Araştırma Çıktıları

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Author: search.filters.author.Bezdan, DanielaHas files: No

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    Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment
    (NATURE RESEARCH, 2020-01-01) 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 V, 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 I, Klas; Ugalde, Juan A.; Valentine, Brandon; Vassilev I, Dimitar; Vayndorf, Elena; Velavan, Thirumalaisamy P.; Zambrano, Maria M.; Zhu, Jifeng; Zhu, Sibo; Consortium, MetaSU. B.
    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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    The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report
    (BMC, 2016-01-01) Chernomoretz, Ariel; Stolovitzky, Gustavo; Labaj, Pawel P.; Graf, Alexandra B.; Darling, Aaron; Burke, Catherine; Noushmehr, Houtan; Moraes, Milton Ozorio; Dias-Neto, Emmanuel; Guo, Yongli; Xie, Zhi; Lee, Patrick; Shi, Leming; Ruiz-Perez, Carlos A.; Mercedes Zambrano, Maria; Siam, Rania; Ouf, Amged; Richard, Hugues; Lafontaine, Ingrid; Wieler, Lothar H.; Semmler, Torsten; Ahmed, Niyaz; Prithi-viraj, Bharath; Nedunuri, Narasimha; Mehr, Shaadi; Banihashemi, Kambiz; Lista, Florigio; Anselmo, Anna; Suzuki, Haruo; Kuroda, Makoto; Yamashita, Riu; Sato, Yukoto; Kaminuma, Eli; Alpuche Aranda, Celia M.; Martinez, Jesus; Dada, Christopher; Dybwad, Marius; Oliveira, Manuela; Schuster, Stephan; Siwo, Geoffrey H.; Jang, Soojin; Seo, Sung Chul; Hwang, Sung Ho; Ossowski, Stephan; Bezdan, Daniela; Chaker, Salama; Chatziefthimiou, Aspassia D.; Udekwu, Klas; Liungdahl, Per; Sezerman, Ugur; Meydan, Cem; Elhaik, Eran; Gonnet, Gaston; Schriml, Lynn M.; Mongodin, Emmanuel; Huttenhower, Curtis; Gilbert, Jack; Mason, Christopher E.; Eisen, Jonathan; Hirschberg, David; Hernandez, Mark; Consortium, MetaSU.B. Int
    The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium is a novel, interdisciplinary initiative comprised of experts across many fields, including genomics, data analysis, engineering, public health, and architecture. The ultimate goal of the MetaSUB Consortium is to improve city utilization and planning through the detection, measurement, and design of metagenomics within urban environments. Although continual measures occur for temperature, air pressure, weather, and human activity, including longitudinal, cross-kingdom ecosystem dynamics can alter and improve the design of cities. The MetaSUB Consortium is aiding these efforts by developing and testing metagenomic methods and standards, including optimized methods for sample collection, DNA/RNA isolation, taxa characterization, and data visualization. The data produced by the consortium can aid city planners, public health officials, and architectural designers. In addition, the study will continue to lead to the discovery of new species, global maps of antimicrobial resistance (AMR) markers, and novel biosynthetic gene clusters (BGCs). Finally, we note that engineered metagenomic ecosystems can help enable more responsive, safer, and quantified cities.