Viral Pathogen Detection by Metagenomics and Pan-Viral Group Polymerase Chain Reaction in Children With Pneumonia Lacking Identifiable Etiology

Details

• Alternative Title:
  J Infect Dis
• Personal Author:
  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
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• 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.
• Keywords:
  • RNA sequencing (RNA-seq)
  • metagenomics
  • pan-viral group polymerase chain reaction (PVG PCR)
  • pneumonia
  • Child, Preschool
  • Cohort Studies
  • Community-Acquired Infections
  • Humans
  • Infant
  • Infant, Newborn
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• 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/
• Volume:
  215
• Issue:
  9
• Download URL:
  https://stacks.cdc.gov/view/cdc/47721/cdc_47721_DS1.pdf
• File Type:
  [PDF - 1.06 MB]
• Collection(s):
  CDC Public Access
• Main Document Checksum:
  urn:sha256:75e495fb928badef0e8c0105aef893c98a158c7ebadd050bf6f4ff5f1e3fbc03