Respiratory pathogen spectrum and co-infection patterns in patients with acute respiratory infection during and after the coronavirus COVID-19 pandemic: a five-year retrospective study, 2021–2025

The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), prompted the widespread implementation of non-pharmaceutical interventions (NPIs) globally. In China, stringent containment measures and mass vaccination were maintained until December 2022. This study aimed to characterize the epidemiological features of respiratory pathogens in patients with acute respiratory infection (ARI) during and after the COVID-19 pandemic, 2021–2025. We retrospectively analyzed 9,674 patients with ARI. All patients were tested using a single multiplex fluorescence polymerase chain reaction (PCR)–capillary electrophoresis panel. The panel detects 13 targets—11 viruses and 2 atypical bacterial pathogens, Mycoplasma pneumoniae and Chlamydia . Of 9,674 patients, 5,289 (54.67%) had lower respiratory tract infection (LRTI) and 4,385 (45.33%) had upper respiratory tract infection (URTI), reflecting the case mix of a hospital-based cohort. The pathogen detection rate was significantly higher in LRTI than in URTI (2,939/5,289 [55.57%] vs. 677/4,385 [15.44%]; difference 40.13% points, 95% CI 38.40–41.80; P < 0.001). Mycoplasma pneumoniae was the leading pathogen in LRTI (954/5,289, 18.04%), followed by rhinovirus (618/5,289, 11.68%) and influenza A virus (456/5,289, 8.62%); rhinovirus predominated in URTI (224/4,385, 5.11%). Temporally, both ARI consultations and positivity were suppressed during 2021–2022 (positives/tested: 326/1,180 [27.63%] and 283/1,161 [24.38%]), rose sharply after NPI relaxation (1,486/4,292 [34.62%] in 2023; 1,046/1,913 [54.68%] in 2024), and remained elevated in 2025 (475/1,128 [42.11%]). After adjustment for age group, the odds of pathogen detection remained significantly higher in 2023 (OR 2.85, 95% CI 2.09–3.88), 2024 (OR 4.19, 95% CI 3.01–5.84), and 2025 (OR 2.19, 95% CI 1.53–3.15) than in 2021. Among 79 patients requiring intensive care for severe LRTI, at least one pathogen was detected in all, and bacterial or fungal co-infection was documented in 72 (91.14%), including multidrug-resistant organisms in 42 (53.16%). During the period of stringent NPIs, respiratory pathogen circulation was suppressed and then resurged after NPI relaxation; this pattern persisted after age adjustment. Mycoplasma pneumoniae and rhinovirus were the leading pathogens in LRTI, in which mixed infections were more frequent than in URTI. Severe LRTI requiring intensive care was characterized by advanced age and a high burden of bacterial and fungal co-infection, including multidrug-resistant organisms, underscoring the need for continued vigilance and optimized management.