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Biosafety and Genomic Epidemiological Surveillance

Эпидемиология и вакцинопрофилактика
The problem of biological safety is extremely relevant today for all countries of the world because of the real and potential threats caused by biological agents that are dangerous to public health and the environment.
V. G. Akimkin, T. A. Semenenko, K. F. Khafizov, S. V. Ugleva, D. V. Dubodelov, E. D. Sverdlov, A. S. Cherkashina, G. A. Gasanov, M. I. Nadtoka, N. P. Rumyantseva, Yu. V. Mikhailova, A. A. Shelenkov, A. S. Esman, I. V. Alekseenko, L. G. Kondratyeva, R. M. Beregovykh   +15 more
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Genomics and epidemiological surveillance [PDF]

Nature Reviews Microbiology, 2020
This month’s Genome Watch highlights how genomic surveillance can provide important information for identifying and tracking emerging pathogens such as SARS-CoV-2.
Lo, Stephanie W., Jamrozy, Dorota
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Overcoming Data Bottlenecks In Genomic Pathogen Surveillance [PDF]

Clinical Infectious Diseases, 2021
Performing whole genome sequencing (WGS) for the surveillance of antimicrobial resistance (AMR) offers the ability to determine not only the antimicrobials to which rates of resistance are increasing, but also the evolutionary mechanisms and transmission routes responsible for the increase at local, national, and global scales.
Ayorinde O. Afolayan, Johan Fabian Bernal, June M Gayeta, Melissa L. Masim, Varun Shamanna, Monica Abrudan, Khalil Abudahab, Silvia Argimón, Celia Carlos, Sonia Sia, Ravikumar Kadahalli Lingegowda, Iruka N. Okeke, Pilar Donado-Godoy, David M. Aanensen, Anthony Underwood, Harry Harste, Mihir Kekre, Dawn Muddyman, Ben Taylor, Nicole Wheeler, Sophia David, Alejandra Arévalo, María Fernanda Valencia, Erik C D Osma Castro, Geetha Nagaraj, Velu Govindan, Akshata Prabhu, D Sravani, M R Shincy, Steffimole Rose, K N Ravishankar, Anderson O. Oaikhena, Jolaade J Ajiboye, Erkison Ewomazino Odih, Marietta L Lagrada, Polle Krystle V Macaranas, Agnettah M Olorosa, Elmer M Herrera, Ali Molloy, John Stelling, Carolin Vegvari   +40 more
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Innovations in genomic antimicrobial resistance surveillance

The Lancet Microbe, 2023
Whole-genome sequencing of antimicrobial-resistant pathogens is increasingly being used for antimicrobial resistance (AMR) surveillance, particularly in high-income countries. Innovations in genome sequencing and analysis technologies promise to revolutionise AMR surveillance and epidemiology; however, routine adoption of these technologies is ...
Wheeler, Nicole E, Price, Vivien, Cunningham-Oakes, Edward, Tsang, Kara K, Nunn, Jamie G, Midega, Janet T, Anjum, Muna F, Wade, Matthew J, Feasey, Nicholas A, Peacock, Sharon J, Jauneikaite, Elita, Baker, Kate S, SEDRIC Genomics Surveillance Working Group   +12 more
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Novel multidrug-resistant sublineages of Staphylococcus aureus clonal complex 22 discovered in India

mSphere, 2023
Staphylococcus aureus is a major pathogen in India causing community and nosocomial infections, but little is known about its molecular epidemiology and mechanisms of resistance in hospital settings.
Monica I. Abrudan, Varun Shamanna, Akshatha Prasanna, Anthony Underwood, Silvia Argimón, Geetha Nagaraj, Sabrina Di Gregorio, Vandana Govindan, Ashwini Vasanth, Sravani Dharmavaram, Mihir Kekre, David M. Aanensen, K. L. Ravikumar   +12 more
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Rectal Colonization and Nosocomial Transmission of Carbapenem-Resistant Acinetobacter baumannii in an Intensive Care Unit, Southwest Nigeria

