AUSGEM 2
Project Member(s): Djordjevic, S., Fourment, M., Bhattacharya, P., Myers, G., Seymour, J.
Funding or Partner Organisation: NSW Department of Primary Industries
NSW Department of Primary Industries
Start year: 2017
Publications:
Hem, S, Cummins, ML, Wyrsch, ER, Drigo, B, Hoye, BJ, Maute, K, Sanderson-Smith, M, Gorman, J, Bogema, DR, Jenkins, C, Deutscher, AT, Yam, J, Hai, F, Donner, E, Jarocki, VM & Djordjevic, SP 2024, 'Genomic analysis of Citrobacter from Australian wastewater and silver gulls reveals novel sequence types carrying critically important antibiotic resistance genes', Science of The Total Environment, vol. 909, pp. 168608-168608.
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Alhamami, T, Roy Chowdhury, P, Venter, H, Veltman, T, Truswell, A, Abraham, S, Sapula, SA, Carr, M, Djordjevic, SP & Trott, DJ 2023, 'Genomic profiling of Pasteurella multocida isolated from feedlot cases of bovine respiratory disease', Veterinary Microbiology, vol. 283, pp. 109773-109773.
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Cummins, ML, Li, D, Ahmad, A, Bushell, R, Noormohammadi, AH, Wijesurendra, DS, Stent, A, Marenda, MS & Djordjevic, SP 2023, 'Whole Genome Sequencing of Avian Pathogenic Escherichia coli Causing Bacterial Chondronecrosis and Osteomyelitis in Australian Poultry', Microorganisms, vol. 11, no. 6, pp. 1513-1513.
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Elankumuran, P, Browning, GF, Marenda, MS, Kidsley, A, Osman, M, Haenni, M, Johnson, JR, Trott, DJ, Reid, CJ & Djordjevic, SP 2023, 'Identification of genes influencing the evolution of Escherichia coli ST372 in dogs and humans', Microbial Genomics, vol. 9, no. 2, p. mgen000930.
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Li, D, Elankumaran, P, Kudinha, T, Kidsley, AK, Trott, DJ, Jarocki, VM & Djordjevic, SP 2023, 'Dominance of Escherichia coli sequence types ST73, ST95, ST127 and ST131 in Australian urine isolates: a genomic analysis of antimicrobial resistance and virulence linked to F plasmids', Microbial Genomics, vol. 9, no. 7.
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Roy Chowdhury, P, Hastak, P, DeMaere, M, Wyrsch, E, Li, D, Elankumaran, P, Dolejska, M, Browning, GF, Marenda, MS, Gottlieb, T, Cheong, E, Merlino, J, Myers, GSA & Djordjevic, SP 2023, 'Phylogenomic analysis of a global collection of Escherichia coli ST38: evidence of interspecies and environmental transmission?', mSystems, vol. 8, no. 5, p. e0123622.
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Elankumaran, P, Browning, GF, Marenda, MS, Reid, CJ & Djordjevic, SP 2022, 'Close genetic linkage between human and companion animal extraintestinal pathogenic Escherichia coli ST127', Current Research in Microbial Sciences, vol. 3, pp. 100106-100106.
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Hem, S, Jarocki, VM, Baker, DJ, Charles, IG, Drigo, B, Aucote, S, Donner, E, Burnard, D, Bauer, MJ, Harris, PNA, Wyrsch, ER & Djordjevic, SP 2022, 'Genomic analysis of Elizabethkingia species from aquatic environments: Evidence for potential clinical transmission', Current Research in Microbial Sciences, vol. 3, pp. 100083-100083.
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Reid, CJ, Cummins, ML, Börjesson, S, Brouwer, MSM, Hasman, H, Hammerum, AM, Roer, L, Hess, S, Berendonk, T, Nešporová, K, Haenni, M, Madec, J-Y, Bethe, A, Michael, GB, Schink, A-K, Schwarz, S, Dolejska, M & Djordjevic, SP 2022, 'A role for ColV plasmids in the evolution of pathogenic Escherichia coli ST58', Nature Communications, vol. 13, no. 1, p. 683.
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Wyrsch, ER, Bushell, RN, Marenda, MS, Browning, GF & Djordjevic, SP 2022, 'Global Phylogeny and F Virulence Plasmid Carriage in Pandemic Escherichia coli ST1193', Microbiology Spectrum, vol. 10, no. 6, p. e0255422.
