Use of multiple imputation to estimate the proportion of respiratory virus detections among patients hospitalized with community-acquired pneumonia

Catherine H. Bozio, W. Dana Flanders, Lyn Finelli, Anna M. Bramley, Carrie Reed, Neel R. Gandhi, Jorge E. Vidal, Dean Erdman, Min Z. Levine, Stephen Lindstrom, Krow Ampofo, Sandra Arnold, Wesley H. Self, Derek J. Williams, Carlos G. Grijalva, Evan J. Anderson, Jonathan Mccullers, Kathryn M. Edwards, Andrew T. Pavia, Richard G. Wunderink & 1 others Seema Jain

Research output: Contribution to journalArticle

Abstract

Background: Real-time polymerase chain reaction (PCR) on respiratory specimens and serology on paired blood specimens are used to determine the etiology of respiratory illnesses for research studies. However, convalescent serology is often not collected. We used multiple imputation to assign values for missing serology results to estimate virus-specific prevalence among pediatric and adult community-acquired pneumonia hospitalizations using data from an active population-based surveillance study. Methods: Presence of adenoviruses, human metapneumovirus, influenza viruses, parainfluenza virus types 1-3, and respiratory syncytial virus was defined by positive PCR on nasopharyngeal/oropharyngeal specimens or a 4-fold rise in paired serology. We performed multiple imputation by developing a multivariable regression model for each virus using data from patients with available serology results. We calculated absolute and relative differences in the proportion of each virus detected comparing the imputed to observed (nonimputed) results. Results: Among 2222 children and 2259 adults, 98.8% and 99.5% had nasopharyngeal/oropharyngeal specimens and 43.2% and 37.5% had paired serum specimens, respectively. Imputed results increased viral etiology assignments by an absolute difference of 1.6%-4.4% and 0.8%-2.8% in children and adults, respectively; relative differences were 1.1-3.0 times higher. Conclusions: Multiple imputation can be used when serology results are missing, to refine virus-specific prevalence estimates, and these will likely increase estimates.

Original languageEnglish (US)
Article number61
JournalOpen Forum Infectious Diseases
Volume5
Issue number4
DOIs
StatePublished - Jan 1 2018

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Serology
Pneumonia
Viruses
Human parainfluenza virus 1
Human parainfluenza virus 3
Population Surveillance
Metapneumovirus
Respiratory Syncytial Viruses
Orthomyxoviridae
Adenoviridae
Human Influenza
Real-Time Polymerase Chain Reaction
Hospitalization
Pediatrics
Polymerase Chain Reaction
Serum
Research

All Science Journal Classification (ASJC) codes

  • Oncology
  • Clinical Neurology

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Use of multiple imputation to estimate the proportion of respiratory virus detections among patients hospitalized with community-acquired pneumonia. / Bozio, Catherine H.; Dana Flanders, W.; Finelli, Lyn; Bramley, Anna M.; Reed, Carrie; Gandhi, Neel R.; Vidal, Jorge E.; Erdman, Dean; Levine, Min Z.; Lindstrom, Stephen; Ampofo, Krow; Arnold, Sandra; Self, Wesley H.; Williams, Derek J.; Grijalva, Carlos G.; Anderson, Evan J.; Mccullers, Jonathan; Edwards, Kathryn M.; Pavia, Andrew T.; Wunderink, Richard G.; Jain, Seema.

In: Open Forum Infectious Diseases, Vol. 5, No. 4, 61, 01.01.2018.

