A 72-year-old man with severe community-acquired pneumonia and concurrent pulmonary embolism had multiple pathogens detected in bronchoalveolar lavage fluid via multiplex pathogen-targeted sequencing, including Chlamydia psittaci, influenza A H3N2, and Streptococcus pneumoniae, and improved with antimicrobial and anticoagulant treatment.
Key Findings
Results
Multiplex pathogen-targeted sequencing of bronchoalveolar lavage fluid detected three principal pathogens simultaneously in a patient with severe community-acquired pneumonia.
The three principal pathogens detected were Chlamydia psittaci, influenza A H3N2, and Streptococcus pneumoniae.
Additional conditionally pathogenic or commensal organisms were also detected beyond the three principal pathogens.
Approximately 10 mL of bronchoalveolar lavage fluid was recovered aseptically, with at least 3 mL allocated to the multiplex pathogen-targeted sequencing assay.
The patient had received antimicrobial therapy prior to bronchoalveolar lavage, which represents an interpretive limitation of the sequencing results.
The three principal detections were interpreted in conjunction with clinical presentation, imaging, inflammatory markers, BALF cytology, conventional testing, and treatment response.
Background
The patient presented with concurrent severe community-acquired pneumonia and pulmonary embolism affecting different lung regions.
Chest computed tomography showed left lower-lobe consolidation and pleural effusion.
Computed tomography pulmonary angiography showed a filling defect in a right upper-lobe pulmonary artery, confirming pulmonary embolism.
The patient was a 72-year-old man presenting with fever, nonproductive cough, vomiting, and hypoxemia.
Laboratory findings included markedly elevated inflammatory markers and an elevated D-dimer concentration.
Hypoxemia and suspected pulmonary embolism prompted the CT pulmonary angiography.
Methods
Bronchoscopy was performed targeting the bronchopulmonary segment corresponding to the radiographic lesion for directed sampling.
Bronchoscopy was performed in the bronchopulmonary segment corresponding to the radiographic lesion.
Approximately 10 mL of bronchoalveolar lavage fluid was recovered aseptically for microbiological and cytological testing.
The authors note that serial imaging and invasive sampling reflected case-specific decisions and 'should not be interpreted as a routine protocol for pneumonia.'
Results
The patient improved and was discharged following combined antimicrobial and anticoagulant treatment.
The patient was discharged on December 3, 2025.
At outpatient follow-up on December 17, rivaroxaban was continued for approximately one further month.
Treatment included both antimicrobial therapy (for the mixed infection) and anticoagulant therapy (for the pulmonary embolism).
Discussion
The case highlights both the adjunctive value and interpretive limitations of targeted sequencing in patients already receiving antimicrobial treatment.
The authors explicitly state the case 'highlights the adjunctive value and interpretive limitations of targeted sequencing in a treated patient.'
Antimicrobial therapy had been administered prior to bronchoalveolar lavage, potentially affecting pathogen detection.
Results required interpretation in conjunction with multiple clinical parameters rather than in isolation.
What This Means
This case report describes a 72-year-old man who developed a serious lung infection (severe community-acquired pneumonia) along with a blood clot in a lung artery (pulmonary embolism) at the same time. What made this case particularly complex was that laboratory testing of fluid collected from his lungs via bronchoscopy — a procedure where a camera is passed into the airways — revealed not one but three significant infectious agents: a bacterium called Chlamydia psittaci (which can be caught from birds), the influenza A H3N2 flu virus, and Streptococcus pneumoniae (a common cause of pneumonia). This type of multi-pathogen infection is called mixed pneumonia and can be challenging to diagnose and treat.
The fluid was analyzed using a modern technique called multiplex pathogen-targeted sequencing, which can scan for many different germs at once. This research suggests that such technology can be a useful additional tool when standard tests may not tell the full story, particularly in severely ill patients. However, the authors are careful to note an important limitation: the patient had already been given antibiotics before the lung fluid was collected, which may have affected which pathogens were detectable and at what levels. The results therefore had to be interpreted carefully alongside the patient's symptoms, scan findings, blood test results, and how he responded to treatment. He ultimately recovered with a combination of antibiotics and blood-thinning medication (rivaroxaban) and was doing well at a follow-up visit two weeks after discharge.
This case is a reminder that serious lung infections can involve multiple germs simultaneously and can occur alongside other complications like blood clots. It also illustrates that advanced sequencing tests, while valuable, are not a standalone diagnostic tool — their results need to be interpreted in the full clinical context, especially when treatment has already started. The authors explicitly caution that the specific tests and procedures used in this case reflected individual clinical decisions and should not be taken as a standard approach for all pneumonia patients.
Chen X. (2026). Mixed Pneumonia with Pulmonary Embolism and Multiple Pathogens Detected in Bronchoalveolar Lavage Fluid: A Case Report.. Journal of visualized experiments : JoVE. https://doi.org/10.3791/72065