title: Identification of pathogens by comprehensive real-time PCR versus conventional methods in community-acquired pneumonia in Japanese adults.
abstract: 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.
authors.affiliation: a Division of Respiratory Diseases, Department of Internal Medicine , The Jikei University School of Medicine , Tokyo , Japan ;
authors.forename: Yutaka
authors.initials: Y
authors.lastname: Yoshii
authors.affiliation: a Division of Respiratory Diseases, Department of Internal Medicine , The Jikei University School of Medicine , Tokyo , Japan ;
authors.forename: Kenichiro
authors.initials: K
authors.lastname: Shimizu
authors.affiliation: b Department of Infectious Diseases , Keio University School of Medicine , Tokyo , Japan ;
authors.forename: Miyuki
authors.initials: M
authors.lastname: Morozumi
authors.affiliation: b Department of Infectious Diseases , Keio University School of Medicine , Tokyo , Japan ;
authors.forename: Naoko
authors.initials: N
authors.lastname: Chiba
authors.affiliation: b Department of Infectious Diseases , Keio University School of Medicine , Tokyo , Japan ;
authors.forename: Kimiko
authors.initials: K
authors.lastname: Ubukata
authors.affiliation: c Department of Respiratory Medicine , Respiratory Center, Toranomon Hospital , Tokyo , Japan ;
authors.forename: Hironori
authors.initials: H
authors.lastname: Uruga
authors.affiliation: c Department of Respiratory Medicine , Respiratory Center, Toranomon Hospital , Tokyo , Japan ;
authors.forename: Shigeo
authors.initials: S
authors.lastname: Hanada
authors.affiliation: a Division of Respiratory Diseases, Department of Internal Medicine , The Jikei University School of Medicine , Tokyo , Japan ;
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Wakui
authors.affiliation: a Division of Respiratory Diseases, Department of Internal Medicine , The Jikei University School of Medicine , Tokyo , Japan ;
authors.forename: Saburo
authors.initials: S
authors.lastname: Ito
authors.affiliation: a Division of Respiratory Diseases, Department of Internal Medicine , The Jikei University School of Medicine , Tokyo , Japan ;
authors.forename: Naoki
authors.initials: N
authors.lastname: Takasaka
authors.affiliation: a Division of Respiratory Diseases, Department of Internal Medicine , The Jikei University School of Medicine , Tokyo , Japan ;
authors.forename: Shunsuke
authors.initials: S
authors.lastname: Minagawa
authors.affiliation: a Division of Respiratory Diseases, Department of Internal Medicine , The Jikei University School of Medicine , Tokyo , Japan ;
authors.forename: Jun
authors.initials: J
authors.lastname: Kojima
authors.affiliation: a Division of Respiratory Diseases, Department of Internal Medicine , The Jikei University School of Medicine , Tokyo , Japan ;
authors.forename: Takanori
authors.initials: T
authors.lastname: Numata
authors.affiliation: a Division of Respiratory Diseases, Department of Internal Medicine , The Jikei University School of Medicine , Tokyo , Japan ;
authors.forename: Hiromichi
authors.initials: H
authors.lastname: Hara
authors.affiliation: a Division of Respiratory Diseases, Department of Internal Medicine , The Jikei University School of Medicine , Tokyo , Japan ;
authors.forename: Makoto
authors.initials: M
authors.lastname: Kawaishi
authors.affiliation: d Department of Respiratory Medicine , The Jikei University Daisan Hospital , Tokyo , Japan.
authors.forename: Keisuke
authors.initials: K
authors.lastname: Saito
authors.affiliation: a Division of Respiratory Diseases, Department of Internal Medicine , The Jikei University School of Medicine , Tokyo , Japan ;
authors.forename: Jun
authors.initials: J
authors.lastname: Araya
authors.affiliation: a Division of Respiratory Diseases, Department of Internal Medicine , The Jikei University School of Medicine , Tokyo , Japan ;
authors.forename: Yumi
authors.initials: Y
authors.lastname: Kaneko
authors.affiliation: a Division of Respiratory Diseases, Department of Internal Medicine , The Jikei University School of Medicine , Tokyo , Japan ;
authors.forename: Katsutoshi
authors.initials: K
authors.lastname: Nakayama
authors.affiliation: c Department of Respiratory Medicine , Respiratory Center, Toranomon Hospital , Tokyo , Japan ;
authors.forename: Kazuma
authors.initials: K
authors.lastname: Kishi
authors.affiliation: a Division of Respiratory Diseases, Department of Internal Medicine , The Jikei University School of Medicine , Tokyo , Japan ;
authors.forename: Kazuyoshi
authors.initials: K
authors.lastname: Kuwano
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D001419:Bacteria / Q000145:classification / Q000302:isolation & purification; D017714:Community-Acquired Infections / Q000175:diagnosis*; D005260:Female; D006801:Humans; D007564:Japan; D008297:Male; D008828:Microbiological Techniques / Q000379:methods*; D008875:Middle Aged; D025202:Molecular Diagnostic Techniques / Q000379:methods*; D009305:Nasopharynx / Q000382:microbiology / Q000821:virology; D011014:Pneumonia / Q000175:diagnosis*; D011446:Prospective Studies; D060888:Real-Time Polymerase Chain Reaction / Q000379:methods*; D012680:Sensitivity and Specificity; D013183:Sputum / Q000382:microbiology / Q000821:virology; D014780:Viruses / Q000145:classification / Q000302:isolation & purification
keywords: Community-acquired pneumonia; mixed infection; pneumococcal pneumonia; real-time polymerase chain reaction