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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 Demographic, clinical and molecular epidemiology of extended-spectrum beta-lactamase-producing Escherichia coli bloodstream infections in Central AustraliaLangham, Freya, Tsai, Danny, Forde, Brian M., Camilleri, Shayne, Harris, Patrick N.A., Roberts, Jason A. and Chiong, Fabian (2024). Demographic, clinical and molecular epidemiology of extended-spectrum beta-lactamase-producing Escherichia coli bloodstream infections in Central Australia. Pathology. doi: 10.1016/j.pathol.2024.04.013 |
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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. doi: 10.1093/cid/ciae341 |
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2024 Journal Article High-risk Escherichia coli clones that cause neonatal meningitis and association with recrudescent infectionNhu, Nguyen Thi Khanh, Phan, Minh-Duy, Hancock, Steven J., Peters, Kate M., Alvarez-Fraga, Laura, Forde, Brian M., Andersen, Stacey B., Miliya, Thyl, Harris, Patrick N. A., Beatson, Scott A., Schlebusch, Sanmarie, Bergh, Haakon, Turner, Paul, Brauner, Annelie, Westerlund-Wikström, Benita, Irwin, Adam D. and Schembri, Mark A (2024). High-risk Escherichia coli clones that cause neonatal meningitis and association with recrudescent infection. eLife, 12 ARTN RP91853. doi: 10.7554/elife.91853.3 |
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2024 Journal Article Correction: Achievement of therapeutic antibiotic exposures using Bayesian dosing software in critically unwell children and adults with sepsisChai, Ming G., Tu, Quyen, Cotta, Menino O., Bauer, Michelle J., Balch, Ross, Okafor, Charles, Comans, Tracy, Kruger, Peter, Meyer, Jason, Shekar, Kiran, Brady, Kara, Fourie, Cheryl, Sharp, Natalie, Vlad, Luminita, Whiley, David, Ungerer, Jacobus P. J., Mcwhinney, Brett C., Farkas, Andras, Paterson, David L., Clark, Julia E., Hajkowicz, Krispin, Raman, Sainath, Bialasiewicz, Seweryn, Lipman, Jeffrey, Forde, Brian M., Harris, Patrick N. A., Schlapbach, Luregn J., Coin, Lachlan, Roberts, Jason A. and Irwin, Adam D. (2024). Correction: Achievement of therapeutic antibiotic exposures using Bayesian dosing software in critically unwell children and adults with sepsis. Intensive Care Medicine, 50 (5), 810-810. doi: 10.1007/s00134-024-07393-9 |
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2024 Journal Article Emergence and clonal expansion of a qacA-harbouring sequence type 45 lineage of methicillin-resistant Staphylococcus aureusNong, Yi, Steinig, Eike, Pollock, Georgina L., Taiaroa, George, Carter, Glen P., Monk, Ian R., Pang, Stanley, Daley, Denise A., Coombs, Geoffrey W., Forde, Brian M., Harris, Patrick N. A., Sherry, Norelle L., Howden, Benjamin P., Pasricha, Shivani, Baines, Sarah L. and Williamson, Deborah A. (2024). Emergence and clonal expansion of a qacA-harbouring sequence type 45 lineage of methicillin-resistant Staphylococcus aureus. Communications Biology, 7 (1) 349, 349. doi: 10.1038/s42003-024-06012-z |
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2024 Journal Article Achievement of therapeutic antibiotic exposures using Bayesian dosing software in critically unwell children and adults with sepsisChai, Gene G., Tu, Quyen, Cotta, Menino O., Bauer, Michelle J., Balch, Ross, Okafor, Charles, Comans, Tracy, Kruger, Peter, Meyer, Jason, Shekar, Kiran, Brady, Kara, Fourie, Cheryl, Sharp, Natalie, Vlad, Luminita, Whiley, David, Ungerer, Jacobus P. J., McWhinney, Brett C., Farkas, Andras, Paterson, David L., Clark, Julia E., Hajkowicz, Krispin, Raman, Sainath, Bialasiewicz, Seweryn, Lipman, Jeffrey, Forde, Brian M., Harris, Patrick N. A., Schlapbach, Luregn J., Coin, Lachlan, Roberts, Jason A. and Irwin, Adam D. (2024). Achievement of therapeutic antibiotic exposures using Bayesian dosing software in critically unwell children and adults with sepsis. Intensive Care Medicine, 50 (4), 1-9. doi: 10.1007/s00134-024-07353-3 |
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2024 Journal Article TcrXY is an acid-sensing two-component transcriptional regulator of Mycobacterium tuberculosis required for persistent infectionStupar, Miljan, Tan, Lendl, Kerr, Edward D., De Voss, Christopher J., Forde, Brian M., Schulz, Benjamin L. and West, Nicholas P. (2024). TcrXY is an acid-sensing two-component transcriptional regulator of Mycobacterium tuberculosis required for persistent infection. Nature Communications, 15 (1) 1615, 1-14. doi: 10.1038/s41467-024-45343-7 |
