Pathogen profiles and co-detection characteristics of acute respiratory infections based on active surveillance in a
Yixiong Chen1, Sheng Zhang1, Zhifeng Ma1
1Bao'an Center for Disease Control and Prevention, Shenzhen, China.
Objective:
The objective of this study is to determine the multipathogen profiles and co-detection characteristics among patients with acute respiratory infections (ARIs) in a large district of southern China.
Methods:
This multicenter study conducted active surveillance of patients with acute respiratory infections (ARIs) at eight sentinel hospitals in a large district of southern China from August 1, 2024, to December 31, 2025. The study employed multiplex polymerase chain reaction (PCR) technology to screen a series of respiratory specimens for 20 respiratory pathogens. Multi-stage logistic regression models were constructed to assess co-detection associations between pathogens at the individual level.
Results:
The median [interquartile range (IQR)] age of the 6,199 patients included in the study was 24 [5, 33] years. The detection rate and co-detection rate for any pathogen were 62.5% (3,876/6,199) and 18.5% (1,148/6,199), respectively. The highest viral detection rate (69.1%, 993/1,437) was observed in children under five, and the highest bacterial detection rate (47.6%, 487/1,022) was observed in school-age children. The three most prevalent viral pathogens were identified as rhinovirus (RV), influenza A virus (IAV) and severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2). The three most prevalent bacterial pathogens were identified as Haemophilus influenzae (H. influenzae), Streptococcus pneumoniae (SPN) and Group A Streptococcus (GAS). The three most prevalent co-detection pairs were SPN with H. influenzae (3.4%, 210/6,199), RV with H. influenzae (2.8%, 171/6,199), and RV with SPN (2.0%, 125/6,199 cases). The detection rates for RV, SARS-CoV-2 and GAS in outpatients were higher than those in inpatients, while the detection rates for RSV, enterovirus (EV), bocavirus (HBoV) and SPN in inpatients were higher than those in outpatients. Virus-virus pairs, such as IAV combined with RV (OR = 0.17, 95%CI: 0.11-0.25) and with RSV (OR = 0.06, 95% CI: 0.02-0.27) exhibited negative co-detection associations. Furthermore, bacteria-bacteria pairs showed positive co-detection associations, such as the combination of SPN and H. influenzae (OR = 2.12, 95% CI: 1.74-2.57).
Conclusion:
The characteristics of the pathogens vary depending on the patient's age, the nature of the pneumonia, and the type of medical care sought. Virus-virus pairs showed negative co-detection associations, whereas bacteria-bacteria pairs showed positive co-detection associations.