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Alhamami, T, Chowdhury, P, Gomes, N, Carr, M, Veltman, T, Khazandi, M, Mollinger, J, Deutscher, A, Turni, C, Mahdi, L, Venter, H, Abraham, S, Djordjevic, S & Trott, D 2021, 'First Emergence of Resistance to Macrolides and Tetracycline Identified in Mannheimia haemolytica and Pasteurella multocida Isolates from Beef Feedlots in Australia', Microorganisms, vol. 9, no. 6, pp. 1322-1322.
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Berry, IJ, Widjaja, M, Jarocki, VM, Steele, JR, Padula, MP & Djordjevic, SP 2021, 'Protein cleavage influences surface protein presentation in Mycoplasma pneumoniae', Scientific Reports, vol. 11, no. 1, p. 6743.
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Dadd-Daigle, P, Kirkby, K, Chowdhury, PR, Labbate, M & Chapman, TA 2021, 'The Verticillium wilt problem in Australian cotton', Australasian Plant Pathology, vol. 50, no. 2, pp. 129-135.
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Gaio, D, DeMaere, MZ, Anantanawat, K, Eamens, GJ, Liu, M, Zingali, T, Falconer, L, Chapman, TA, Djordjevic, SP & Darling, AE 2021, 'A large-scale metagenomic survey dataset of the post-weaning piglet gut lumen', GigaScience, vol. 10, no. 6.
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Jarocki, VM, Heß, S, Anantanawat, K, Berendonk, TU & Djordjevic, SP 2021, 'Multidrug-Resistant Lineage of Enterotoxigenic Escherichia coli ST182 With Serotype O169:H41 in Airline Waste', Frontiers in Microbiology, vol. 12, p. 731050.
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Li, D, Wyrsch, ER, Elankumaran, P, Dolejska, M, Marenda, MS, Browning, GF, Bushell, RN, McKinnon, J, Chowdhury, PR, Hitchick, N, Miller, N, Donner, E, Drigo, B, Baker, D, Charles, IG, Kudinha, T, Jarocki, VM & Djordjevic, SP 2021, 'Genomic comparisons of Escherichia coli ST131 from Australia', Microbial Genomics, vol. 7, no. 12.
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Tarabai, H, Wyrsch, ER, Bitar, I, Dolejska, M & Djordjevic, SP 2021, 'Epidemic HI2 Plasmids Mobilising the Carbapenemase Gene blaIMP-4 in Australian Clinical Samples Identified in Multiple Sublineages of Escherichia coli ST216 Colonising Silver Gulls', Microorganisms, vol. 9, no. 3, pp. 567-567.
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Djordjevic, SP, Jarocki, VM, Morgan, B & Donner, E 2020, 'Genomic Surveillance for One Health Antimicrobial Resistance: Understanding Human, Animal, and Environmental Reservoirs and Transmission' in The Handbook of Environmental Chemistry, Springer International Publishing, pp. 71-100.
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Bogema, DR, McKinnon, J, Liu, M, Hitchick, N, Miller, N, Venturini, C, Iredell, J, Darling, AE, Roy Chowdury, P & Djordjevic, SP 2020, 'Whole-genome analysis of extraintestinal Escherichia coli sequence type 73 from a single hospital over a 2 year period identified different circulating clonal groups', Microbial Genomics, vol. 6, no. 1, pp. 1-18.
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Cummins, ML, Hamidian, M & Djordjevic, SP 2020, 'Salmonella Genomic Island 1 is Broadly Disseminated within Gammaproteobacteriaceae', Microorganisms, vol. 8, no. 2, pp. 161-161.
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Cummins, ML, Sanderson-Smith, M, Newton, P, Carlile, N, Phalen, DN, Maute, K, Monahan, LG, Hoye, BJ & Djordjevic, SP 2020, 'Whole-Genome Sequence Analysis of an Extensively Drug-Resistant Salmonella enterica Serovar Agona Isolate from an Australian Silver Gull (Chroicocephalus novaehollandiae) Reveals the Acquisition of Multidrug Resistance Plasmids', mSphere, vol. 5, no. 6.
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Daigle, PD, Kirkby, K, Collins, D, Cuddy, W, Lonergan, P, Roser, S, Chowdhury, PR, Labbate, M & Chapman, TA 2020, 'Virulence not linked with vegetative compatibility groups in Australian cotton Verticillium dahliae isolates', Australian Journal of Crop Science, vol. 14, no. 14(04):2020, pp. 633-640.
