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1. A global metagenomic map of urban microbiomes and antimicrobial resistance.

Author

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 JA, Hernandez, Mark, Iraola, Gregorio, Jang, Soojin, Kahles, Andre, Kelly, Frank J, Knights, Kaymisha, Kyrpides, Nikos C, Łabaj, Paweł P, Lee, Patrick KH, Leung, Marcus HY, 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, and International MetaSUB Consortium

Subjects
International MetaSUB Consortium, AMR, BGC, NGS, antimicrobial resistance, built Environment, de novo assembly, global health, metagenome, microbiome, shotgun sequencing, Antimicrobial Resistance, Biotechnology, Human Genome, Genetics, Infection, Developmental Biology, Biological Sciences, Medical and Health Sciences
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
2021

5. Annotating unknown species of urban microorganisms on a global scale unveils novel functional diversity and local environment association

Author

Wu, Jun, Danko, David, Afshinnekoo, Ebrahim, Bezdan, Daniela, Bhattacharyya, Malay, Castro-Nallar, Eduardo, Chmielarczyk, Agnieszka, Hazrin-Chong, Nur Hazlin, Deng, Youping, Dias-Neto, Emmanuel, Frolova, Alina, Mason-Buck, Gabriella, Iraola, Gregorio, Jang, Soojin, Łabaj, Paweł, Lee, Patrick K.H., Nieto-Caballero, Marina, Osuolale, Olayinka O., Ouzounis, Christos A., Perlin, Michael H., Prithiviraj, Bharath, Rascovan, Nicolás, Różańska, Anna, Schriml, Lynn M., Semmler, Torsten, Suzuki, Haruo, Ugalde, Juan A., Young, Ben, Werner, Johannes, Zambrano, Maria Mercedes, Zhao, Yongxiang, Mason, Christopher, and Shi, Tieliu

Published
2022
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7. Real-Time Genomic Surveillance for SARS-CoV-2 Variants of Concern, Uruguay

Author

Rego, Natalia, Costabile, Alicia, Paz, Mercedes, Salazar, Cecilia, Perbolianachis, Paula, Spangenberg, Lucia, Ferres, Ignacio, Arce, Rodrigo, Fajardo, Alvaro, Arleo, Mailen, Possi, Tania, Reyes, Natalia, Bentancor, Ma Noel, Lizasoain, Andres, Benitez, Maria Jose, Bortagaray, Viviana, Moller, Ana, Bello, Gonzalo, Arantes, Ighor, Brandes, Mariana, Smircich, Pablo, Chappos, Odhille, Duquia, Melissa, Gonzalez, Belen, Griffero, Luciana, Mendez, Mauricio, Techera, Ma Pia, Zanetti, Juan, Rivera, Bernardina, Maidana, Matias, Alonso, Martina, Alonso, Cecilia, Medina, Julio, Albornoz, Henry, Colina, Rodney, Noya, Veronica, Iraola, Gregorio, Fernandez-Calero, Tamara, Moratorio, Gonzalo, and Moreno, Pilar

Subjects
Statistics, Identification and classification, Distribution, Methods, Company distribution practices, Polymerase chain reaction -- Methods, Disease transmission -- Statistics, SARS-CoV-2 variants -- Identification and classification -- Distribution, Epidemics -- Statistics -- Uruguay, COVID-19 -- Statistics, Genomics -- Methods
Abstract

By late 2020, because of natural viral evolution, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genetic variants emerged, some of which show increased transmissibility and cause more severe coronavirus disease [...]

Published
2021
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8. A global metagenomic map of urban microbiomes and antimicrobial resistance

