Study design, patient enrolment, and data collection
The Adult Pneumonia Study Group-Japan (APSG-J) conducted multicentre prospective hospital-based surveillance for community-onset pneumonia at four community-based hospitals in Japan. In our previous paper, the burden and aetiology of adult pneumonia were reported based on the data and clinical samples collected during the 1st phase of the study (September 2011 to January 2013) [9]. The current study included all data and samples collected during the whole study period (September 2011 to August 2014). Details of the study settings and enrolment criteria were described previously [9]. In brief, all outpatients and inpatients were screened by hospital physicians, and eligible patients were identified using a standardized case definition: patients aged ≥15 years with respiratory symptoms compatible with pneumonia and new infiltrative shadows on chest X-rays or computed tomography scans. Clinical information was collected from patients and medical charts using a standardized data collection form.
Microbiological test
Sputum, blood, and urine samples were collected at the time of diagnosis. Gram staining, sputum culture, and blood culture were performed on site. Sputum samples were further tested by in-house multiplex polymerase chain reaction (PCR) assays to identify viral and bacterial pathogens at the Institute of Tropical Medicine, Nagasaki University. Thirteen viral pathogens (influenza A virus, influenza B virus, RSV, human metapneumovirus [hMPV], human parainfluenza virus [HPIV] type 1–4, HRV, HCoV 229E/OC43, human adenovirus [HAdV], and human bocavirus [HBoV]) and six bacterial pathogens (Streptococcus pneumoniae, Haemophilus influenzae, Moraxella Catarrhalis, Mycoplasma pneumoniae, Chlamydophila pneumoniae, and Legionella pneumophila) were tested using multiplex PCR assays. Details about the primers and PCR methods used have been described previously [10, 11]. Urinary antigen testing was performed for the detection of S. pneumoniae and L. pneumophila (Binax NOW Streptococcus Pneumoniae, Binax NOW Legionella; Alere Inc., Waltham, MA, USA).
Definitions of variables
Diagnosis of viral infection was made according to PCR results. Bacterial infection was diagnosed when any of the following criteria were fulfilled: 1) culture yielded pathogenic bacteria from microscopically purulent sputum samples (i.e., Geckler’s classification groups 4 and 5) or normally sterile site samples; 2) PCR assays were positive for bacterial DNA in microscopically purulent sputum samples; or 3) urinary antigen tests showed a positive result.
Patients were categorized into four age groups: 15–64 years, 65–74 years, 75–84 years, and ≥85 years. Patients’ disability status was evaluated using the Eastern Cooperative Oncology Group Performance Status (PS) score [12]. Pneumonia severity was assessed using the CURB65 scoring system [13]. To estimate the effect on pneumonia mortality, viruses were categorized into four groups: 1) HRV; 2) influenza A and B viruses; 3) paramyxoviruses (RSV, hMPV, and PIV type 1–4); and 4) other viruses (HAdV, HBoV, and HCoV).
We divided patients into three groups according to comorbidity status: 1) patients without comorbidity; 2) patients with chronic respiratory disease; and 3) patients with comorbidities other than chronic respiratory disease (i.e., other comorbidities). Chronic respiratory disease included bronchial asthma, chronic obstructive pulmonary disease (COPD), interstitial pneumonia, pneumoconiosis, and bronchiectasis. Other comorbidities included diabetes mellitus, cerebrovascular disease, dementia, neuromuscular disease, cardiac failure, ischaemic heart disease, collagen disease, malignancy, renal disease, and liver disease. Patients were considered to have aspiration risk factors when they had any of the following factors: episodes of aspiration, the presence of dysphagia, consciousness disturbances, neuromuscular diseases, cerebrovascular diseases, tube feeding, and bedridden status [14].
The in-hospital death was defined as any death occurred during the hospitalization. During the first year of study, we followed up our patients after the enrolment and confirmed that no outpatient had died within 30 days of enrolment. We therefore considered the in-hospital death as a good marker of short-term mortality in pneumonia patients regardless of their hospitalization status.
Statistical analysis
Patients were categorized according to their comorbidity status (i.e., patients without comorbidity, with chronic respiratory disease, or with other comorbidities) and compared using chi-squared tests. Viral and bacterial infection status were compared by age group and comorbidity status using chi-squared tests, Fisher’s exact tests, and chi-squared tests for trend. In-hospital mortality rates were calculated by viral and bacterial infection status and compared with those of the virus-negative group. The effects of viral infection on in-hospital mortality were expressed as risk ratios with 95% confidence intervals (CI) and estimated using Poisson regression models with robust standard errors. Age, study site, comorbidity status, duration of symptoms, month of diagnosis, antibiotic use, and presence of bacteria were considered potential confounders based on prior knowledge and were included in the multiple regression models. For patients whose onset of symptoms were unknown (<5%), we coded those missing values as “unknown” and included all patients in our analysis. The data were analysed using STATA version 13 (STATA Corp., College Station, TX, USA).
Ethics
This study was approved by the institutional review boards (IRBs) of the Institute of Tropical Medicine, Nagasaki University, Ebetsu City Hospital, Kameda Medical Center, Chikamori Hospital, and Juzenkai Hospital. The requirement for obtaining written consent from all participants was waived by all IRBs because of the study’s observational nature without any deviation from the current medical practice. Anonymized data were used for the analyses.
