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Research article - Peer-reviewed, 2021

A global metagenomic map of urban microbiomes and antimicrobial resistance

Danko, David; Bezdan, Daniela; Afshin, Evan E.; Ahsanuddin, Sofia; Bhattacharya, Chandrima; Butler, Daniel J.; Chng, Kern Rei; Donnellan, Daisy; Hecht, Jochen; Jackson, Katelyn; Kuchin, Katerina; Karasikov, Mikhail; Lyons, Abigail; Mak, Lauren; Meleshko, Dmitry; Mustafa, Harun; Mutai, Beth; Neches, Russell Y.; Ng, Amanda; Nikolayeva, Olga;
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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.

Published in

Cell

2021, volume: 184, number: 13, pages: 3376-+
Publisher: CELL PRESS

Authors' information

Danko, David
Cornell University
Bezdan, Daniela
Eberhard Karls University of Tubingen
Bezdan, Daniela
Cornell University
Afshin, Evan E.
Cornell University
Ahsanuddin, Sofia
Icahn School of Medicine at Mount Sinai
Bhattacharya, Chandrima
Cornell University
Butler, Daniel J.
Cornell University
Chng, Kern Rei
Genome Institute of Singapore (GIS)
Donnellan, Daisy
Cornell University
Hecht, Jochen
Pompeu Fabra University
Jackson, Katelyn
Cornell University
Kuchin, Katerina
Cornell University
Karasikov, Mikhail
Univ Hosp Zurich
Karasikov, Mikhail
ETH Zurich
Karasikov, Mikhail
Swiss Institute of Bioinformatics
Lyons, Abigail
Cornell University
Mak, Lauren
Cornell University
Meleshko, Dmitry
Cornell University
Mustafa, Harun
Swiss Institute of Bioinformatics
Mustafa, Harun
Univ Hosp Zurich
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Sustainable Development Goals

SDG3 Good health and wellbeing

UKÄ Subject classification

Bioinformatics and Systems Biology

Publication Identifiers

DOI: https://doi.org/10.1016/j.cell.2021.05.002

URI (permanent link to this page)

https://res.slu.se/id/publ/113028