Author

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, Hastings, Jaden J.A., 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., III, 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., Knights, Kaymisha, 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, Leung, Marcus H.Y., 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, Meydan, Cem, 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, Noushmehr, Houtan, 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., Shaaban, Heba, Shakil, Maheen, Shalaby, Sarah, Shari, Aliyah, Shim, Hyenah, Shirahata, Hikaru, Shiwa, Yuh, Siam, Rania, 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, Tang, Anyi, Man Tang, Yuk, Tarcitano, Emilio, Tassinari, Andrea, Taye, Mahdi, Terrero, Alexis, Thambiraja, Eunice, Thiébaut, Antonin, Thomas, Sade, Thomas, Andrew M., Togashi, Yuto, Togashi, Takumi, Tomaselli, Anna, Tomita, Masaru, Tomita, Itsuki, Tong, Xinzhao, Toth, Oliver, Toussaint, Nora C., Tran, Jennifer M., Truong, Catalina, Tsonev, Stefan I., Tsuda, Kazutoshi, Tsurumaki, Takafumi, Tuz, Michelle, Tymoshenko, Yelyzaveta, Urgiles, Carmen, Usui, Mariko, Vacant, Sophie, Valentine, Brandon, Vann, Laura E., Velter, Fabienne, Ventorino, Valeria, Vera-Wolf, Patricia, Vicedomini, Riccardo, Suarez-Villamil, Michael A., Vincent, Sierra, Vivancos-Koopman, Renee, Wan, Andrew, Wang, Cindy, Warashina, Tomoro, Watanabe, Ayuki, Weekes, Samuel, Werner, Johannes, Westfall, David, Wieler, Lothar H., Williams, Michelle, Wolf, Silver A., Wong, Brian, Wong, Yan Ling, Wong, Tyler, Wright, Rasheena, Wunderlin, Tina, Yamanaka, Ryota, Yang, Jingcheng, Yano, Hirokazu, Yeh, George C., Yemets, Olena, Yeskova, Tetiana, Yoshikawa, Shusei, Zafar, Laraib, Zhang, Yang, Zhang, Shu, Zhang, Amy, Zheng, Yuanting, Zubenko, Stas, 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., 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, Hernandez, Mark, Iraola, Gregorio, Jang, Soojin, Kahles, Andre, Kelly, Frank J., Kyrpides, Nikos C., Łabaj, Paweł P., Lee, Patrick K.H., Ljungdahl, Per O., Mason-Buck, Gabriella, McGrath, Ken, Mongodin, Emmanuel F., Moraes, Milton Ozorio, Nagarajan, Niranjan, Nieto-Caballero, Marina, 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, Song, Le Huu, Suzuki, Haruo, Court, Denise Syndercombe, Tighe, Scott W., Udekwu, Klas I., Ugalde, Juan A., Vassilev, Dimitar I., Vayndorf, Elena M., Velavan, Thirumalaisamy P., Wu, Jun, Zambrano, María M., Zhu, Jifeng, Zhu, Sibo, and Mason, Christopher E.

Published
2021
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14. Integrated genomic epidemiology and phenotypic profiling of Clostridium difficile across intra-hospital and community populations in Colombia

Author

Muñoz, Marina, Restrepo-Montoya, Daniel, Kumar, Nitin, Iraola, Gregorio, Camargo, Milena, Díaz-Arévalo, Diana, Roa-Molina, Nelly S., Tellez, Mayra A., Herrera, Giovanny, Ríos-Chaparro, Dora I., Birchenall, Claudia, Pinilla, Darío, Pardo-Oviedo, Juan M., Rodríguez-Leguizamón, Giovanni, Josa, Diego F., Lawley, Trevor D., Patarroyo, Manuel A., and Ramírez, Juan David

Published
2019
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19. Comprehensive Phenotyping in Inflammatory Bowel Disease: Search for Biomarker Algorithms in the Transkingdom Interactions Context

Author

Rosso, Ayelén D., primary, Aguilera, Pablo, additional, Quesada, Sofía, additional, Mascardi, Florencia, additional, Mascuka, Sebastian N., additional, Cimolai, María C., additional, Cerezo, Jimena, additional, Spiazzi, Renata, additional, Conlon, Carolina, additional, Milano, Claudia, additional, Iraola, Gregorio M., additional, Penas-Steinhardt, Alberto, additional, and Belforte, Fiorella S., additional

Published
2022
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20. A history of the MetaSUB consortium: Tracking urban microbes around the globe

Author

Ryon, Krista A., primary, Tierney, Braden T., additional, Frolova, Alina, additional, Kahles, Andre, additional, Desnues, Christelle, additional, Ouzounis, Christos, additional, Gibas, Cynthia, additional, Bezdan, Daniela, additional, Deng, Youping, additional, He, Ding, additional, Dias-Neto, Emmanuel, additional, Elhaik, Eran, additional, Afshin, Evan, additional, Grills, George, additional, Iraola, Gregorio, additional, Suzuki, Haruo, additional, Werner, Johannes, additional, Udekwu, Klas, additional, Schriml, Lynn, additional, Bhattacharyya, Malay, additional, Oliveira, Manuela, additional, Zambrano, Maria Mercedes, additional, Hazrin-Chong, Nur Hazlin, additional, Osuolale, Olayinka, additional, Łabaj, Paweł P., additional, Tiasse, Prisca, additional, Rapuri, Sampath, additional, Borras, Silvia, additional, Pozdniakova, Sofya, additional, Shi, Tieliu, additional, Sezerman, Ugur, additional, Rodo, Xavier, additional, Sezer, Zehra Hazal, additional, and Mason, Christopher E., additional

