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Background: Community acquired pneumonia remains a leading infectious cause of hospitalization with substantial morbidity and mortality in China. At present, the role of atypical pathogens in CAP arouses peoples' concern. Previous studies indicated that MP was the dominant pathogen of CAP, but the associated factors of MP infection were rarely reported. Methods: We retrospectively investigated the distribution of atypical pathogens related with CAP and compared their differences among various populations. Furthermore, we accessed the associated factors of MP infection in various population. Results: A total of 3,675 patients were enrolled and divided into three groups. One thousand and eighty-nine subjects (29.6%) were infected with at least one atypical pathogen. MP was the most predominant pathogen in these CAP patients. Our study found that infection rates of the atypical pathogens were significantly different among three groups. Our results also revealed, in a pediatric group, as the temperature increased, so did the infection rate of MP, while it was the opposite in adult and elderly groups. Furthermore, in preschool and school-age children, high temperature, female, PIVs, ADV, and INFB infection were independent risk factors for MP infection, INFA infection was a protection factor for MP infection. However, in adult and elderly groups, the associated factors might be different. Conclusions: The infection of atypical pathogens related with CAP is quite serious, and MP infection plays a key role in CAP. Besides, the infection rates of the atypical pathogens are different in various populations, as are the associated factors for MP infection. [ABSTRACT FROM AUTHOR]