Research output: Contribution to journalArticle

Bozio, CH, Dana Flanders, W, Finelli, L, Bramley, AM, Reed, C, Gandhi, NR, Vidal, JE, Erdman, D, Levine, MZ, Lindstrom, S, Ampofo, K, Arnold, S, Self, WH, Williams, DJ, Grijalva, CG, Anderson, EJ, Mccullers, J, Edwards, KM, Pavia, AT, Wunderink, RG & Jain, S 2018, 'Use of multiple imputation to estimate the proportion of respiratory virus detections among patients hospitalized with community-acquired pneumonia', Open Forum Infectious Diseases, vol. 5, no. 4, 61. https://doi.org/10.1093/ofid/ofy061
Bozio, Catherine H. ; Dana Flanders, W. ; Finelli, Lyn ; Bramley, Anna M. ; Reed, Carrie ; Gandhi, Neel R. ; Vidal, Jorge E. ; Erdman, Dean ; Levine, Min Z. ; Lindstrom, Stephen ; Ampofo, Krow ; Arnold, Sandra ; Self, Wesley H. ; Williams, Derek J. ; Grijalva, Carlos G. ; Anderson, Evan J. ; Mccullers, Jonathan ; Edwards, Kathryn M. ; Pavia, Andrew T. ; Wunderink, Richard G. ; Jain, Seema. / Use of multiple imputation to estimate the proportion of respiratory virus detections among patients hospitalized with community-acquired pneumonia. In: Open Forum Infectious Diseases. 2018 ; Vol. 5, No. 4.
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abstract = "Background: Real-time polymerase chain reaction (PCR) on respiratory specimens and serology on paired blood specimens are used to determine the etiology of respiratory illnesses for research studies. However, convalescent serology is often not collected. We used multiple imputation to assign values for missing serology results to estimate virus-specific prevalence among pediatric and adult community-acquired pneumonia hospitalizations using data from an active population-based surveillance study. Methods: Presence of adenoviruses, human metapneumovirus, influenza viruses, parainfluenza virus types 1-3, and respiratory syncytial virus was defined by positive PCR on nasopharyngeal/oropharyngeal specimens or a 4-fold rise in paired serology. We performed multiple imputation by developing a multivariable regression model for each virus using data from patients with available serology results. We calculated absolute and relative differences in the proportion of each virus detected comparing the imputed to observed (nonimputed) results. Results: Among 2222 children and 2259 adults, 98.8{\%} and 99.5{\%} had nasopharyngeal/oropharyngeal specimens and 43.2{\%} and 37.5{\%} had paired serum specimens, respectively. Imputed results increased viral etiology assignments by an absolute difference of 1.6{\%}-4.4{\%} and 0.8{\%}-2.8{\%} in children and adults, respectively; relative differences were 1.1-3.0 times higher. Conclusions: Multiple imputation can be used when serology results are missing, to refine virus-specific prevalence estimates, and these will likely increase estimates.",
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AU - Bozio, Catherine H.

AU - Dana Flanders, W.

AU - Finelli, Lyn

AU - Bramley, Anna M.

AU - Reed, Carrie

AU - Gandhi, Neel R.

AU - Vidal, Jorge E.

AU - Erdman, Dean

AU - Levine, Min Z.

AU - Lindstrom, Stephen

AU - Ampofo, Krow

AU - Arnold, Sandra

AU - Self, Wesley H.

AU - Williams, Derek J.

AU - Grijalva, Carlos G.

AU - Anderson, Evan J.

AU - Mccullers, Jonathan

AU - Edwards, Kathryn M.

AU - Pavia, Andrew T.

AU - Wunderink, Richard G.

AU - Jain, Seema

PY - 2018/1/1

Y1 - 2018/1/1

N2 - Background: Real-time polymerase chain reaction (PCR) on respiratory specimens and serology on paired blood specimens are used to determine the etiology of respiratory illnesses for research studies. However, convalescent serology is often not collected. We used multiple imputation to assign values for missing serology results to estimate virus-specific prevalence among pediatric and adult community-acquired pneumonia hospitalizations using data from an active population-based surveillance study. Methods: Presence of adenoviruses, human metapneumovirus, influenza viruses, parainfluenza virus types 1-3, and respiratory syncytial virus was defined by positive PCR on nasopharyngeal/oropharyngeal specimens or a 4-fold rise in paired serology. We performed multiple imputation by developing a multivariable regression model for each virus using data from patients with available serology results. We calculated absolute and relative differences in the proportion of each virus detected comparing the imputed to observed (nonimputed) results. Results: Among 2222 children and 2259 adults, 98.8% and 99.5% had nasopharyngeal/oropharyngeal specimens and 43.2% and 37.5% had paired serum specimens, respectively. Imputed results increased viral etiology assignments by an absolute difference of 1.6%-4.4% and 0.8%-2.8% in children and adults, respectively; relative differences were 1.1-3.0 times higher. Conclusions: Multiple imputation can be used when serology results are missing, to refine virus-specific prevalence estimates, and these will likely increase estimates.

AB - Background: Real-time polymerase chain reaction (PCR) on respiratory specimens and serology on paired blood specimens are used to determine the etiology of respiratory illnesses for research studies. However, convalescent serology is often not collected. We used multiple imputation to assign values for missing serology results to estimate virus-specific prevalence among pediatric and adult community-acquired pneumonia hospitalizations using data from an active population-based surveillance study. Methods: Presence of adenoviruses, human metapneumovirus, influenza viruses, parainfluenza virus types 1-3, and respiratory syncytial virus was defined by positive PCR on nasopharyngeal/oropharyngeal specimens or a 4-fold rise in paired serology. We performed multiple imputation by developing a multivariable regression model for each virus using data from patients with available serology results. We calculated absolute and relative differences in the proportion of each virus detected comparing the imputed to observed (nonimputed) results. Results: Among 2222 children and 2259 adults, 98.8% and 99.5% had nasopharyngeal/oropharyngeal specimens and 43.2% and 37.5% had paired serum specimens, respectively. Imputed results increased viral etiology assignments by an absolute difference of 1.6%-4.4% and 0.8%-2.8% in children and adults, respectively; relative differences were 1.1-3.0 times higher. Conclusions: Multiple imputation can be used when serology results are missing, to refine virus-specific prevalence estimates, and these will likely increase estimates.

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