Published
2022
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22. What have we learned from a case of convalescent plasma treatment in a two-time kidney transplant recipient COVID-19 patient? A case report from the perspective of viral load evolution and immune response.

Author

Aldunate, Fabian, Fajardo, Alvaro, Ibañez, Natalia, Rammauro, Florencia, Daghero, Hellen, Arce, Rodrigo, Ferla, Diego, Pereira-Gomez, Marianoel, Salazar, Cecilia, Iraola, Gregorio, Pritsch, Otto, Hurtado, Javier, Tenzi, Jordan, Bollati-Fogolín, Mariela, Bianchi, Sergio, Nin, Nicolas, Moratorio, Gonzalo, and Moreno, Pilar

Published
2023
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24. ¿What did we learn from Convalescent plasma treatment in a COVID-19 patient two-time kidney transplanted? A case report from the viral and immune response evolution perspective

Author

Aldunate, Fabian, primary, Fajardo, Alvaro, additional, Rammauro, Florencia, additional, Daghero, Hellen, additional, Arce, Rodrigo, additional, Ferla, Diego, additional, Pereira-Gomez, Marianoel, additional, Ibañez, Natalia, additional, Salazar, Cecilia, additional, Iraola, Gregorio, additional, Pritsch, Otto, additional, Bollati, Mariella, additional, Hurtado, Javier, additional, Tenzi, Jordan, additional, Bianchi, Sergio, additional, Nin, Nicolas, additional, Moratorio, Gonzalo, additional, and Moreno, Pilar, additional

Published
2022
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26. Human microbiota drives hospital-associated antimicrobial resistance dissemination in the urban environment and mirrors patient case rates

Author

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

Published
2022
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27. A history of the MetaSUB consortium:Tracking urban microbes around the globe

Author

Ryon, Krista A., Tierney, Braden T., Frolova, Alina, Kahles, Andre, Desnues, Christelle, Ouzounis, Christos, Gibas, Cynthis, Bezdan, Daniela, Deng, Youping, He, Ding, Dias-Neto, Emmanuel, Elhaik, Eran, Afshin, Evan, Grills, George, Iraola, Gregorio, Suzuki, Haruo, Werner, Johannes, Udekwu, Klas, Schriml, Lynn, Bhattacharyya, Malay, Oliveira, Manuela, Zambrano, Maria Mercedes, Hazrin-Chong, Nur Hazlin, Osuolale, Olayinka, Łabaj, Paweł P., Tiasse, Prisca, Rapuri, Sampath, Borras, Silvia, Pozdniakova, Sofya, Shi, Tieliu, Sezerman, Ugur, Rodo, Xavier, Sezer, Zehra Hazal, Mason, Christopher E., Ryon, Krista A., Tierney, Braden T., Frolova, Alina, Kahles, Andre, Desnues, Christelle, Ouzounis, Christos, Gibas, Cynthis, Bezdan, Daniela, Deng, Youping, He, Ding, Dias-Neto, Emmanuel, Elhaik, Eran, Afshin, Evan, Grills, George, Iraola, Gregorio, Suzuki, Haruo, Werner, Johannes, Udekwu, Klas, Schriml, Lynn, Bhattacharyya, Malay, Oliveira, Manuela, Zambrano, Maria Mercedes, Hazrin-Chong, Nur Hazlin, Osuolale, Olayinka, Łabaj, Paweł P., Tiasse, Prisca, Rapuri, Sampath, Borras, Silvia, Pozdniakova, Sofya, Shi, Tieliu, Sezerman, Ugur, Rodo, Xavier, Sezer, Zehra Hazal, and Mason, Christopher E.

