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Metagenomic insights into resistome, mobilome and virulome in different fecal waste

Zhiguo Su1, Saishi Cui2, Donghui Wen3

  • 1School of Environment, Tsinghua University, Beijing 100084, China.

Environmental Research
|August 29, 2024
PubMed

Insights

Fecal waste significantly contributes to antimicrobial resistance (AMR) pollution. Cattle feces show the lowest AMR risk determinants, while specific genes and microbes indicate pollution sources.

Area of Science:

  • Environmental microbiology
  • Antimicrobial resistance
  • One Health

Background:

  • Fecal waste is a major source of antimicrobial resistance (AMR) pollution.
  • Antimicrobial resistance determinants (ARDs) include antibiotic resistance genes (ARGs), biocide and metal resistance genes (BMGs), mobile genetic elements (MGEs), and virulence factor genes (VFGs).
  • Limited research exists on ARD compositional differences across various fecal types.

Purpose of the Study:

  • To analyze the compositional characteristics of ARDs in human, pig, chicken, and cattle feces.
  • To identify key ARDs and their hosts in fecal waste.
  • To develop methods for tracking AMR pollution from fecal sources.

Main Methods:

  • Analysis of 753 public metagenomes from diverse fecal sources.
  • Comparative analysis of ARD richness and abundance.
  • Correlation analysis between microbial composition and ARDs using Procrustes analysis.
  • Identification of indicator genes using random forest methods.

Main Results:

  • Significant variations in ARD richness and abundance were observed across fecal types, with cattle samples exhibiting the lowest levels.
  • Tetracycline, multi-metal, and multi-biocide resistance genes were the dominant resistome.
  • Microbial composition strongly correlated with ARGs and BMGs.
  • Gammaproteobacteria were identified as major hosts for ARDs, particularly in human and pig feces.
  • MGEs positively influenced ARGs and BMGs, with indirect effects on VFGs.

Conclusions:

  • Fecal waste composition significantly impacts AMR pollution profiles.
  • Specific microbial communities and genetic elements are key drivers of AMR in fecal waste.
  • Identified indicator genes provide a tool for monitoring environmental AMR pollution from fecal origins.
Keywords:
Antimicrobial resistance (AMR)FecesIndicator genesMetagenomicsMicrobial community

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