A global metagenomic map of urban microbiomes and antimicrobial resistance

David Danko; Daniela Bezdan; Evan E Afshin; Sofia Ahsanuddin; Chandrima Bhattacharya; Daniel J Butler; Kern Rei Chng; Daisy Donnellan; Jochen Hecht; Katelyn Jackson; Katerina Kuchin; Mikhail Karasikov; Abigail Lyons; Lauren Mak; Dmitry Meleshko; Harun Mustafa; Beth Mutai; Russell Y Neches; Amanda Ng; Olga Nikolayeva; Tatyana Nikolayeva; Eileen Png; Krista A Ryon; Jorge L Sanchez; Heba Shaaban; Maria A Sierra; Dominique Thomas; Ben Young; Omar O Abudayyeh; Josue Alicea; Malay Bhattacharyya; Ran Blekhman; Eduardo Castro-Nallar; Ana M Cañas; Aspassia D Chatziefthimiou; Robert W Crawford; Francesca De Filippis; Youping Deng; Christelle Desnues; Emmanuel Dias-Neto; Marius Dybwad; Eran Elhaik; Danilo Ercolini; Alina Frolova; Dennis Gankin; Jonathan S Gootenberg; Alexandra B Graf; David C Green; Iman Hajirasouliha; Jun Wu; Christopher E Mason; International MetaSUB Consortium

doi:10.1016/j.cell.2021.05.002

A global metagenomic map of urban microbiomes and antimicrobial resistance

David Danko, Daniela Bezdan, Evan E Afshin, Sofia Ahsanuddin, Chandrima Bhattacharya, Daniel J Butler, Kern Rei Chng, Daisy Donnellan, Jochen Hecht, Katelyn Jackson, Katerina Kuchin, Mikhail Karasikov, Abigail Lyons, Lauren Mak, Dmitry Meleshko, Harun Mustafa, Beth Mutai, Russell Y Neches, Amanda Ng, Olga NikolayevaTatyana Nikolayeva, Eileen Png, Krista A Ryon, Jorge L Sanchez, Heba Shaaban, Maria A Sierra, Dominique Thomas, Ben Young, Omar O Abudayyeh, Josue Alicea, Malay Bhattacharyya, Ran Blekhman, Eduardo Castro-Nallar, Ana M Cañas, Aspassia D Chatziefthimiou, Robert W Crawford, Francesca De Filippis, Youping Deng, Christelle Desnues, Emmanuel Dias-Neto, Marius Dybwad, Eran Elhaik, Danilo Ercolini, Alina Frolova, Dennis Gankin, Jonathan S Gootenberg, Alexandra B Graf, David C Green, Iman Hajirasouliha, Jun Wu, Christopher E Mason, International MetaSUB Consortium

Bioinformatics

Research output: Contribution to journal › Article › peer-review

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
DOIs	https://doi.org/10.1016/j.cell.2021.05.002
Publication status	Published - 2021 Jun 24

Subject classification (UKÄ)

Microbiology

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1016/j.cell.2021.05.002

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Danko, D., Bezdan, D., Afshin, E. E., Ahsanuddin, S., Bhattacharya, C., Butler, D. J., Chng, K. R., Donnellan, D., Hecht, J., Jackson, K., Kuchin, K., Karasikov, M., Lyons, A., Mak, L., Meleshko, D., Mustafa, H., Mutai, B., Neches, R. Y., Ng, A., ... International MetaSUB Consortium (2021). A global metagenomic map of urban microbiomes and antimicrobial resistance. Cell, 184(13), 3376-3393.e17. https://doi.org/10.1016/j.cell.2021.05.002

@article{7304c8991454487992fc774e334c8248,

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.",

author = "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 Green, {David C} and Iman Hajirasouliha and Jun Wu and Mason, {Christopher E} and {International MetaSUB Consortium}",

year = "2021",

month = jun,

day = "24",

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

language = "English",

volume = "184",

pages = "3376--3393.e17",

journal = "Cell",

issn = "1097-4172",

publisher = "Cell Press",

number = "13",

}

Danko, D, Bezdan, D, Afshin, EE, Ahsanuddin, S, Bhattacharya, C, Butler, DJ, Chng, KR, Donnellan, D, Hecht, J, Jackson, K, Kuchin, K, Karasikov, M, Lyons, A, Mak, L, Meleshko, D, Mustafa, H, Mutai, B, Neches, RY, Ng, A, Nikolayeva, O, Nikolayeva, T, Png, E, Ryon, KA, Sanchez, JL, Shaaban, H, Sierra, MA, Thomas, D, Young, B, Abudayyeh, OO, Alicea, J, Bhattacharyya, M, Blekhman, R, Castro-Nallar, E, Cañas, AM, Chatziefthimiou, AD, Crawford, RW, De Filippis, F, Deng, Y, Desnues, C, Dias-Neto, E, Dybwad, M, Elhaik, E, Ercolini, D, Frolova, A, Gankin, D, Gootenberg, JS, Graf, AB, Green, DC, Hajirasouliha, I, Wu, J, Mason, CE & International MetaSUB Consortium 2021, 'A global metagenomic map of urban microbiomes and antimicrobial resistance', Cell, vol. 184, no. 13, pp. 3376-3393.e17. https://doi.org/10.1016/j.cell.2021.05.002

TY - JOUR

T1 - A global metagenomic map of urban microbiomes and antimicrobial resistance

AU - Danko, David

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 - Green, David C

AU - Hajirasouliha, Iman

AU - Wu, Jun

AU - Mason, Christopher E

AU - 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.

U2 - 10.1016/j.cell.2021.05.002

DO - 10.1016/j.cell.2021.05.002

M3 - Article

C2 - 34043940

SN - 1097-4172

VL - 184

SP - 3376-3393.e17

JO - Cell

JF - Cell

IS - 13

ER -

A global metagenomic map of urban microbiomes and antimicrobial resistance

Abstract

Subject classification (UKÄ)

UN SDGs

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