Table 3_Post-COVID-19 era pathogen profiles and influencing factors for hospital patients with lower respiratory tract infections in Shenzhen, China.docx

BackgroundLower respiratory tract infections (LRTIs) are associated with significant morbidity, hospitalizations, and mortality globally. The aim of this study was to investigate the causative pathogens and epidemiological characteristics of LRTIs including the factors influencing the severity of illness and the length of hospital stay (LOS).
MethodsFrom November 2023 to June 2024, a prospective study including 121 patients was performed at four hospitals in Shenzhen, China. The bronchoalveolar lavage fluid (BALF) samples from inpatients with LRTIs were strictly collected and tested using targeted next-generation sequencing (tNGS). A total of 108 respiratory pathogens were included in the detection list.
ResultsOf the total inpatients, 89.3% tested positive for one or more pathogens (108/121). The three leading pathogens were Staphylococcus aureus (S. aureus), Pseudomonas aeruginosa (P. aeruginosa), and Haemophilus influenzae (H. influenzae). Patients aged over 70 years showed the highest pathogen detection rate (23/24, 95.8%), with P. aeruginosa being the most frequently detected pathogen in this age group (9/24, 37.5%). Profound sex differences were observed in S. aeruginosa infections. Multiple infections were found in 53.8% of all patients (65/121), in which 22.0% exhibited bacterial–viral co-infections (28/121). Positive interactions were identified in P. aeruginosa–Acinetobacter baumannii or S. aureus. High-risk factors of LOS were considerably associated with older age, multiple infections, pleural effusion, diabetes mellitus, hypertension, shortness of breath, and infection with P. aeruginosa, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), or human herpes virus (HHV).
ConclusionsDifferent age groups of hospitalized patients showed different pathogen profiles and types of co-infection, indicating the significance of age-targeted clinical medical practice. The most common pathogens that caused LRTIs were S. aureus, P. aeruginosa, and H. influenzae. Older age, multiple infections, pleural effusion, diabetes mellitus, hypertension, shortness of breath, and infection with P. aeruginosa, SARS-CoV-2, or HHV contribute to prolonged LOS. tNGS testing should be prioritized for immunocompromised and critically ill patients.