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Hastak, P, Cummins, ML, Gottlieb, T, Cheong, E, Merlino, J, Myers, GSA, Djordjevic, SP & Roy Chowdhury, P 2020, 'Genomic profiling of Escherichia coli isolates from bacteraemia patients: a 3-year cohort study of isolates collected at a Sydney teaching hospital', Microbial Genomics, vol. 6, no. 5, pp. 1-16.
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Hastak, P, Fourment, M, Darling, AE, Gottlieb, T, Cheong, E, Merlino, J, Myers, GSA, Djordjevic, SP & Roy Chowdhury, P 2020, 'Escherichia coli ST8196 is a novel, locally evolved, and extensively drug resistant pathogenic lineage within the ST131 clonal complex', Emerging Microbes & Infections, vol. 9, no. 1, pp. 1780-1792.
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Hudson, BJ, Chicken, C, Blishen, A, Todhunter, KH, Begg, AP, Chan, L, Karagiannis, T, Raymond, B, Bogema, D, Adkins, AR, O’Sullivan, CB, O’Rourke, BA, Roy Chowdhury, P, Djordjevic, SP, Charles, IG, Edgar, A & Mitsakos, K 2020, 'Osteoarticular Infection in Three Young Thoroughbred Horses Caused by a Novel Gram Negative Cocco-Bacillus', Case Reports in Veterinary Medicine, vol. 2020, pp. 1-8.
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King, WL, Siboni, N, Kahlke, T, Dove, M, O'Connor, W, Mahbub, KR, Jenkins, C, Seymour, JR & Labbate, M 2020, 'Regional and oyster microenvironmental scale heterogeneity in the Pacific oyster bacterial community', FEMS Microbiology Ecology, vol. 96, no. 5.
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Li, D, Reid, CJ, Kudinha, T, Jarocki, VM & Djordjevic, SP 2020, 'Genomic analysis of trimethoprim-resistant extraintestinal pathogenic Escherichia coli and recurrent urinary tract infections', Microbial Genomics, vol. 6, no. 12.
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Massella, E, Reid, CJ, Cummins, ML, Anantanawat, K, Zingali, T, Serraino, A, Piva, S, Giacometti, F & Djordjevic, SP 2020, 'Snapshot Study of Whole Genome Sequences of Escherichia coli from Healthy Companion Animals, Livestock, Wildlife, Humans and Food in Italy', Antibiotics, vol. 9, no. 11, pp. 782-782.
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McKinnon, J, Roy Chowdhury, P & Djordjevic, SP 2020, 'Molecular Analysis of an IncF ColV-Like Plasmid Lineage That Carries a Complex Resistance Locus with a Trackable Genetic Signature', Microbial Drug Resistance, vol. 26, no. 7, pp. 787-793.
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Nesporova, K, Wyrsch, ER, Valcek, A, Bitar, I, Chaw, K, Harris, P, Hrabak, J, Literak, I, Djordjevic, SP & Dolejska, M 2020, 'Escherichia coli Sequence Type 457 Is an Emerging Extended-Spectrum-β-Lactam-Resistant Lineage with Reservoirs in Wildlife and Food-Producing Animals', Antimicrobial Agents and Chemotherapy, vol. 65, no. 1, pp. 1-18.
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Poulsen, LL, Kudirkiene, E, Jørgensen, SL, Djordjevic, SP, Cummins, ML, Christensen, JP, Christensen, H, Bisgaard, M & Thøfner, I 2020, 'Whole genome sequence comparison of avian pathogenic Escherichia coli from acute and chronic salpingitis of egg laying hens', BMC Veterinary Research, vol. 16, no. 1, p. 148.
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Wyrsch, ER, Chowdhury, PR, Jarocki, VM, Brandis, KJ & Djordjevic, SP 2020, 'Duplication and diversification of a unique chromosomal virulence island hosting the subtilase cytotoxin in Escherichia coli ST58', Microbial Genomics, vol. 6, no. 6, pp. 1-8.
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Wyrsch, ER, Chowdhury, PR, Wallis, L, Cummins, ML, Zingali, T, Brandis, KJ & Djordjevic, SP 2020, 'Whole-genome sequence analysis of environmental Escherichia coli from the faeces of straw-necked ibis (Threskiornis spinicollis) nesting on inland wetlands', Microbial Genomics, vol. 6, no. 6, pp. 1-16.
