title: Pathogen profiles and molecular epidemiology of respiratory viruses in Japanese inpatients with community-acquired pneumonia.
abstract: BACKGROUND
  The etiological profile of viruses among adult patients with community-acquired pneumonia (CAP) has not been characterized yet. The aim of this study was twofold: first, investigate the pathogen profiles and the molecular epidemiology of respiratory viruses among Japanese CAP patients; and second, explore the clinical significance of viral infections.
  
  
  METHODS
  A cross-sectional observational study was conducted at Kyorin University Hospital. To identify respiratory pathogens, hospitalized CAP patients were enrolled, and reverse transcriptase-polymerase chain reaction technology was applied alongside conventional microbiological methods. Phylogenetic and pairwise distance analyses of 10 viruses were performed. CAP patients were divided into four etiological groups (virus alone, bacteria alone, co-detection of virus and bacteria, and not detected) and the clinical findings were compared.
  
  
  RESULTS
  Seventy-six patients were enrolled. Bacteria alone were detected in 39.5% (n=30) of CAP patients. Virus alone or co-detection were found in 10.5% (n=8) and 11.8% (n=9) of cases, respectively. Streptococcus pneumoniae and human metapneumovirus were the most frequently detected bacterium and virus, respectively. Phylogenetic analyses of human metapneumovirus, human rhinovirus, and human respiratory syncytial virus showed that different subgroups and genotypes might be associated with CAP. Respiratory failure was more common when a virus was detected (both virus alone and co-detection groups; n=17, 100%, p<0.05) than when a bacteria alone was detected (n=17, 56.7%).
  
  
  CONCLUSIONS
  Prevalence of respiratory virus infection in CAP inpatients was 22.3%. The detected viruses display high genetic divergence and correlate with increased respiratory failure.
authors.affiliation: Department of Respiratory Medicine, Kyorin University School of Medicine, 6-20-2 Shinkawa, Mitaka-shi, Tokyo 181-8611, Japan. Electronic address: kuraida@aol.com.
authors.forename: Daisuke
authors.initials: D
authors.lastname: Kurai
authors.affiliation: Gunma Prefectural Institute of Public Health and Environmental Science, 378 Kamioki-machi, Maebashi-shi, Gunma 371-0052, Japan. Electronic address: sasa-yosi@pref.gunma.lg.jp.
authors.forename: Yoshiko
authors.initials: Y
authors.lastname: Sasaki
authors.affiliation: Department of Respiratory Medicine, Kyorin University School of Medicine, 6-20-2 Shinkawa, Mitaka-shi, Tokyo 181-8611, Japan. Electronic address: sara@yd5.so-net.ne.jp.
authors.forename: Takeshi
authors.initials: T
authors.lastname: Saraya
authors.affiliation: Department of Respiratory Medicine, Kyorin University School of Medicine, 6-20-2 Shinkawa, Mitaka-shi, Tokyo 181-8611, Japan. Electronic address: h141@ks.kyorin-u.ac.jp.
authors.forename: Haruyuki
authors.initials: H
authors.lastname: Ishii
authors.affiliation: Gunma Prefectural Institute of Public Health and Environmental Science, 378 Kamioki-machi, Maebashi-shi, Gunma 371-0052, Japan. Electronic address: tsuka-hiro@pref.gunma.lg.jp.
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Tsukagoshi
authors.affiliation: Department of Microbiology, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama-shi, Kanagawa 236-0004, Japan. Electronic address: kkozawa-gi@umin.net.
authors.forename: Kunihisa
authors.initials: K
authors.lastname: Kozawa
authors.affiliation: Department of Microbiology, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama-shi, Kanagawa 236-0004, Japan. Electronic address: aryo@yokohama-cu.ac.jp.
authors.forename: Akihide
authors.initials: A
authors.lastname: Ryo
authors.affiliation: Takasaki City Health Center, 5-28 Takamatsu-cho, Takasaki-shi, Gunma 370-0829, Japan. Electronic address: ishioka@nih.go.jp.
authors.forename: Taisei
authors.initials: T
authors.lastname: Ishioka
authors.affiliation: Pathogen Genomics Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan. Electronic address: makokuro@niid.go.jp.
authors.forename: Makoto
authors.initials: M
authors.lastname: Kuroda
authors.affiliation: Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo 208-0011, Japan. Electronic address: oishik@nih.go.jp.
authors.forename: Kazunori
authors.initials: K
authors.lastname: Oishi
authors.affiliation: Department of Respiratory Medicine, Kyorin University School of Medicine, 6-20-2 Shinkawa, Mitaka-shi, Tokyo 181-8611, Japan. Electronic address: hajime@ks.kyorin-u.ac.jp.
authors.forename: Hajime
authors.initials: H
authors.lastname: Takizawa
authors.affiliation: Department of Microbiology, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama-shi, Kanagawa 236-0004, Japan; Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo 208-0011, Japan. Electronic address: kimhiro@nih.go.jp.
authors.forename: Hirokazu
authors.initials: H
authors.lastname: Kimura
mesh_terms: D000368:Aged; D017714:Community-Acquired Infections / Q000382:microbiology* / Q000821:virology; D003430:Cross-Sectional Studies; D005260:Female; D006801:Humans; D007297:Inpatients; D007564:Japan; D008297:Male; D008875:Middle Aged; D011014:Pneumonia / Q000382:microbiology* / Q000821:virology; D011024:Pneumonia, Viral / Q000821:virology
keywords: Community-acquired pneumonia; Metapneumovirus; Pathogen profile; Respiratory virus