Abstract
BackgroundFew 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.ResultsDominant 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.ConclusionsWe 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.
Highlights
Over recent years the composition of the gastrointestinal (GI) microbiota has been increasingly implicated in health and disease, with bacterial populations harbouring both beneficial commensals and pathogens
Using shotgun metagenomic sequencing we have captured an early snapshot of the antimicrobial resistance landscape within the gut microbiota of eleven premature infants who did not have proven sepsis or necrotizing enterocolitis
A mixture of benchtop to medium throughput Illumina platforms were used to generate a dataset of 145.6 million paired end (PE) reads (51.4 Gbp sequence data) (Table 1), enabling us to characterise taxonomic and antimicrobial resistance profiles
Summary
Over recent years the composition of the gastrointestinal (GI) microbiota has been increasingly implicated in health and disease, with bacterial populations harbouring both beneficial commensals and pathogens. Previous studies have implicated the GI microbiota as a reservoir of antimicrobial resistance (AMR) genes (Penders et al, 2013), held by, or capable of being transferred to, potential pathogens. How to cite this article Rose et al (2017), Antibiotic resistance potential of the healthy preterm infant gut microbiome. We describe the gut microbiomes from preterm but healthy infants, characterising the taxonomic diversity identified and frequency of antibiotic resistance genes detected. 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
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