Molecular Diagnostics, Antimicrobial Resistance Patterns, and Clinical Outcomes in Hospitalized Pneumonia Patients: A Prospective Study from Jordan and a Call for National Guideline Integration.

Purpose: Pneumonia is still a leading cause of morbidity and death globally, with a significant percentage of cases having an unknown aetiology, and management becoming more difficult due to growing antimicrobial resistance (AMR). This study assessed clinical outcomes, antimicrobial susceptibility patterns, and pathogen detection using both conventional and molecular techniques in hospitalized pneumonia patients in Jordan. Patients and Methods: 111 adults (≥18 years) who were admitted to a tertiary private hospital in Amman between May 2021 and January 2022 with either hospital-acquired (HAP) or community-acquired pneumonia (CAP) were included in this prospective study. Multiplex real-time PCR and conventional culture were performed on lower respiratory tract samples (FTD Respiratory Pathogens 33). Data on outcomes, microbiology, antimicrobial susceptibility, clinical, and demographics were gathered. McNemar's test was used to compare diagnostic performance, and logistic regression and chi-square analyses were used to evaluate the relationships between outcomes and adherence to guidelines. Results: The average age was 64.0±20.6 years, and 58.6% of the population was male. 78.4% of cases were CAP. PCR detected pathogens in 74.8% of patients, whereas culture detected them in 57.7% (p<0.001). PCR showed a higher false-positive rate but a significantly higher sensitivity than culture (96.9% vs 86.3%, p=0.039). In 36.9% of cases, bacterial-viral co-infections were found. The overall death rate was 27.0%. Although not an independent predictor in logistic regression, non-guideline-concordant antibiotic therapy was substantially associated with mortality (p=0.023). High ampicillin resistance and notable trends in resistance to specific broad-spectrum agents were among the notable variations in AMR patterns observed. Conclusion: Multiplex PCR reveals complex co-infection patterns in pneumonia and greatly enhances pathogen detection when compared to culture. Antimicrobial stewardship initiatives that incorporate molecular diagnostics may improve targeted treatment. To address changing AMR patterns in Jordan, national guidelines that include molecular testing are necessary.