Longitudinal genomics reveals carbapenem-resistant Acinetobacter baumannii population changes with emergence of highly resistant ST164 clone
Liu, Haiyang, Moran, Robert A., Doughty, Emma L., Hua, Xiaoting, Snaith, Ann E., Zhang, Linghong, Chen, Xiangping, Guo, Feng, van Schaik, Willem, McNally, Alan, Yu, Yunsong
Published in Nature communications (02.11.2024)
Published in Nature communications (02.11.2024)
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Global emergence of a hypervirulent carbapenem-resistant Escherichia coli ST410 clone
Ba, Xiaoliang, Guo, Yingyi, Moran, Robert A., Doughty, Emma L., Liu, Baomo, Yao, Likang, Li, Jiahui, He, Nanhao, Shen, Siquan, Li, Yang, van Schaik, Willem, McNally, Alan, Holmes, Mark A., Zhuo, Chao
Published in Nature communications (12.01.2024)
Published in Nature communications (12.01.2024)
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Culture-independent detection and characterisation of Mycobacterium tuberculosis and M. africanum in sputum samples using shotgun metagenomics on a benchtop sequencer
Doughty, Emma L, Sergeant, Martin J, Adetifa, Ifedayo, Antonio, Martin, Pallen, Mark J
Published in PeerJ (San Francisco, CA) (23.09.2014)
Published in PeerJ (San Francisco, CA) (23.09.2014)
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Whole-genome sequencing illuminates the evolution and spread of multidrug-resistant tuberculosis in Southwest Nigeria
Senghore, Madikay, Otu, Jacob, Witney, Adam, Gehre, Florian, Doughty, Emma L, Kay, Gemma L, Butcher, Phillip, Salako, Kayode, Kehinde, Aderemi, Onyejepu, Nneka, Idigbe, Emmanuel, Corrah, Tumani, de Jong, Bouke, Pallen, Mark J, Antonio, Martin
Published in PloS one (19.09.2017)
Published in PloS one (19.09.2017)
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TheiaEuk: a species-agnostic bioinformatics workflow for fungal genomic characterization
Ambrosio, Frank J., Scribner, Michelle R., Wright, Sage M., Otieno, James R., Doughty, Emma L., Gorzalski, Andrew, Siao, Danielle Denise, Killian, Steve, Hua, Chi, Schneider, Emily, Tran, Michael, Varghese, Vici, Libuit, Kevin G., Pandori, Mark, Sevinsky, Joel R., Hess, David
Published in Frontiers in public health (01.08.2023)
Published in Frontiers in public health (01.08.2023)
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Estimating the time-varying reproduction number of SARS-CoV-2 using national and subnational case counts
Abbott, Sam, Hellewell, Joel, Thompson, Robin N., Sherratt, Katharine, Gibbs, Hamish P., Bosse, Nikos I., Munday, James D., Meakin, Sophie, Doughty, Emma L., Chun, June Young, Chan, Yung-Wai Desmond, Finger, Flavio, Campbell, Paul, Endo, Akira, Pearson, Carl A. B., Gimma, Amy, Russell, Tim, Flasche, Stefan, Kucharski, Adam J., Eggo, Rosalind M., Funk, Sebastian
Published in Wellcome open research (01.06.2020)
Published in Wellcome open research (01.06.2020)
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Transferable Acinetobacter baumannii plasmid pDETAB2 encodes OXA-58 and NDM-1 and represents a new class of antibiotic resistance plasmids
Liu, Haiyang, Moran, Robert A, Chen, Ying, Doughty, Emma L, Hua, Xiaoting, Jiang, Yan, Xu, Qingye, Zhang, Linghong, Blair, Jessica M A, McNally, Alan, van Schaik, Willem, Yu, Yunsong
Published in Journal of antimicrobial chemotherapy (13.04.2021)
Published in Journal of antimicrobial chemotherapy (13.04.2021)
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Extended-Spectrum β-Lactamase Genes Traverse the Escherichia coli Populations of Intensive Care Unit Patients, Staff, and Environment
Moran, Robert A, Baomo, Liu, Doughty, Emma L, Guo, Yingyi, Ba, Xiaoliang, van Schaik, Willem, Zhuo, Chao, McNally, Alan
