Standard-of-care test: Bacterial and fungal testing: BAL and ETA or sputum specimens are subjected to Gram staining, and aerobic, anaerobic, and fungal cultures are performed. Mycobacterium culture is performed, and PCR is used to detect mycobacterial DNA. Other tests included atypical pathogen, aspergillus and virus survey.

FilmArray PP can detect 15 bacterial species, 3 atypical bacteria, 8 viruses, and detect 7 antimicrobial resistance genes.

Respiratory Pathogen ID/AMR enrichment (RPIP): According to the manufacturer's instructions, the workflow includes nucleic acid extraction, cDNA synthesis, sequencing library construction, target amplification, library quality testing, sequencing, and analysis.

Untargeted mNGS: The sample is outsourced to a biotechnology company for mNGS analysis.

The turnaround time between RPIP results and the final report of the standard test is compared to evaluate the time saved by using RPIP. The proportion of clinical treatment strategy adjustments prompted by RPIP results is analyzed, as well as the proportion of inappropriate empirical treatments. It also analyzes whether adjustments in treatment strategies have an impact on mortality.

The data will collect from the medical records of patients, which contained demographic data (age, gender, smoking status, alcohol consumption, source of admission, and type of ICU and supportive care), comorbidities (malignancy, liver disease, including chronic hepatitis or cirrhosis, heart failure, hypertension, cerebral vascular disease, neurodegenerative disorder, chronic kidney disease, chronic lung disease, diabetes mellitus, immunocompromised due to long-term use of steroid or other immunosuppressants, autoimmune disease), clinical manifestations, laboratory findings, severity of illness on the day of pneumonia diagnosis evaluated by the Acute Physiology and Chronic Health Evaluation (APACHE) II score and SOFA score, microbiological profile, antimicrobial therapy, and other outcome measures included 90-day mortality, clinical cure/improvement, and microbiological eradication at day 14 following pneumonia diagnosis evaluation.