Details:

Alternative Title:
J Infect Dis
Publisher's site:
http://dx.doi.org/10.1093/infdis/jix148
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
Pan-viral Group Polymerase Chain Reaction (PVG PCR)
Pneumonia
Pneumonia, Viral
Polymerase Chain Reaction
RNA Sequencing (RNA-seq)
Sequence Analysis, RNA
Viruses
Metagenomics

Source:
J Infect Dis. 215(9):1407-1415
Pubmed ID:
28368491
Pubmed Central ID:
PMC5565793
Document Type:
Journal Article
Funding:
CC999999/ImCDC/Intramural CDC HHSUnited States/ ; T32 HL007576/HL/NHLBI NIH HHSUnited States/ ; UL1 TR001067/TR/NCATS NIH HHSUnited States/
CC999999/ImCDC/Intramural CDC HHSUnited States/ ; T32 HL007576/HL/NHLBI NIH HHSUnited States/ ; UL1 TR001067/TR/NCATS NIH HHSUnited States/ Less -
Collection(s):
CDC Public Access
Main Document Checksum:
[+]
urn:sha256:75e495fb928badef0e8c0105aef893c98a158c7ebadd050bf6f4ff5f1e3fbc03
File Type:

Supporting Files

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