Vertical Transmission of Gut Microbiome and Antimicrobial Resistance Genes in Infants Exposed to Antibiotics at Birth

Weizhong Li, Terhi Tapiainen, Lauren Brinkac, Hernan A Lorenzi, Kelvin Moncera, Mysore V Tejesvi, Jarmo Salo, Karen E Nelson, Weizhong Li, Terhi Tapiainen, Lauren Brinkac, Hernan A Lorenzi, Kelvin Moncera, Mysore V Tejesvi, Jarmo Salo, Karen E Nelson

Abstract

Vertical transmission of maternal microbes is a major route for establishing the gut microbiome in newborns. The impact of perinatal antibiotics on vertical transmission of microbes and antimicrobial resistance is not well understood. Using a metagenomic approach, we analyzed the fecal samples from mothers and vaginally delivered infants from a control group (10 pairs) and a treatment group (10 pairs) receiving perinatal antibiotics. Antibiotic-usage had a significant impact on the main source of inoculum in the gut microbiome of newborns. The control group had significantly more species transmitted from mothers to infants (P = .03) than the antibiotic-treated group. Approximately 72% of the gut microbial population of infants at 3-7 days after birth in the control group was transmitted from their mothers, versus only 25% in the antibiotic-treated group. In conclusion, perinatal antibiotics markedly disturbed vertical transmission and changed the source of gut colonization towards horizontal transfer from the environment to the infants.

Keywords: AMR; antibiotics; antimicrobial resistance genes; gut microbiome; infant microbiome; microbiome; microbiome transmission.

© The Author(s) 2020. Published by Oxford University Press for the Infectious Diseases Society of America.

Figures

Figure 1.
Figure 1.
Transmitted species and exclusively shared genes of different adult/mother-infant groups. P values (Wilcoxon rank sum test) for unrelated woman-infant antibiotic-treated group, unrelated woman-infant control group, and paired mother-infant antibiotic-treated group all represent comparisons with the paired mother-infant/child control group. Abbreviations: ESGs, exclusively shared genes.
Figure 2.
Figure 2.
Relative abundance at phylum level.
Figure 3.
Figure 3.
Relative species abundance of children’s fecal samples. Infant samples obtained 3–7 days after birth are shown on the bottom, and samples obtained at 12 months on the top. Species on the left side of the x-axis are species transmitted from the maternal gut microbiome. Only species that with ≥5% relative abundance in any sample are shown. (Individual species and their abundances are available in Supplementary Table 5.)
Figure 4.
Figure 4.
Antimicrobial-resistant (AMR) gene abundance and source of AMR genes in infants’ gut microbiome. The unit of abundance unit is copies per million (the number of reads mapped to the AMR gene per million reads mapped to all genes in the sample). AMR genes in infants transmitted from mothers are not necessarily exclusively shared genes (as listed in Table 1); exclusively shared genes must exist in both mother and infant and must be 100% identical in full gene length. In this figure, an AMR gene in an infant’s sample is considered transmitted if the gene is from a species that can be traced back to the mother’s sample, even if the AMR gene was not found in the mother’s sequencing data.
Figure 5.
Figure 5.
Nonmetric multidimensional scaling (MDS) plot of samples and taxonomic distance between groups. A, X-axis and y-axis are the two MDS dimensions. Each point is a sample. A dashed line connects a mother’s sample to an infant’s sample at 3–7 days after birth, then to that child’s sample at 12 months. The 2 overlapping ellipses cover the mothers’ samples in the control and the antibiotic-treated groups. B, Taxonomic distance (range, 0.0–1.0) between different groups. Both plots were based on Bray-Curtis distance on species relative abundance.

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Source: PubMed

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