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Evolution and Global Transmission of a Multidrug-Resistant, Community-Associated Methicillin-Resistant Staphylococcus aureus Lineage from the Indian Subcontinent.
Eike J Steinig, Sebastian Duchene, D Ashley Robinson, Stefan Monecke, Maho Yokoyama, Maisem Laabei, Peter Slickers, Patiyan Andersson, Deborah Williamson, Angela Kearns, Richard V Goering, Elizabeth Dickson, Ralf Ehricht, Margaret Ip, Matthew V N O'Sullivan, Geoffrey W Coombs, Andreas Petersen, Grainne Brennan, Anna C Shore, David C Coleman, Annalisa Pantosti, Herminia de Lencastre, Henrik Westh, Nobumichi Kobayashi, Helen Heffernan, Birgit Strommenger, Franziska Layer, Stefan Weber, Hege Vangstein Aamot, Leila Skakni, Sharon J Peacock, Derek Sarovich, Simon Harris, Julian Parkhill, Ruth C Massey, Mathew T G Holden, Stephen D Bentley, Steven Y C Tong
Jan 03, 2020
The evolution and global transmission of antimicrobial resistance have been well documented for Gram-negative bacteria and health care-associated epidemic pathogens, often emerging from regions with heavy antimicrobial use....
Genomic epidemiology of a national outbreak of post-surgical Mycobacterium abscessus wound infections in Brazil.
Izzy Everall, Christiane Lourenço Nogueira, Josephine M Bryant, Leonor Sánchez-Busó, Erica Chimara, Rafael da Silva Duarte, Jesus Pais Ramos, Karla Valéria Batista Lima, Maria Luíza Lopes, Moises Palaci, Andre Kipnis, Fernanda Monego, R Andres Floto, Julian Parkhill, Sylvia Cardoso Leão, Simon R Harris
Oct 23, 2019
An epidemic of post-surgical wound infections, caused by a non-tuberculous mycobacterium, has been on-going in Brazil. It has been unclear whether one or multiple lineages are responsible and whether their wide geographical...
genomic epidemiology Mycobacterium abscessus Nosocomial infections outbreak transmission Adaptation Biological Bacterial Typing Techniques Brazil Cross Infection Disease Outbreaks Disease Transmission Infectious Gene Deletion Genes Bacterial Genomics Humans Mycobacterium Infections Nontuberculous Mycobacterium abscessus Phenotype Phylogeny Plasmids Surgical Wound Infection whole genome sequencing
An open dataset of <i>Plasmodium vivax</i> genome variation in 1,895 worldwide samples.
Ishag Adam, Mohammad Shafiul Alam, Sisay Alemu, Chanaki Amaratunga, Roberto Amato, Voahangy Andrianaranjaka, Nicholas M Anstey, Abraham Aseffa, Elizabeth Ashley, Ashenafi Assefa, Sarah Auburn, Bridget E Barber, Alyssa Barry, Dhelio Batista Pereira, Jun Cao, Nguyen Hoang Chau, Kesinee Chotivanich, Cindy Chu, Arjen M Dondorp, Eleanor Drury, Diego F Echeverry, Berhanu Erko, Fe Espino, Rick Fairhurst, Abdul Faiz, María Fernanda Villegas, Qi Gao, Lemu Golassa, Sonia Goncalves, Matthew J Grigg, Yaghoob Hamedi, Tran Tinh Hien, Ye Htut, Kimberly J Johnson, Nadira Karunaweera, Wasif Khan, Srivicha Krudsood, Dominic P Kwiatkowski, Marcus Lacerda, Benedikt Ley, Pharath Lim, Yaobao Liu, Alejandro Llanos-Cuentas, Chanthap Lon, Tatiana Lopera-Mesa, Jutta Marfurt, Pascal Michon, Olivo Miotto, Rezika Mohammed, Ivo Mueller, Chayadol Namaik-Larp, Paul N Newton, Thuy-Nhien Nguyen, Francois Nosten, Rintis Noviyanti, Zuleima Pava, Richard D Pearson, Beyene Petros, Aung P Phyo, Ric N Price, Sasithon Pukrittayakamee, Awab Ghulam Rahim, Milijaona Randrianarivelojosia, Julian C Rayner, Angela Rumaseb, Sasha V Siegel, Victoria J Simpson, Kamala Thriemer, Alberto Tobon-Castano, Hidayat Trimarsanto, Marcelo Urbano Ferreira, Ivan D Vélez, Sonam Wangchuk, Thomas E Wellems, Nicholas J White, Timothy William, Maria F Yasnot, Daniel Yilma
Jul 02, 2022
This report describes the MalariaGEN Pv4 dataset, a new release of curated genome variation data on 1,895 samples of Plasmodium vivax collected at 88 worldwide locations between 2001 and 2017. It includes 1,370 new...
