|
2024 Journal Article Evolution of the pheV-tRNA integrated genomic island in Escherichia coliNhu, Nguyen Thi Khanh, Forde, Brian M., Ben Zakour, Nouri L., Phan, Minh-Duy, Roberts, Leah W., Beatson, Scott A. and Schembri, Mark A. (2024). Evolution of the pheV-tRNA integrated genomic island in Escherichia coli. PLoS Genetics, 20 (10) e1011459, e1011459. doi: 10.1371/journal.pgen.1011459 |
|
2024 Journal Article Diversity, functional classification and genotyping of SHV β-lactamases in Klebsiella pneumoniaeTsang, Kara K., Lam, Margaret M. C., Wick, Ryan R., Wyres, Kelly L., Bachman, Michael, Baker, Stephen, Barry, Katherine, Brisse, Sylvain, Campino, Susana, Chiaverini, Alexandra, Cirillo, Daniela Maria, Clark, Taane, Corander, Jukka, Corbella, Marta, Cornacchia, Alessandra, Cuénod, Aline, D'Alterio, Nicola, Di Marco, Federico, Donado-Godoy, Pilar, Egli, Adrian, Farzana, Refath, Feil, Edward J., Fostervold, Aasmund, Gorrie, Claire L., Hassan, Brekhna, Hetland, Marit Andrea Klokkhammer, Hoa, Le Nguyen Minh, Hoi, Le Thi, Howden, Benjamin ... KlebNET-GSP AMR Genotype-Phenotype Group (2024). Diversity, functional classification and genotyping of SHV β-lactamases in Klebsiella pneumoniae. Microbial Genomics, 10 (10). doi: 10.1099/mgen.0.001294 |
|
2024 Journal Article The complete genome sequence of five pre-2013 Escherichia coli sequence type (ST)1193 strains reveals insights into an emerging pathogenWhite, Rhys T., Ashcroft, Melinda M., Bauer, Michelle J., Bell, Jan, Butkiewicz, Dominika, Álvarez-Fraga, Laura, Gibson, Justine S., Kidsley, Amanda K., Mollinger, Joanne L., Peters, Kate M., Phan, Minh-Duy, Roberts, Leah W., Rogers, Benjamin A., Schembri, Mark A., Trott, Darren J., Turnidge, John, Forde, Brian M. and Beatson, Scott A. (2024). The complete genome sequence of five pre-2013 Escherichia coli sequence type (ST)1193 strains reveals insights into an emerging pathogen. Access Microbiology, 6 (10) 000894.v3, 1-15. doi: 10.1099/acmi.0.000894.v3 |
|
2024 Journal Article Applying rearrangement distances to enable plasmid epidemiology with plingFrolova, Daria, Lima, Leandro, Roberts, Leah Wendy, Bohnenkämper, Leonard, Wittler, Roland, Stoye, Jens and Iqbal, Zamin (2024). Applying rearrangement distances to enable plasmid epidemiology with pling. Microbial Genomics, 10 (10) 001300. doi: 10.1099/mgen.0.001300 |
|
2024 Journal Article Exploiting human immune repertoire transgenic mice for protective monoclonal antibodies against antimicrobial resistant Acinetobacter baumanniiBaker, Stephen, Krishna, Aishwarya, Higham, Sophie, Naydenova, Plamena, O’Leary, Siobhan, Scott, Josefin Bartholdson, Harcourt, Katherine, Forrest, Sally, Goulding, David, Thi Nguyen, To Nguyen, Toan, Nguyen Duc, Alekseeva, Elizaveta, Zhou, Qingqing, Andreozzi, Ilaria, Sobotic, Barbara, Craig, Hannah, Wong, Vivian, Forrest-Owen, Nichola, Sanchez, Dana Moreno, Pearce, Claire, Roberts, Leah, Watson, Simon, Clare, Simon, Torok, Mili Estee, Dougan, Gordon, Kellam, Paul, Tregoning, John S. and Reece, Stephen T. (2024). Exploiting human immune repertoire transgenic mice for protective monoclonal antibodies against antimicrobial resistant Acinetobacter baumannii. Nature Communications, 15 (1) 7979, 1-14. doi: 10.1038/s41467-024-52357-8 |
|
2024 Other Outputs The complete genome sequence of five pre-2013 Escherichia coli sequence type (ST)1193 strains reveals insights into an emerging pathogen.White, Rhys T., Ashcroft, Melinda A., Bauer, Michelle J., Bell, Jan, Butkiewicz, Dominika, Álvarez-Fraga, Laura, Gibson, Justine S., Kidsley, Amanda K., Mollinger, Joanne L., Peters, Kate M., Phan, Duy, Roberts, Leah W., Rogers, Benjamin, Schembri, Mark, Trott, Darren J., Turnidge, John, Forde, Brian M. and Beatson, Scott A. (2024). The complete genome sequence of five pre-2013 Escherichia coli sequence type (ST)1193 strains reveals insights into an emerging pathogen.. doi: 10.1099/acmi.0.000894.v2 |
|