Abstract

The MetaSUB Consortium, founded in 2015, is a global consortium with an interdisciplinary team of clinicians, scientists, bioinformaticians, engineers, and designers, with members from more than 100 countries across the globe. This network has continually collected samples from urban and rural sites including subways and transit systems, sewage systems, hospitals, and other environmental sampling. These collections have been ongoing since 2015 and have continued when possible, even throughout the COVID-19 pandemic. The consortium has optimized their workflow for the collection, isolation, and sequencing of DNA and RNA collected from these various sites and processing them for metagenomics analysis, including the identification of SARS-CoV-2 and its variants. Here, the Consortium describes its foundations, and its ongoing work to expand on this network and to focus its scope on the mapping, annotation, and prediction of emerging pathogens, mapping microbial evolution and antibiotic resistance, and the discovery of novel organisms and biosynthetic gene clusters.

Published
2022

28. A history of the MetaSUB consortium : Tracking urban microbes around the globe

Author

Ryon, Krista A., Tierney, Braden T., Frolova, Alina, Kahles, Andre, Desnues, Christelle, Ouzounis, Christos, Gibas, Cynthis, Bezdan, Daniela, Deng, Youping, He, Ding, Dias-Neto, Emmanuel, Elhaik, Eran, Afshin, Evan, Grills, George, Iraola, Gregorio, Suzuki, Haruo, Werner, Johannes, Udekwu, Klas, Schriml, Lynn, Bhattacharyya, Malay, Oliveira, Manuela, Zambrano, Maria Mercedes, Hazrin-Chong, Nur Hazlin, Osuolale, Olayinka, Labaj, Pawel P., Tiasse, Prisca, Rapuri, Sampath, Borras, Silvia, Pozdniakova, Sofya, Shi, Tieliu, Sezerman, Ugur, Rodo, Xavier, Sezer, Zehra Hazal, Mason, Christopher E., Ryon, Krista A., Tierney, Braden T., Frolova, Alina, Kahles, Andre, Desnues, Christelle, Ouzounis, Christos, Gibas, Cynthis, Bezdan, Daniela, Deng, Youping, He, Ding, Dias-Neto, Emmanuel, Elhaik, Eran, Afshin, Evan, Grills, George, Iraola, Gregorio, Suzuki, Haruo, Werner, Johannes, Udekwu, Klas, Schriml, Lynn, Bhattacharyya, Malay, Oliveira, Manuela, Zambrano, Maria Mercedes, Hazrin-Chong, Nur Hazlin, Osuolale, Olayinka, Labaj, Pawel P., Tiasse, Prisca, Rapuri, Sampath, Borras, Silvia, Pozdniakova, Sofya, Shi, Tieliu, Sezerman, Ugur, Rodo, Xavier, Sezer, Zehra Hazal, and Mason, Christopher E.

Abstract

The MetaSUB Consortium, founded in 2015, is a global consortium with an interdisciplinary team of clinicians, scientists, bioinformaticians, engineers, and designers, with members from more than 100 countries across the globe. This network has continually collected samples from urban and rural sites including subways and transit systems, sewage systems, hospitals, and other environmental sampling. These collections have been ongoing since 2015 and have continued when possible, even throughout the COVID-19 pandemic. The consortium has optimized their workflow for the collection, isolation, and sequencing of DNA and RNA collected from these various sites and processing them for metagenomics analysis, including the identification of SARS-CoV-2 and its variants. Here, the Consortium describes its foundations, and its ongoing work to expand on this network and to focus its scope on the mapping, annotation, and prediction of emerging pathogens, mapping microbial evolution and antibiotic resistance, and the discovery of novel organisms and biosynthetic gene clusters.

Published
2022
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29. A Two-Time Point Analysis of Gut Microbiota in the General Population of Buenos Aires and Its Variation Due to Preventive and Compulsory Social Isolation During the COVID-19 Pandemic

Author

Aguilera, Pablo, primary, Mascardi, María Florencia, additional, Belforte, Fiorella Sabrina, additional, Rosso, Ayelén Daiana, additional, Quesada, Sofía, additional, Llovet, Ignacio, additional, Iraola, Gregorio, additional, Trinks, Julieta, additional, and Penas-Steinhardt, Alberto, additional

Published
2022
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31. One-Year Monitoring SARS-CoV-2 RNA Surface Contamination in Hospitals Reveals No Correlation with Organic Material and Negative Pressure as a Limiting Factor for Contamination

Author

Pereira-Gomez, Marianoel, primary, Arce, Rodrigo, additional, Ferla, Diego, additional, Simon, Diego, additional, Salazar, Cecilia, additional, Perbolianachis, Paula, additional, Costábile, Alicia, additional, Fajardo, Alvaro, additional, Aldunate, Fabian, additional, Nin, Nicolas, additional, Hurtado, José Francisco, additional, Iraola, Gregorio, additional, Moreno, Pilar, additional, and Moratorio, Gonzalo, additional

Published
2022
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35. Emergence and Spread of a B.1.1.28-Derived P.6 Lineage with Q675H and Q677H Spike Mutations in Uruguay

Author

Rego, Natalia, primary, Salazar, Cecilia, additional, Paz, Mercedes, additional, Costábile, Alicia, additional, Fajardo, Alvaro, additional, Ferrés, Ignacio, additional, Perbolianachis, Paula, additional, Fernández-Calero, Tamara, additional, Noya, Veronica, additional, Machado, Matias R., additional, Brandes, Mariana, additional, Arce, Rodrigo, additional, Arleo, Mailen, additional, Possi, Tania, additional, Reyes, Natalia, additional, Bentancor, María Noel, additional, Lizasoain, Andrés, additional, Bortagaray, Viviana, additional, Moller, Ana, additional, Chappos, Odhille, additional, Nin, Nicolas, additional, Hurtado, Javier, additional, Duquía, Melissa, additional, González, Maria Belén, additional, Griffero, Luciana, additional, Méndez, Mauricio, additional, Techera, Maria Pía, additional, Zanetti, Juan, additional, Pereira, Emiliano, additional, Rivera, Bernardina, additional, Maidana, Matías, additional, Alonso, Martina, additional, Smircich, Pablo, additional, Arantes, Ighor, additional, Mir, Daiana, additional, Alonso, Cecilia, additional, Medina, Julio, additional, Albornoz, Henry, additional, Colina, Rodney, additional, Bello, Gonzalo, additional, Moreno, Pilar, additional, Moratorio, Gonzalo, additional, Iraola, Gregorio, additional, and Spangenberg, Lucía, additional

Published
2021
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36. Case Report: Early Transcontinental Import of SARS-CoV-2 Variant of Concern 202012/01 (B.1.1.7) From Europe to Uruguay

Author

Salazar, Cecilia, primary, Costabile, Alicia, additional, Ferrés, Ignacio, additional, Perbolianachis, Paula, additional, Pereira-Gómez, Marianoel, additional, Simón, Diego, additional, Galiana, Antonio, additional, Pi, Beatriz, additional, Antelo, Virginia, additional, García, Rosario, additional, Moreno, Pilar, additional, Moratorio, Gonzalo, additional, and Iraola, Gregorio, additional

Published
2021
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37. Implementation of a qPCR assay coupled with genomic surveillance for real-time monitoring of SARS-CoV-2 variants of concern

Author

Rego, Natalia, primary, Costábile, Alicia, additional, Paz, Mercedes, additional, Salazar, Cecilia, additional, Perbolianachis, Paula, additional, Spangenberg, Lucía, additional, Ferrés, Ignacio, additional, Arce, Rodrigo, additional, Fajardo, Alvaro, additional, Arleo, Mailen, additional, Possi, Tania, additional, Bellini, Inés, additional, Bilbao, Lucia, additional, Reyes, Natalia, additional, Bentancor, Ma Noel, additional, Lizasoain, Andrés, additional, Benítez, María José, additional, Castells, Matías, additional, Victoria, Matías, additional, Maya, Leticia, additional, Bortagaray, Viviana, additional, Moller, Ana, additional, Bello, Gonzalo, additional, Arantes, Ighor, additional, Brandes, Mariana, additional, Smircich, Pablo, additional, Chappos, Odhille, additional, Duquía, Melissa, additional, González, Belén, additional, Griffero, Luciana, additional, Méndez, Mauricio, additional, Techera, Ma Pía, additional, Zanetti, Juan, additional, Rivera, Bernardina, additional, Maidana, Matías, additional, Alonso, Martina, additional, Alonso, Cecilia, additional, Medina, Julio, additional, Albornoz, Henry, additional, Colina, Rodney, additional, Noya, Veronica, additional, Iraola, Gregorio, additional, Fernández-Calero, Tamara, additional, Moratorio, Gonzalo, additional, and Moreno, Pilar, additional