Published by: Wellcome open research
Generation and transmission of interlineage recombinants in the SARS-CoV-2 pandemic.
Ben Jackson, Maciej F Boni, Matthew J Bull, Amy Colleran, Rachel M Colquhoun, Alistair C Darby, Sam Haldenby, Verity Hill, Anita Lucaci, John T McCrone, Samuel M Nicholls, Áine O'Toole, Nicole Pacchiarini, Radoslaw Poplawski, Emily Scher, Flora Todd, Hermione J Webster, Mark Whitehead, Claudia Wierzbicki, COVID-19 Genomics UK (COG-UK) Consortium, Nicholas J Loman, Thomas R Connor, David L Robertson, Oliver G Pybus, Andrew Rambaut
Oct 06, 2021
B.1.1.7 SARS-CoV-2 evolution genomic epidemiology Genomics Recombination variants Base Sequence covid-19 Computational Biology Gene Frequency Genome Viral Genotype Humans Mutation Pandemics Phylogeny Polymorphism Single Nucleotide Recombination Genetic SARS-CoV-2 United Kingdom whole genome sequencing
Large-scale sequencing of SARS-CoV-2 genomes from one region allows detailed epidemiology and enables local outbreak management.
Andrew J Page, Alison E Mather, Thanh Le-Viet, Emma J Meader, Nabil-Fareed Alikhan, Gemma L Kay, Leonardo de Oliveira Martins, Alp Aydin, David J Baker, Alexander J Trotter, Steven Rudder, Ana P Tedim, Anastasia Kolyva, Rachael Stanley, Muhammad Yasir, Maria Diaz, Will Potter, Claire Stuart, Lizzie Meadows, Andrew Bell, Ana Victoria Gutierrez, Nicholas M Thomson, Evelien M Adriaenssens, Tracey Swingler, Rachel AJ Gilroy, Luke Griffith, Dheeraj K Sethi, Dinesh Aggarwal, Colin S Brown, Rose K Davidson, Robert A Kingsley, Luke Bedford, Lindsay J Coupland, Ian G Charles, Ngozi Elumogo, John Wain, Reenesh Prakash, Mark A Webber, SJ Louise Smith, Meera Chand, Samir Dervisevic, Justin O'Grady, The Covid-Genomics Uk Cog-Uk Consortium
Jul 08, 2021
Comparative Genomics of Disease and Carriage Serotype 1 Pneumococci.
Chrispin Chaguza, Chinelo Ebruke, Madikay Senghore, Stephanie W Lo, Peggy-Estelle Tientcheu, Rebecca A Gladstone, Gerry Tonkin-Hill, Jennifer E Cornick, Marie Yang, Archibald Worwui, Lesley McGee, Robert F Breiman, Keith P Klugman, Aras Kadioglu, Dean B Everett, Grant Mackenzie, Nicholas J Croucher, Anna Roca, Brenda A Kwambana-Adams, Martin Antonio, Stephen D Bentley
May 21, 2022
The isolation of Streptococcus pneumoniae serotypes in systemic tissues of patients with invasive disease versus the nasopharynx of healthy individuals with asymptomatic carriage varies widely. Some serotypes are hyper-invasive...