2024 Journal Article CELEBRIMBOR: core and accessory genes from metagenomesHellewell, Joel, Horsfield, Samuel T., von Wachsmann, Johanna, Gurbich, Tatiana A., Finn, Robert D., Iqbal, Zamin, Roberts, Leah W. and Lees, John A. (2024). CELEBRIMBOR: core and accessory genes from metagenomes. Bioinformatics, 40 (9) btae542. doi: 10.1093/bioinformatics/btae542 |
|
2024 Journal Article MmpR5 protein truncation and bedaquiline resistance in Mycobacterium tuberculosis isolates from South Africa: a genomic analysisRoberts, Leah W., Malone, Kerri M., Hunt, Martin, Joseph, Lavania, Wintringer, Penelope, Knaggs, Jeff, Crook, Derrick, Farhat, Maha R., Iqbal, Zamin and Omar, Shaheed (2024). MmpR5 protein truncation and bedaquiline resistance in Mycobacterium tuberculosis isolates from South Africa: a genomic analysis. The Lancet Microbe, 5 (8) 100847, 100847. doi: 10.1016/s2666-5247(24)00053-3 |
|
2024 Journal Article HAIviz: an interactive dashboard for visualising and integrating healthcare-associated genomic epidemiological dataPermana, Budi, Harris, Patrick N. A., Roberts, Leah W., Cuddihy, Thom, Paterson, David L., Beatson, Scott A. and Forde, Brian M. (2024). HAIviz: an interactive dashboard for visualising and integrating healthcare-associated genomic epidemiological data. Microbial Genomics, 10 (2) 001200. doi: 10.1099/mgen.0.001200 |
|
2024 Journal Article Antibiotic resistance determination using Enterococcus faecium whole-genome sequences: a diagnostic accuracy study using genotypic and phenotypic dataColl, Francesc, Gouliouris, Theodore, Blane, Beth, Yeats, Corin A., Raven, Kathy E., Ludden, Catherine, Khokhar, Fahad A., Wilson, Hayley J., Roberts, Leah W., Harrison, Ewan M., Horner, Carolyne S., Hoi, Le Thi, Hoa, Nguyen Thi, Trung, Nguyen Vu, Brown, Nicholas M., Holmes, Mark A., Parkhill, Julian, Toeroek, Mili Estee and Peacock, Sharon J. (2024). Antibiotic resistance determination using Enterococcus faecium whole-genome sequences: a diagnostic accuracy study using genotypic and phenotypic data. The Lancet Microbe, 5 (2), e151-e163. doi: 10.1016/s2666-5247(23)00297-5 |
|
2023 Journal Article Long- read sequencing reveals genomic diversity and associated plasmid movement of carbapenemase- producing bacteria in a UK hospital over 6 yearsRoberts, Leah W., Enoch, David A., Khokhar, Fahad, Blackwell, Grace A., Wilson, Hayley, Warne, Ben, Gouliouris, Theodore, Iqbal, Zamin and Toeroek, M. Estee (2023). Long- read sequencing reveals genomic diversity and associated plasmid movement of carbapenemase- producing bacteria in a UK hospital over 6 years. Microbial Genomics, 9 (7) 001048. doi: 10.1099/mgen.0.001048 |
|
2022 Journal Article Genomic characterisation of multidrug-resistant Escherichia coli, Klebsiella pneumoniae, and Acinetobacter baumannii in two intensive care units in Hanoi, Viet Nam: a prospective observational cohort studyRoberts, Leah W., Le Thi Hoi,, Khokhar, Fahad A., Nguyen Thi Hoa,, Tran Van Giang,, Cuong Bui,, Tran Hai Ninh,, Dao Xuan Co,, Nguyen Gia Binh,, Hoang Bao Long,, Dang Thi Huong,, Bryan, James E., Herrick, Archie, Feltwell, Theresa, Nadjm, Behzad, van Doorn, H. Rogier, Parkhill, Julian, Nguyen Vu Trung,, Nguyen Van Kinh,, Iqbal, Zamin and Torok, M. Estee (2022). Genomic characterisation of multidrug-resistant Escherichia coli, Klebsiella pneumoniae, and Acinetobacter baumannii in two intensive care units in Hanoi, Viet Nam: a prospective observational cohort study. The Lancet Microbe, 3 (11), E857-E866. doi: 10.1016/s2666-5247(22)00181-1 |
|
2022 Journal Article Differential Afa/Dr fimbriae expression in the multidrug-resistant Escherichia coli ST131 cloneAlvarez-Fraga, Laura, Phan, Minh-Duy, Goh, Kelvin G. K., Nhu, Nguyen Thi Khanh, Hancock, Steven J., Allsopp, Luke P., Peters, Kate M., Forde, Brian M., Roberts, Leah W., Sullivan, Matthew J., Totsika, Makrina, Beatson, Scott A., Ulett, Glen C. and Schembri, Mark A. (2022). Differential Afa/Dr fimbriae expression in the multidrug-resistant Escherichia coli ST131 clone. mBio, 13 (1) e03519, e0351921. doi: 10.1128/mbio.03519-21 |
