGS) test using cell-free DNA from body fluids to identify pathogens. The performance of mNGS testing of 182 body fluids from 160 patients with acute illness was evaluated using two sequencing p

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d1960b297ae4abf07fe54e3a4f3965ce
https://doi.org/10.1038/s41591-020-1105-z

Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance

Autor: Shaun Arevalo, Jean-Jacques Muyembe-Tamfum, Guixia Yu, Asim A. Ahmed, Steve Ahuka-Mundeke, Mary A. Rodgers, Mars Stone, César González-Bonilla, Nuno R. Faria, Carole McArthur, Xianding Deng, Charles Y. Chiu, Lazare Kaptue, Zoraima Neto, Jean L. Patterson, Vijay S. Ganesh, Sneha Somasekar, Kristina Hsieh, Carlos F. Arias, Jimmy Kapetshi, Manasi Tamhankar, Nuno Taveira, Asmeeta Achari, Oliver G. Pybus, Placide Mbala-Kingebeni, Scot Federman, Shigeo Yagi, Sharon Messenger, Inês Bártolo, Nicaise Ndembi, Michael P. Busch, Debra A. Wadford, Steve Miller, Dora Mbanya, John R. Hackett, Susana López, José Esteban Muñoz-Medina, Gavin Cloherty, Joana Morais, Julien Thézé

Publikováno v: Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
Agência para a Sociedade do Conhecimento (UMIC)-FCT-Sociedade da Informação
instacron:RCAAP
Nature Microbiology
Nature Microbiology, Nature Publishing Group, 2020, ⟨10.1038/s41564-019-0637-9⟩

Metagenomic next-generation sequencing (mNGS), the shotgun sequencing of RNA and DNA from clinical samples, has proved useful for broad-spectrum pathogen detection and the genomic surveillance of viral outbreaks. An additional target enrichment step

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::b5cea654862ffd7f7b40e12f0140e022
https://doi.org/10.1038/s41564-019-0637-9