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. 2023 Jun 15:11:1177069.
doi: 10.3389/fpubh.2023.1177069. eCollection 2023.

Metagenomic-based pathogen surveillance for children with severe pneumonia in pediatric intensive care unit

Meijin Li  1 , Jing Wang  2 , Zhongwei Yao  1 , Hailing Liao  1 , Shufen Su  1 , Xuying Yang  2 , Mingzhou Xie  2 , Yinan Zheng  1
Affiliations

Metagenomic-based pathogen surveillance for children with severe pneumonia in pediatric intensive care unit

Meijin Li et al. Front Public Health. .

Abstract

Background: Pneumonia is a significant cause of morbidity and mortality in children. Metagenomic next-generation sequencing (mNGS) has the potential to assess the landscape of pathogens responsible for severe pulmonary infection.

Methods: Bronchoalveolar lavage fluid (BALF) samples of 262 children with suspected pulmonary infections were collected from April 2019 to October 2021 in the Pediatric Intensive Care Unit (PICU) of Guangdong Women and Children Hospital. Both mNGS and conventional tests were utilized for pathogen detection.

Results: A total of 80 underlying pathogens were identified using both mNGS and conventional tests. Respiratory syncytial virus (RSV), Staphylococcus aureus and rhinovirus were the most frequently detected pathogens in this cohort. The incidence rate of co-infection was high (58.96%, 148/251), with bacterial-viral agents most co-detected. RSV was the main pathogen in children younger than 6 months of age, and was also commonly found in older pediatric patients. Rhinovirus was prevalent in children older than 6 months. Adenovirus and Mycoplasma pneumoniae were more prevalent in children older than 3 years than in other age groups. Pneumocystis jirovecii was detected in nearly 15% of children younger than 6 months. Besides, influenza virus and adenovirus were rarely found in 2020 and 2021.

Conclusions: Our study highlights the importance of using advanced diagnostic techniques like mNGS to improve our understanding of the microbial epidemiology of severe pneumonia in pediatric patients.

Keywords: PICU; co-infection; mNGS; pathogens; severe pneumonia.

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Conflict of interest statement

JW, XY, and MX were employed by Hugobiotech. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
The landscape of potential pathogens detected by metagenomic next generation sequencing (mNGS) and conventional methods. The pathogens consisted of identical detection (the green) of mNGS with conventional tests (CTM), extra detection (the red) of mNGS, false positive detection (the blue) of mNGS, extra detection (the yellow) of CTM, false positive detection (the grey) of CTM. The false positive detection of mNGS represent those microorganisms detected only by mNGS and diagnosed as non-causitive pathogens. The false positive detection of CTM represent those microorganisms detected only by CTM and diagnosed as non-causitive pathogens. CMV, cytomegalovirus; EBV, Epstein–Barr virus; RSV, respiratory syncytial virus.
Figure 2
Figure 2
Proportions of the dominant pathogens detected in each age group. Proportions are calculated as the case numbers of the pathogen out of the total number of patients in the age group. M, months of age; Y, years of age. Statistical significance was determined by χ2 test. *p < 0.05. **p < 0.01. ***p < 0.001. CMV, cytomegalovirus; RSV, respiratory syncytial virus.
Figure 3
Figure 3
Proportions of several respiratory viruses detected in 2019–2021. Proportions are calculated as the case numbers of the pathogen out of the total number of patients in the year. RSV, respiratory syncytial virus.
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