key: cord-0947303-5s6b22o1
authors: Qin, Tian; Zhou, Haijian; Ren, Hongyu; Meng, Jiantong; Du, Yinju; Mahemut, Mahemut; Wang, Peng; Luo, Nana; Tian, Fei; Li, Ming; Zhou, Pu; Li, Fang; Duan, Pengyuan; Li, Yinan; Zhao, Na; Yuan, Qiwu; Zhang, Jinzhong; Cheng, Lihong; Luo, Longze; Fang, Ming; Huang, Xin; Gu, Changguo; Zhou, Huifang; Yang, Min; Lu, Shan; Jiang, Xiangkun; Lin, Hualiang; Tian, Huaiyu; Kan, Biao; Xu, Jianguo
title: Incidence, aetiology, and enviromental risk factors of community-acquired pneumonia requiring hospitalization in China: a 3-year, prospective, age-stratified, multi-centre case-control study
date: 2021-10-06
journal: Open Forum Infect Dis
DOI: 10.1093/ofid/ofab499
sha: f010314f92c541727cd4eaa62a9e70a4ecca03b0
doc_id: 947303
cord_uid: 5s6b22o1

BACKGROUND: Community-acquired pneumonia (CAP) is a leading infectious cause of hospitalisation and death worldwide. The knowledge about the incidence and aetiology of CAP in China was fragmented. METHODS: A multicenter study performed at four hospitals in four regions in China and clinical samples from CAP patients were collected and used for pathogen identification from July 2016 to June 2019. RESULTS: A total of 1,674 patients were enrolled and the average annual incidence of hospitalized CAP was 18.7 cases per 10,000 people (95% confidence interval 18.5–19.0). The most common viral and bacterial agents found in patients were respiratory syncytial virus (19.2%) and Streptococcus pneumoniae (9.3%). The co-infections percentage was 13.8%. Pathogen distribution displayed variations within age groups, and seasonal and regional differences. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was not detected. Respiratory virus detection was significantly positively correlated with air pollutants, including PM(2.5), PM(10), NO(2) and SO(2); and significantly negatively correlated with ambient temperature and O(3) content; bacteria detection was opposite. CONCLUSION: The hospitalized CAP incidence in China was higher than previously known. CAP etiology showed differences in age, seasons, regions, and respiratory viruses were detected at a higher rate than bacterial infection overall. Air pollutants and temperature have influence on the detection of pathogens.

Following the Coronavirus Disease 2019 (COVID-19) outbreak, community-acquired pneumonia (CAP) has remained a serious challenge for infectious disease prevention and control, and has caused high morbidity and treatment costs worldwide 1, 2 . Although the diagnosis and treatment of CAP have been improved over the past two decades, it has remained a health burden 3, 4 . Even in the United States, Canada, and other countries with high levels of medical care, CAP is a leading cause of death among infectious diseases 3 .

The etiology of CAP is difficult to identify using clinical manifestations, imaging results, and routine laboratory test results. The distribution of major pathogens may vary from country to country. Recently, most of the data have been reported from western countries [5] [6] [7] [8] . However, the last surveys of the etiology of CAP in China were carried out approximately 20 years ago 9,10 . To gain additional insight into the epidemiology of CAP in China, estimated incidence and contemporary etiologic studies of CAP in the Chinese population are required.

The investigation of the etiology of CAP is helpful to guide the use of anti-infective drugs and vaccines, the formulation and implementation of respiratory infection prevention and control measures, so as to reduce the spread of respiratory viruses and bacteria. This will be an important part of global respiratory infection prevention and control as frequent international travel of Chinese population. Thus, we performed a prospective observational study of CAP etiology and estimated the incidence of CAP in China.

