Viral pathogen detection by metagenomics and pan-viral group polymerase chain reaction in children with pneumonia lacking identifiable etiology
R Schlaberg, K Queen, K Simmon… - The Journal of …, 2017 - academic.oup.com
R Schlaberg, K Queen, K Simmon, K Tardif, C Stockmann, S Flygare, B Kennedy…
The Journal of infectious diseases, 2017•academic.oup.comBackground. 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 …
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 …
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.
Oxford University Press