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2025 Journal Article Snapshot genomic surveillance reveals insights into antimicrobial resistance and lineage diversity of uropathogens in older adults in QueenslandPermana, Budi, Falconer, Caitlin, Mayer-Coverdale, Johanna, Robson, Jennifer, Cuddihy, Thom, Schembri, Mark A., Paterson, David L., Harris, Patrick N. A. and Forde, Brian M. (2025). Snapshot genomic surveillance reveals insights into antimicrobial resistance and lineage diversity of uropathogens in older adults in Queensland. Open Forum Infectious Diseases, 12 (10) ofaf610, 10. doi: 10.1093/ofid/ofaf610 |
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2025 Journal Article Emergence of a carbapenem-resistant atypical uropathogenic Escherichia coli clone as an increasing cause of urinary tract infectionWalker, Lachlan L., Phan, Minh-Duy, Permana, Budi, Lian, Zheng Jie, Nhu, Nguyen Thi Khanh, Cuddihy, Thom, Peters, Kate M., Ramsay, Kay A., Stewart, Chelsea, Pfennigwerth, Niels, Kidd, Timothy J., Harris, Patrick N. A., Paterson, David L., Sweet, Matthew J., Forde, Brian M. and Schembri, Mark A. (2025). Emergence of a carbapenem-resistant atypical uropathogenic Escherichia coli clone as an increasing cause of urinary tract infection. Nature Communications, 16 (1) 8200, 1-10. doi: 10.1038/s41467-025-63477-0 |
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2025 Journal Article PIRT-Seq: a high-resolution whole-genome assay to identify protein-coding genesGoodall, Emily C. A., Hodges, Freya, Kok, Weine, Permana, Budi, Cuddihy, Thom, Yang, Zihao, Kahler, Nicole, Shires, Kenneth, Pullela, Karthik, Torres, Von Vergel L., Rooke, Jessica L., Delhaye, Antoine, Collet, Jean-François, Bryant, Jack A., Forde, Brian M., Hemm, Matthew R. and Henderson, Ian R. (2025). PIRT-Seq: a high-resolution whole-genome assay to identify protein-coding genes. Nucleic Acids Research, 53 (15) gkaf774, 1-16. doi: 10.1093/nar/gkaf774 |
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2024 Conference Publication Loss of OmpK35 and Glycine-aspartic acid Duplication in ompK36 Negatively Affect the in vitro Synergy of Meropenem in Combination with Piperacillin/tazobactam or Imipenem Against OXA-48-like Carbapenemase-producing Klebsiella pneumoniaeAslan, Abdullah Tarik, Demir, Mervenur, Tanriverdi, Elif Seren, Permana, Budi, Izuagbe, Rhys, Ramsay, Kay A., Forde, Brian, Otlu, Baris, Paterson, David L., Harris, Patrick, Akova, Murat and Hazirolan, Gulsen (2024). Loss of OmpK35 and Glycine-aspartic acid Duplication in ompK36 Negatively Affect the in vitro Synergy of Meropenem in Combination with Piperacillin/tazobactam or Imipenem Against OXA-48-like Carbapenemase-producing Klebsiella pneumoniae. 33rd International Congress of Antimicrobial Chemotherapy (ICC), Istanbul, Turkey, 3-6 November 2024. Amsterdam, Netherlands: Elsevier. doi: 10.1016/j.jgar.2024.10.019 |
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2024 Journal Article Characterization of gram-negative bloodstream infections in hospitalised Australian children and their clinical outcomesWen, Sophie C. H., Harris, Patrick N. A., Forde, Brian, Permana, Budi, Chatfield, Mark D., Lau, Colleen L., Spurling, Geoffrey, Bauer, Michelle J., Balch, Ross, Chambers, Henry, Schlapbach, Luregn J., Clark, Julia E., Dougherty, Sonia, Blyth, Christopher C., Britton, Philip N., Clifford, Vanessa, Haeusler, Gabrielle M., McMullan, Brendan, Wadia, Ushma, Paterson, David L., Irwin, Adam D., on behalf of the PAEDS network, Carr, Jeremy, Vasilunas, Nan, Francis, Joshua R., Macartney, Kristine, Crawford, Nigel W., Wood, Nicholas, Buttery, Jim ... Glover, Catherine (2024). Characterization of gram-negative bloodstream infections in hospitalised Australian children and their clinical outcomes. Clinical Infectious Diseases, 79 (3), 734-743. doi: 10.1093/cid/ciae341 |
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2024 Journal Article The genomic epidemiology of clinical Burkholderia pseudomallei isolates in North Queensland, AustraliaGassiep, Ian, Chatfield, Mark D., Permana, Budi, Burnard, Delaney, Bauer, Michelle J., Cuddihy, Thom, Forde, Brian M., Mayer-Coverdale, Johanna, Norton, Robert E. and Harris, Patrick N. A. (2024). The genomic epidemiology of clinical Burkholderia pseudomallei isolates in North Queensland, Australia. Pathogens, 13 (7) 584, 584. doi: 10.3390/pathogens13070584 |
