Systematic review of human gut resistome studies revealed variable definitions and approaches

Gut Microbes. 2020 Nov 9;12(1):1700755. doi: 10.1080/19490976.2019.1700755. Epub 2020 Jan 16.

Abstract

In this review, we highlight the variations of gut resistome studies, which may preclude comparisons and translational interpretations. Of 22 included studies, a range of 12 to 2000 antibiotic resistance (AR) genes were profiled. Overall, studies defined a healthy gut resistome as subjects who had not taken antibiotics in the last three to 12 months prior to sampling. In studies with de novo assembly, AR genes were identified based on variable nucleotide or amino acid sequence similarities. Different marker genes were used for defining resistance to a given antibiotic class. Validation of phenotypic resistance in the laboratory is frequently lacking. Cryptic resistance, collateral sensitivity and the interaction with repressors or promotors were not investigated. International consensus is needed for selecting marker genes to define resistance to a given antibiotic class in addition to uniformity in phenotypic validation and bioinformatics pipelines.

Keywords: Resistome; antibiotic resistance; fecal microbiota transplantation; gut microbiota; meta-genomics.

Publication types

  • Research Support, Non-U.S. Gov't
  • Systematic Review

MeSH terms

  • Anti-Bacterial Agents / pharmacology
  • Bacteria / classification
  • Bacteria / drug effects*
  • Bacteria / genetics*
  • Drug Resistance, Bacterial / genetics*
  • Gastrointestinal Microbiome / drug effects*
  • Gastrointestinal Microbiome / genetics*
  • Gastrointestinal Tract / microbiology
  • Genes, Bacterial
  • Humans

Substances

  • Anti-Bacterial Agents

Grants and funding

We thank the support of funding from Health and Medical Research Fund (Project number 18170082, PI: MI), Food and Health Bureau of the Hong Kong Special Administrative Region, People’s Republic of China. The study was partially supported by a seed fund for gut microbiota research provided by the Faculty of Medicine, The Chinese University of Hong Kong. The funding bodies did not involve in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript.