Severe pneumonia with multiorgan dysfunction associated with probable Chlamydia abortus infection: a case report

Human Chlamydia abortus infection can present as severe pneumonia with multiorgan dysfunction. In patients with relevant animal exposure, interpretation of sequencing results depends on both the organisms covered by the assay and the specimen tested. We describe these diagnostic considerations in a patient with probable C. abortus pneumonia. A 45-year-old woman with 10 years of occupational exposure to poultry slaughter presented with fever, dyspnoea, and profound hypoxaemia. She developed severe community-acquired pneumonia with hypoxaemic respiratory failure, shock requiring vasopressors, acute kidney injury, and liver injury. A predefined targeted next-generation sequencing panel of bronchoalveolar lavage fluid (BALF) did not include C. abortus. Untargeted DNA metagenomic next-generation sequencing (mNGS) of whole blood detected C. abortus (1,157 species-level reads). Four blood-suculture sets showed no growth, and respiratory cultures yielded only normal oropharyngeal flora. The exposure history, compatible clinical and radiological findings, absence of pathogenic growth on conventional cultures, negative admission viral tests, and blood mNGS result supported a probable diagnosis. Treatment included doxycycline, invasive mechanical ventilation, prone positioning, vasopressors, and continuous renal replacement therapy for acute kidney injury. She was extubated on hospital day 8 and discharged without fever or supplemental oxygen on December 26, 2024. At follow-up on January 21, 2025, she had no respiratory symptoms, and chest computed tomography showed complete resolution of the pulmonary opacities. C. abortus merits consideration in severe pneumonia in patients with relevant animal exposure. In this case, whole-blood mNGS contributed to the aetiological assessment, whereas the BALF targeted panel did not cover the organism. This case highlights the importance of reviewing assay coverage and interpreting sequencing results in their clinical context. The diagnosis remained probable because respiratory and independent species-specific confirmation were unavailable.