A c c e p t e d M a n u s c r i p t 6 We conducted a prospective observational study at four hospitals in four cities located in the east, south, west, and northwest regions of China, including Chengdu, Liaocheng, Dali and Kashi (see Supplementary Figure 1 ). Three different cohorts were defined. The first cohort was conducted in Chengdu across all age groups from July 2016 to June 2019. The second cohort was conducted for a 0 to 4-year-old age group in Chengdu and Liaocheng from July 2017 to June 2019. The third cohort included a ≥50-year-old age group in Chengdu, Dali, and Kashi from July 2017 to June 2019 (see Supplementary Figure 2 Unified technical training, monthly teleconferences, enrollment reports, data audits, and annual study-site visits were conducted to ensure uniform procedures were being followed at the study sites. See the methods within the supplementary materials for detailed descriptions of study design, rationale, and overall conduct.

The criteria for a diagnosis of CAP were reported in the respiratory branch of the Chinese Medical Association Guidelines on the diagnosis and treatment of CAP 11 . A clinical diagnosis of CAP was established if a patient had any of the following 1-4 symptoms plus number 5: (1) symptoms of cough, expectoration, or original respiratory diseases that were recently aggravated, with A c c e p t e d M a n u s c r i p t 7 the appearance of purulent sputum, (2) fever, (3) signs of pulmonary consolidation and/or moist rales, (4) white blood cell count > 10 × 10 9 / L or < 4 × 10 9 / L, and (5) X-ray examination of the chest that showed an infiltrative shadow or interstitial change. Patients were excluded if they had been recently hospitalized (<28 days for immunocompetent patients and <90 days for immunosuppressed patients), had been enrolled in other clinical investigation studies within the previous 28 days, or had a clear alternative diagnosis, including tuberculosis, lung tumors, noninfective pulmonary interstitial disease, pulmonary oedema, atelectasis, pulmonary embolism, pulmonary eosinophilic infiltration, and / or pulmonary vasculitis.

The number of CAP patients with radiographic evidence in hospitals was found to be very large. Therefore, we selected one day (the 15th of each month) to collect patient samples that were included in this project. For example, in Wenjiang, Chengdu, there were 28,030 CAP patients with radiographic evidence between July 2016 and June 2019, and 900 cases were included for pathogen detection in this study.

The study was approved by the ethics committee of the National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention. Oral consent process by using a researcher record of oral consent template before providing information on the study, including sex, age, occupation, and date of onset. Only routinely obtained microbiology results were used and diagnostic strategy was not determined by the study design.

A c c e p t e d M a n u s c r i p t 8

Specimen collection and bacterial culture were performed according to standard methods 12 . Blood and urine samples were obtained from the patients as soon as possible after case presentation. In the case of patients with a productive cough, sputum was obtained. Pleural fluid, endotracheal aspirates, and bronchoalveolar lavage samples obtained for clinical care were analyzed. Only specimens obtained within 72 hours before or after admission were considered. Urinary antigen testing was performed for the detection of Legionella pneumophila and Streptococcus pneumoniae (BinaxNOW, Alere). A c c e p t e d M a n u s c r i p t 9 pneumoniae, C. pneumoniae or L. pneumophila were detected in sputum via PCR assay; or if L. pneumophila or S. pneumoniae were detected in urine via antigen detection.

A viral pathogen was determined to be present if viruses were detected in sputum, pleural fluid, endotracheal aspirates, or bronchoalveolar lavage samples via PCR assay.

In summer 2017 and winter 2018, we enrolled a sample of asymptomatic patients from Zigong, a city around Chengdu. Oropharyngeal swabs were obtained to assess the prevalence of respiratory pathogens among asymptomatic children and adults. Exclusion criteria were the same as those for patients with pneumonia, except that control patients were excluded if they exhibited fever or respiratory symptoms within 14 days before or after enrollment (based on information obtained during sample collection or if patients had received a live attenuated influenza vaccination within seven days prior to enrollment).

We collected ambient air pollutants data from Chengdu for the entire study period from China's 

The differences in detection rates between different groups, including age and seasons, were compared using the 2 test with the row × column table (McNemar's test). Differences were considered statistically significant if P-values were < 0.05.