Published
2021
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38. COVID-19 drug practices risk antimicrobial resistance evolution

Author

Afshinnekoo, Ebrahim, primary, Bhattacharya, Chandrima, additional, Burguete-García, Ana, additional, Castro-Nallar, Eduardo, additional, Deng, Youping, additional, Desnues, Christelle, additional, Dias-Neto, Emmanuel, additional, Elhaik, Eran, additional, Iraola, Gregorio, additional, Jang, Soojin, additional, Łabaj, Paweł P, additional, Mason, Christopher E, additional, Nagarajan, Niranjan, additional, Poulsen, Michael, additional, Prithiviraj, Bharath, additional, Siam, Rania, additional, Shi, Tieliu, additional, Suzuki, Haruo, additional, Werner, Johannes, additional, Zambrano, Maria Mercedes, additional, and Bhattacharyya, Malay, additional

Published
2021
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40. New insights in Ulcerative Colitis Associated Gut Microbiota in South American Population: Akkermansia and Collinsella, two distinctive genera found in Argentine subjects

Author

Ayelén, Rosso, primary, Pablo, Aguilera, additional, Sofía, Quesada, additional, Jimena, Cerezo, additional, Renata, Spiazzi, additional, Carolina, Conlon, additional, Claudia, Milano, additional, Iraola, Gregorio, additional, Federico, Coluccio Leskow, additional, Alberto, Penas-Steinhardt, additional, and Belforte Fiorella, S., additional

Published
2020
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44. First detection and origin of multi-drug resistant Klebsiella pneumoniaeST15 harboring OXA-48 in South America

Author

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

Abstract

•First detection of Klebsiella pneumoniaeepidemic clone ST15 in South America.•This clone originated from Spanish strains circulating since 2013.•Whole-genome sequencing revealed duplication of ESBL genes and OXA-48 carbapenemase.•Carriage in the urinary tract highlights the importance of active surveillance.

Published
2022
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45. Phylogenetic analyses of Mycobacterium ulcerans from French Guiana using combination of core and accessory genomes

Author

Reynaud, Yann, Fresia, P., Iraola, Gregorio, Institut Pasteur de la Guadeloupe, Réseau International des Instituts Pasteur (RIIP), Bioinformatics / Bioinformática [Montevideo], Institut Pasteur de Montevideo, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), and FALCO, Eliane

Subjects
[SDV.MHEP] Life Sciences [q-bio]/Human health and pathology, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract

International audience; In South America, French Guiana is the only Buruli ulcer endemic area, even though the incidence remains low over the years, with a total of 245 cases reported between 1969 and 2013. In a previous study, we reported evidence for uncommon heterogeneity in M. ulcerans (usually characterized by a very low level of genetic variability) and we identified two main contrasted sublineages. Nevertheless, this study was based on classical molecular typing approaches which can sometimes lead to discrepancies in Mycobacterium classification. To overcome these issues, and to move forward in the exploration of M. ulcerans genetic variability, we performed cgMLST (Core Genome Multi Locus Sequence Typing) using whole genome sequences of 25 M. ulcerans strains originated from French Guiana (n=5) and from other countries in the world were Buruli is endemic (n=20). Maximum likelihood phylogeny revealed a total of 5 lineages clearly delineated. As expected lineage L3 previously described by Doig et al. (2012) comprised all isolates from Africa and from Papua New Guinea and, lineage L2 includes Asian isolates from China and Japan. Concerning the lineage L1, Doig et al. initially proposed a clusterization of the M. ulcerans strains Mu_1G897 isolated in French Guiana with MPM isolates (Mycolactone Producing Mycobacteria: M. liflandii, M. pseudoshotsii, M. shinshuense), known to be pathogenic to ectotherms fishes and frogs. In our study, as we included 5 additional M. ulcerans samples from French Guiana that clearly clustered together, we were able to reveal for the first time an independent phylogenetic group called lineage L1.2, while MPM isolates were grouped into L1.1. Finally, the Mexican isolate and the strain Mu_FG102 recently identified in French Guiana constitute the lineage L4; this lineage was also characterized for the first time in this work using WGS.

