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We assessed the clinical characteristics of three patients with associated pneumonia. Clinical data for three patients with -associated pneumonia admitted to our hospital from June 2020 to December 2020 were retrospectively analyzed, and the diagnosis, clinical features, and treatment of the disease are summarized. Fever, headache, and fatigue were the main symptoms in all three patients, whereas local respiratory symptoms such as cough and expectoration were not obvious. Not all patients had a definite contact history with poultry and birds. Chest computed tomography (CT) showed inflammatory exudation, consolidation, and bronchial inflation signs on one side of the lungs, which progressed rapidly. Treatment with beta-amides did not result in positive clinical responses. Combined with clinical manifestations, the disease was confirmed by detection of nucleic acid sequences in alveolar lavage fluid and blood by metagenomic second-generation sequencing technology. Fever and malaise were rapidly relieved after the administration of moxifloxacin-based regimens and levels of infectious blood markers decreased; and the consolidation shadow on chest CT was gradually absorbed. Early application of metagenomic second-generation sequencing in patients with community-acquired pneumonia due to rare and complex pathogens that cannot be diagnosed by conventional tests and for whom empirical anti-infective therapy is ineffective is important for definitive diagnosis and selection of appropriate antibacterial drugs.