Investigations of Genomic and Microbial Markers Associated with Adverse Pregnancy and Birth Outcomes

Abstract

Background: Adverse pregnancy and birth outcomes (APBOs), such as preterm birth, preeclampsia, gestational diabetes, and stillbirth, represent a major global public health crisis, driving maternal mortality rates of 211-223 per 100,000 live births and neonatal mortality of 17-20 per 1,000 live births, with short-term effects like respiratory distress requiring intensive care and long-term consequences including cardiovascular issues and delayed growth. Key causes include genomic variations (such as, single nucleotide polymorphisms (SNPs), copy number variants (CNVs), gene mutations) that impair placental development, hormone signaling, and immune responses, leading to complications like fetal growth restriction and miscarriage, as well as microbial infections that provoke inflammation, chorioamnionitis, preterm labor, and stillbirth. Microbial infections are often worsened by antimicrobial resistance causing treatment failures. While GWAS and metagenomics studies have linked genetic variants and maternal microbiota dysbiosis to APBOs, inconsistent findings across regions underscore the need for population-specific research, thus, this study investigated genomic and microbial markers contributing to APBOs in the Vhembe district of Limpopo province, South Africa. Methodology: Pregnant women were recruited into the study after providing informed consent. The umbilical cord blood samples collected immediately post-delivery by trained health care providers. Pathogen profiling used culture methods on different agar media, including nutrient agar, blood agar, MacConkey agar, EMB, and MSA, followed by antimicrobial susceptibility testing on the isolates and WGS to detect virulence and antibiotic resistance genes. DNA extracted from blood samples via QIAamp DNA Blood Mini Kit was used for molecular genotyping to detect the rs12255372 (G/T) polymorphism in the TCFL2 gene and TNF-α promoter polymorphisms at G-308A. Results: This study identified clinically significant bacterial isolates including E. coli, Klebsiella pneumoniae, Staphylococcus aureus, and Staphylococcus epidermidis, with evidence of variable antimicrobial resistance patterns among the isolates. Gentamicin showed a significant association with pregnancy outcomes (p = 0.042) while Ertepenem showed the least association (p > 0.05). Whole genome sequencing revealed antibiotic resistant genes of E. coli that can exacerbate the infections, however, there were no significant virulence genes detected within the isolate. Genotypic analysis revealed that the TNF-α GA genotype was the most prevalent, however, no statistically significant association was observed between TNF polymorphisms and overall adverse pregnancy outcomes. In contrast, TCF genotype distribution showed a statistically significant association with adverse pregnancy outcome categories (p = 0.005), suggesting a potential role in susceptibility to adverse obstetric complications. The overall findings support the multifactorial nature of adverse pregnancy outcomes involving both microbial and host genetic factors.