Association between vaginal microbiomes and neonatal septicemia in pregnant women with preterm premature rupture of membranes based on metagenome sequencing

Abstract

Background: Preterm premature rupture of membranes (PPROM) is closely associated with pathogenic microbiomes in the female reproductive tract, and can lead to neonatal septicemia. The current study aimed to investigate potential pathogenic microbiomes associated with neonatal septicemia based on DNA metagenome sequencing.

Methods: In this study, a total of 7 pregnant women with PPROM presenting neonatal septicemia (experimental group) and 3 pregnant women with normal newborns (control group) were enrolled. Vaginal secretions at admission and before parturition as well as placental tissues after parturition were collected for DNA metagenome sequencing using whole genome shotgun method on the Illumina NovaSeq/HiSeq platform. Raw data were processed by BioBakery workflow, and MetaPhlAn4 was implemented for qualitative and quantitative analyses of microbiome. Lactobacillus crispatus, Gardneralla vaginalis, Fannyhessea vaginae and Streptococcus suis were specifically detected from the experimental group. The two groups were compared using Student's t-tests.

Results: The indexes of Chao1 (P=0.00028/P=0.00072), abundance-based coverage estimator (ACE, P=0.00059/P=0.00026), Shannon (P=0.036/P=0.0065) and Simpson (P=0.007/P=0.041) in the experimental group were increased at admission and before parturition as compared with the control group. Several microbiomes, such as Lactobacillus crispatus, Gardneralla vaginalis, Fannyhessea vaginae and Streptococcus suis, were specifically detected in the experimental group. Notably, Gardnerella vaginalis and Streptococcus gallolyticus were identified from the vaginal secretions and placenta tissues of women with neonatal septicemia. Moreover, nucleic acid synthesis and carbohydrate metabolism-related pathways were enriched in the experimental group.

Conclusion: This study enhanced the current understanding of the mechanisms underlying pathogenic microbiomes in PPROM-induced neonatal septicemia. The trial registry number is ChiCTR2300070666 (URL: https://www.chictr.org.cn/showproj.html?proj=195648).

Keywords: Preterm premature rupture of membranes; metabolic pathways; microbiomes; neonatal septicemia; whole genome shotgun.

Figure 1

Differences of microbial diversity in vaginal secretions between the experimental group and control group at admission. A: The difference of Simpson between EG and CG group. B: The difference of chao1 between EG and CG group. C: The difference of ACE between EG and CG group. D: The difference of Shannon between EG and CG group. EG, experimental group; CG, control group; abundance-based coverage estimator (ACE). *P<0.05, **P<0.01, ***P<0.001.

Figure 2

Alterations of microbial abundance in vaginal secretions between experimental group and control group at admission. A. PCoA ordination of genera abundance using Bray-Curtis dissimilarity. B. Genera abundance of top 25 species. PCoA: principal coordinate analysis.

Figure 3

Differences of microbial diversity in vaginal secretions between experimental group and control group before parturition. A: The difference of Simpson between EG and CG group. B: The difference of chao1 between EG and CG group. C: The difference of ACE between EG and CG group. D: The difference of Shannon between EG and CG group. EG, experimental group; CG, control group; abundance-based coverage estimator (ACE). *P<0.05, **P<0.01, ***P<0.001.

Figure 4

Alterations of microbial abundance in vaginal secretions before parturition. A. PCoA ordination of genera abundance using Bray-Curtis dissimilarity to distinguish the experimental group and the control group. B. Genera abundance of top 25 species in the experimental group and the control group. C. PCoA ordination of genera abundance shows a high consistency in genera abundance of vaginal secretions at admission and before parturition. D. Genera abundance of top 25 species at admission and before parturition. E. The abundance of Streptococcus suis in the experimental group and the control group before parturition. EG, experimental group; CG, control group. PCoA: principal coordinate analysis.

Figure 5

Relationship of vaginal microbial abundance and intrauterine infection before parturition. A. PCoA ordination of genera abundance portrays a separation of microbiome between the experimental group and the control group. B. Genera abundance of top 25 species of placenta tissue in the experimental and control groups. PCoA: principal coordinate analysis.

Figure 6

Identification of potential pathogen for neonatal septicemia in PPROM women. A. Potential pathogenic microbiomes in vaginal secretions at admission. B. Potential pathogenic microbiomes in vaginal secretions before parturition. C. Differences of pathogenic microbiomes in vaginal secretions at admission vs. before parturition. D. Potential pathogenic microbiomes in placenta tissue after parturition. PPROM: Preterm premature rupture of membranes.

Figure 7

Perturbation of metabolic pathways. A. Perturbed metabolic pathways in vaginal secretions at admission. B. Perturbed metabolic pathways in vaginal secretions before parturition. C. Differential perturbed metabolic pathways in vaginal secretions at admission vs. before parturition. D. Perturbed metabolic pathways in placenta tissue after parturition.