Selected article for: "dna rna and RNA sequencing"
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
Title: Viral Pathogen Detection by Metagenomics and Pan-Viral Group Polymerase Chain Reaction in Children With Pneumonia Lacking Identifiable Etiology
  • Cord-id: 0k8y86pf
  • Document date: 2017_5_1
    • ID: 0k8y86pf
    Snippet: 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 asymptoma
    Document: 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.

    Search related documents:
    Co phrase search for related documents
    • active replication and acute infection: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14
    • active replication and acute respiratory illness: 1
    • active replication and additional virus: 1, 2
    • active replication and logistic regression: 1
    • active replication and logistic regression model: 1
    • acute infection and additional virus: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10
    • acute infection and adjusted odd ratio: 1
    • acute infection and lobar pneumonia: 1, 2
    • acute infection and logistic regression: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25
    • acute infection and logistic regression model: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25
    • acute infection and low frequency: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11
    • acute respiratory illness and additional virus: 1, 2, 3, 4, 5
    • acute respiratory illness and logistic regression: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25
    • acute respiratory illness and logistic regression model: 1, 2, 3
    • additional band and logistic regression: 1
    • additional band and logistic regression model: 1
    • additional virus and logistic regression: 1
    • adjusted odd ratio and logistic regression: 1, 2, 3, 4, 5
    • adjusted odd ratio and logistic regression model: 1, 2