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  1. Article ; Online: First detection and origin of multi-drug resistant Klebsiella pneumoniae ST15 harboring OXA-48 in South America.

    Salazar, Cecilia / Antelo, Verónica / Vieytes, Mariela / Dávila, Cristina / Grill, Fabio / Galiana, Antonio / Iraola, Gregorio

    Journal of global antimicrobial resistance

    2022  Volume 30, Page(s) 480–484

    Abstract: Objectives: The emergence and spread of carbapenem resistant clones is of major concern for global health. This study aimed to characterize the first detected Klebsiella pneumoniae ST15 harboring the epidemic carbapenemase OXA-48 in South America.: ... ...

    Abstract Objectives: The emergence and spread of carbapenem resistant clones is of major concern for global health. This study aimed to characterize the first detected Klebsiella pneumoniae ST15 harboring the epidemic carbapenemase OXA-48 in South America.
    Methods: During a routine colonization screening with carbapenem-resistant bacteria, one K. pneumoniae strain (CGHM01) was isolated from the urine of a hospitalized patient suffering from a neurodegenerative disease in Uruguay. We used long-read whole-genome sequencing and a phylogenomic approach to characterize the emergence of K. pneumoniae CGHM01.
    Results: K. pneumoniae CGHM01 is a multi-drug resistant strain carrying an IncL/M plasmid that encodes the carbapenemase gene bla
    Conclusions: The asymptomatic carriage of this strain in the urinary tract warns of difficulties for detection and reporting of emerging carbapenem-resistant clones in new geographic areas where these are not endemic.
    MeSH term(s) Carbapenems ; Humans ; Klebsiella Infections/epidemiology ; Klebsiella Infections/microbiology ; Klebsiella pneumoniae/genetics ; Microbial Sensitivity Tests ; Neurodegenerative Diseases ; beta-Lactamases/genetics
    Chemical Substances Carbapenems ; beta-Lactamases (EC 3.5.2.6)
    Language English
    Publishing date 2022-08-09
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2710046-7
    ISSN 2213-7173 ; 2213-7173
    ISSN (online) 2213-7173
    ISSN 2213-7173
    DOI 10.1016/j.jgar.2022.08.005
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Human microbiota drives hospital-associated antimicrobial resistance dissemination in the urban environment and mirrors patient case rates.

    Salazar, Cecilia / Giménez, Matias / Riera, Nadia / Parada, Andrés / Puig, Josefina / Galiana, Antonio / Grill, Fabio / Vieytes, Mariela / Mason, Christopher E / Antelo, Verónica / D'Alessandro, Bruno / Risso, Jimena / Iraola, Gregorio

    Microbiome

    2022  Volume 10, Issue 1, Page(s) 208

    Abstract: Background: The microbial community composition of urban environments is primarily determined by human activity. The use of metagenomics to explore how microbial communities are shaped in a city provides a novel input that can improve decisions on ... ...

