title: A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples.
abstract: Unbiased next-generation sequencing (NGS) approaches enable comprehensive pathogen detection in the clinical microbiology laboratory and have numerous applications for public health surveillance, outbreak investigation, and the diagnosis of infectious diseases. However, practical deployment of the technology is hindered by the bioinformatics challenge of analyzing results accurately and in a clinically relevant timeframe. Here we describe SURPI ("sequence-based ultrarapid pathogen identification"), a computational pipeline for pathogen identification from complex metagenomic NGS data generated from clinical samples, and demonstrate use of the pipeline in the analysis of 237 clinical samples comprising more than 1.1 billion sequences. Deployable on both cloud-based and standalone servers, SURPI leverages two state-of-the-art aligners for accelerated analyses, SNAP and RAPSearch, which are as accurate as existing bioinformatics tools but orders of magnitude faster in performance. In fast mode, SURPI detects viruses and bacteria by scanning data sets of 7-500 million reads in 11 min to 5 h, while in comprehensive mode, all known microorganisms are identified, followed by de novo assembly and protein homology searches for divergent viruses in 50 min to 16 h. SURPI has also directly contributed to real-time microbial diagnosis in acutely ill patients, underscoring its potential key role in the development of unbiased NGS-based clinical assays in infectious diseases that demand rapid turnaround times.
authors.affiliation: Department of Laboratory Medicine, UCSF, San Francisco, California 94107, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California 94107, USA;
authors.forename: Samia N
authors.initials: SN
authors.lastname: Naccache
authors.affiliation: Department of Laboratory Medicine, UCSF, San Francisco, California 94107, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California 94107, USA;
authors.forename: Scot
authors.initials: S
authors.lastname: Federman
authors.affiliation: Department of Laboratory Medicine, UCSF, San Francisco, California 94107, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California 94107, USA;
authors.forename: Narayanan
authors.initials: N
authors.lastname: Veeraraghavan
authors.affiliation: Department of Computer Science, University of California, Berkeley, California 94720, USA;
authors.forename: Matei
authors.initials: M
authors.lastname: Zaharia
authors.affiliation: Department of Laboratory Medicine, UCSF, San Francisco, California 94107, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California 94107, USA;
authors.forename: Deanna
authors.initials: D
authors.lastname: Lee
authors.affiliation: Department of Laboratory Medicine, UCSF, San Francisco, California 94107, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California 94107, USA;
authors.forename: Erik
authors.initials: E
authors.lastname: Samayoa
authors.affiliation: Department of Laboratory Medicine, UCSF, San Francisco, California 94107, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California 94107, USA;
authors.forename: Jerome
authors.initials: J
authors.lastname: Bouquet
authors.affiliation: Department of Biochemistry, UCSF, San Francisco, California 94107, USA;
authors.forename: Alexander L
authors.initials: AL
authors.lastname: Greninger
authors.affiliation: Abbott Diagnostics, Abbott Park, Illinois 60064, USA;
authors.forename: Ka-Cheung
authors.initials: KC
authors.lastname: Luk
authors.affiliation: Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, California 94804, USA;
authors.forename: Barryett
authors.initials: B
authors.lastname: Enge
authors.affiliation: Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, California 94804, USA;
authors.forename: Debra A
authors.initials: DA
authors.lastname: Wadford
authors.affiliation: Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, California 94804, USA;
authors.forename: Sharon L
authors.initials: SL
authors.lastname: Messenger
authors.affiliation: Department of Laboratory Medicine, UCSF, San Francisco, California 94107, USA;
authors.forename: Gillian L
authors.initials: GL
authors.lastname: Genrich
authors.affiliation: Department of Family and Community Medicine, UCSF, San Francisco, California 94143, USA;
authors.forename: Kristen
authors.initials: K
authors.lastname: Pellegrino
authors.affiliation: Viral Emergent Diseases Unit, Centre International de Recherches Médicales de Franceville, Franceville, BP 769, Gabon;
authors.forename: Gilda
authors.initials: G
authors.lastname: Grard
authors.affiliation: Viral Emergent Diseases Unit, Centre International de Recherches Médicales de Franceville, Franceville, BP 769, Gabon;
authors.forename: Eric
authors.initials: E
authors.lastname: Leroy
authors.affiliation: Metabiota, Inc., San Francisco, California 94104, USA;
authors.forename: Bradley S
authors.initials: BS
authors.lastname: Schneider
authors.affiliation: Metabiota, Inc., San Francisco, California 94104, USA;
authors.forename: Joseph N
authors.initials: JN
authors.lastname: Fair
authors.affiliation: Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, 62260, Mexico;
authors.forename: Miguel A
authors.initials: MA
authors.lastname: Martínez
authors.affiliation: Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, 62260, Mexico;
authors.forename: Pavel
authors.initials: P
authors.lastname: Isa
authors.affiliation: Division of Infectious Diseases and International Health and the Duke Global Health Institute, Duke University Medical Center, Durham, North Carolina 27708, USA; Kilimanjaro Christian Medical Centre, Moshi, Kilimanjaro, 7393, Tanzania; Centre for International Health, University of Otago, Dunedin, 9054, New Zealand;
authors.forename: John A
authors.initials: JA
authors.lastname: Crump
authors.affiliation: Department of Biochemistry, UCSF, San Francisco, California 94107, USA;
authors.forename: Joseph L
authors.initials: JL
authors.lastname: DeRisi
authors.affiliation: Department of Laboratory Medicine, UCSF, San Francisco, California 94107, USA;
authors.forename: Taylor
authors.initials: T
authors.lastname: Sittler
authors.affiliation: Abbott Diagnostics, Abbott Park, Illinois 60064, USA;
authors.forename: John
authors.initials: J
authors.lastname: Hackett
authors.affiliation: Department of Laboratory Medicine, UCSF, San Francisco, California 94107, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California 94107, USA;
authors.forename: Steve
authors.initials: S
authors.lastname: Miller
authors.affiliation: Department of Laboratory Medicine, UCSF, San Francisco, California 94107, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California 94107, USA; Department of Medicine, Division of Infectious Diseases, UCSF, San Francisco, California 94143, USA.
authors.forename: Charles Y
authors.initials: CY
authors.lastname: Chiu
mesh_terms: D019295:Computational Biology / Q000379:methods*; D030561:Databases, Nucleic Acid; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D056186:Metagenomics / Q000379:methods*; D012372:ROC Curve; D015203:Reproducibility of Results; D012984:Software