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Difei Academic | mNGS reveals changes in intestinal flora and related drug resistance genes in children in PICU after antibiotic treatment

Views: 0     Author: Diffei Medical     Publish Time: 2024-05-10      Origin: 迪飞医学

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Recently, Diffei Medical collaborated with the team of Zhu Xiaodong, PICU of Xinhua Hospital Affiliated to Shanghai Jiao Tong University, and published 'Pediatric intensive care unit treatment alters the diversity and

composition of the gut microbiota and antimicrobial resistance gene expression in critically ill children'.This article comprehensively reveals the community structure of the intestinal flora of children in PICU, and compares the differences in intestinal flora, gene functions, and changes in metabolism-related pathways in children before and after short-term antibiotic treatment.

Research Background

Common critical illnesses include sepsis, acute respiratory distress syndrome, and multiple organ failure syndrome, which impose a heavy economic burden on the global healthcare sector.A large number of studies have confirmed that intestinal flora can participate in the occurrence and development of various diseases; at the same time, its structural state is affected by the physiological and pathological changes of critically ill patients, and it has a symbiotic relationship with the human host.The use of antibiotics may induce the up-regulation of the expression of some drug-resistant genes in intestinal flora, thereby affecting the treatment of diseases.Therefore, intestinal flora, as an important factor in the treatment of childhood diseases and the management of critically ill patients, has attracted more and more attention from clinicians.

this researchThe aim is to use mNGS technology to reveal the changes in intestinal microbiota composition, gene function and drug resistance genes in children in PICU, and to provide a theoretical basis for rational medication use in children and reducing the incidence of adverse events in the intensive care unit.

Enrolled patients

This study collected 71 children from March 2021 to March 2022 as research subjects (Figure 1). Anal swabs were collected on D1 and D7 who were admitted to the PICU for treatment, and then mNGS testing was performed (PE150; 50M ).

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Figure 1. Patient admission and discharge flow chart

Research result

1. Patient characteristics and clinical information

According to statistics, most children have underlying diseases and are complicated by infectious complications.All children received intravenous antibiotics upon admission.More than half of the children received two or more classes of antibiotics within 7 days of PICU admission.

The study found that after 7 days of PICU treatment,C-reactive protein (P<0.01), procalcitonin (P<0.01), creatinine (P<0.01) and lactic acid (P<0.01) and white blood cell count decreased significantly (P=0.01); platelet count increased significantly (P=0.01).In terms of clinical outcomes, 7 children died during the 28-day follow-up period (Table 1).

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Table 1. Clinical information of enrolled patients

2. PICUShort-term treatment alters richness of gut microbiota in children

Alpha diversity analysis based on Shannon index, Simpson index, Chao1 and ACE index showed that compared with the D1 group, the bacterial flora richness of the D7 group was significantly reduced (Table 2).There was no significant difference in the beta diversity of intestinal microbiota between the two groups (P>0.05).Our results show that the community structure of children's gut microbiota remains somewhat stable even under the influence of antibiotics and other treatments

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Table 2. Alpha diversity between D1 and D7 groups

3. PICUShort-term treatment alters species abundance in children's gut microbiota

Changes in species abundance of intestinal microbiota in groups D1 and D7 were analyzed from multiple taxonomic levels.At the phylum level, the relative abundance of Bacteroidetes and Actinobacteria in the intestinal flora of children in group D7 decreased, while the relative abundance of Firmicutes and Proteobacteria increased (Figure 2).At other classification levels we findThe relative abundance of Bacillus and Lactobacillales in the intestinal flora of children in group D7 increased significantly (P=0.03,P=0.04), while the relative abundance of human Campylobacter was significantly reduced (P=0.02)(image 3).

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Figure 2. Overall bacterial composition at portal level in critically ill children before and after PICU treatment

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Figure 3. Distribution of the top 20 bacterial communities at the (A) class, (B) order and (C) species levels among D1 and D7 taxa.*P < 0.05.

4. Significant changes in gene function of gut microbiota

After short-term PICU treatment, children's gut microbiota gene function changed significantly (Figure 4).A total of 30 significantly altered KEGG pathways were obtained (P<0.01), and the expression of 30 pathways was inhibited.They mainly include changes in the activity of enzymes and transcription factors in the metabolic process represented by phosphoribosamide formyltransferase 1, and in the DNA catabolism and repair process represented by the DNA repair protein RadA/Sms and deoxyribonuclease I. Changes in enzyme and protein activity.In addition, changes in the activity of the ExbD biopolymer transporter were also observed.this meansIntestinal microbial imbalance is also accompanied by changes in material metabolism, material transport, and genetic material decomposition and repair processes..Likewise, we useP<0.01, the significantly changed GO pathways were screened and found to be consistent with the results of KEGG pathway analysis.

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Figure 4. Gene function prediction of KEGG pathway

5. Differential analysis of antimicrobial resistance gene expression in intestinal microbiota

A total of 31 significantly different antibiotic resistance genes (ARGs) were detected in the D7 group and the D1 group, and the expression of 19 resistance genes was up-regulated.The top 10 significantly up-regulated resistance genes are Erm(A), ErmX, LptD, eptB, SAT-4, tetO, adeJ, adeF, APH(3′)-IIIa and tetM, among which LptD and adeJ are closely related to Carbapenem Related to ene antibiotic resistance (Figure 5)

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Figure 5. Volcano plot of antimicrobial resistance gene expression in groups D1 and D7


1. PICUAfter short-term treatment, the richness of intestinal flora in critically ill children was significantly reduced, but the bacterial diversity and community structure remained stable to a certain extent between groups;

2. After 7 days of short-term treatment in PICU, the relative abundance of Bacillus and Lactobacillus in the intestinal tract of children increased significantly, while the relative abundance of human Campylobacter decreased significantly;

3. GOand KEGG analysis showed that the gene function of the intestinal flora has also undergone certain changes, mainly the down-regulation of genes responsible for metabolism, DNA catabolism and transmembrane transport.

4. PICUAfter short-term treatment, there were significant changes in the expression of drug-resistant genes in critically ill children. The top 10 significantly up-regulated resistance genes were Erm(A), ErmX, LptD, eptB, SAT-4, tetO, adeJ, adeF, and APH(3′ )-IIIa and tetM.


Xu J, Kong X, Li J, Mao H, Zhu Y, Zhu X, Xu Y. Pediatric intensive care unit treatment alters the diversity and composition of the gut microbiota and antimicrobial resistance gene expression in critically ill children. Front Microbiol. 2023 Nov 13;14:1237993. doi: 10.3389/fmicb.2023.1237993. PMID: 38029168; PMCID: PMC10679412.

Compiler: Zen-Master Reviewer: Jia, Eleven Typesetting: Lin

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