29 results on '"Mutai, Beth"'
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2. A global metagenomic map of urban microbiomes and antimicrobial resistance.
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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.
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- 2021
3. Temporal lineage replacements and dominance of imported variants of concern during the COVID-19 pandemic in Kenya
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Kimita, Gathii, Nyataya, Josphat, Omuseni, Esther, Sigei, Faith, Lemtudo, Alan, Muthanje, Eric, Andika, Brian, Liyai, Rehema, Githii, Rachel, Masakwe, Clement, Ochola, Stephen, Awinda, George, Kifude, Carol, Mutai, Beth, Gatata, Robert M., and Waitumbi, John
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- 2022
- Full Text
- View/download PDF
4. A global metagenomic map of urban microbiomes and antimicrobial resistance
- Author
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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.
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- 2021
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5. The evolution of dengue-2 viruses in Malindi, Kenya and greater East Africa: Epidemiological and immunological implications
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Pollett, Simon, Gathii, Kimita, Figueroa, Katherine, Rutvisuttinunt, Wiriya, Srikanth, Abhi, Nyataya, Josphat, Mutai, Beth K., Awinda, George, Jarman, Richard G., Berry, Irina Maljkovic, and Waitumbi, J.N.
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- 2021
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6. COVID-19 mass testing and sequencing: Experiences from a laboratory in Western Kenya
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Waitumbi, John N., primary, Omuseni, Esther, additional, Nyataya, Josphat, additional, Masakhwe, Clement, additional, Sigei, Faith, additional, Lemtudo, Allan, additional, Awinda, George, additional, Muthanje, Eric, additional, Andika, Brian, additional, Githii, Rachel, additional, Liyai, Rehema, additional, Kimita, Gathii, additional, and Mutai, Beth, additional
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- 2022
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7. March 2019 dengue fever outbreak at the Kenyan south coast involving dengue virus serotype 3, genotypes III and V
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Muthanje, Eric M., primary, Kimita, Gathii, additional, Nyataya, Josphat, additional, Njue, Winrose, additional, Mulili, Cyrus, additional, Mugweru, Julius, additional, Mutai, Beth, additional, Kituyi, Sarah N., additional, and Waitumbi, John, additional
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- 2022
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8. Bacteriome in Ticks Collected from Domestic Livestock in Kenya
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Mutai, Beth, primary, Njaanake, Kariuki, additional, Gathii, Kimita, additional, Estambale, Benson B., additional, and Waitumbi, John N., additional
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- 2022
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9. A genomics dissection of Kenya’s COVID-19 waves: temporal lineage replacements and dominance of imported variants of concern
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Kimita, Gathii, primary, Nyataya, Josphat, additional, Omuseni, Esther, additional, Sigei, Faith, additional, Lemtudo, Allan, additional, Muthanje, Eric, additional, Andika, Brian, additional, Liyai, Rehema, additional, Githii, Rachel, additional, Masakhwe, Clement, additional, Ochola, Stephen, additional, Awinda, George, additional, Kifude, Carol, additional, Mutai, Beth, additional, and Waitumbi, John, additional
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- 2021
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10. The spleen bacteriome of wild rodents and shrews from Marigat, Baringo County, Kenya
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Liyai, Rehema, primary, Kimita, Gathii, additional, Masakhwe, Clement, additional, Abuom, David, additional, Mutai, Beth, additional, Onyango, David Miruka, additional, and Waitumbi, John, additional
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- 2021
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11. Seroprevalence ofCoxiella burnetiiin patients presenting with acute febrile illness at Marigat District Hospital, Baringo County, Kenya
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Lemtudo, Allan P., primary, Mutai, Beth K., additional, Mwamburi, Lizzy, additional, and Waitumbi, John N., additional
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- 2021
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12. Apoptosis stalks Plasmodium falciparum maintained in continuous culture condition
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Waitumbi John N and Mutai Beth K
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Arctic medicine. Tropical medicine ,RC955-962 ,Infectious and parasitic diseases ,RC109-216 - Abstract
Abstract Background Growth kinetic of Plasmodium falciparum in culture or in the host fall short of expected growth rate considering that there are 4 x 106/µL red blood cell (RBCs) available for invasion and about 16 merozoites growing in each infected RBC. This study determined whether apoptotic machinery is operable to keep the parasite population under check. Methods A synchronized culture of P. falciparum (Dd2 strain) was initiated at 0.5% ring stage parasitaemia and kept under conditions not limiting for RBCs and nutrient by adjusting hematocrit to 5% at each schizogony and changing growth media daily. Parasite growth pattern and morphology was evaluated by blood smear microscopy and flow-cytometry using SYBR green. The apoptotic processes were evaluated for evidence of: DNA fragmentation by TUNEL, collapse of mitochondria membrane potential (ΔΨm) by TMRE, expression of metacaspse gene by RT-qPCR and by probing parasite proteins with anti-caspase antibodies. Results From the seeding parasitaemia of 0.5%, the parasites doubled every 48 hours to a parasitaemia of 4%. Thereafter, the growth stagnated and the culture consistently crashed at about 6% parasitaemia. ΔΨm potential collapsed as the parasite density increased and DNA fragmentation increased steadily from 0.2% to ~6%. The expression of metacaspase gene and protein was observed in all stages, but their abundance was variable among the stages. Conclusion These findings suggest existence of P. falciparum quorum sensing that keep the parasite population under check.
