This review will consider the gut as a reservoir for antimicrobial resistance, colonization resistance, and how disruption of the microbiome can lead to colonization by pathogenic organisms. There is a focus on the gut as a reservoir for β-lactam and plasmid-mediated quinolone resistance. Finally, the role of functional metagenomics and long-read sequencing technologies to detect and understand antimicrobial resistance genes within the gut microbiome is discussed, along with the potential for future microbiome-directed methods to detect and prevent infection.

Original languageEnglish
Pages (from-to)S209-S213
JournalJournal of Infectious Diseases
StatePublished - Jun 15 2021


  • Antibiotic resistance
  • Antimicrobial resistance
  • Microbiome
  • Resistome


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