Published in Microbiology spectrum (14.03.2023)
Published in Microbiology spectrum (14.03.2023)
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Endemicity and diversification of carbapenem-resistant Acinetobacter baumannii in an intensive care unit
Doughty, Emma L., Liu, Haiyang, Moran, Robert A., Hua, Xiaoting, Ba, Xiaoliang, Guo, Feng, Chen, Xiangping, Zhang, Linghong, Holmes, Mark, van Schaik, Willem, McNally, Alan, Yu, Yunsong
Published in The Lancet regional health. Western Pacific (01.08.2023)
Published in The Lancet regional health. Western Pacific (01.08.2023)
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GR13-type plasmids in Acinetobacter potentiate the accumulation and horizontal transfer of diverse accessory genes
Moran, Robert A., Liu, Haiyang, Doughty, Emma L., Hua, Xiaoting, Cummins, Elizabeth A., Liveikis, Tomas, McNally, Alan, Zhou, Zhihui, van Schaik, Willem, Yu, Yunsong
Published in Microbial genomics (01.06.2022)
Published in Microbial genomics (01.06.2022)
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Transmission of Staphylococcus aureus from Humans to Green Monkeys in The Gambia as Revealed by Whole-Genome Sequencing
Senghore, Madikay, Bayliss, Sion C, Kwambana-Adams, Brenda A, Foster-Nyarko, Ebenezer, Manneh, Jainaba, Dione, Michel, Badji, Henry, Ebruke, Chinelo, Doughty, Emma L, Thorpe, Harry A, Jasinska, Anna J, Schmitt, Christopher A, Cramer, Jennifer D, Turner, Trudy R, Weinstock, George, Freimer, Nelson B, Pallen, Mark J, Feil, Edward J, Antonio, Martin
Published in Applied and environmental microbiology (01.10.2016)
Published in Applied and environmental microbiology (01.10.2016)
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Accelerating bioinformatics implementation in public health
Libuit, Kevin G, Doughty, Emma L, Otieno, James R, Ambrosio, Frank, Kapsak, Curtis J, Smith, Emily A, Wright, Sage M, Scribner, Michelle R, Petit Iii, Robert A, Mendes, Catarina Inês, Huergo, Marcela, Legacki, Gregory, Loreth, Christine, Park, Daniel J, Sevinsky, Joel R
Published in Microbial genomics (01.07.2023)
Published in Microbial genomics (01.07.2023)
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Estimating the time-varying reproduction number of SARS-CoV-2 using national and subnational case counts
Abbott, Sam, Hellewell, Joel, Thompson, Robin N., Sherratt, Katharine, Gibbs, Hamish P., Bosse, Nikos I., Munday, James D., Meakin, Sophie, Doughty, Emma L., Chun, June Young, Chan, Yung-Wai Desmond, Finger, Flavio, Campbell, Paul, Endo, Akira, Pearson, Carl A. B., Gimma, Amy, Russell, Tim, Flasche, Stefan, Kucharski, Adam J., Eggo, Rosalind M., Funk, Sebastian
Published in Wellcome open research (08.12.2020)
Published in Wellcome open research (08.12.2020)
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Journal Article
Culture-independent detection and characterisation of Mycobacterium tuberculosis and M. africanum in sputum samples using shotgun metagenomics on a benchtop sequencer
Doughty, Emma L, Sergeant, Martin J, Adetifa, Ifedayo MO, Martin, Antonio, Pallen, Mark J
Published in PeerJ preprints (30.08.2014)
Published in PeerJ preprints (30.08.2014)
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Journal Article
GR13-type plasmids in Acinetobacter potentiate the accumulation and horizontal transfer of diverse accessory genes
Moran, Robert A, Liu, Haiyang, Doughty, Emma L, Hua, Xiaoting, Cummins, Elizabeth A, Liveikis, Tomas, Mcnally, Alan, Zhou, Zhihui, Willem Van Schaik, Yu, Yunsong
Published in bioRxiv (12.01.2022)
Published in bioRxiv (12.01.2022)
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