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- 2010
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13. Serological Evidence of Yersiniosis, Tick-Borne Encephalitis, West Nile, Hepatitis E, Crimean-Congo Hemorrhagic Fever, Lyme Borreliosis, and Brucellosis in Febrile Patients Presenting at Diverse Hospitals in Kenya
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Nyataya, Josphat, primary, Maraka, Moureen, additional, Lemtudo, Allan, additional, Masakhwe, Clement, additional, Mutai, Beth, additional, Njaanake, Kariuki, additional, Estambale, Benson B., additional, Nyakoe, Nancy, additional, Siangla, Joram, additional, and Waitumbi, John Njenga, additional
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- 2020
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14. Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment
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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.
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- 2020
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15. Seroprevalence of Coxiella burnetii in patients presenting with acute febrile illness at Marigat District Hospital, Baringo County, Kenya.
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Lemtudo, Allan P., Mutai, Beth K., Mwamburi, Lizzy, and Waitumbi, John N.
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COXIELLA burnetii , *Q fever , *ACUTE diseases , *IMMUNOGLOBULIN G , *SENSITIVITY & specificity (Statistics) , *SEROPREVALENCE - Abstract
Q fever is not routinely diagnosed in Kenyan hospitals. This study reports on Q fever in patients presenting at Marigat District Hospital, Kenya, with febrile illness. ELISA was used to detect Coxiella burnetii phase antigens. Of 406 patients, 45 (11.1%) were judged to have acute disease (phase II IgM or IgG > phase I IgG), 2 (0.5%) were chronic (phase I IgG titer >800 or phase I IgG > phase II IgG), while 26 (6.4%) had previous exposure (phase I IgG titer <800). Age (6–10 years, p = 0.002) and contact with goats (p = 0.014) were significant risk factors. Compared to immunofluorescence antibody test, the sensitivity and specificity for phase I IgG were 84% and 98%, respectfully, 46% and 100% for phase II IgG and 35% and 89% for phase II IgM. It is concluded that the low sensitivity of phase II ELISA underestimated the true burden of acute Q fever in the study population. [ABSTRACT FROM AUTHOR]
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- 2021
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16. A Duo 4-Plex Real Time PCR for Detection of Eight Tick-Borne Zoonoses in Kenya
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Mutai, Beth, primary, Njaanake, Kariuki, additional, Gathii, Kimita, additional, Estambale, Benson B., additional, and Waitumbi, John N., additional
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- 2019
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17. Identification and Characterization of Orientia chuto in Trombiculid Chigger Mites Collected from Wild Rodents in Kenya
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Masakhwe, Clement, primary, Linsuwanon, Piyada, additional, Kimita, Gathii, additional, Mutai, Beth, additional, Leepitakrat, Surachai, additional, Yalwala, Santos, additional, Abuom, David, additional, Auysawasi, Nutthanun, additional, Gilbreath, Tom, additional, Wanja, Elizabeth, additional, and Waitumbi, John, additional
- Published
- 2018
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18. Complete Coding Sequences of Dengue Virus Type 2 Strains from Febrile Patients Seen in Malindi District Hospital, Kenya, during the 2017 Dengue Fever Outbreak
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Gathii, Kimita, primary, Nyataya, Josphat N., additional, Mutai, Beth K., additional, Awinda, George, additional, and Waitumbi, John N., additional
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- 2018
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19. Identification of a novel flavivirus, Nakiwogo virus, in Kenyan Mosquitoes
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Collins Morang, Kimita Gathii, Abuom, David, Mutai, Beth, Gilbreath, Thomas, and Waitumbi, John
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- 2017
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20. Zoonotic Pathogens in Ticks Collected from Livestock in Kenya
