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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 |
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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 |
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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 |
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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 |
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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 |
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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), 9. doi: 10.1093/bioinformatics/btae542 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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2021 Other Outputs MicroPIPE: An end-to-end solution 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: An end-to-end solution for high-quality complete bacterial genome construction. doi: 10.1101/2021.02.02.429319 |
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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 |
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2020 Other Outputs Genomic surveillance, characterisation and intervention of a carbapenem-resistant Acinetobacter baumannii 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. (2020). Genomic surveillance, characterisation and intervention of a carbapenem-resistant Acinetobacter baumannii outbreak in critical care. doi: 10.1101/2020.08.10.20166652 |
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2019 Journal Article Control of bacterial sulfite detoxification by conserved and species-specific regulatory circuitsTan, Yi Jie Chelsea, Zhao, Chengzhi, Nasreen, Marufa, O'Rourke, Leo, Dhouib, Rabeb, Roberts, Leah, Wan, Ying, Beatson, Scott A. and Kappler, Ulrike (2019). Control of bacterial sulfite detoxification by conserved and species-specific regulatory circuits. Frontiers in Microbiology, 10 (MAY) 960, 960. doi: 10.3389/fmicb.2019.00960 |
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2019 Other Outputs Genomic investigation reveals contaminated detergent as the source of an ESBL-producing Klebsiella michiganensis outbreak in a neonatal unitChapman, Paul, Forde, Brian M., Roberts, Leah W., Bergh, Haakon, Vesey, Debra, Jennison, Amy V., Moss, Susan, Paterson, David L., Beatson, Scott A. and Harris, Patrick N. A. (2019). Genomic investigation reveals contaminated detergent as the source of an ESBL-producing Klebsiella michiganensis outbreak in a neonatal unit. doi: 10.1101/568154 |
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2018 Journal Article Discovery of mcr-1-mediated colistin resistance in a highly virulent Escherichia coli lineageForde, Brian M., Zowawi, Hosam M., Harris, Patrick N. A., Roberts, Leah, Ibrahim, Emad, Shaikh, Nissar, Deshmukh, Anand, Sid Ahmed, Mazen A., Al Maslamani, Muna, Cottrell, Kyra, Trembizki, Ella, Sundac, Lana, Yu, Heidi H., Li, Jian, Schembri, Mark A., Whiley, David M., Paterson, David L. and Beatson, Scott A. (2018). Discovery of mcr-1-mediated colistin resistance in a highly virulent Escherichia coli lineage. mSphere, 3 (5) e00486-18. doi: 10.1128/msphere.00486-18 |
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2018 Journal Article Effect of piperacillin-tazobactam vs meropenem on 30-day mortality for patients with E coli or Klebsiella pneumoniae bloodstream infection and ceftriaxone resistance: a randomized clinical trialHarris, Patrick N. A., Tambyah, Paul A., Lye, David C., Mo, Yin, Lee, Tau H., Yilmaz, Mesut, Alenazi, Thamer H., Arabi, Yaseen, Falcone, Marco, Bassetti, Matteo, Righi, Elda, Rogers, Benjamin A., Kanj, Souha, Bhally, Hasan, Iredell, Jon, Mendelson, Marc, Boyles, Tom H., Looke, David, Miyakis, Spiros, Walls, Genevieve, Al Khamis, Mohammed, Zikri, Ahmed, Crowe, Amy, Ingram, Paul, Daneman, Nick, Griffin, Paul, Athan, Eugene, Lorenc, Penelope, Baker, Peter ... MERINO Trial Investigators and the Australasian Society for Infectious Disease Clinical Research Network (ASID-CRN) (2018). Effect of piperacillin-tazobactam vs meropenem on 30-day mortality for patients with E coli or Klebsiella pneumoniae bloodstream infection and ceftriaxone resistance: a randomized clinical trial. JAMA, 320 (10), 984-994. doi: 10.1001/jama.2018.12163 |
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2017 Journal Article Whole genome analysis of cephalosporin-resistant Escherichia coli from bloodstream infections in Australia, New Zealand and Singapore: high prevalence of CMY-2 producers and ST131 carrying blaCTX-M-15 and blaCTX-M-27Harris, Patrick N. A., Ben Zakour, Nouri L., Roberts, Leah W., Wailan, Alexander M., Zowawi, Hosam M., Tambyah, Paul A., Lye, David C., Jureen, Roland, Lee, Tau H., Yin, Mo, Izharuddin, Ezlyn, Looke, David, Runnegar, Naomi, Rogers, Benjamin, Bhally, Hasan, Crowe, Amy, Schembri, Mark A., Beatson, Scott A. and Paterson, David L. (2017). Whole genome analysis of cephalosporin-resistant Escherichia coli from bloodstream infections in Australia, New Zealand and Singapore: high prevalence of CMY-2 producers and ST131 carrying blaCTX-M-15 and blaCTX-M-27. The Journal of Antimicrobial Chemotherapy, 73 (3), 634-642. doi: 10.1093/jac/dkx466 |
