Post COVID-19 era pathogen profiles and influencing factors for Hospital patients with Lower Respiratory Tract Infections in Shenzhen, China

Tong Li¹Tiejian Feng^1*Dandan Niu¹Renli Zhang¹Yongchao Guo²Yingluan Zhang¹Tengyingzi Liu¹Peng Bo¹Dana Huang¹Zhen Zhang¹Zhanhong Rao¹Xiaomin Zhang^1*Xiaolu Shi¹

• ¹Shenzhen Center for Disease Control and Prevention, Shenzhen, China
• ²Shenzhen Uni-medical Techonology Co., Ltd, Shenzhen, Shenzhen, China

Background. Lower respiratory tract infections (LRTIs) are associated with significant morbidity, hospitalizations and mortality globally. This study aimed to investigate the causative pathogens and epidemiology characteristics of LRTIs including the factors influencing the severity of illness and the length of hospital stay (LOS). Methods. From November 2023 to June 2024, a prospective study containing 121 patients was performed at four hospitals in Shenzhen, China. The bronchoalveolar lavage fluid (BALF) samples from LRTIs inpatients were strictly collected and tested using targeted next-generation sequencing (tNGS). 108 respiratory pathogens were included in the detection list. Results. 89.3% of inpatients tested positive for one or more pathogens (108/121). The three leading pathogens were Staphylococcus aureus (S. aureus), Pseudomonas aeruginosa (P. aeruginosa), 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 the infections of S. aeruginosa. Multiple infections were found in 53.8% of all patients group (65/121), in which 22.0% exhibited bacterial-viral co-infections (28/121). Positive interactions were identified in P. aeruginosa-A. 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, SARS-CoV-2 or HHV. Conclusions. Different age groups of hospitalized patients showed different pathogens profiles and types of co-infection, indicating the significance of age-targeted clinical medical practice. The most common pathogens caused LRTIs were S. aureus, P. aeruginosa, H. influenzae. Older age, multiple infections, pleural effusion, diabetes mellitus, hypertension, shortness of breath and infection with P. aeruginosa, SARS-CoV-2 or HHV preferred to prolong LOS. TNGS testing should be prioritized for immunocompromised and critically ill patients.