A global metagenomic map of urban microbiomes and antimicrobial resistance

670 authors, including; David Danko; Patrick K.H. Lee; Marcus H.Y. Leung; Xinzhao Tong; Christopher E. Mason; The International MetaSUB Consortium

doi:10.1016/j.cell.2021.05.002

A global metagenomic map of urban microbiomes and antimicrobial resistance

670 authors, including
, David Danko
, Patrick K.H. Lee
, Marcus H.Y. Leung
, Xinzhao Tong
, Christopher E. Mason^*
, The International MetaSUB Consortium

^*Corresponding author for this work

School of Energy and Environment

Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review

299 Citations (Scopus)

119 Downloads (CityUHK Scholars)

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.

Original language	English
Pages (from-to)	3376-3393.e17
Journal	Cell
Volume	184
Issue number	13
Online published	26 May 2021
DOIs	https://doi.org/10.1016/j.cell.2021.05.002
Publication status	Published - 24 Jun 2021

Research Keywords

AMR
antimicrobial resistance
BGC
built Environment
de novo assembly
global health
metagenome
microbiome
NGS
shotgun sequencing

Publisher's Copyright Statement

This full text is made available under CC-BY 4.0. https://creativecommons.org/licenses/by/4.0/

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10.1016/j.cell.2021.05.002

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@article{be18925c520a4778a39c6a7f5ef56b4b,

title = "A global metagenomic map of urban microbiomes and antimicrobial resistance",

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.",

keywords = "AMR, antimicrobial resistance, BGC, built Environment, de novo assembly, global health, metagenome, microbiome, NGS, shotgun sequencing",

author = "\{670 authors, including\} and David Danko and Daniela Bezdan and Afshin, \{Evan E.\} and Sofia Ahsanuddin and Chandrima Bhattacharya and Butler, \{Daniel J.\} and Chng, \{Kern Rei\} and Daisy Donnellan and Jochen Hecht and Katelyn Jackson and Katerina Kuchin and Mikhail Karasikov and Abigail Lyons and Lauren Mak and Dmitry Meleshko and Harun Mustafa and Beth Mutai and Neches, \{Russell Y.\} and Amanda Ng and Olga Nikolayeva and Tatyana Nikolayeva and Eileen Png and Ryon, \{Krista A.\} and Sanchez, \{Jorge L.\} and Heba Shaaban and Sierra, \{Maria A.\} and Dominique Thomas and Ben Young and Abudayyeh, \{Omar O.\} and Josue Alicea and Malay Bhattacharyya and Ran Blekhman and Eduardo Castro-Nallar and Ca{\~n}as, \{Ana M.\} and Chatziefthimiou, \{Aspassia D.\} and Crawford, \{Robert W.\} and \{De Filippis\}, Francesca and Youping Deng and Christelle Desnues and Emmanuel Dias-Neto and Marius Dybwad and Eran Elhaik and Danilo Ercolini and Alina Frolova and Dennis Gankin and Gootenberg, \{Jonathan S.\} and Graf, \{Alexandra B.\} and Lee, \{Patrick K.H.\} and Leung, \{Marcus H.Y.\} and Xinzhao Tong and Mason, \{Christopher E.\} and \{The International MetaSUB Consortium\}",

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month = jun,

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doi = "10.1016/j.cell.2021.05.002",

language = "English",

volume = "184",

pages = "3376--3393.e17",

journal = "Cell",

issn = "0092-8674",

publisher = "Elsevier B.V.",

number = "13",

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AU - 670 authors, including

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AU - Bezdan, Daniela

AU - Afshin, Evan E.

AU - Ahsanuddin, Sofia

AU - Bhattacharya, Chandrima

AU - Butler, Daniel J.

AU - Chng, Kern Rei

AU - Donnellan, Daisy

AU - Hecht, Jochen

AU - Jackson, Katelyn

AU - Kuchin, Katerina

AU - Karasikov, Mikhail

AU - Lyons, Abigail

AU - Mak, Lauren

AU - Meleshko, Dmitry

AU - Mustafa, Harun

AU - Mutai, Beth

AU - Neches, Russell Y.

AU - Ng, Amanda

AU - Nikolayeva, Olga

AU - Nikolayeva, Tatyana

AU - Png, Eileen

AU - Ryon, Krista A.

AU - Sanchez, Jorge L.

AU - Shaaban, Heba

AU - Sierra, Maria A.

AU - Thomas, Dominique

AU - Young, Ben

AU - Abudayyeh, Omar O.

AU - Alicea, Josue

AU - Bhattacharyya, Malay

AU - Blekhman, Ran

AU - Castro-Nallar, Eduardo

AU - Cañas, Ana M.

AU - Chatziefthimiou, Aspassia D.

AU - Crawford, Robert W.

AU - De Filippis, Francesca

AU - Deng, Youping

AU - Desnues, Christelle

AU - Dias-Neto, Emmanuel

AU - Dybwad, Marius

AU - Elhaik, Eran

AU - Ercolini, Danilo

AU - Frolova, Alina

AU - Gankin, Dennis

AU - Gootenberg, Jonathan S.

AU - Graf, Alexandra B.

AU - Lee, Patrick K.H.

AU - Leung, Marcus H.Y.

AU - Tong, Xinzhao

AU - Mason, Christopher E.

AU - The International MetaSUB Consortium

PY - 2021/6/24

Y1 - 2021/6/24

N2 - 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.

AB - 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.

KW - AMR

KW - antimicrobial resistance

KW - BGC

KW - built Environment

KW - de novo assembly

KW - global health

KW - metagenome

KW - microbiome

KW - NGS

KW - shotgun sequencing

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UR - https://www.scopus.com/record/pubmetrics.uri?eid=2-s2.0-85106902108&origin=recordpage

UR - https://app-overton-io.ezproxy.cityu.edu.hk/articles.php?query=10.1016/j.cell.2021.05.002

U2 - 10.1016/j.cell.2021.05.002

DO - 10.1016/j.cell.2021.05.002

M3 - RGC 21 - Publication in refereed journal

C2 - 34043940

SN - 0092-8674

VL - 184

SP - 3376-3393.e17

JO - Cell

JF - Cell

IS - 13

ER -

A global metagenomic map of urban microbiomes and antimicrobial resistance

Abstract

Research Keywords

Publisher's Copyright Statement

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GRF: A Meta-analysis of the Hong Kong Built Environment Microbiomes

Cite this

A global metagenomic map of urban microbiomes and antimicrobial resistance

Abstract

Research Keywords

Publisher's Copyright Statement

Policy Impact

ESI Highly Cited Papers

Access Output

Other Access Options

Permanent Link

Other Files and Links

Fingerprint

Projects

GRF: A Meta-analysis of the Hong Kong Built Environment Microbiomes

Cite this