BACKGROUND: Rapid diagnosis is critical for effective treatment of severe pneumonia during the COVID-19 pandemic. Chlamydia psittaci, an atypical community-acquired pathogen, typically exhibits nonspecific clinical signs and requires stringent conditions for microbiological culture, complicating its identification. Metagenomic next-generation sequencing (mNGS), which involves shotgun sequencing of DNA or RNA from clinical samples, is a key technology in clinical settings. Although mNGS technology identifies nucleic acids, it should not be directly equated with the presence of pathogenic microorganisms. Nonetheless, it shows promise as a principal method for detecting atypical pathogens in severe infectious diseases in the future.

CASE REPORT: We present a case of severe community-acquired Chlamydia psittaci pneumonia, highlighting the ongoing mutations and frequent spread of COVID-19. The patient’s severe pulmonary infection rapidly advanced, resulting in multiple organ failure, necessitating extracorporeal membrane oxygenation (ECMO) support. Despite initial inconclusive routine laboratory tests, diagnosis of Chlamydia psittaci pneumonia was confirmed through mNGS. Antibiotic treatment and multi-organ functional support were administered, leading to the patient’s successful recovery and hospital discharge.

CONCLUSIONS: Diagnosing severe pneumonia caused by atypical pathogens amid the COVID-19 pandemic presents significant challenges. Initiating ECMO support without effective infection control poses considerable risks, such as increasing risk of catheter-related infections and antimicrobial treatment failure. In the case presented, mNGS proved instrumental in screening for atypical pathogens in critical infectious diseases. Application of multi-organ function support in reversible conditions affords clinicians time for pathogen identification and treatment, offering novel approaches for diagnosing and treating severe pneumonia induced by unconventional pathogens during epidemic outbreaks.

Keywords: Chlamydophila psittaci, Metagenomics, Prone Position