Antibiotic resistance potential of the healthy preterm infant gut microbiome

Abstract

Background: Few studies have investigated the gut microbiome of infants, fewer still preterm infants. In this study we sought to quantify and interrogate the resistome within a cohort of premature infants using shotgun metagenomic sequencing. We describe the gut microbiomes from preterm but healthy infants, characterising the taxonomic diversity identified and frequency of antibiotic resistance genes detected.

Results: Dominant clinically important species identified within the microbiomes included C. perfringens, K. pneumoniae and members of the Staphylococci and Enterobacter genera. Screening at the gene level we identified an average of 13 antimicrobial resistance genes per preterm infant, ranging across eight different antibiotic classes, including aminoglycosides and fluoroquinolones. Some antibiotic resistance genes were associated with clinically relevant bacteria, including the identification of mecA and high levels of Staphylococci within some infants. We were able to demonstrate that in a third of the infants the S. aureus identified was unrelated using MLST or metagenome assembly, but low abundance prevented such analysis within the remaining samples.

Conclusions: We found that the healthy preterm infant gut microbiomes in this study harboured a significant diversity of antibiotic resistance genes. This broad picture of resistances and the wider taxonomic diversity identified raises further caution to the use of antibiotics without consideration of the resident microbial communities.

Keywords: Antibiotic resistance; Gut microbiome; Preterm infants; Shotgun metagenomics.

Figure 1. Healthy premature infant gut microbiome.

(A) Metagenomic profiles for the eleven preterm samples and four replicates at the species level. Samples clustered by UPGMA using Bray–Curtis distances shown on left, with replicates highlighted by filled nodes. Relative abundances by rank order shown on right, with the top 8 most abundant species coloured and labelled, leaving remaining species in white. (B) Dominant species, based on ≥50% abundance, shown on x-axis, with overall prevalence of the species across samples shown on y-axis. Sample number reflects eleven neonates as replicates are averaged. The five labelled species are present in five or more samples with at least one in >50% abundance. (C) Principal coordinates analysis (PCoA) using Bray–Curtis distances at the species level for all fifteen samples. Separation of the three broad sample groups shown by biplot of the top five species.

Figure 2. Antibiotic resistance genes detected.

Heatmap showing distribution of the 39 AMR genes detected within the eleven metagenomic samples. Genes grouped by antibiotic class are demarcated by black lines under gene names: AGly (aminoglycosides), Bla (β-lactam), Fos (Fosfomycin), Flq (fluoroquinolones), MLS (macrolide-lincosamide- streptogramin), Phe (phenicols), Tet (tetracyclines), Tmt (trimethoprim). Colours show read depth in bp: undetected (grey), 3–199 bp (blue), 200–399 bp (yellow), 400–1,437 (red). Rows clustered by UPGMA method using Euclidean distances.