Liner regression methods were fitted to explore the association of environmental factors with the positive rate of bacterial infection and virus infection during the same period 22 . The correlation coefficients with p-values were used to assess the associations. Generalized additive models were used to derive the estimates adjusted for environmental factors.

Estimated annual incidence rates of hospitalization for CAP according to year of study and detected pathogen were analyzed based on 5,000,000 person/years of observation. Pathogenspecific incidence is calculated for the patients who showed radiographic evidence of pneumonia during the incidence period.

The incidence rate of CAP is estimated by the data of this study. The positive rate, age and seasonal differences of each pathogen were counted and analyzed. Related environmental factors of CAP pathogen distribution were assessed.

A c c e p t e d M a n u s c r i p t 11

We conducted a multicenter study, and a total of 1674 patients were enrolled, including 900 patients spanning all ages in Chengdu (first cohort), 383 patients less than 5 year old in Liaocheng (second cohort), and 129 and 262 patients greater than 50 year old in Dali and Kashi, respectively (third cohort) (see Supplementary Table 1 ). All patients showed radiographic evidence of pneumonia.

Between July 2016 and June 2019, 28,030 CAP patients with radiographic evidence were diagnosed in Chengdu Fifth People's Hospital located in the Wenjiang District of Chengdu City, which provides medical services to approximately 526,000 people in the surrounding area (see Supplementary   Table 2 ). All patients were asked if they have symptoms of cough, expectoration, or original respiratory diseases that were recently aggravated, with the appearance of purulent sputum, and tested for fever, signs of pulmonary consolidation and moist rales, white blood cell count, X-ray examination of the chest and tuberculosis, lung tumors, noninfective pulmonary interstitial disease, pulmonary oedema, atelectasis, pulmonary embolism, pulmonary eosinophilic infiltration, and pulmonary vasculitis, and then diagnose CAP according to the judgment criteria. During 2016-2019, 59.8% (538/900) of the enrolled patients were male, and the median age was 23.4 years old (interquartile range of 1 to 54.0). The average annual incidence of hospitalized CAP was 177.6 cases per 10,000 people (95% CI 100.0, 250.0). Pathogen-specific incidences ranged between 0.1 (0.0-0.1) to 10.8 (10.5-11.0) per 10,000 people (see Supplementary Table 3) .

A c c e p t e d M a n u s c r i p t 12 Overall, pathogens were identified in 58.8% (528/900) of patients in Chengdu (Figure 1 ). Single-viral and single-bacterial pathogens were detected in 30.7% and 14.3% of patients, respectively, whereas multiple pathogen co-detection was found in 13.8% of patients, including viral-bacterial (6.8%), viralviral (6.2%), and bacterial-bacterial (0.8%). When mono-infections and co-infection were considered at the same time, respiratory syncytial virus was the major cause of CAP (19.2% of patients), followed by S. pneumoniae (9.3%), coronavirus (8.3%), human rhinovirus (7. The etiology differed across ages ( Figure 2) . Overall, pathogen detection rates in the lower age groups were higher than the older age groups, including single viral and bacterial infection as well as co-infections with multiple pathogens (P < 0.05). In the younger age groups (0-4 years old and 5-17 years old), 49.6% and 54.9% of patients, respectively, showed at least one pathogen versus 40.0% and 36.6% in the older age groups (18-49 years old and ≥ 50 years old), respectively. Respiratory syncytial virus was the major etiology in the 0-4, 18-49, and ≥50 age groups, and coronavirus in the 5-17 age group. S. pneumoniae, human rhinovirus, M. pneumoniae, and influenza virus were the second-most frequently detected agents in the 0-4, 5-17, 18-49, and ≥50-year age groups, respectively ( Figure 2) . The older the age group, the lower the detection rate of respiratory syncytial virus (27.36%, 12.68%, 9.33%, and 7.32% in the 0-4, 5-17, 18-49, and ≥50-year age groups, respectively), and the higher the detection rate of influenza virus (0.98%, 1.41%, 2.67%, and 5.69% in the 0-4, 5-17, 18-49, and ≥50-year age groups, respectively) ( Figure 2, Supplementary Table 4) .

