The epidemiology and estimated etiology of pathogens detected from the upper respiratory tract of adults with severe acute respiratory infections in multiple countries, 2014-2015

PLoS One. 2020 Oct 19;15(10):e0240309. doi: 10.1371/journal.pone.0240309. eCollection 2020.


Introduction: Etiology studies of severe acute respiratory infections (SARI) in adults are limited. We studied potential etiologies of SARI among adults in six countries using multi-pathogen diagnostics.

Methods: We enrolled both adults with SARI (acute respiratory illness onset with fever and cough requiring hospitalization) and asymptomatic adults (adults hospitalized with non-infectious illnesses, non-household members accompanying SARI patients, adults enrolled from outpatient departments, and community members) in each country. Demographics, clinical data, and nasopharyngeal and oropharyngeal specimens were collected from both SARI patients and asymptomatic adults. Specimens were tested for presence of 29 pathogens utilizing the Taqman® Array Card platform. We applied a non-parametric Bayesian regression extension of a partially latent class model approach to estimate proportions of SARI caused by specific pathogens.

Results: We enrolled 2,388 SARI patients and 1,135 asymptomatic adults from October 2013 through October 2015. We detected ≥1 pathogen in 76% of SARI patients and 67% of asymptomatic adults. Haemophilus influenzae and Streptococcus pneumoniae were most commonly detected (≥23% of SARI patients and asymptomatic adults). Through modeling, etiology was attributed to a pathogen in most SARI patients (range among countries: 57.3-93.2%); pathogens commonly attributed to SARI etiology included influenza A (14.4-54.4%), influenza B (1.9-19.1%), rhino/enterovirus (1.8-42.6%), and RSV (3.6-14.6%).

Conclusions: Use of multi-pathogen diagnostics and modeling enabled attribution of etiology in most adult SARI patients, despite frequent detection of multiple pathogens in the upper respiratory tract. Seasonal flu vaccination and development of RSV vaccine would likely reduce the burden of SARI in these populations.

Publication types

  • Multicenter Study
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Adult
  • Aged
  • Asymptomatic Diseases / epidemiology
  • Bacteria / classification*
  • Bacteria / genetics
  • Bacteria / isolation & purification
  • Bangladesh
  • Bayes Theorem
  • Female
  • Guatemala
  • Humans
  • Male
  • Middle Aged
  • Models, Theoretical
  • Molecular Epidemiology
  • Nasopharynx / microbiology
  • Oropharynx / microbiology
  • Polymerase Chain Reaction
  • Respiratory Tract Infections / epidemiology*
  • Respiratory Tract Infections / microbiology*
  • Viruses / classification*
  • Viruses / genetics
  • Viruses / isolation & purification
  • Young Adult

Grants and funding

Funding was provided by the Centers for Disease Control and Prevention.