Antibiotic resistance potential of the healthy preterm infant gut microbiome.
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 includedC. perfringens,K. pneumoniaeand members of theStaphylococciandEnterobactergenera. 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 ofmecAand high levels ofStaphylococciwithin some infants. We were able to demonstrate that in a third of the infants theS. aureusidentified 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.
Genomics Research Unit, Public Health England , London , United Kingdom.
Graham
G
Rose
Department of Medicine, Imperial College London , London , United Kingdom.
Alexander G
AG
Shaw
Department of Medicine, Imperial College London , London , United Kingdom.
Kathleen
K
Sim
Genomics Research Unit, Public Health England , London , United Kingdom.
David J
DJ
Wooldridge
Department of Medicine, Imperial College London , London , United Kingdom.
Ming-Shi
MS
Li
Genomics Research Unit, Public Health England , London , United Kingdom.
Saheer
S
Gharbia
Genomics Research Unit, Public Health England , London , United Kingdom.
Raju
R
Misra
Section of Paediatrics, Department of Medicine, Imperial College London , London , United Kingdom.
John Simon
JS
Kroll
Antibiotic resistance; Gut microbiome; Preterm infants; Shotgun metagenomics