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Oswe, Mishael, primary, Odhiambo, Rose, additional, Mutai, Beth, additional, Nyakoe, Nancy, additional, Awinda, George, additional, and Waitumbi, John N., additional
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- 2018
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21. Phylogenetic Variants of Rickettsia africae, and Incidental Identification of "Candidatus Rickettsia Moyalensis" in Kenya
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Kimita, Gathii, primary, Mutai, Beth, additional, Nyanjom, Steven Ger, additional, Wamunyokoli, Fred, additional, and Waitumbi, John, additional
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- 2016
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22. High Seroprevalence of Antibodies against Spotted Fever and Scrub Typhus Bacteria in Patients with Febrile Illness, Kenya
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Thiga, Jacqueline W., primary, Mutai, Beth K., additional, Eyako, Wurapa K., additional, Ng’ang’a, Zipporah, additional, Jiang, Ju, additional, Richards, Allen L., additional, and Waitumbi, John N., additional
- Published
- 2015
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23. Zoonotic Surveillance for Rickettsiae in Domestic Animals in Kenya
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Mutai, Beth K., primary, Wainaina, James M., additional, Magiri, Charles G., additional, Nganga, Joseph K., additional, Ithondeka, Peter M., additional, Njagi, Obadiah N., additional, Jiang, Ju, additional, Richards, Allen L., additional, and Waitumbi, John N, additional
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- 2013
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24. Humoral immune responses to Plasmodium falciparum among HIV-1-infected Kenyan adults
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Nnedu, Obinna N., primary, O'Leary, Michael P., additional, Mutua, Daniel, additional, Mutai, Beth, additional, Kalantari-Dehaghi, Mina, additional, Jasinskas, Al, additional, Nakajima-Sasaki, Rie, additional, John-Stewart, Grace, additional, Otieno, Phelgona, additional, Liang, Xiaowu, additional, Waitumbi, John, additional, Kimani, Francis, additional, Camerini, David, additional, Felgner, Philip L., additional, Walson, Judd L., additional, and Vigil, Adam, additional
- Published
- 2011
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25. Apoptosis stalks Plasmodium falciparum maintained in continuous culture condition
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Mutai, Beth K, primary and Waitumbi, John N, additional
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- 2010
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26. Identification and Characterization of Orientia chutoin Trombiculid Chigger Mites Collected from Wild Rodents in Kenya
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Masakhwe, Clement, Linsuwanon, Piyada, Kimita, Gathii, Mutai, Beth, Leepitakrat, Surachai, Yalwala, Santos, Abuom, David, Auysawasi, Nutthanun, Gilbreath, Tom, Wanja, Elizabeth, and Waitumbi, John
- Abstract
We present data that concurs with the reported geographical expansion of scrub typhus outside the “Tsutsugamushi Triangle” and addition of Orientia chutoas a second species in the Orientiagenus. Wild rodents were caught in Marigat, Baringo County, Kenya, and ectoparasites, including chiggers, were recovered.
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- 2018
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27. Complete coding sequence of Rift Valley fever virus identified by metagenomic sequencing in patient with undifferentiated febrile illness at Marigat sub-district hospital, Kenya.
- Author
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Lemtudo A, Kimita G, Awinda G, Mutai B, and Waitumbi J
- Abstract
We report on the complete coding sequence of Rift Valley Fever Virus inadvertently identified through metagenomics in a child with undifferentiated fever at Marigat sub-county hospital, Kenya. On phylogeny, the genome clustered with sequences obtained during the 2017 human outbreak in Uganda and the 2021 cattle outbreak in Kiambu, Kenya., Competing Interests: The authors declare no conflict of interest.
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- 2024
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28. Zoonotic surveillance for rickettsiae in domestic animals in Kenya.
