Details:

Alternative Title:
J Infect Dis
Personal Author:
Schlaberg, Robert ; Queen, Krista ; Simmon, Keith ; Tardif, Keith ; Stockmann, Chris ; ... More +
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 ; Less -
Description:
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.
Subject:
[+]
Article
Child, Preschool
Cohort Studies
Community-Acquired Infections
Humans
Infant
Infant, Newborn
Metagenomics
Pneumonia, Viral
Polymerase Chain Reaction
Sequence Analysis, RNA
Viruses

Source:
J Infect Dis. 215(9):1407-1415
Pubmed ID:
28368491
Pubmed Central ID:
PMC5565793
Document Type:
Journal Article ;
Funding:
CC999999/Intramural CDC HHS/United States ; T32 HL007576/HL/NHLBI NIH HHS/United States ;
CC999999/Intramural CDC HHS/United States ; T32 HL007576/HL/NHLBI NIH HHS/United States ; Less -
Collection(s):
CDC Public Access
Main Document Checksum:
[+]
urn:sha256:75e495fb928badef0e8c0105aef893c98a158c7ebadd050bf6f4ff5f1e3fbc03
File Type:

Supporting Files

• 	nihms890990f4.gif	gif
  	nihms890990f4.jpg	jpeg
  	NIHMS890990-supplement-Supplemental_figure_and_legend.pdf	pdf
  	nihms890990.nxml	xml
  	nihms890990f1.gif	gif
  	nihms890990f1.jpg	jpeg
  	nihms890990f2.gif	gif
  	nihms890990f2.jpg	jpeg
  	nihms890990f3.gif	gif
  	nihms890990f3.jpg	jpeg

More +