A c c e p t e d M a n u s c r i p t 13 The dominant pathogens found in CAP in Chengdu were not observed to differ in years, however seasonal differences were detected. Respiratory syncytial virus was the most frequently detected viral agent across all three epidemic years, and S. pneumoniae was the most frequently identified bacterial pathogen across all three epidemic years ( Figure 3A 

Among the 595 asymptomatic control patients, 144 (24.2%) were 0 to 4 years of age, 271 (45.6%) were 5 to 17 years of age, 86 (14.5%) were 18 to 49 years of age, and 94 (15.8%) were ≥50 years of age (see Supplementary Table 4 ). Among asymptomatic control patients, 2.6% and 1.2% of the 5-17-year-old and 18-49-year-old groups, respectively, tested positive for M. pneumoniae, which was significantly lower than the proportion of CAP patients within the same age groups. Human rhinovirus was detected in 2.1% and 0.7% of 0-4-year-olds and 5-17-year-old control groups, respectively, which was significantly lower than the proportion of CAP patients within the same age groups. No other pathogens were detected among the controls.

Based on correlation analysis, the total detection rate of virus was significantly positively correlated with the four kinds of air pollutants, including PM 2.5 , PM 10 , NO 2 and SO 2 , and significantly negatively correlated with ambient temperature and O 3 content; bacteria detection was opposite ( Table 6 ). The detection rates of bacteria (0.76%) increased and virus (1.11%) decreased when the temperature increased by 1℃ (see Supplementary Table 6 ).

In the present study, we revealed the characteristics of CAP etiology in the Chinese population and the results demonstrate the differences in pathogens between regions and age groups. The detection rates of respiratory syncytial virus in younger age groups were higher than in older age groups. Therefore, respiratory syncytial virus is the key to reduce the CAP incidence in children. However, older age groups showed higher detection rates of influenza virus, which underscores the need for improving influenza vaccine uptake as well as vaccine effectiveness in adults and the elderly.

Our study found that S. pneumoniae, H. influenzae, M. pneumoniae, and M. catarrhalis were the main bacterial pathogens present in the enrolled patients, which was consistent with the results of two previous studies carried out in 2003-2004 and 2004-2005 , and was supported by a small-scale survey data collected during the same period 23, 24 . S. pneumoniae is a major bacterial pathogen that causes CAP worldwide 5, 6, 25 . Pneumococcal vaccination should be focused on children and the elderly, as the detection rates of S. pneumoniae in these two age A c c e p t e d M a n u s c r i p t 16 groups were higher than in middle-aged groups. In our previous investigation, 3.85% of patients with severe pneumonia, due to unknown causes, tested positive for the L. pneumophila serogroup 1 antigen 26 . In the present study, Legionella was detected in three cities, suggesting that Legionnaires' disease may be an underestimated disease in China.

Previous studies on the relationship between respiratory viral infectious diseases and temperature have shown that increasing temperature can reduce the ability to spread both SARS and influenza, but not COVID-19 22, 27, 28 . In the present study, increased temperature reduced the detection rate of viruses but increased the detection rate of bacteria. These findings suggest the occurrence of two types of infectious diseases during seasonal changes.

A previous study presented a hypothesis regarding why warmer seasons reduce the spread of viruses, which included higher vitamin D levels that may result in better immune responses 29 .

The results of this study suggest that low temperature is helpful for virus survival and transmission, while bacteria prefer higher temperature, which is consistent with the difference of temperature sensitivity between these two types of pathogens.

