Study on pathogen spectrum of 1,046 hospitalized children with respiratory tract infections during COVID-19

Objectives This study aimed to describe the pathogen spectrum of bacteria and viruses of RTIs in hospitalized children during the Coronavirus disease 2019 (COVID-19) epidemic in Shenzhen. Methods From October 2020 to October 2021, the results of pathogenic tests causing RTIs were retrospectively analyzed in hospitalized children in Shenzhen Luohu Hospital Group. Results 829 sputum samples for bacterial isolation and 1,037 nasopharyngeal swabs for virus detection in total. The positive detection rate (PDR) of bacteria was 42.1%. Staphylococcus aureus (18.8%) was the predominant bacteria detected in positive cases, with Moraxella catarrhalis (10.9%), Streptococcus pneumoniae (9.5%) following. The PDR of the virus was 65.6%. The viruses ranking first to third were Human Rhinovirus (HRV), Respiratory syncytial virus (RSV), and Human Parainfluenza (HPIV), with rates of 28.0, 18.1, and 13.5%, respectively. Children under 3 years were the most susceptible population to RTIs. The pathogens of S. aureus, M. catarrhalis, S. pneumoniae, HRV, and HPIV were more prevalent in autumn. Meanwhile, RSV had a high rate of infection in summer and autumn. S. aureus and HRV had higher co-infection rates. Conclusions Our findings demonstrate the pathogen spectrum of 1,046 hospitalized children with RTIs in Shenzhen, China, during the COVID-19 outbreak.