Metagenomic Next-Generation Sequencing of Bloodstream Microbial Cell-Free Nucleic Acid in Children With Suspected Sepsis in Pediatric Intensive Care Unit

Abstract

Bloodstream infection is a life-threatening complication in critically ill patients. Multi-drug resistant bacteria or fungi may increase the risk of invasive infections in hospitalized children and are difficult to treat in intensive care units. The purpose of this study was to use metagenomic next-generation sequencing (mNGS) to understand the bloodstream microbiomes of children with suspected sepsis in a pediatric intensive care unit (PICU). mNGS were performed on microbial cell-free nucleic acid from 34 children admitted to PICU, and potentially pathogenic microbes were identified. The associations of serological inflammation indicators, lymphocyte subpopulations, and other clinical phenotypes were also examined. mNGS of blood samples from children in PICU revealed potential eukaryotic microbial pathogens. The abundance of Pneumocystis jirovecii was positively correlated with a decrease in total white blood cell count and immunodeficiency. Hospital-acquired pneumonia patients showed a significant increase in blood bacterial species richness compared with community-acquired pneumonia children. The abundance of bloodstream bacteria was positively correlated with serum procalcitonin level. Microbial genome sequences from potential pathogens were detected in the bloodstream of children with suspected sepsis in PICU, suggesting the presence of bloodstream infections in these children.

Keywords: Pneumocystis jirovecii; bloodstream infection; metagenomic next-generation sequencing; pediatric intensive care unit; sepsis.

Figure 1

Bloodstream microbial ecological diversity in children in PICU. (A) The number of bloodstream bacterial species in children with hospital-acquired pneumonia (HAP) was significantly higher than in those with community-acquired pneumonia (CAP), P < 0.05, Wilcoxon rank-sum test. (B) The number of bloodstream fungi and protozoa in children with immunodeficiency disease was significantly higher compared with non-deficient children, P < 0.05, Wilcoxon rank-sum test; (C) PCT was positively correlated with the bacteria abundance. *P < 0.05.

Figure 2

Potential pathogenic bacteria in the bloodstream of children with suspected sepsis in PICU. (A) Identified bloodstream pathogenic bacteria, where red dots represent potential pathogenic bacteria, Z-score > 6, uniformly assigned value was Z-score = 6. (B) Heat map of bloodstream potential pathogenic bacteria; each line on the horizontal represents a sample and lines on the vertical represent potential pathogenic bacteria; the “+” and “-” signs represent significant positive and negative correlations, respectively; the top is the clinical phenotype, and the color block on the right represents the specific value of clinical phenotype. (C) The correlation between bloodstream pathogenic bacteria and clinical phenotype; each line on the horizontal represents a clinical phenotype and on the vertical represents potential pathogenic bacteria; the “+” and “-” represent significant positive and negative correlations, respectively; the color block on the right represents the value of the correlation coefficient: positive correlation is red and negative correlation is blue. (D) The species richness (chao 1) of hospital-acquired pneumonia (HAP) bacteria was significantly higher than that of community-acquired pneumonia (CAP), P < 0.05, Wilcoxon rank- sum test. *P < 0.05.

Figure 3

Potential pathogenic viruses in the bloodstream of children with suspected sepsis in PICU. (A) Identified bloodstream potential pathogenic viruses. (B) Heat map of bloodstream potential pathogenic viruses. (C) Heat map of the correlation between clinical phenotypes and candidate viruses. (D) Compared with children with negative microbial culture, the bloodstream abundance of human mastadenovirus B in children with positive microbial culture was significantly increased, P < 0.05, Wilcoxon rank-sum test. *P < 0.05.

Figure 4

Potential pathogenic fungi in blood of children in PICU. (A) Identified bloodstream pathogenic fungi. (B) Heatmap of bloodstream pathogenic fungi. (C) Correlation of potential pathogenic fungi and white blood cell count (WBC). (D) Compared with non-immune deficient children, the bloodstream abundance of Pneumocystis jirovecii was significantly higher in children with immunodeficiency disease, P < 0.05, Wilcoxon rank-sum test. *P < 0.05.