    Abstract Background: The microbial community composition of urban environments is primarily determined by human activity. The use of metagenomics to explore how microbial communities are shaped in a city provides a novel input that can improve decisions on public health measures, architectural design, and urban resilience. Of note, the sewage system in a city acts as a complex reservoir of bacteria, pharmaceuticals, and antimicrobial resistant (AMR) genes that can be an important source of epidemiological information. Hospital effluents are rich in patient-derived bacteria and can thus readily become a birthplace and hotspot reservoir for antibiotic resistant pathogens which are eventually incorporated into the environment. Yet, the scope to which nosocomial outbreaks impact the urban environment is still poorly understood.
    Results: In this work, we extensively show that different urban waters from creeks, beaches, sewage spillways and collector pipes enclose discrete microbial communities that are characterized by a differential degree of contamination and admixture with human-derived bacteria. The abundance of human bacteria correlates with the abundance of AMR genes in the environment, with beta-lactamases being the top-contributing class to distinguish low vs. highly-impacted urban environments. Indeed, the abundance of beta-lactamase resistance and carbapenem resistance determinants in the urban environment significantly increased in a 1-year period. This was in line with a pronounced increase of nosocomial carbapenem-resistant infections reported during the same period that was mainly driven by an outbreak-causing, carbapenemase-producing Klebsiella pneumoniae (KPC) ST-11 strain. Genome-resolved metagenomics of urban waters before and after this outbreak, coupled with high-resolution whole-genome sequencing, confirmed the dissemination of the ST-11 strain and a novel KPC megaplasmid from the hospital to the urban environment. City-wide analysis showed that geospatial dissemination of the KPC megaplasmid in the urban environment inversely depended on the sewage system infrastructure.
    Conclusions: We show how urban metagenomics and outbreak genomic surveillance can be coupled to generate relevant information for infection control, antibiotic stewardship, and pathogen epidemiology. Our results highlight the need to better characterize and understand how human-derived bacteria and antimicrobial resistance disseminate in the urban environment to incorporate this information in the development of effluent treatment infrastructure and public health policies. Video Abstract.
    MeSH term(s) Humans ; Anti-Bacterial Agents/pharmacology ; Sewage ; Drug Resistance, Bacterial/genetics ; Microbiota/genetics ; Hospitals ; Cross Infection ; Carbapenems
    Chemical Substances Anti-Bacterial Agents ; Sewage ; Carbapenems
    Language English
    Publishing date 2022-12-02
    Publishing country England
    Document type Video-Audio Media ; Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2697425-3
    ISSN 2049-2618 ; 2049-2618
    ISSN (online) 2049-2618
    ISSN 2049-2618
    DOI 10.1186/s40168-022-01407-8
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Urban metagenomics uncover antibiotic resistance reservoirs in coastal beach and sewage waters.

    Fresia, Pablo / Antelo, Verónica / Salazar, Cecilia / Giménez, Matías / D'Alessandro, Bruno / Afshinnekoo, Ebrahim / Mason, Christopher / Gonnet, Gastón H / Iraola, Gregorio

    Microbiome

    2019  Volume 7, Issue 1, Page(s) 35

    Abstract: Background: Microbial communities present in environmental waters constitute a reservoir for antibiotic-resistant pathogens that impact human health. For this reason, a diverse variety of water environments are being analyzed using metagenomics to ... ...

    Abstract Background: Microbial communities present in environmental waters constitute a reservoir for antibiotic-resistant pathogens that impact human health. For this reason, a diverse variety of water environments are being analyzed using metagenomics to uncover public health threats. However, the composition of these communities along the coastal environment of a whole city, where sewage and beach waters are mixed, is poorly understood.
    Results: We shotgun-sequenced 20 coastal areas from the city of Montevideo (capital of Uruguay) including beach and sewage water samples to characterize bacterial communities and their virulence and antibiotic resistance repertories. As expected, we found that sewage and beach environments present significantly different bacterial communities. This baseline allowed us to detect a higher prevalence and a more diverse repertory of virulence and antibiotic-resistant genes in sewage samples. Many of these genes come from well-known enterobacteria and represent carbapenemases and extended-spectrum betalactamases reported in hospital infections in Montevideo. Additionally, we were able to genotype the presence of both globally disseminated pathogenic clones and emerging antibiotic-resistant bacteria in sewage waters.
    Conclusions: Our study represents the first in using metagenomics to jointly analyze beaches and the sewage system from an entire city, allowing us to characterize antibiotic-resistant pathogens circulating in urban waters. The data generated in this initial study represent a baseline metagenomic exploration to guide future longitudinal (time-wise) studies, whose systematic implementation will provide useful epidemiological information to improve public health surveillance.
    MeSH term(s) Anti-Bacterial Agents/pharmacology ; Bacteria/classification ; Bacteria/genetics ; Bacteria/isolation & purification ; Bacteria/pathogenicity ; Bacterial Proteins/genetics ; Bathing Beaches ; Cross-Sectional Studies ; Drug Resistance, Bacterial ; Humans ; Metagenomics/methods ; Sequence Analysis, DNA ; Sewage/microbiology ; Uruguay ; Water Microbiology
    Chemical Substances Anti-Bacterial Agents ; Bacterial Proteins ; Sewage
    Language English
    Publishing date 2019-02-28
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2697425-3
    ISSN 2049-2618 ; 2049-2618
    ISSN (online) 2049-2618
    ISSN 2049-2618
    DOI 10.1186/s40168-019-0648-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Metagenomic strategies identify diverse integron-integrase and antibiotic resistance genes in the Antarctic environment.

