RNA-seq was also able to identify 90% of previously unknown pathogens in patients with unknown cause

The use of broad-spectrum detection methods identified pathogens in more than one-third of children hospitalized with community-acquired pneumonia without a previously identified cause.

“Pathogens vary by age but viruses are the most common cause of CAP in children less than or equal to 5 years, especially in the absence of lobar pneumonia and pleural effusion. However, a pathogen cannot be identified in 14% to 23% of children with CAP, even with extensive testing,” Robert Schlaberg, MD, MPH, from the department of pathology at the University of Utah and the ARUP Institute for Clinical and Experimental Pathology, and colleagues wrote. “More effective pathogen identification will improve our understanding of pneumonia and guide treatment and site of care decisions.”

To distinguish the pathogens in children with CAP and asymptomatic controls whose tests were negative, the researchers tested for 19 viral families in nasopharyngeal and oropharyngeal specimens using next-generation sequencing (RNA-seq) and pan viral group (PVG) PCR. Seventy children younger than 5 years of age with CAP and 90 asymptomatic controls were included in the study.

For patients diagnosed with CAP without an identified etiology, the two types of swabs could identify viruses in 34% of patients, including human parainfluenza virus 4, human bocavirus, Coxsackieviruses, rhinovirus A, and rhinovirus C. More RNA viruses were detected with RNA-seq, and PVG PCR detected more DNA viruses in patients with CAP.

Putative pathogens by RNA-seq and/or PVG PCRin children with pneumonia with no identifiable etiology


RNA-seq was also able to identify 90% of previously unknown pathogens; PVG PCR identified 57%. When human rhinoviruses and Mycoplasma pneumoniae were excluded, PVG PCR was more effective at detecting viruses (78%).

“Data from our proof of concept study of upper respiratory specimens suggest that RNA-seq and PVG PCR enable more comprehensive pathogen detection compared with virus-specific, real-time PCR–based tests,” the researchers wrote. “While specimens from the upper respiratory can be collected without invasive procedure, they are most useful for identifying viral infections and have limited utility in testing for bacterial pneumonia.” – by Katherine Bortz

Schlaberg R, Queen K, Simmon K, Tardif K, Stockmann C, Flygare S, Kennedy B, Voelkerding K, Bramley A, Zhang J, Eilbeck K, Yandell M, Jain S, Pavia AT, Tong S, Ampofo K. (2017) Viral Pathogen Detection by Metagenomics and Pan Viral Group PCR in Children with Pneumonia Lacking Identifiable Etiology. J Infect Dis [Epub ahead of print]. [abstract]

Source – Healio.com

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