|
2021 Journal Article Pandora: nucleotide-resolution bacterial pan-genomics with reference graphsColquhoun, Rachel M., Hall, Michael B., Lima, Leandro, Roberts, Leah W., Malone, Kerri M., Hunt, Martin, Letcher, Brice, Hawkey, Jane, George, Sophie, Pankhurst, Louise and Iqbal, Zamin (2021). Pandora: nucleotide-resolution bacterial pan-genomics with reference graphs. Genome Biology, 22 (1) 267, 267. doi: 10.1186/s13059-021-02473-1 |
|
2021 Journal Article Characterisation of DtrJ as an IncC plasmid conjugative DNA transfer componentHancock, Steven J., Phan, Minh‐Duy, Roberts, Leah, Vu, Thu Ngoc Minh, Harris, Patrick N.A., Beatson, Scott A. and Schembri, Mark A. (2021). Characterisation of DtrJ as an IncC plasmid conjugative DNA transfer component. Molecular Microbiology, 116 (1), 154-167. doi: 10.1111/mmi.14697 |
|
2021 Journal Article MicroPIPE: validating an end-to-end workflow for high-quality complete bacterial genome constructionMurigneux, Valentine, Roberts, Leah W., Forde, Brian M., Phan, Minh-Duy, Nhu, Nguyen Thi Khanh, Irwin, Adam D., Harris, Patrick N. A., Paterson, David L., Schembri, Mark A., Whiley, David M. and Beatson, Scott A. (2021). MicroPIPE: validating an end-to-end workflow for high-quality complete bacterial genome construction. BMC Genomics, 22 (1) 474, 474. doi: 10.1186/s12864-021-07767-z |
|
2021 Journal Article Genomic surveillance, characterization and intervention of a polymicrobial multidrug-resistant outbreak in critical careRoberts, Leah W., Forde, Brian M., Hurst, Trish, Ling, Weiping, Nimmo, Graeme R., Bergh, Haakon, George, Narelle, Hajkowicz, Krispin, McNamara, John F., Lipman, Jeffrey, Permana, Budi, Schembri, Mark A., Paterson, David, Beatson, Scott A. and Harris, Patrick N. A. (2021). Genomic surveillance, characterization and intervention of a polymicrobial multidrug-resistant outbreak in critical care. Microbial Genomics, 7 (3) 000530. doi: 10.1099/mgen.0.000530 |
|
2021 Journal Article Cost-effectiveness analysis of whole-genome sequencing during an outbreak of carbapenem-resistant Acinetobacter baumanniiElliott, Thomas M., Harris, Patrick N., Roberts, Leah W., Doidge, Michelle, Hurst, Trish, Hajkowicz, Krispin, Forde, Brian, Paterson, David L. and Gordon, Louisa G. (2021). Cost-effectiveness analysis of whole-genome sequencing during an outbreak of carbapenem-resistant Acinetobacter baumannii. Antimicrobial Stewardship and Healthcare Epidemiology, 1 (1) e62, e62. doi: 10.1017/ash.2021.233 |
|
2020 Journal Article Association between minimum inhibitory concentration, beta-lactamase genes and mortality for patients treated with piperacillin/tazobactam or meropenem from the MERINO studyHenderson, A., Paterson, D. L., Chatfield, M. D., Tambyah, P. A., Lye, D. C., De, P. P., Lin, R. T. P., Chew, K. L., Yin, M., Lee, T. H., Yilmaz, M., Cakmak, R., Alenazi, T. H., Arabi, Y. M., Falcone, M., Bassetti, M., Righi, E., Rogers, B.A., Kanj, S. S., Bhally, H., Iredell, J., Mendelson, M., Boyles, T. H., Looke, D. F. M., Runnegar, N. J., Miyakis, S., Walls, G., AI Khamis, M., Zikri, A. ... For the MERINO Trial Investigators and the Australasian Society for Infectious Disease Clinical Research Network (ASID-CRN) (2020). Association between minimum inhibitory concentration, beta-lactamase genes and mortality for patients treated with piperacillin/tazobactam or meropenem from the MERINO study. Clinical Infectious Diseases, 73 (11), e3842-e3850. doi: 10.1093/cid/ciaa1479 |
|
2020 Other Outputs Strain and lineage-level methylome heterogeneity in the multi-drug resistant pathogenic Escherichia coli ST101 cloneAshcroft, Melinda M., Forde, Brian M., Phan, Minh-Duy, Peters, Kate M., Roberts, Leah W., Chan, Kok-Gan, Chong, Teik Min, Yin, Wai-Fong, Paterson, David L., Walsh, Timothy R., Schembri, Mark A. and Beatson, Scott A. (2020). Strain and lineage-level methylome heterogeneity in the multi-drug resistant pathogenic Escherichia coli ST101 clone. doi: 10.1101/2020.06.07.138552 |