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Zingali, T, Chapman, TA, Webster, J, Roy Chowdhury, P & Djordjevic, SP 2020, 'Genomic Characterisation of a Multiple Drug Resistant IncHI2 ST4 Plasmid in Escherichia coli ST744 in Australia', Microorganisms, vol. 8, no. 6, pp. 896-896.
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Zingali, T, Reid, CJ, Chapman, TA, Gaio, D, Liu, M, Darling, AE & Djordjevic, SP 2020, 'Whole Genome Sequencing Analysis of Porcine Faecal Commensal Escherichia coli Carrying Class 1 Integrons from Sows and Their Offspring', Microorganisms, vol. 8, no. 6, pp. 843-843.
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Gaio, D, DeMaere, MZ, Anantanawat, K, Chapman, TA, Djordjevic, SP & Darling, AE 2020, 'Post-weaning shifts in microbiome composition and metabolism revealed by over 25,000 pig gut metagenome assembled genomes', Cold Spring Harbor Laboratory.
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Gaio, D, DeMaere, MZ, Anantanawat, K, Eamens, GJ, Liu, M, Zingali, T, Falconer, L, Chapman, TA, Djordjevic, SP & Darling, AE 2020, 'Community composition and development of the post-weaning piglet gut microbiome', Research Square Platform LLC, Research Square.
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Gaio, D, DeMaere, MZ, Anantanawat, K, Eamens, GJ, Zingali, T, Falconer, L, Chapman, TA, Djordjevic, S & Darling, AE 2020, 'Phylogenetic diversity analysis of shotgun metagenomic reads describes gut microbiome development and treatment effects in the post-weaned pig', Cold Spring Harbor Laboratory.
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Cummins, ML, Reid, CJ, Roy Chowdhury, P, Bushell, RN, Esbert, N, Tivendale, KA, Noormohammadi, AH, Islam, S, Marenda, MS, Browning, GF, Markham, PF & Djordjevic, SP 2019, 'Whole genome sequence analysis of Australian avian pathogenic Escherichia coli that carry the class 1 integrase gene', Microbial Genomics, vol. 5, no. 2.
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Cummins, ML, Roy Chowdhury, P, Marenda, MS, Browning, GF & Djordjevic, SP 2019, 'Salmonella Genomic Island 1B Variant Found in a Sequence Type 117 Avian Pathogenic Escherichia coli Isolate', mSphere, vol. 4, no. 3.
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Djordjevic, SP & Morgan, BS 2019, 'A One Health genomic approach to antimicrobial resistance is essential for generating relevant data for a holistic assessment of the biggest threat to public health', Microbiology Australia, vol. 40, no. 2, pp. 73-73.
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Espinoza-Vergara, G, Noorian, P, Silva-Valenzuela, CA, Raymond, BBA, Allen, C, Hoque, MM, Sun, S, Johnson, MS, Pernice, M, Kjelleberg, S, Djordjevic, SP, Labbate, M, Camilli, A & McDougald, D 2019, 'Vibrio cholerae residing in food vacuoles expelled by protozoa are more infectious in vivo', Nature Microbiology, vol. 4, no. 12, pp. 2466-2474.
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Fourment, M & Darling, AE 2019, 'Evaluating probabilistic programming and fast variational Bayesian inference in phylogenetics', PeerJ, vol. 7, no. 12, pp. e8272-e8272.
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Harvey, KL, Jarocki, VM, Charles, IG & Djordjevic, SP 2019, 'The Diverse Functional Roles of Elongation Factor Tu (EF-Tu) in Microbial Pathogenesis', Frontiers in Microbiology, vol. 10, no. OCT, p. 2351.
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Jarocki, VM, Reid, CJ, Chapman, TA & Djordjevic, SP 2019, 'Escherichia coli ST302: Genomic Analysis of Virulence Potential and Antimicrobial Resistance Mediated by Mobile Genetic Elements', Frontiers in Microbiology, vol. 10, p. 3098.
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Jarocki, VM, Steele, JR, Widjaja, M, Tacchi, JL, Padula, MP & Djordjevic, SP 2019, 'Formylated N-terminal methionine is absent from the Mycoplasma hyopneumoniae proteome: Implications for translation initiation', International Journal of Medical Microbiology, vol. 309, no. 5, pp. 288-298.
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King, WL, Jenkins, C, Go, J, Siboni, N, Seymour, JR & Labbate, M 2019, 'Characterisation of the Pacific Oyster Microbiome During a Summer Mortality Event', Microbial Ecology, vol. 77, no. 2, pp. 502-512.