    Antelo, Verónica / Giménez, Matías / Azziz, Gastón / Valdespino-Castillo, Patricia / Falcón, Luisa I / Ruberto, Lucas A M / Mac Cormack, Walter P / Mazel, Didier / Batista, Silvia

    MicrobiologyOpen

    2021  Volume 10, Issue 5, Page(s) e1219

    Abstract: The objective of this study is to identify and analyze integrons and antibiotic resistance genes (ARGs) in samples collected from diverse sites in terrestrial Antarctica. Integrons were studied using two independent methods. One involved the construction ...

    Abstract The objective of this study is to identify and analyze integrons and antibiotic resistance genes (ARGs) in samples collected from diverse sites in terrestrial Antarctica. Integrons were studied using two independent methods. One involved the construction and analysis of intI gene amplicon libraries. In addition, we sequenced 17 metagenomes of microbial mats and soil by high-throughput sequencing and analyzed these data using the IntegronFinder program. As expected, the metagenomic analysis allowed for the identification of novel predicted intI integrases and gene cassettes (GCs), which mostly encode unknown functions. However, some intI genes are similar to sequences previously identified by amplicon library analysis in soil samples collected from non-Antarctic sites. ARGs were analyzed in the metagenomes using ABRIcate with CARD database and verified if these genes could be classified as GCs by IntegronFinder. We identified 53 ARGs in 15 metagenomes, but only four were classified as GCs, one in MTG12 metagenome (Continental Antarctica), encoding an aminoglycoside-modifying enzyme (AAC(6´)acetyltransferase) and the other three in CS1 metagenome (Maritime Antarctica). One of these genes encodes a class D β-lactamase (blaOXA-205) and the other two are located in the same contig. One is part of a gene encoding the first 76 amino acids of aminoglycoside adenyltransferase (aadA6), and the other is a qacG2 gene.
    MeSH term(s) Antarctic Regions ; Bacteria/genetics ; Computational Biology/methods ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; High-Throughput Nucleotide Sequencing ; Integrases/genetics ; Integrons/genetics ; Metagenome ; Metagenomics/methods ; Phylogeny ; Soil Microbiology
    Chemical Substances Integrases (EC 2.7.7.-)
    Language English
    Publishing date 2021-09-03
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2661368-2
    ISSN 2045-8827 ; 2045-8827
    ISSN (online) 2045-8827
    ISSN 2045-8827
    DOI 10.1002/mbo3.1219
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: First Release of the Bacterial Biobank of the Urban Environment (BBUE).

    Antelo, Verónica / Salazar, Cecilia / Martínez, Arací / D'Alessandro, Bruno / Castro, Marta / Betancor, Laura / Barcala, María Victoria / Míguez, Diana / Gonnet, Gastón H / Iraola, Gregorio

    Microbiology resource announcements

    2018  Volume 7, Issue 16

    Abstract: Metagenomics is providing a broad overview of bacterial functional diversity; however, culturing and biobanking are still essential for microbiology. Here, we present the Bacterial Biobank of the Urban Environment (BBUE), a sizable culture collection for ...