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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 Conference Publication The molecular epidemiology of Burkholderia pseudomallei in North QueenslandGassiep, Ian, Burnard, Delaney, Permana, Budi, Bauer, Michelle J., Cuddihy, Thom, Forde, Brian M., Chatfield, Mark D., Ling, Weiping, Mayer-Coverdale, Johanna, Norton, Robert and Harris, Patrick N.A. (2024). The molecular epidemiology of Burkholderia pseudomallei in North Queensland. Pathology Update 2024, Adelaide, VIC, Australia, 1 - 3 March 2024. Oxford, United Kingdom: Elsevier. doi: 10.1016/j.pathol.2023.12.133 |
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2023 Journal Article The opportunities and challenges for artificial intelligence to improve sepsis outcomes in the paediatric intensive care unitAslan, Abdullah Tarik, Permana, Budi, Harris, Patrick N. A., Naidoo, Kuban D., Pienaar, Michael A. and Irwin, Adam D. (2023). The opportunities and challenges for artificial intelligence to improve sepsis outcomes in the paediatric intensive care unit. Current Infectious Disease Reports, 25 (11), 243-253. doi: 10.1007/s11908-023-00818-4 |
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2023 Journal Article Melioidosis Queensland: an analysis of clinical outcomes and genomic factorsGassiep, Ian, Burnard, Delaney, Permana, Budi, Bauer, Michelle J., Cuddihy, Thom, Forde, Brian M., Chatfield, Mark D., Ling, Weiping, Norton, Robert and Harris, Patrick N. A. (2023). Melioidosis Queensland: an analysis of clinical outcomes and genomic factors. PLoS Neglected Tropical Diseases, 17 (10) e0011697, 1-13. doi: 10.1371/journal.pntd.0011697 |
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2023 Journal Article Characterization of antibiotic resistance genes and mobile elements in extended-spectrum β-lactamase-producing Escherichia coli strains isolated from hospitalized patients in Guangdong, ChinaShafiq, Muhammad, Bilal, Hazrat, Permana, Budi, Xu, Danhong, Cai, Gengzhong, Li, Xin, Zeng, Mi, Yuan, Yumeng, Jiao, Xiaoyang and Yao, Fen (2023). Characterization of antibiotic resistance genes and mobile elements in extended-spectrum β-lactamase-producing Escherichia coli strains isolated from hospitalized patients in Guangdong, China. Journal of Applied Microbiology, 134 (7) lxad125, 1-12. doi: 10.1093/jambio/lxad125 |
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2023 Journal Article GraphSNP: an interactive distance viewer for investigating outbreaks and transmission networks using a graph approachPermana, Budi, Beatson, Scott A. and Forde, Brian M. (2023). GraphSNP: an interactive distance viewer for investigating outbreaks and transmission networks using a graph approach. BMC Bioinformatics, 24 (1) 209, 1-9. doi: 10.1186/s12859-023-05332-x |
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2023 Journal Article Using genomics to investigate an outbreak of vancomycin-resistant Enterococcus faecium ST78 at a large tertiary hospital in QueenslandPermana, Budi, Harris, Patrick N. A., Runnegar, Naomi, Lindsay, Margaret, Henderson, Belinda C., Playford, E. G., Paterson, David L., Beatson, Scott A. and Forde, Brian M. (2023). Using genomics to investigate an outbreak of vancomycin-resistant Enterococcus faecium ST78 at a large tertiary hospital in Queensland. Microbiology Spectrum, 11 (3) e0420422, 1-10. doi: 10.1128/spectrum.04204-22 |
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2022 Journal Article Coexistence of blaNDM–5 and tet(X4) in international high-risk Escherichia coli clone ST648 of human origin in ChinaShafiq, Muhammad, Zeng, Mi, Permana, Budi, Bilal, Hazrat, Huang, Jinhu, Yao, Fen, Algammal, Abdelazeem Mohamed, Li, Xin, Yuan, Yumeng and Jiao, Xiaoyang (2022). Coexistence of blaNDM–5 and tet(X4) in international high-risk Escherichia coli clone ST648 of human origin in China. Frontiers in Microbiology, 13 1031688, 1031688. doi: 10.3389/fmicb.2022.1031688 |
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2022 Other Outputs New approaches in visualising genomic data for surveillance and control of drug-resistant bacteria in healthcare settingsPermana, Budi (2022). New approaches in visualising genomic data for surveillance and control of drug-resistant bacteria in healthcare settings. PhD Thesis, School of Chemistry and Molecular Biosciences, The University of Queensland. doi: 10.14264/ed99fc0 |
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2022 Journal Article CATHAI: cluster analysis tool for healthcare-associated infectionsCuddihy, Thom, Harris, Patrick N. A., Permana, Budi, Beatson, Scott A. and Forde, Brian M. (2022). CATHAI: cluster analysis tool for healthcare-associated infections. Bioinformatics Advances, 2 (1) vbac040, vbac040. doi: 10.1093/bioadv/vbac040 |
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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 |
