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

Yuqing Li¹, Mingwei Wei^1,2, Lunbiao Cui²

¹School of Public Health, National Vaccine Innovation Platform, Nanjing Medical University, Nanjing, China.

Frontiers in Public Health

|August 20, 2025

Insights

A 2023 surge in infant acute respiratory infections (ARIs) was studied. Cytomegalovirus (CMV), Acinetobacter baumannii, and Rhinovirus (HRV) were common in general ARI cases, while Adenovirus (HAdV) and RSV dominated severe cases.

Area of Science:

Pediatric infectious diseases
Respiratory pathogen epidemiology
Molecular diagnostics in infants

Background:

Infants face high risks from acute respiratory infections (ARIs), leading to significant pediatric morbidity and mortality.
A notable increase in ARIs among young children in China during 2023 prompted global health concern.
Understanding the specific pathogens driving these infections is crucial for effective public health interventions.

Purpose of the Study:

To investigate the frequency and types of respiratory pathogens linked to acute respiratory illnesses in infants.
To analyze pathogen prevalence during the 2023 surge of ARIs in young children.
To correlate pathogen detection with disease severity, including hospitalization.

Main Methods:

Established a cohort of 796 healthy 2-month-old infants in Suqian City, China.
Collected throat swabs at enrollment and during follow-up for active ARI monitoring.
Utilized targeted next-generation sequencing (tNGS) to identify respiratory pathogens in collected specimens.

Main Results:

Baseline pathogen carriers included Staphylococcus aureus (17.9%), Cytomegalovirus (CMV) (16.0%), and Acinetobacter baumannii (A. baumannii) (15.3%).
During follow-up, 1,412 ARI episodes were recorded; 636 (94.2%) specimens showed pathogen detection.
Common ARIs frequently involved CMV (43.7%), A. baumannii (35.6%), and Rhinovirus (HRV) (29.3%); hospitalized cases showed higher rates of human adenovirus (HAdV) and RSV.

Conclusions:

Data offer insights into respiratory pathogen epidemiology in infants from 2023-2024.
CMV, A. baumannii, and HRV were prevalent in common ARI cases; HAdV and RSV were more common in severe, hospitalized ARIs.
Pathogen spectrum shifts correlate with disease severity, necessitating targeted prevention and control strategies.

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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 across 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 7 February and 17 April 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 carriers 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 30 April 2024, 1,412 episodes of common ARIs were recorded (164.5 per 100 person-years). A total of 675 specimens were collected during the episodes of common ARIs and qualified for analysis, 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%). Among the pathogens, human adenovirus (HAdV) and human respiratory syncytial virus (RSV) (18, 36.0%) were the most common pathogens detected among 50 hospitalized cases of ARIs.

Conclusion:

Our data provide a better understanding of epidemiological patterns of respiratory pathogens in infants and young children from 2023 to 2024. CMV, A. baumannii, and HRV were the 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.

Keywords:

acute respiratory infections cohort study infants and young children pathogens targeted next-generation sequencing

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