Detection profiles and co-detection patterns of respiratory pathogens in hospitalized patients with acute respiratory infections after the COVID-19 pandemic in Nantong, China

Abstract Background Respiratory-pathogen circulation may have changed after relaxation of coronavirus disease 2019 (COVID-19) control measures. We characterized the pathogen spectrum, clinical-site distribution, age-specific patterns, co-detection patterns, and seasonality among hospitalized patients with acute respiratory tract infections (ARTIs) in Nantong, China. Methods This retrospective cross-sectional study included 5,808 patients hospitalized with ARTIs at the Affiliated Hospital of Nantong University between December 2023 and December 2025. Respiratory specimens collected at admission were tested for 16 pathogens using multiplex real-time quantitative polymerase chain reaction. Pathogen detection was compared by infection site, age group, and season. False discovery rate correction, multivariable logistic regression, and Cochran-Armitage trend tests were applied as appropriate. Results At least one pathogen was detected in 3,129 of 5,808 patients (53.87%). Single and mixed detections occurred in 2,103 (36.21%) and 1,026 (17.67%) patients, respectively. Klebsiella pneumoniae , Staphylococcus aureus , and Haemophilus influenzae were the most frequently detected bacterial targets. After false discovery rate correction, Mycoplasma pneumoniae , adenovirus, human metapneumovirus, H. influenzae , parainfluenza virus type III, and influenza B virus were more frequently detected in lower than upper respiratory tract infections (all q < 0.05). In adjusted analyses, M. pneumoniae and H. influenzae remained associated with lower respiratory tract infections. M. pneumoniae detection peaked among children aged 6–17 years (30.92%, 81/262; P-trend < 0.001). Among patients with mixed detections, bacterial-bacterial pairs were most frequent, particularly S. aureus with K. pneumoniae . Influenza A virus showed a marked winter peak (21.31% vs. 1.20–2.54% in other seasons; q < 0.001). Conclusion Hospitalized patients in eastern China showed frequent bacterial-target detection, age-related heterogeneity, and distinct seasonal patterns. The school-age peak in M. pneumoniae and the winter peak in influenza A virus support age- and season-informed surveillance. Because molecular detection cannot distinguish active infection from colonization, bacterial findings should be interpreted alongside clinical, culture, and biomarker data.