Published
2019

46. Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment

Author

Chng, Kern Rei, Li, Chenhao, Bertrand, Denis, Ng, Amanda Hui Qi, Kwah, Junmei Samantha, Low, Hwee Meng, Tong, Chengxuan, Natrajan, Maanasa, Zhang, Michael Hongjie, Xu, Licheng, Ko, Karrie Kwan Ki, Ho, Eliza Xin Pei, Av-Shalom, Tamar, Teo, Jeanette Woon Pei, Khor, Chiea Chuen, Chen, Swaine L., Mason, Christopher E., Ng, Oon Tek, Marimuthu, Kalisvar, Ang, Brenda, Nagarajan, Niranjan, Danko, David, Bezdan, Daniela, Afshinnekoo, Ebrahim, Ahsanuddin, Sofia, Bhattacharya, Chandrima, Butler, Daniel J., De Filippis, Francesca, Hecht, Jochen, Kahles, Andre, Karasikov, Mikhail, Kyrpides, Nikos C., Leung, Marcus H. Y., Meleshko, Dmitry, Mustafa, Harun, Mutai, Beth, Neches, Russell Y., Ng, Amanda, Nieto-Caballero, Marina, Nikolayeva, Olga, Nikolayeva, Tatyana, Png, Eileen, Sanchez, Jorge L., Shaaban, Heba, Sierra, Maria A., Tong, Xinzhao, Young, Ben, Alicea, Josue, Bhattacharyya, Malay, Blekhman, Ran, Castro-Nallar, Eduardo, Canas, Ana M., Chatziefthimiou, Aspassia D., Crawford, Robert W., Deng, Youping, Desnues, Christelle, Dias-Neto, Emmanuel, Donnellan, Daisy, Dybwad, Marius, Elhaik, Eran, Ercolini, Danilo, Frolova, Alina, Graf, Alexandra B., Green, David C., Hajirasouliha, Iman, Hernandez, Mark, Iraola, Gregorio, Jang, Soojin, Jones, Angela, Kelly, Frank J., Knights, Kaymisha, Labaj, Pawel P., Lee, Patrick K. H., Shawn, Levy, Ljungdahl, Per, Lyons, Abigail, Mason-Buck, Gabriella, McGrath, Ken, Mongodin, Emmanuel F., Moraes, Milton Ozorio, Noushmehr, Houtan, Oliveira, Manuela, Ossowski, Stephan, Osuolale, Olayinka O., Ozcan, Orhan, Paez-Espino, David, Rascovan, Nicolas, Richard, Hugues, Raetsch, Gunnar, Schriml, Lynn M., Semmler, Torsten, Sezerman, Osman U., Shi, Leming, Song, Le Huu, Suzuki, Haruo, Court, Denise Syndercombe, Thomas, Dominique, Tighe, Scott W., Udekwu, Klas, Ugalde, Juan A., Valentine, Brandon, Vassilev, Dimitar, Vayndorf, Elena, Velavan, Thirumalaisamy P., Zambrano, Maria M., Zhu, Jifeng, Zhu, Sibo, Chng, Kern Rei, Li, Chenhao, Bertrand, Denis, Ng, Amanda Hui Qi, Kwah, Junmei Samantha, Low, Hwee Meng, Tong, Chengxuan, Natrajan, Maanasa, Zhang, Michael Hongjie, Xu, Licheng, Ko, Karrie Kwan Ki, Ho, Eliza Xin Pei, Av-Shalom, Tamar, Teo, Jeanette Woon Pei, Khor, Chiea Chuen, Chen, Swaine L., Mason, Christopher E., Ng, Oon Tek, Marimuthu, Kalisvar, Ang, Brenda, Nagarajan, Niranjan, Danko, David, Bezdan, Daniela, Afshinnekoo, Ebrahim, Ahsanuddin, Sofia, Bhattacharya, Chandrima, Butler, Daniel J., De Filippis, Francesca, Hecht, Jochen, Kahles, Andre, Karasikov, Mikhail, Kyrpides, Nikos C., Leung, Marcus H. Y., Meleshko, Dmitry, Mustafa, Harun, Mutai, Beth, Neches, Russell Y., Ng, Amanda, Nieto-Caballero, Marina, Nikolayeva, Olga, Nikolayeva, Tatyana, Png, Eileen, Sanchez, Jorge L., Shaaban, Heba, Sierra, Maria A., Tong, Xinzhao, Young, Ben, Alicea, Josue, Bhattacharyya, Malay, Blekhman, Ran, Castro-Nallar, Eduardo, Canas, Ana M., Chatziefthimiou, Aspassia D., Crawford, Robert W., Deng, Youping, Desnues, Christelle, Dias-Neto, Emmanuel, Donnellan, Daisy, Dybwad, Marius, Elhaik, Eran, Ercolini, Danilo, Frolova, Alina, Graf, Alexandra B., Green, David C., Hajirasouliha, Iman, Hernandez, Mark, Iraola, Gregorio, Jang, Soojin, Jones, Angela, Kelly, Frank J., Knights, Kaymisha, Labaj, Pawel P., Lee, Patrick K. H., Shawn, Levy, Ljungdahl, Per, Lyons, Abigail, Mason-Buck, Gabriella, McGrath, Ken, Mongodin, Emmanuel F., Moraes, Milton Ozorio, Noushmehr, Houtan, Oliveira, Manuela, Ossowski, Stephan, Osuolale, Olayinka O., Ozcan, Orhan, Paez-Espino, David, Rascovan, Nicolas, Richard, Hugues, Raetsch, Gunnar, Schriml, Lynn M., Semmler, Torsten, Sezerman, Osman U., Shi, Leming, Song, Le Huu, Suzuki, Haruo, Court, Denise Syndercombe, Thomas, Dominique, Tighe, Scott W., Udekwu, Klas, Ugalde, Juan A., Valentine, Brandon, Vassilev, Dimitar, Vayndorf, Elena, Velavan, Thirumalaisamy P., Zambrano, Maria M., Zhu, Jifeng, and Zhu, Sibo

