Identification of pathogens by comprehensive real-time PCR versus conventional methods in community-acquired pneumonia in Japanese adults

Yutaka Yoshii, Kenichiro Shimizu, Miyuki Morozumi, Naoko Chiba, Kimiko Ubukata, Hironori Uruga, Shigeo Hanada, Hiroshi Wakui, Saburo Ito, Naoki Takasaka, Shunsuke Minagawa, Jun Kojima, Takanori Numata, Hiromichi Hara, Makoto Kawaishi, Keisuke Saito, Jun Araya, Yumi Kaneko, Katsutoshi Nakayama, Kazuma KishiKazuyoshi Kuwano

Research output: Contribution to journalArticlepeer-review

19 Citations (Scopus)


Background: Community-acquired pneumonia (CAP) has high morbidity and mortality. Unfortunately, the pathogen detection rate using conventional culture methods is relatively low. We compared comprehensive real-time polymerase chain reaction (real-time PCR) analysis of nasopharyngeal swab specimens (NPS) and sputum samples against conventional methods for ability to detect causative pathogens of CAP. Methods: We prospectively enrolled adult CAP patients, including those with prior antibiotic use, from December 2012 to May 2014. For each patient, causative pathogens were investigated conventionally and by real-time PCR that can identify 6 bacterial and 11 viral pathogens. Results: Patients numbered 92 (mean age, 63 years; 59 male), including 30 (33%) with prior antibiotic use. Considering all patients, identification of causative pathogens by real-time PCR was significantly more frequent than by conventional methods in all patients (72% vs. 57%, p = 0.018). In patients with prior antibiotic use, identification rates also differed significantly (PCR, 77%; conventional, 50%; p = 0.027). Mixed infections were more frequent according to real-time PCR than conventional methods (26% vs. 4%, p < 0.001). By the real-time PCR, Streptococcus pneumoniae was most frequently identified (38%) as a causative pathogen, followed by Haemophilus influenzae (37%) and Mycoplasma pneumoniae (5%). PCR also identified viral pathogens (21%), with sensitivity enhanced by simultaneous examination of both NPS and sputum samples rather than only NPS samples. Conclusions: Real-time PCR of NPS and sputum samples could better identify bacterial and viral pathogens in CAP than conventional methods, both overall and in patients with prior antibiotic treatment.

Original languageEnglish
Pages (from-to)782-788
Number of pages7
JournalInfectious Diseases
Issue number11-12
Publication statusPublished - 2016 Dec 1


  • Community-acquired pneumonia
  • mixed infection
  • pneumococcal pneumonia
  • real-time polymerase chain reaction

ASJC Scopus subject areas

  • Immunology and Microbiology(all)
  • Microbiology (medical)
  • Infectious Diseases


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