Viral Pathogen Detection by Metagenomics and Pan-Viral Group Polymerase Chain Reaction in Children With Pneumonia Lacking Identifiable Etiology. (31st May 2017)

• Record Type: Journal Article
• Authors: Schlaberg, Robert; Queen, Krista; Simmon, Keith; Tardif, Keith; Stockmann, Chris; Flygare, Steven; Kennedy, Brett; Voelkerding, Karl; Bramley, Anna; Zhang, Jing; Eilbeck, Karen; Yandell, Mark; Jain, Seema; Pavia, Andrew T.; Tong, Suxiang; Ampofo, Krow
• Is Part Of: Journal of infectious diseases. Volume 215:Number 9(2017:May 01)
• Page Start: 1407
• Page End: 1415
• Publication Date: 2017-05-31
• Subjects: RNA sequencing (RNA-seq) -- metagenomics -- pan-viral group polymerase chain reaction (PVG PCR) -- pneumonia.; Communicable diseases -- Periodicals; Diseases -- Causes and theories of causation -- Periodicals; Medicine -- Periodicals; Communicable Diseases -- Periodicals; Electronic journals; 616.9
• DOI: 10.1093/infdis/jix148
• Languages: English
• ISSNs: 0022-1899

Abstract

Summary: Two broad-spectrum pathogen detection methods, next-generation sequencing and pan-viral group polymerase chain reaction, detected previously missed, putative pathogens in 34% of children hospitalized with community-acquired pneumonia with no identified etiology. Abstract: Background: Community-acquired pneumonia (CAP) is a leading cause of pediatric hospitalization. Pathogen identification fails in approximately 20% of children but is critical for optimal treatment and prevention of hospital-acquired infections. We used two broad-spectrum detection strategies to identify pathogens in test-negative children with CAP and asymptomatic controls. Methods: Nasopharyngeal/oropharyngeal (NP/OP) swabs from 70 children <5 years with CAP of unknown etiology and 90 asymptomatic controls were tested by next-generation sequencing (RNA-seq) and pan viral group (PVG) PCR for 19 viral families. Association of viruses with CAP was assessed by adjusted odds ratios (aOR) and 95% confidence intervals controlling for season and age group. Results: RNA-seq/PVG PCR detected previously missed, putative pathogens in 34% of patients. Putative viral pathogens included human parainfluenza virus 4 (aOR 9.3, P = .12), human bocavirus (aOR 9.1, P < .01), Coxsackieviruses (aOR 5.1, P = .09), rhinovirus A (aOR 3.5, P = .34), and rhinovirus C (aOR 2.9, P = .57). RNA-seq was more sensitive for RNA viruses whereas PVG PCR detected more DNA viruses. Conclusions: RNA-seq and PVG PCR identified additional viruses, some known to be pathogenic, in NP/OP specimens from one-third of children hospitalized with CAP without a previously identified etiology. Both broad-range methods could be useful tools in future epidemiologic and diagnostic studies.