Metagenomic next-generation sequencing for accurate diagnosis and management of lower respiratory tract infections.

OBJECTIVES

This study aimed to evaluate the clinical value of metagenomic next-generation sequencing (mNGS) in patients with suspected lower respiratory tract infections.

METHODS

This retrospective study reviewed patients with suspected lower respiratory tract infections at the Wuhan Union Hospital. Data including demographic, laboratory, and radiological profiles; treatment; and outcomes were recorded and analyzed.

RESULTS

mNGS identified pathogenic microbes in 100/140 (71.4%) patients, although 135 (96.4%) had received empiric antibiotic treatment before the mNGS tests. Single bacterial infection (35/100, 35%) was the most common type of infection in patients with positive mNGS results, followed by single fungal infection (14/100, 14%), bacterial-viral coinfection (14/100, 14%), single viral infection (12/100, 12%), bacterial-fungal coinfection (9/100, 9%), fungal-viral coinfection (9/100, 9%), and bacterial-fungal-viral coinfection (7/100, 7%). Moreover, compared with culture test, mNGS showed higher sensitivity (63/85, 74.1% vs 22/85, 25.9% P = 0.001) and lower processing time (24 hours vs 48 hours). Antibiotic treatment was adjusted or confirmed based on the mNGS results in 123 (87.9%) patients, including five (3.6%), 33 (23.6%), and 85 (60.7%) patients, in whom treatment was downgraded, upgraded, and unchanged, respectively. Almost all patients, regardless of escalation, de-escalation, or no change in treatment, showed significant improvement in clinical symptoms and inflammatory indicators. In addition, 17 (12.1%) patients were referred to Wuhan Pulmonary Hospital for further treatment because of confirmed or suspected tuberculosis.

CONCLUSION

mNGS could be a promising technique for microbiological diagnosis and antibiotic management, potentially improving outcomes for patients.