Frontiers in Medicine, 2022
BackgroundAcinetobacter baumannii are of major human health importance because they cause life-threatening nosocomial infections and often are highly resistant to antimicrobials. Specific multidrug-resistant A.
Erkison Ewomazino Odih, Erkison Ewomazino Odih, Emmanuel Oladayo Irek, Temitope O. Obadare, Anderson O. Oaikhena, Ayorinde O. Afolayan, Anthony Underwood, Anthony Underwood, Anthony T. Adenekan, Veronica O. Ogunleye, Silvia Argimon, Silvia Argimon, Anders Dalsgaard, David M. Aanensen, David M. Aanensen, Iruka N. Okeke, A. Oladipo Aboderin   +16 more
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WHOLE GENOME SEQUENCING REVEALS DIVERSE MODES OF CARBAPENEMASE GENE DISSEMINATION IN INDIAN KLEBSIELLA PNEUMONIAE CLINICAL ISOLATES

International Journal of Infectious Diseases, 2023
Intro: Mobile genetic elements and plasmids harboring multiple drug resistance genes are a significant concern in Klebsiella pneumoniae causing nosocomial infections.
V. Shamanna, A. Underwood, S. Argimón, A. Prasanna, G. Nagaraj, V. Govindan, D. Aanensen, K.L. Ravikumar   +7 more
doaj   +1 more source

Combining genomics and epidemiology to track mumps virus transmission in the United States. [PDF]

, 2020
Unusually large outbreaks of mumps across the United States in 2016 and 2017 raised questions about the extent of mumps circulation and the relationship between these and prior outbreaks.
Bankamp, Bettina, Barreira, Paul, Burns, Meagan, Byrne, Elizabeth H, Chak, Bridget, Fitzgerald, Susan, Fleming, Stephen, Gharib, Soheyla, Grad, Yonatan H, Hennigan, Scott, Krasilnikova, Lydia A, Lett, Susan, Lewnard, Joseph A, MacInnis, Bronwyn L, Madoff, Lawrence C, Matranga, Christian B, McNall, Rebecca J, Metsky, Hayden C, Park, Daniel J, Piantadosi, Anne, Qu, James, Rota, Paul A, Sabeti, Pardis C, Sabina, Brandon, Schaffner, Stephen F, Shah, Rickey R, Siddle, Katherine J, Smole, Sandra, Wohl, Shirlee, Yozwiak, Nathan L   +29 more
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Integrating whole-genome sequencing within the National Antimicrobial Resistance Surveillance Program in the Philippines

Nature Communications, 2020
Whole-genome sequencing (WGS) can support drug resistance surveillance, but is rare in low- and middle-income countries. Here, the authors integrate WGS within the national antimicrobial resistance surveillance program in the Philippines and conduct a ...
Silvia Argimón, Melissa A. L. Masim, June M. Gayeta, Marietta L. Lagrada, Polle K. V. Macaranas, Victoria Cohen, Marilyn T. Limas, Holly O. Espiritu, Janziel C. Palarca, Jeremiah Chilam, Manuel C. Jamoralin, Alfred S. Villamin, Janice B. Borlasa, Agnettah M. Olorosa, Lara F. T. Hernandez, Karis D. Boehme, Benjamin Jeffrey, Khalil Abudahab, Charmian M. Hufano, Sonia B. Sia, John Stelling, Matthew T. G. Holden, David M. Aanensen, Celia C. Carlos   +23 more
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A community-driven resource for genomic epidemiology and antimicrobial resistance prediction of Neisseria gonorrhoeae at Pathogenwatch

Genome Medicine, 2021
Background Antimicrobial-resistant (AMR) Neisseria gonorrhoeae is an urgent threat to public health, as strains resistant to at least one of the two last-line antibiotics used in empiric therapy of gonorrhoea, ceftriaxone and azithromycin, have spread ...
Leonor Sánchez-Busó, Corin A. Yeats, Benjamin Taylor, Richard J. Goater, Anthony Underwood, Khalil Abudahab, Silvia Argimón, Kevin C. Ma, Tatum D. Mortimer, Daniel Golparian, Michelle J. Cole, Yonatan H. Grad, Irene Martin, Brian H. Raphael, William M. Shafer, Katy Town, Teodora Wi, Simon R. Harris, Magnus Unemo, David M. Aanensen   +19 more
doaj   +1 more source