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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 Genomic epidemiology reveals geographical clustering of multidrug-resistant Escherichia coli ST131 associated with bacteraemia in WalesWhite, Rhys T., Bull, Matthew J., Barker, Clare R., Arnott, Julie M., Wootton, Mandy, Jones, Lim S., Howe, Robin A., Morgan, Mari, Ashcroft, Melinda M., Forde, Brian M., Connor, Thomas R. and Beatson, Scott A. (2024). Genomic epidemiology reveals geographical clustering of multidrug-resistant Escherichia coli ST131 associated with bacteraemia in Wales. Nature Communications, 15 (1) 1371, 1-10. doi: 10.1038/s41467-024-45608-1 |
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2024 Journal Article Differences in antimicrobial resistance gene abundance and microbial diversity of the gut microbiome in patients on antibiotics enrolled in a clinical trialStewart, Adam G., Harris, Patrick N.A., Graham, Rikki M.A., Jennison, Amy V., Schlebusch, Sanmarie, Harris-Brown, Tiffany, Paterson, David L. and Forde, Brian M. (2024). Differences in antimicrobial resistance gene abundance and microbial diversity of the gut microbiome in patients on antibiotics enrolled in a clinical trial. Pathology, 56, S36-S37. doi: 10.1016/j.pathol.2023.12.137 |
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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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2024 Journal Article Rapid nanopore sequencing and predictive susceptibility testing of positive blood cultures from intensive care patients with sepsisHarris, Patrick N. A., Bauer, Michelle J., Lüftinger, Lukas, Beisken, Stephan, Forde, Brian M., Balch, Ross, Cotta, Menino, Schlapbach, Luregn, Raman, Sainath, Shekar, Kiran, Kruger, Peter, Lipman, Jeff, Bialasiewicz, Seweryn, Coin, Lachlan, Roberts, Jason A., Paterson, David L. and Irwin, Adam D. (2024). Rapid nanopore sequencing and predictive susceptibility testing of positive blood cultures from intensive care patients with sepsis. Microbiology spectrum, 12 (2) e0306523, e0306523. doi: 10.1128/spectrum.03065-23 |
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2024 Book Chapter Microbiome-based approaches to food allergy treatmentYao, Lu, Forde, Brian, Lunjani, Nonhlanhla, Cronin, Caoimhe and O'Mahony, Liam (2024). Microbiome-based approaches to food allergy treatment. Encyclopedia of Food Allergy. (pp. 610-623) Amsterdam, Netherlands: Elsevier. doi: 10.1016/b978-0-323-96018-2.00109-7 |
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2024 Journal Article Association between gut microbiota development and allergy in infants born during pandemic-related social distancing restrictionsKorpela, Katri, Hurley, Sadhbh, Ford, Sinead Ahearn, Franklin, Ruth, Byrne, Susan, Lunjani, Nonhlanhla, Forde, Brian, Neogi, Ujjwal, Venter, Carina, Walter, Jens, Hourihane, Jonathan and O'Mahony, Liam (2024). Association between gut microbiota development and allergy in infants born during pandemic-related social distancing restrictions. Allergy: European Journal of Allergy and Clinical Immunology, 79 (7), 1938-1951. doi: 10.1111/all.16069 |
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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 Higher rates of cefiderocol resistance among NDM producing Klebsiella bloodstream isolates applying EUCAST over CLSI breakpointsIsler, Burcu, Vatansever, Cansel, Özer, Berna, Çınar, Güle, Aslan, Abdullah Tarık, Falconer, Caitlin, Bauer, Michelle J., Forde, Brian, Şimşek, Funda, Tülek, Necla, Demirkaya, Hamiyet, Menekşe, Şirin, Akalin, Halis, Balkan, İlker İnanç, Aydın, Mehtap, Tigen, Elif Tükenmez, Demir, Safiye Koçulu, Kapmaz, Mahir, Keske, Şiran, Doğan, Özlem, Arabacı, Çiğdem, Yağcı, Serap, Hazırolan, Gülşen, Bakır, Veli Oğuzalp, Gönen, Mehmet, Saltoğlu, Neşe, Azap, Alpay, Azap, Özlem, Akova, Murat ... Harris, Patrick N. A. (2023). Higher rates of cefiderocol resistance among NDM producing Klebsiella bloodstream isolates applying EUCAST over CLSI breakpoints. Infectious Diseases, 55 (9), 607-613. doi: 10.1080/23744235.2023.2226709 |
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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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2023 Journal Article Integrative omics identifies conserved and pathogen-specific responses of sepsis-causing bacteriaMu, Andre, Klare, William P., Baines, Sarah L., Ignatius Pang, C. N., Guérillot, Romain, Harbison-Price, Nichaela, Keller, Nadia, Wilksch, Jonathan, Nhu, Nguyen Thi Khanh, Phan, Minh-Duy, Keller, Bernhard, Nijagal, Brunda, Tull, Dedreia, Dayalan, Saravanan, Chua, Hwa Huat Charlie, Skoneczny, Dominik, Koval, Jason, Hachani, Abderrahman, Shah, Anup D., Neha, Nitika, Jadhav, Snehal, Partridge, Sally R., Cork, Amanda J., Peters, Kate, Bertolla, Olivia, Brouwer, Stephan, Hancock, Steven J., Álvarez-Fraga, Laura, De Oliveira, David M. P. ... Walker, Mark J. (2023). Integrative omics identifies conserved and pathogen-specific responses of sepsis-causing bacteria. Nature Communications, 14 (1) 1530, 1-21. doi: 10.1038/s41467-023-37200-w |