Air pollution, including PM 2.5 , PM 10 , NO 2, and SO 2 , have a serious impact on human health and increase the risk of hospital admission due to respiratory diseases 29 . However, in the present study, the total detection rate of bacteria was significantly negatively correlated with air pollutants, which may be related to the fact that generally people wear masks during high pollution days. This result is supported by our previous data that showed wearing masks could reduce bacterial infections from sources of air pollution 30 . One limitation of the present study was that no data on the incidence rates of CAP in different age groups were obtained.

However, the overall incidence rate was similar to the incidence rate reported in the United A c c e p t e d M a n u s c r i p t 17 States 5,6 . This limitation might be attributed to the year and region that the analyses were performed, differences in the populations studied, and the differing criteria of CAP, as defined by different studies. Another limitation was that the detection methods of this study covered a limited number of CAP pathogens. Endemic fungal diseases (such as Histoplasmosis), melioidosis and other pathogens (such as Q fever) that are common in China (or at least in some regions), were not within the scope of the study.. In the future study, more advanced detection methods should be included, such as broad-spectrum pathogen screening technologies, metagenomics next-generation sequencing technology and so on.

In conclusion, our study has provided a better understanding of the incidence, etiology, and related environmental factors of CAP in China, which is conducive to the clinical diagnosis and treatment, epidemiological monitoring, disease burden assessment, prevention, and control of CAP. In the future, it will be necessary to carry out nationwide routine monitoring to grasp the incidence and pathogenic changes of CAP in real time, followed by targeted prevention and control measures. 

Community-acquired pneumonia

The influence of age and gender on the population-based incidence of community-acquired pneumonia caused by different microbial pathogens

Global, regional, and national disability-adjusted life years (DALYs) for 306 diseases and injuries and healthy life expectancy (HALE) for 188 countries, 1990-2013: Quantifying the epidemiological transition

Mortality differences among hospitalized patients with community-acquired pneumonia in three world regions: Results from the Community-Acquired Pneumonia Organization (CAPO) International Cohort Study

Community-Acquired Pneumonia Requiring Hospitalization among U.S. Adults

Community-acquired pneumonia requiring hospitalization among U.S. children

The etiology of community-acquired pneumonia in Australia: why penicillin plus doxycycline or a macrolide is the most appropriate therapy

Community-acquired pneumonia in outpatients: aetiology and outcomes

Clinical Practice Guidelines by the Chinese Thoracic Society, Chinese Medical Association

Manual of Clinical Microbiology 11th Edition

World Health Organization. CDC protocol of realtime RTPCR for swine influenza A (H1N1)

An economical tandem multiplex real-time PCR technique for the detection of a comprehensive range of respiratory pathogens

Simultaneous Detection, Subgrouping, and Quantitation of Respiratory Syncytial Virus A and B by Real-Time PCR

Human coronavirus infections in rural Thailand: a comprehensive study using real-time reverse-transcription polymerase chain reaction assays

Real-Time PCR Assays for Detection of Bocavirus in Human Specimens

Real-Time Reverse Transcriptase PCR Assay for Detection of Human Metapneumoviruses from All Known Genetic Lineages

Simultaneous Detection of 13 Key Bacterial Respiratory Pathogens by Combination of Multiplex PCR and Capillary Electrophoresis

No association of COVID-19 transmission with temperature or UV radiation in Chinese cities

The incidence and etiology of community-acquired pneumonia in fever outpatients

Etiological analysis and predictive diagnostic model building of community-acquired pneumonia in adult outpatients in Beijing, China

A visual review of the human pathogen Streptococcus pneumoniae

National Surveillance of Legionnaires' Disease, China

Decline in temperature and humidity increases the occurrence of influenza in cold climate

The effects of temperature and relative humidity on the viability of the SARS coronavirus

Vitamin D and the immune system

High-Level PM2.5/PM10 Exposure Is Associated With Alterations in the Human Pharyngeal Microbiota Composition

The present work was supported We thank Elsevier Language Editing Services for language editing.

A c c e p t e d M a n u s c r i p t 19 A c c e p t e d M a n u s c r i p t 21