A global metagenomic map of urban microbiomes and antimicrobial resistance

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dc.contributor.authorDanko, David
dc.contributor.authorBezdan, Daniela
dc.contributor.authorAfshin, Evan E.
dc.contributor.authorAhsanuddin, Sofia
dc.contributor.authorBhattacharya, Chandrima
dc.contributor.authorButler, Daniel J.
dc.contributor.authorChng, Kern Rei
dc.contributor.authorDonnellan, Daisy
dc.contributor.authorHecht, Jochen
dc.contributor.authorJackson, Katelyn
dc.contributor.authorKuchin, Katerina
dc.contributor.authorKarasikov, Mikhail
dc.contributor.authorLyons, Abigail
dc.contributor.authorMak, Lauren
dc.contributor.authorMeleshko, Dmitry
dc.contributor.authorMustafa, Harun
dc.contributor.authorMutai, Beth
dc.contributor.authorNeches, Russell Y.
dc.contributor.authorNg, Amanda
dc.contributor.authorNikolayeva, Olga
dc.contributor.authorNikolayeva, Tatyana
dc.contributor.authorPng, Eileen
dc.contributor.authorRyon, Krista A.
dc.contributor.authorSanchez, Jorge L.
dc.contributor.authorShaaban, Heba
dc.contributor.authorSierra, Maria A.
dc.contributor.authorThomas, Dominique
dc.contributor.authorYoung, Ben
dc.contributor.authorAbudayyeh, Omar O.
dc.contributor.authorAlicea, Josue
dc.contributor.authorBhattacharyya, Malay
dc.contributor.authorBlekhman, Ran
dc.contributor.authorCastro-Nallar, Eduardo
dc.contributor.authorCanas, Ana M.
dc.contributor.authorChatziefthimiou, Aspassia D.
dc.contributor.authorCrawford, Robert W.
dc.contributor.authorDe Filippis, Francesca
dc.contributor.authorDeng, Youping
dc.contributor.authorDesnues, Christelle
dc.contributor.authorDias-Neto, Emmanuel
dc.contributor.authorDybwad, Marius
dc.contributor.authorElhaik, Eran
dc.contributor.authorErcolini, Danilo
dc.contributor.authorFrolova, Alina
dc.contributor.authorGankin, Dennis
dc.contributor.authorGootenberg, Jonathan S.
dc.contributor.authorGraf, Alexandra B.
dc.contributor.authorGreen, David C.
dc.contributor.authorHajirasouliha, Iman
dc.contributor.authorHastings, Jaden J. A.
dc.contributor.authorHernandez, Mark
dc.contributor.authorIraola, Gregorio
dc.contributor.authorJang, Soojin
dc.contributor.authorKahles, Andre
dc.contributor.authorKelly, Frank J.
dc.contributor.authorKnights, Kaymisha
dc.contributor.authorKyrpides, Nikos C.
dc.contributor.authorLabaj, Pawel P.
dc.contributor.authorLee, Patrick K. H.
dc.contributor.authorLeung, Marcus H. Y.
dc.contributor.authorLjungdahl, Per O.
dc.contributor.authorMason-Buck, Gabriella
dc.contributor.authorMcGrath, Ken
dc.contributor.authorMeydan, Cem
dc.contributor.authorMongodin, Emmanuel F.
dc.contributor.authorMoraes, Milton Ozorio
dc.contributor.authorNagarajan, Niranjan
dc.contributor.authorNieto-Caballero, Marina
dc.contributor.authorNoushmehr, Houtan
dc.contributor.authorOliveira, Manuela
dc.contributor.authorOssowski, Stephan
dc.contributor.authorOsuolale, Olayinka O.
dc.contributor.authorOzcan, Orhan
dc.contributor.authorPaez-Espino, David
dc.contributor.authorRascovan, Nicolas
dc.contributor.authorRichard, Hugues
dc.contributor.authorRatsch, Gunnar
dc.contributor.authorSchriml, Lynn M.
dc.contributor.authorSemmler, Torsten
dc.contributor.authorSezerman, Osman U.
dc.contributor.authorShi, Leming
dc.contributor.authorShi, Tieliu
dc.contributor.authorSiam, Rania
dc.contributor.authorSong, Le Huu
dc.contributor.authorSuzuki, Haruo
dc.contributor.authorCourt, Denise Syndercombe
dc.contributor.authorTighe, Scott W.
dc.contributor.authorTong, Xinzhao
dc.contributor.authorUdekwu I, Klas
dc.contributor.authorUgalde, Juan A.
dc.contributor.authorValentine, Brandon
dc.contributor.authorVassilev I, Dimitar
dc.contributor.authorVayndorf, Elena M.
dc.contributor.authorVelavan, Thirumalaisamy P.
dc.contributor.authorWu, Jun
dc.contributor.authorZambrano, Maria M.
dc.contributor.authorZhu, Jifeng
dc.contributor.authorZhu, Sibo
dc.contributor.authorMason, Christopher E.
dc.contributor.authorConsortium, Int MetaSU. B.
dc.date.accessioned2023-02-21T12:43:08Z
dc.date.available2023-02-21T12:43:08Z
dc.date.issued2021-01-01
dc.description.abstractWe 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.
dc.description.issue13
dc.description.issueJUN 24
dc.description.pages3376+
dc.description.volume184
dc.identifier.doi10.1016/j.cell.2021.05.002
dc.identifier.urihttps://hdl.handle.net/11443/2879
dc.identifier.urihttp://dx.doi.org/10.1016/j.cell.2021.05.002
dc.identifier.wosWOS:000665547300006
dc.publisherCELL PRESS
dc.relation.ispartofCELL
dc.titleA global metagenomic map of urban microbiomes and antimicrobial resistance
dc.typeArticle

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