Targeted sequencing-based analysis of respiratory pathogen profiles in Shenzhen, China

Abstract Background Respiratory tract infections (RTIs) are caused by diverse viral, bacterial, and fungal pathogens and remain a major public health burden worldwide. Rapid and accurate identification of respiratory pathogens is important for clinical diagnosis and epidemiological surveillance. Shenzhen is a highly populated metropolitan city characterized by substantial population mobility and intensive domestic and international travel, which may influence the regional circulation patterns of respiratory pathogens. However, sequencing-based epidemiological data regarding respiratory pathogens in Shenzhen remain limited. Methods Clinical specimens from 392 patients with suspected RTIs who underwent targeted sequencing at Longgang District People’s Hospital of Shenzhen between 2023 and 2025 were analyzed using a respiratory pathogen targeted sequencing panel. Clinical information was retrospectively collected. Microorganism detection profiles, co-detection patterns, age-associated detection frequencies, and associations with clinical manifestations were analyzed. Results Among the 392 enrolled patients, at least one panel-targeted respiratory microorganism was detected in 273/392 samples (69.6%), whereas 119/392 samples (30.4%) were negative. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was the most frequently detected microorganism, followed by influenza A(H1N1) virus, Klebsiella pneumoniae , Epstein-Barr virus, Haemophilus influenzae , and Streptococcus pneumoniae . Among the 273 positive samples, 195/273 (71.4%) showed single-microorganism detection, whereas 78/273 (28.6%) showed multiple-microorganism detection. Cough and fever were the most frequently observed symptoms across most microorganism groups. In addition, Bordetella pertussis and Mycoplasma pneumoniae were more frequently detected in younger patients, whereas Klebsiella pneumoniae , Aspergillus , and Epstein-Barr virus were more commonly detected in elderly individuals. The clinical relevance of some detected microorganisms should be interpreted cautiously, as their detection does not necessarily indicate active infection or etiological causality. Conclusion Targeted sequencing detected a diverse range of respiratory microorganisms in patients with suspected RTIs and provided regional data on their detection patterns in Shenzhen, China. These findings may contribute to respiratory pathogen surveillance, although individual sequencing results should be interpreted together with clinical and microbiological information when assessing etiological relevance.