Unveiling the impact of intrapartum antimicrobial prophylaxis in the early microbiome through metagenomics analysis

Abstract

[Introduction] The correct establishment of the intestinal microbiome (IM) at the beginning of life plays a key role in infant and later health. Some factors affecting this process have been studied; however, other like the intrapartum antimicrobial prophylaxis (IAP), in spite of been present on over 30% of total deliveries, have been much less studied. Given the increasingly evident relationship between early microbiota, later disease risk and the rising worries regarding antimicrobial resistances, there is an urgent need to assess the potential adverse consequences of IAP in the establishment of the IM. [Objectives] The objective of this study was to assess the effect of the IAP on the IM composition in full-term 30-days-old infants by metagenomics approach. Methods: Gut microbial DNA was extracted from faecal samples of nine one-month-old babies, five of which were born from mothers receiving IAP. Trying to avoid possible cofounders the recruited cohort of babies were in all cases full-term, vaginally delivered. Illumina shotgun sequencing of the DNA extracted was performed and reconstruction of the microbiomes allowed taxonomic and functional characterization. [Results] In spite of the large inter-individual differences, IAP-exposed babies showed slight microbiota differences when compared with babies which mothers did not received prophylaxis, being the bifidobacteria and bacteriodes populations affected. The functional classification of coding reads by means of different databases allowed to identify differences on the abundance of transporters and enzymes involved in the antibiotic resistance in infants exposed to IAP compared with the not exposed counterparts. [Conclusions] Our results confirm an impact of the IAP treatment on the correct establishment of the IM by using metagenomics analysis and highlight the need of new dietary strategies development based on microbial modulation with the objective to minimize the IAP effect at the early stage of life.