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Mutai BK, Wainaina JM, Magiri CG, Nganga JK, Ithondeka PM, Njagi ON, Jiang J, Richards AL, and Waitumbi JN
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- Animals, Animals, Domestic, Arachnid Vectors classification, Bacterial Outer Membrane Proteins genetics, Bacterial Proteins genetics, Cattle, DNA Primers genetics, DNA, Bacterial chemistry, DNA, Bacterial genetics, Geography, Goats, Humans, Kenya epidemiology, Population Surveillance, Rickettsia classification, Rickettsia genetics, Rickettsia Infections microbiology, Sequence Analysis, DNA, Sheep, Ticks classification, Zoonoses, Arachnid Vectors microbiology, Citrate (si)-Synthase genetics, Rickettsia isolation & purification, Rickettsia Infections epidemiology, Ticks microbiology
- Abstract
Abstract Rickettsiae are obligate intracellular bacteria that cause zoonotic and human diseases. Arthropod vectors, such as fleas, mites, ticks, and lice, transmit rickettsiae to vertebrates during blood meals. In humans, the disease can be life threatening. This study was conducted amidst rising reports of rickettsioses among travelers to Kenya. Ticks and whole blood were collected from domestic animals presented for slaughter at major slaughterhouses in Nairobi and Mombasa that receive animals from nearly all counties in the country. Blood samples and ticks were collected from 1019 cattle, 379 goats, and 299 sheep and were screened for rickettsiae by a quantitative PCR (qPCR) assay (Rick17b) using primers and probe that target the genus-specific 17-kD gene (htrA). The ticks were identified using standard taxonomic keys. All Rick17b-positive tick DNA samples were amplified and sequenced with primers sets that target rickettsial outer membrane protein genes (ompA and ompB) and the citrate-synthase encoding gene (gltA). Using the Rick17b qPCR, rickettsial infections in domestic animals were found in 25/32 counties sampled (78.1% prevalence). Infection rates were comparable in cattle (16.3%) and sheep (15.1%) but were lower in goats (7.1%). Of the 596 ticks collected, 139 had rickettsiae (23.3%), and the detection rates were highest in Amblyomma (62.3%; n=104), then Rhipicephalus (45.5%; n=120), Hyalomma (35.9%; n=28), and Boophilus (34.9%; n=30). Following sequencing, 104 out of the 139 Rick17b-positive tick DNA had good reverse and forward sequences for the 3 target genes. On querying GenBank with the generated consensus sequences, homologies of 92-100% for the following spotted fever group (SFG) rickettsiae were identified: Rickettsia africae (93.%, n=97), Rickettsia aeschlimannii (1.9%, n=2), Rickettsia mongolotimonae (0.96%, n=1), Rickettsia conorii subsp. israelensis (0.96%, n=1), Candidatus Rickettsia kulagini (0.96% n=1), and Rickettsia spp. (1.9% n=2). In conclusion, molecular methods were used in this study to detect and identify rickettsial infections in domestic animals and ticks throughout Kenya.
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- 2013
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29. Humoral immune responses to Plasmodium falciparum among HIV-1-infected Kenyan adults.
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Nnedu ON, O'Leary MP, Mutua D, Mutai B, Kalantari-Dehaghi M, Jasinskas A, Nakajima-Sasaki R, John-Stewart G, Otieno P, Liang X, Waitumbi J, Kimani F, Camerini D, Felgner PL, Walson JL, and Vigil A
- Subjects
- Adult, Antibodies, Protozoan immunology, Antigens, Protozoan immunology, CD4 Lymphocyte Count, Endemic Diseases prevention & control, Female, HIV-1, Humans, Kenya epidemiology, Malaria Vaccines immunology, Malaria, Falciparum epidemiology, Malaria, Falciparum immunology, Male, Plasmodium falciparum pathogenicity, Species Specificity, HIV Infections immunology, HIV Infections parasitology, Immunity, Humoral, Plasmodium falciparum immunology
- Abstract
Introduction: Humoral immune responses play a pivotal role in naturally acquired immunity to malaria. Understanding which humoral responses are impaired among individuals at higher risk for malaria may improve our understanding of malaria immune control and contribute to vaccine development., Methods: We compared humoral responses with 483 Plasmodium falciparum antigens between adults in, Kisumu (high, year-long malaria transmission leading to partial immunity), and adults in Kisii (low, seasonal malaria transmission). Then within each site, we compared malaria-specific humoral responses between those at higher risk for malaria (CD4(+) ≤500) and those at lower risk for malaria (CD4(+) >500). A protein microarray chip containing 483 P. falciparum antigens and 71 HIV antigens was used. Benjamini-Hochberg adjustments were made to control for multiple comparisons., Results: Fifty-seven antigens including CSP, MSP1, LSA1 and AMA1 were identified as significantly more reactive in Kisumu than in Kisii. Ten of these antigens had been identified as protective in an earlier study. CD4(+) T-cell count did not significantly impact humoral responses., Conclusion: Protein microarrays are a useful method to screen multiple humoral responses simultaneously. This study provides useful clues for potential vaccine candidates. Modest decreases in CD4 counts may not significantly impact malaria-specific humoral immunity., (Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)
- Published
- 2011
- Full Text
- View/download PDF
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