A global metagenomic map of urban microbiomes and antimicrobial resistance. Academic Article uri icon

Overview

abstract

  • We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic elements, including 10,928 viruses, 1,302 bacteria, 2 archaea, and 838,532 CRISPR arrays not found in reference databases. We identified 4,246 known species of urban microorganisms and a consistent set of 31 species found in 97% of samples that were distinct from human commensal organisms. Profiles of AMR genes varied widely in type and density across cities. Cities showed distinct microbial taxonomic signatures that were driven by climate and geographic differences. These results constitute a high-resolution global metagenomic atlas that enables discovery of organisms and genes, highlights potential public health and forensic applications, and provides a culture-independent view of AMR burden in cities.

authors

publication date

  • May 26, 2021

Research

keywords

  • Drug Resistance, Bacterial
  • Metagenomics
  • Microbiota
  • Urban Population

Identity

PubMed Central ID

  • PMC8238498

Scopus Document Identifier

  • 85106902108

Digital Object Identifier (DOI)

  • 10.1145/2792745.2792775

PubMed ID

  • 34043940

Additional Document Info

volume

  • 184

issue

  • 13