Abstract

Although disinfection is key to infection control, the colonization patterns and resistomes of hospital-environment microbes remain underexplored. We report the first extensive genomic characterization of microbiomes, pathogens and antibiotic resistance cassettes in a tertiary-care hospital, from repeated sampling (up to 1.5 years apart) of 179 sites associated with 45 beds. Deep shotgun metagenomics unveiled distinct ecological niches of microbes and antibiotic resistance genes characterized by biofilm-forming and human-microbiome-influenced environments with corresponding patterns of spatiotemporal divergence. Quasi-metagenomics with nanopore sequencing provided thousands of high-contiguity genomes, phage and plasmid sequences (>60% novel), enabling characterization of resistome and mobilome diversity and dynamic architectures in hospital environments. Phylogenetics identified multidrug-resistant strains as being widely distributed and stably colonizing across sites. Comparisons with clinical isolates indicated that such microbes can persist in hospitals for extended periods (>8 years), to opportunistically infect patients. These findings highlight the importance of characterizing antibiotic resistance reservoirs in hospitals and establish the feasibility of systematic surveys to target resources for preventing infections. Spatiotemporal characterization of microbial diversity and antibiotic resistance in a tertiary-care hospital reveals broad distribution and persistence of antibiotic-resistant organisms that could cause opportunistic infections in a healthcare setting.

Published
2020
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50. MLSTar: automatic multilocus and core genome sequence typing in R

Author

Ferrés, Ignacio and Iraola, Gregorio

Subjects
Population genomics, Whole genome sequencing, R package, Bacterial genomics, Core (graph theory), Multilocus sequence typing, Computational biology, Typing, Biology
Abstract

Multilocus sequence typing (MLST) is a standard tool in population genetics and bacterial epidemiology that assesses the genetic variation present in a reduced number of housekeeping genes (typically seven) along the genome. This methodology assigns arbitrary integer identifiers to genetic variations at these loci allowing to efficiently compare bacterial isolates using allele-based methods. Now, the increasing availability of whole-genome sequences for hundreds to thousands of strains from the same bacterial species has motivated to upgrade the resolution of traditional MLST schemes using larger gene sets or even the core genome (cgMLST). The PubMLST database is the most comprehensive resource of described MLST and cgMLST schemes available for a wide variety of species. Here we present MLSTar as the first R package that allows to i) connect with the PubMLST database to select a target scheme, ii) screen a desired set of genomes to assign alleles and sequence types and iii) interact with other widely used R packages to analyze and produce graphical representations of the data. We applied MLSTar to analyze a set of 400 Campylobacter coli genomes, showing great accuracy and comparable performance with previously published command-line tools. MLSTar can be freely downloaded from http://github.com/iferres/MLSTar.

Published
2018
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