In silico analysis of antibiotic resistance genes in the gut microflora of individuals from diverse geographies and age-groups

PLoS One. 2013 Dec 31;8(12):e83823. doi: 10.1371/journal.pone.0083823. eCollection 2013.

Abstract

The spread of antibiotic resistance, originating from the rampant and unrestrictive use of antibiotics in humans and livestock over the past few decades has emerged as a global health problem. This problem has been further compounded by recent reports implicating the gut microbial communities to act as reservoirs of antibiotic resistance. We have profiled the presence of probable antibiotic resistance genes in the gut flora of 275 individuals from eight different nationalities. For this purpose, available metagenomic data sets corresponding to 275 gut microbiomes were analyzed. Sequence similarity searches of the genomic fragments constituting each of these metagenomes were performed against genes conferring resistance to around 240 antibiotics. Potential antibiotic resistance genes conferring resistance against 53 different antibiotics were detected in the human gut microflora analysed in this study. In addition to several geography/country-specific patterns, four distinct clusters of gut microbiomes, referred to as 'Resistotypes', exhibiting similarities in their antibiotic resistance profiles, were identified. Groups of antibiotics having similarities in their resistance patterns within each of these clusters were also detected. Apart from this, mobile multi-drug resistance gene operons were detected in certain gut microbiomes. The study highlighted an alarmingly high abundance of antibiotic resistance genes in two infant gut microbiomes. The results obtained in the present study presents a holistic 'big picture' on the spectra of antibiotic resistance within our gut microbiota across different geographies. Such insights may help in implementation of new regulations and stringency on the existing ones.

Publication types

  • Comparative Study

MeSH terms

  • Adult
  • Age Factors
  • Anti-Bacterial Agents / pharmacology*
  • Biomarkers / metabolism
  • Child
  • Computational Biology
  • DNA, Bacterial / genetics
  • Drug Resistance, Bacterial / genetics*
  • Drug Resistance, Multiple / genetics
  • Gastrointestinal Tract / drug effects*
  • Gastrointestinal Tract / metabolism
  • Gastrointestinal Tract / microbiology
  • Gene Expression Profiling*
  • Genes, Bacterial / genetics*
  • Geography
  • Humans
  • Metagenome / genetics*
  • Microbiota / drug effects
  • Microbiota / genetics*
  • Oligonucleotide Array Sequence Analysis

Substances

  • Anti-Bacterial Agents
  • Biomarkers
  • DNA, Bacterial

Grants and funding

The authors have no support or funding to report.