Genomic survey of Clostridium difficile reservoirs in the East of England implicates environmental contamination of wastewater treatment plants by clinical lineages.
Danesh Moradigaravand, Theodore Gouliouris, Catherine Ludden, Sandra Reuter, Dorota Jamrozy, Beth Blane, Plamena Naydenova, Kim Judge, Sani H Aliyu, Nazreen F Hadjirin, Mark A Holmes, Estée Török, Nicholas M Brown, Julian Parkhill, Sharon Peacock
May 22, 2018
There is growing evidence that patients with Clostridiumdifficile-associated diarrhoea often acquire their infecting strain before hospital admission. Wastewater is known to be a potential source of surface water that is...
Clostridium difficile One Health genomic epidemiology wastewater treatment plants Bayes Theorem Clostridioides difficile Cross-Sectional Studies DNA Bacterial Diarrhea England Genome Bacterial Genomics Humans Multilocus Sequence Typing Retrospective Studies Sequence Analysis DNA Waste Management Wastewater
Pf7
Muzamil Mahdi Abdel Hamid, Mohamed Hassan Abdelraheem, Desmond Omane Acheampong, Ambroise Ahouidi, Mozam Ali, Jacob Almagro-Garcia, Alfred Amambua-Ngwa, Chanaki Amaratunga, Lucas Amenga-Etego, Ben Andagalu, Tim Anderson, Voahangy Andrianaranjaka, Ifeyinwa Aniebo, Enoch Aninagyei, Felix Ansah, Patrick O Ansah, Tobias Apinjoh, Paulo Arnaldo, Elizabeth Ashley, Sarah Auburn, Gordon A Awandare, Hampate Ba, Vito Baraka, Alyssa Barry, Philip Bejon, Gwladys I Bertin, Maciej F Boni, Steffen Borrmann, Teun Bousema, Marielle Bouyou-Akotet, Oralee Branch, Peter C Bull, Huch Cheah, Keobouphaphone Chindavongsa, Thanat Chookajorn, Kesinee Chotivanich, Antoine Claessens, David J Conway, Vladimir Corredor, Erin Courtier, Alister Craig, Umberto D'Alessandro, Souleymane Dama, Nicholas Day, Brigitte Denis, Mehul Dhorda, Mahamadou Diakite, Abdoulaye Djimde, Christiane Dolecek, Arjen Dondorp, Seydou Doumbia, Chris Drakeley, Eleanor Drury, Patrick Duffy, Diego F Echeverry, Thomas G Egwang, Sonia Maria Mauricio Enosse, Berhanu Erko, Rick M Fairhurst, Abdul Faiz, Caterina A Fanello, Mark Fleharty, Matthew Forbes, Mark Fukuda, Dionicia Gamboa, Anita Ghansah, Lemu Golassa, Sonia Goncalves, G L Abby Harrison, Sara Anne Healy, Jason A Hendry, Anastasia Hernandez-Koutoucheva, Tran Tinh Hien, Catherine A Hill, Francis Hombhanje, Amanda Hott, Ye Htut, Mazza Hussein, Mallika Imwong, Deus Ishengoma, Scott A Jackson, Chris G Jacob, Julia Jeans, Kimberly J Johnson, Claire Kamaliddin, Edwin Kamau, Jon Keatley, Theerarat Kochakarn, Drissa S Konate, Abibatou Konaté, Aminatou Kone, Dominic P Kwiatkowski, Myat P Kyaw, Dennis Kyle, Mara Lawniczak, Samuel K Lee, Martha Lemnge, Pharath Lim, Chanthap Lon, Kovana M Loua, Celine I Mandara, Jutta Marfurt, Kevin Marsh, Richard James Maude, Mayfong Mayxay, Oumou Maïga-Ascofaré, Olivo Miotto, Toshihiro Mita, Victor Mobegi, Abdelrahim Osman Mohamed, Olugbenga A Mokuolu, Jaqui Montgomery, Collins Misita Morang'a, Ivo Mueller, Kathryn Murie, Paul N Newton, Thang Ngo Duc, Thuy Nguyen, Thuy-Nhien