title: Application of broad-spectrum, sequence-based pathogen identification in an urban population.
abstract: A broad spectrum detection platform that provides sequence level resolution of target regions would have a significant impact in public health, case management, and means of expanding our understanding of the etiology of diseases. A previously developed respiratory pathogen microarray (RPM v.1) demonstrated the capability of this platform for this purpose. This newly developed RPM v.1 was used to analyze 424 well-characterized nasal wash specimens from patients presenting with febrile respiratory illness in the Washington, D. C. metropolitan region. For each specimen, the RPM v.1 results were compared against composite reference assay (viral and bacterial culture and, where appropriate, RT-PCR/PCR) results. Across this panel, the RPM assay showed >or=98% overall agreement for all the organisms detected compared with reference methods. Additionally, the RPM v.1 results provide sequence information which allowed phylogenetic classification of circulating influenza A viruses in approximately 250 clinical specimens, and allowed monitoring the genetic variation as well as antigenic variability prediction. Multiple pathogens (2-4) were detected in 58 specimens (13.7%) with notably increased abundances of respiratory colonizers (esp. S. pneumoniae) during viral infection. This first-ever comparison of a broad-spectrum viral and bacterial identification technology of this type against a large battery of conventional "gold standard" assays confirms the utility of the approach for both medical surveillance and investigations of complex etiologies of illness caused by respiratory co-infections.
authors.affiliation: Center for Bio/Molecular Science and Engineering, Code 6900, Naval Research Laboratory, Washington, DC, United States of America. baochuan.lin@nrl.navy.mil
authors.forename: Baochuan
authors.initials: B
authors.lastname: Lin
authors.forename: Anthony P
authors.initials: AP
authors.lastname: Malanoski
authors.forename: Zheng
authors.initials: Z
authors.lastname: Wang
authors.forename: Kate M
authors.initials: KM
authors.lastname: Blaney
authors.forename: Adam G
authors.initials: AG
authors.lastname: Ligler
authors.forename: Robb K
authors.initials: RK
authors.lastname: Rowley
authors.forename: Eric H
authors.initials: EH
authors.lastname: Hanson
authors.forename: Erik
authors.initials: E
authors.lastname: von Rosenvinge
authors.forename: Frances S
authors.initials: FS
authors.lastname: Ligler
authors.forename: Anne W
authors.initials: AW
authors.lastname: Kusterbeck
authors.forename: David
authors.initials: D
authors.lastname: Metzgar
authors.forename: Christopher P
authors.initials: CP
authors.lastname: Barrozo
authors.forename: Kevin L
authors.initials: KL
authors.lastname: Russell
authors.forename: Clark
authors.initials: C
authors.lastname: Tibbetts
authors.forename: Joel M
authors.initials: JM
authors.lastname: Schnur
authors.forename: David A
authors.initials: DA
authors.lastname: Stenger
mesh_terms: D001419:Bacteria / Q000235:genetics / Q000276:immunology / Q000302:isolation & purification; D006801:Humans; D009975:Orthomyxoviridae / Q000235:genetics / Q000276:immunology / Q000302:isolation & purification; D010802:Phylogeny; D012140:Respiratory Tract Diseases / Q000382:microbiology* / Q000821:virology; D020133:Reverse Transcriptase Polymerase Chain Reaction; D014505:Urban Population