    Abstract Metagenomics is providing a broad overview of bacterial functional diversity; however, culturing and biobanking are still essential for microbiology. Here, we present the Bacterial Biobank of the Urban Environment (BBUE), a sizable culture collection for long-term storage and characterization of the microbiota associated with urban environments relevant for public health.
    Language English
    Publishing date 2018-10-25
    Publishing country United States
    Document type Journal Article
    ISSN 2576-098X
    ISSN (online) 2576-098X
    DOI 10.1128/MRA.01201-18
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: 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 / Nikolayeva, Tatyana / Png, Eileen / Ryon, Krista A / Sanchez, Jorge L / Shaaban, Heba / Sierra, Maria A / Thomas, Dominique / Young, Ben / Abudayyeh, Omar O / Alicea, Josue / Bhattacharyya, Malay / Blekhman, Ran / Castro-Nallar, Eduardo / Cañas, Ana M / Chatziefthimiou, Aspassia D / Crawford, Robert W / De Filippis, Francesca / Deng, Youping / Desnues, Christelle / Dias-Neto, Emmanuel / Dybwad, Marius / Elhaik, Eran / Ercolini, Danilo / Frolova, Alina / Gankin, Dennis / Gootenberg, Jonathan S / Graf, Alexandra B / Green, David C / Hajirasouliha, Iman / Hastings, Jaden J.A / Hernandez, Mark / Iraola, Gregorio / Jang, Soojin / Kahles, Andre / Kelly, Frank J / Knights, Kaymisha / Kyrpides, Nikos C / Łabaj, Paweł P / Lee, Patrick K.H / Leung, Marcus H.Y / Ljungdahl, Per O / Mason-Buck, Gabriella / McGrath, Ken / Meydan, Cem / Mongodin, Emmanuel F / Moraes, Milton Ozorio / Nagarajan, Niranjan / Nieto-Caballero, Marina / Noushmehr, Houtan / Oliveira, Manuela / Ossowski, Stephan / Osuolale, Olayinka O / Özcan, Orhan / Paez-Espino, David / Rascovan, Nicolás / Richard, Hugues / Rätsch, Gunnar / Schriml, Lynn M / Semmler, Torsten / Sezerman, Osman U / Shi, Leming / Shi, Tieliu / Siam, Rania / Song, Le Huu / Suzuki, Haruo / Court, Denise Syndercombe / Tighe, Scott W / Tong, Xinzhao / Udekwu, Klas I / Ugalde, Juan A / Valentine, Brandon / Vassilev, Dimitar I / Vayndorf, Elena M / Velavan, Thirumalaisamy P / Wu, Jun / Zambrano, María M / Zhu, Jifeng / Zhu, Sibo / Mason, Christopher E / Abdullah, Natasha / Abraao, Marcos / Adel, Ait-hamlat / Afaq, Muhammad / Al-Quaddoomi, Faisal S / Alam, Ireen / Albuquerque, Gabriela E / Alexiev, Alex / Ali, Kalyn / Alvarado-Arnez, Lucia E / Aly, Sarh / Amachee, Jennifer / Amorim, Maria G / Ampadu, Majelia / Amran, Muhammad Al-Fath / An, Nala / Andrew, Watson / Andrianjakarivony, Harilanto / Angelov, Michael / Antelo, Verónica / Aquino, Catharine / Aranguren, Álvaro / Araujo, Luiza F / Vasquez Arevalo, Hitler Francois / Arevalo, Jenny / Arnan, Carme / Alvarado Arnez, Lucia Elena / Arredondo, Fernanda / Arthur, Matthew / Asenjo, Freddy / Aung, Thomas Saw / Auvinet, Juliette / Aventin, Nuria / Ayaz, Sadaf / Baburyan, Silva / Bakere, Abd-Manaaf / Bakhl, Katrin / Bartelli, Thais F / Batdelger, Erdenetsetseg / Baudon, François / Becher, Kevin / Bello, Carla / Benchouaia, Médine / Benisty, Hannah / Benoiston, Anne-Sophie / Benson, Joseph / Benítez, Diego / Bernardes, Juliana / Bertrand, Denis / Beurmann, Silvia / Bitard-Feildel, Tristan / Bittner, Lucie / Black, Christina / Blanc, Guillaume / Blyther, Brittany / Bode, Toni / Boeri, Julia / Boldgiv, Bazartseren / Bolzli, Kevin / Bordigoni, Alexia / Borrelli, Ciro / Bouchard, Sonia / Bouly, Jean-Pierre / Boyd, Alicia / Branco, Gabriela P / Breschi, Alessandra / Brindefalk, Björn / Brion, Christian / Briones, Alan / Buczansla, Paulina / Burke, Catherine M / Burrell, Aszia / Butova, Alina / Buttar, Irvind / Bynoe, Jalia / Bönigk, Sven / Bøifot, Kari O / Caballero, Hiram / Cai, Xiao Wen / Calderon, Dayana / Cantillo, Angela / Carbajo, Miguel / Carbone, Alessandra / Cardenas, Anais / Carrillo, Katerine / Casalot, Laurie / Castro, Sofia / Castro, Ana V / Castro, Astred / Castro, Ana Valeria B / Cawthorne, Simone / Cedillo, Jonathan / Chaker, Salama / Chalangal, Jasna / Chan, Allison / Chasapi, Anastasia I / Chatziefthimiou, Starr / Chaudhuri, Sreya Ray / Chavan, Akash Keluth / Chavez, Francisco / Chem, Gregory / Chen, Xiaoqing / Chen, Michelle / Chen, Jenn-Wei / Chernomoretz, Ariel / Chettouh, Allaeddine / Cheung, Daisy / Chicas, Diana / Chiu, Shirley / Choudhry, Hira / Chrispin, Carl / Ciaramella, Kianna / Cifuentes, Erika / Cohen, Jake / Coil, David A / Collin, Sylvie / Conger, Colleen / Conte, Romain / Corsi, Flavia / Cossio, Cecilia N / Costa, Ana F / Cuebas, Delisia / D’Alessandro, Bruno / Dahlhausen, Katherine E / Darling, Aaron E / Das, Pujita / Davenport, Lucinda B / David, Laurent / Davidson, Natalie R / Dayama, Gargi / Delmas, Stéphane / Deng, Chris K / Dequeker, Chloé / Desert, Alexandre / Devi, Monika / Dezem, Felipe S / Dias, Clara N / Donahoe, Timothy Ryan / Dorado, Sonia / Dorsey, LaShonda / Dotsenko, Valeriia / Du, Steven / Dutan, Alexandra / Eady, Naya / Eisen, Jonathan A / Elaskandrany, Miar / Epping, Lennard / Escalera-Antezana, Juan P / Ettinger, Cassie L / Faiz, Iqra / Fan, Luice / Farhat, Nadine / Faure, Emile / Fauzi, Fazlina / Feigin, Charlie / Felice, Skye / Ferreira, Laís Pereira / Figueroa, Gabriel / Fleiss, Aubin / Flores, Denisse / Velasco Flores, Jhovana L / Fonseca, Marcos A.S / Foox, Jonathan / Forero, Juan Carlos / Francis, Aaishah / French, Kelly / Fresia, Pablo / Friedman, Jacob / Fuentes, Jaime J / Galipon, Josephine / Garcia, Mathilde / Garcia, Laura / García, Catalina / Geiger, Annie / Gerner, Samuel M / Ghose, Sonia L / Giang, Dao Phuong / Giménez, Matías / Giovannelli, Donato / Githae, Dedan / Gkotzis, Spyridon / Godoy, Liliana / Goldman, Samantha / Gonnet, Gaston H / Gonzalez, Juana / Gonzalez, Andrea / Gonzalez-Poblete, Camila / Gray, Andrew / Gregory, Tranette / Greselle, Charlotte / Guasco, Sophie / Guerra, Juan / Gurianova, Nika / Haehr, Wolfgang / Halary, Sebastien / Hartkopf, Felix / Hawkins-Zafarnia, Arya / Hazrin-Chong, Nur Hazlin / Helfrich, Eric / Hell, Eva / Henry, Tamera / Hernandez, Samuel / Hernandez, Pilar Lopez / Hess-Homeier, David / Hittle, Lauren E / Hoan, Nghiem Xuan / Holik, Aliaksei / Homma, Chiaki / Hoxie, Irene / Huber, Michael / Humphries, Elizabeth / Hyland, Stephanie / Hässig, Andrea / Häusler, Roland / Hüsser, Nathalie / Petit, Robert A / Iderzorig, Badamnyambuu / Igarashi, Mizuki / Iqbal, Shaikh B / Ishikawa, Shino / Ishizuka, Sakura / Islam, Sharah / Islam, Riham / Ito, Kohei / Ito, Sota / Ito, Takayuki / Ivankovic, Tomislav / Iwashiro, Tomoki / Jackson, Sarah / Jacobs, JoAnn / James, Marisano / Jaubert, Marianne / Jerier, Marie-Laure / Jiminez, Esmeralda / Jinfessa, Ayantu / De Jong, Ymke / Joo, Hyun Woo / Jospin, Guilllaume / Kajita, Takema / Ahmad Kassim, Affifah Saadah / Kato, Nao / Kaur, Amrit / Kaur, Inderjit / de Souza Gomes Kehdy, Fernanda / Khadka, Vedbar S / Khan, Shaira / Khavari, Mahshid / Ki, Michelle / Kim, Gina / Kim, Hyung Jun / Kim, Sangwan / King, Ryan J / KoLoMonaco, Giuseppe / Koag, Ellen / Kobko-Litskevitch, Nadezhda / Korshevniuk, Maryna / Kozhar, Michael / Krebs, Jonas / Kubota, Nanami / Kuklin, Andrii / Kumar, Sheelta S / Kwong, Rachel / Kwong, Lawrence / Lafontaine, Ingrid / Lago, Juliana / Lai, Tsoi Ying / Laine, Elodie / Laiola, Manolo / Lakhneko, Olha / Lamba, Isha / de Lamotte, Gerardo / Lannes, Romain / De Lazzari, Eleonora / Leahy, Madeline / Lee, Hyunjung / Lee, Yunmi / Lee, Lucy / Lemaire, Vincent / Leong, Emily / Lewandowska, Dagmara / Li, Chenhao / Liang, Weijun / Lin, Moses / Lisboa, Priscilla / Litskevitch, Anna / Liu, Eric Minwei / Liu, Tracy / Livia, Mayra Arauco / Lo, Yui Him / Losim, Sonia / Loubens, Manon / Lu, Jennifer / Lykhenko, Olexandr / Lysakova, Simona / Mahmoud, Salah / Majid, Sara Abdul / Makogon, Natalka / Maldonado, Denisse / Mallari, Krizzy / Malta, Tathiane M / Mamun, Maliha / Manoir, Dimitri / Marchandon, German / Marciniak, Natalia / Marinovic, Sonia / Marques, Brunna / Mathews, Nicole / Matsuzaki, Yuri / Matthys, Vincent / May, Madelyn / McComb, Elias / Meagher, Annabelle / Melamed, Adiell / Menary, Wayne / Mendez, Katterinne N / Mendez, Ambar / Mendy, Irène Mauricette / Meng, Irene / Menon, Ajay / Menor, Mark / Meoded, Roy / Merino, Nancy / Miah, Karishma / Mignotte, Mathilde / Miketic, Tanja / Miranda, Wilson / Mitsios, Athena / Miura, Ryusei / Miyake, Kunihiko / Moccia, Maria D / Mohan, Natasha / Mohsin, Mohammed / Moitra, Karobi / Moldes, Mauricio / Molina, Laura / Molinet, Jennifer / Molomjamts, Orgil-Erdene / Moniruzzaman, Eftar / Moon, Sookwon / de Oliveira Moraes, Isabelle / Moreno, Mario / Mosella, Maritza S / Moser, Josef W / Mozsary, Christopher / Muehlbauer, Amanda L / Muner, Oasima / Munia, Muntaha / Munim, Naimah / Muscat, Maureen / Mustac, Tatjana / Muñoz, Cristina / Nadalin, Francesca / Naeem, Areeg / Nagy-Szakal, Dorottya / Nakagawa, Mayuko / Narce, Ashanti / Nasu, Masaki / Navarrete, Irene González / Naveed, Hiba / Nazario, Bryan / Nedunuri, Narasimha Rao / Neff, Thomas / Nesimi, Aida / Ng, Wan Chiew / Ng, Synti / Nguyen, Gloria / Ngwa, Elsy / Nicolas, Agier / Nicolas, Pierre / Nika, Abdollahi / Noorzi, Hosna / Nosrati, Avigdor / Nunes, Diana N / O’Brien, Kathryn / O’Hara, Niamh B / Oken, Gabriella / Olawoyin, Rantimi A / Oliete, Javier Quilez / Olmeda, Kiara / Oluwadare, Tolulope / Oluwadare, Itunu A / Ordioni, Nils / Orpilla, Jenessa / Orrego, Jacqueline / Ortega, Melissa / Osma, Princess / Osuolale, Israel O / Osuolale, Oluwatosin M / Ota, Mitsuki / Oteri, Francesco / Oto, Yuya / Ounit, Rachid / Ouzounis, Christos A / Pakrashi, Subhamitra / Paras, Rachel / Pardo-Este, Coral / Park, Young-Ja / Pastuszek, Paulina / Patel, Suraj / Pathmanathan, Jananan / Patrignani, Andrea / Perez, Manuel / Peros, Ante / Persaud, Sabrina / Peters, Anisia / Phillips, Adam / Pineda, Lisbeth / Pizzi, Melissa P / Plaku, Alma / Plaku, Alketa / Pompa-Hogan, Brianna / Portilla, María Gabriela / Posada, Leonardo / Priestman, Max / Prithiviraj, Bharath / Priya, Sambhawa / Pugdeethosal, Phanthira / Pugh, Catherine E / Pulatov, Benjamin / Pupiec, Angelika / Pyrshev, Kyrylo / Qing, Tao / Rahiel, Saher / Rahmatulloev, Savlatjon / Rajendran, Kannan / Ramcharan, Aneisa / Ramirez-Rojas, Adan / Rana, Shahryar / Ratnanandan, Prashanthi / Read, Timothy D / Rehrauer, Hubert / Richer, Renee / Rivera, Alexis / Rivera, Michelle / Robertiello, Alessandro / Robinson, Courtney / Rodríguez, Paula / Rojas, Nayra Aguilar / Roldán, Paul / Rosario, Anyelic / Roth, Sandra / Ruiz, Maria / Boja Ruiz, Stephen Eduard / Russell, Kaitlan / Rybak, Mariia / Sabedot, Thais S / Sabina, Mahfuza / Saito, Ikuto / Saito, Yoshitaka / Malca Salas, Gustavo Adolfo / Salazar, Cecilia / San, Kaung Myat / Sanchez, Jorge / Sanchir, Khaliun / Sankar, Ryan / de Souza Santos, Paulo Thiago / Saravi, Zulena / Sasaki, Kai / Sato, Yuma / Sato, Masaki / Sato, Seisuke / Sato, Ryo / Sato, Kaisei / Sayara, Nowshin / Schaaf, Steffen / Schacher, Oli / Schinke, Anna-Lena M / Schlapbach, Ralph / Schori, Christian / Schriml, Jason R / Segato, Felipe / Sepulveda, Felipe / Serpa, Marianna S / De Sessions, Paola F / Severyn, Juan C / Shakil, Maheen / Shalaby, Sarah / Shari, Aliyah / Shim, Hyenah / Shirahata, Hikaru / Shiwa, Yuh / Da Silva, Ophélie / Silva, Jordana M / Simon, Gwenola / Singh, Shaleni K / Sluzek, Kasia / Smith, Rebecca / So, Eunice / Andreu Somavilla, Núria / Sonohara, Yuya / Rufino de Sousa, Nuno / Souza, Camila / Sperry, Jason / Sprinsky, Nicolas / Stark, Stefan G / La Storia, Antonietta / Suganuma, Kiyoshi / Suliman, Hamood / Sullivan, Jill / Supie, Arif Asyraf Md / Suzuki, Chisato / Takagi, Sora / Takahara, Fumie / Takahashi, Naoya / Takahashi, Kou / Takeda, Tomoki / Takenaka, Isabella K / Tanaka, Soma / 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    Cell. 2021 June 24, v. 184, no. 13

    2021  

    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 ... ...

    Institution The International MetaSUB Consortium
    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 Archaea ; antibiotic resistance ; climate ; forensic sciences ; humans ; metagenomics ; microbial ecology ; microbiome ; public health
    Language English
    Dates of publication 2021-0624
    Size p. 3376-3393.e17.
    Publishing place Elsevier Inc.
    Document type Article
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2021.05.002
    Database NAL-Catalogue (AGRICOLA)

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