Nguyen, Tuyen Nguyen Thi Kim, Hong Nguyen Van, Harald Noedl, Francois Nosten, Rintis Noviyanti, Vincent Ntui-Njock Ntui, Alexis Nzila, Lynette Isabella Ochola-Oyier, Harold Ocholla, Abraham Oduro, Irene Omedo, Marie A Onyamboko, Jean-Bosco Ouedraogo, Kolapo Oyebola, Wellington Aghoghovwia Oyibo, Richard Pearson, Norbert Peshu, Aung P Phyo, Christopher V Plowe, Ric N Price, Sasithon Pukrittayakamee, Huynh Hong Quang, Milijaona Randrianarivelojosia, Julian C Rayner, Pascal Ringwald, Anna Rosanas-Urgell, Eduard Rovira-Vallbona, Valentin Ruano-Rubio, Lastenia Ruiz, David Saunders, Alex Shayo, Peter Siba, Victoria J Simpson, Mahamadou S Sissoko, Christen Smith, Xin-Zhuan Su, Colin Sutherland, Shannon Takala-Harrison, Arthur Talman, Livingstone Tavul, Ngo Viet Thanh, Vandana Thathy, Aung Myint Thu, Mahamoudou Toure, Antoinette Tshefu, Federica Verra, Joseph Vinetz, Thomas E Wellems, Jason Wendler, Nicholas J White, Georgia Whitton, William Yavo, Rob W van der Pluijm
Apr 02, 2023
We describe the MalariaGEN Pf7 data resource, the seventh release of Plasmodium falciparum genome variation data from the MalariaGEN network. It comprises over 20,000 samples from 82 partner studies in 33 countries...
Published by: Wellcome open research
Evolution and Global Transmission of a Multidrug-Resistant, Community-Associated Methicillin-Resistant Staphylococcus aureus Lineage from the Indian Subcontinent.
Eike J Steinig, Sebastian Duchene, D Ashley Robinson, Stefan Monecke, Maho Yokoyama, Maisem Laabei, Peter Slickers, Patiyan Andersson, Deborah Williamson, Angela Kearns, Richard V Goering, Elizabeth Dickson, Ralf Ehricht, Margaret Ip, Matthew VN O'Sullivan, Geoffrey W Coombs, Andreas Petersen, Grainne Brennan, Anna C Shore, David C Coleman, Annalisa Pantosti, Herminia de Lencastre, Henrik Westh, Nobumichi Kobayashi, Helen Heffernan, Birgit Strommenger, Franziska Layer, Stefan Weber, Hege Vangstein Aamot, Leila Skakni, Sharon J Peacock, Derek Sarovich, Simon Harris, Julian Parkhill, Ruth C Massey, Mathew TG Holden, Stephen D Bentley, Steven YC Tong
Jan 06, 2020
The evolution and global transmission of antimicrobial resistance have been well documented for Gram-negative bacteria and health care-associated epidemic pathogens, often emerging from regions with heavy antimicrobial use....
Bengal Bay CA-MRSA india St772 South Asia Staphylococcus aureus WGS Antimicrobial resistance genomic epidemiology Global Transmission Phenotyping phylodynamics Anti-Bacterial Agents Asia Community-Acquired Infections Drug Resistance Multiple Bacterial evolution Molecular Genome Bacterial Humans india Methicillin-Resistant Staphylococcus aureus Phylogeny Staphylococcal Infections Staphylococcus aureus
Modifiable lifestyle factors and severe COVID-19 risk
BACKGROUND: Lifestyle factors including obesity and smoking are suggested to be correlated with increased risk of COVID-19 severe illness or related death. However, whether these relationships are causal is not well known;...