Respiratory pathogens in infants and young children with acute respiratory illness: a prospective cohort study, China, 2023-2024

Yuqing Li¹Mingwei Wei¹Lunbiao Cui²Xiang Huo²Lisha Ma³Ran Tao²Tao Wu²Suyang Qi⁴Baolong Wang⁵Xiuyun Shi⁶Yuanbao Liu²Wenqing Liu¹Yiyue Ge²Li Chen⁶Xiujuan Zhao⁵Jingjing Wu⁴Runjie Qi¹Fengcai Zhu¹Jingxin Li^1*

• ¹School of Public Health, Nanjing Medical University, Nanjing, China
• ²Jiangsu Provincial Center for Disease Control And Prevention, Nanjing, China
• ³School of Public Health, Southeast University, Nanjing, Jiangsu Province, China
• ⁴Sucheng District Center for Disease Control and Prevention, Suqian, China
• ⁵Suyu District Center for Disease Control and Prevention, Suqian, China
• ⁶Siyang County Center for Disease Control and Prevention, Suqian, China

Abstract Background. Infants are vulnerable to acute respiratory infections (ARIs), which result in pediatric morbidity and even fatalities. A surge of ARIs among infants and young children was reported in China in 2023, garnering global attention. We aimed to investigate the frequency and types of respiratory pathogens associated with the risk of acute respiratory illnesses in infants and young children during this period. Methods. We established a cohort of 2-month-old healthy infants in three counties in Suqian City, Jiangsu Province, China. The infants in the cohort donated throat swabs at enrollment and then underwent a follow-up for active monitoring of common ARIs. Throat swabs collected from infants experiencing common ARIs were analyzed for respiratory pathogens using targeted next-generation sequencing (tNGS). Results. Between February 7 and April 17, 2023, a total of 804 infants were invited to participate. Among them, 796 participants were enrolled (423 [53.1%] male, 373 [46.9%] female) with a median age of 71.0 days. Frequently detected respiratory pathogen carriages at baseline included Staphylococcus aureus (S.aureus) (17.9%), Cytomegalovirus (CMV) (16.0%) and Acinetobacter baumannii (A.baumannii) (15.3%). In the follow-up period up to April 30, 2024, 1412 episodes of common ARIs were recorded (164.5 per 100 person-year). A total of 675 specimens were collected during the episodes of common ARIs and qualified for analysis, and of which 636 (94.2%) had at least one positive detection of respiratory pathogens, with the most frequently detected pathogens being CMV (43.7%), A.baumannii (35.6%) and Rhinovirus (HRV) (29.3%). While, Human adenovirus (HAdV) and Human respiratory syncytial virus (RSV) (18, 36.0%) were the most common pathogens detected among 50 hospitalized cases of ARIs. Conclusions. Our data provide a better understanding of epidemiological patterns of respiratory pathogens in infants and young children from 2023 to 2024 year. CMV, A.baumannii and HRV were most commonly detected pathogens in common ARI cases, while HAdV and RSV were more frequently observed in hospitalized cases with ARIs. These findings suggest that shifts in the pathogen spectrum are closely linked to disease severity, highlighting the need for targeted prevention and control strategies.