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King, WL, Jenkins, C, Seymour, JR & Labbate, M 2019, 'Oyster disease in a changing environment: Decrypting the link between pathogen, microbiome and environment', Marine Environmental Research, vol. 143, pp. 124-140.
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King, WL, Siboni, N, Kahlke, T, Green, TJ, Labbate, M & Seymour, JR 2019, 'A New High Throughput Sequencing Assay for Characterizing the Diversity of Natural Vibrio Communities and Its Application to a Pacific Oyster Mortality Event', Frontiers in Microbiology, vol. 10, pp. 2907-2907.
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Monahan, LG, DeMaere, MZ, Cummins, ML, Djordjevic, SP, Roy Chowdhury, P & Darling, AE 2019, 'High contiguity genome sequence of a multidrug-resistant hospital isolate of Enterobacter hormaechei', Gut Pathogens, vol. 11, no. 1.
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Reid, CJ, Blau, K, Jechalke, S, Smalla, K & Djordjevic, SP 2019, 'Whole Genome Sequencing of Escherichia coli From Store-Bought Produce', Frontiers in Microbiology, vol. 10, p. 3050.
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Reid, CJ, DeMaere, MZ & Djordjevic, SP 2019, 'Australian porcine clonal complex 10 (CC10) Escherichia coli belong to multiple sublineages of a highly diverse global CC10 phylogeny', Microbial Genomics, vol. 5, no. 3, pp. ---.
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Reid, CJ, McKinnon, J & Djordjevic, SP 2019, 'Clonal ST131-H22 Escherichia coli strains from a healthy pig and a human urinary tract infection carry highly similar resistance and virulence plasmids', Microbial Genomics, vol. 5, no. 9.
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Roy Chowdhury, P, Fourment, M, DeMaere, MZ, Monahan, L, Merlino, J, Gottlieb, T, Darling, AE & Djordjevic, SP 2019, 'Identification of a novel lineage of plasmids within phylogenetically diverse subclades of IncHI2-ST1 plasmids', Plasmid, vol. 102, pp. 56-61.
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Roy Chowdhury, P, McKinnon, J, Liu, M & Djordjevic, SP 2019, 'Multidrug Resistant Uropathogenic Escherichia coli ST405 With a Novel, Composite IS26 Transposon in a Unique Chromosomal Location', Frontiers in Microbiology, vol. 9, no. JAN, pp. 3212-3212.
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Venturini, C, Zingali, T, Wyrsch, ER, Bowring, B, Iredell, J, Partridge, SR & Djordjevic, SP 2019, 'Diversity of P1 phage-like elements in multidrug resistant Escherichia coli', Scientific Reports, vol. 9, no. 1.
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Wyrsch, ER, Hawkey, J, Judd, LM, Haites, R, Holt, KE, Djordjevic, SP & Billman-Jacobe, H 2019, 'Z/I1 Hybrid Virulence Plasmids Carrying Antimicrobial Resistance genes in S. Typhimurium from Australian Food Animal Production', Microorganisms, vol. 7, no. 9, pp. 299-299.
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Wyrsch, ER, Reid, CJ, DeMaere, MZ, Liu, MY, Chapman, TA, Roy Chowdhury, P & Djordjevic, SP 2019, 'Complete Sequences of Multiple-Drug Resistant IncHI2 ST3 Plasmids in Escherichia coli of Porcine Origin in Australia', Frontiers in Sustainable Food Systems, vol. 3.
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Bogema, DR, McKinnon, J, Liu, M, Hitchick, N, Miller, N, Venturini, C, Iredell, J, Darling, AE, Roy Chowdury, P & Djordjevic, SP 2018, 'Whole genome analysis of ExPEC ST73 from a single hospital over a 2-year period identified different circulating clonal groups', Microbial Genomics, vol. 6, no. 1, p. 428599.
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Fourment, M, Claywell, BC, Dinh, V, McCoy, C, Matsen IV, FA & Darling, AE 2018, 'Effective Online Bayesian Phylogenetics via Sequential Monte Carlo with Guided Proposals', Systematic Biology, vol. 67, no. 3, pp. 490-502.
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McKinnon, J, Roy Chowdhury, P & Djordjevic, SP 2018, 'Genomic analysis of multidrug-resistant Escherichia coli ST58 causing urosepsis', International Journal of Antimicrobial Agents, vol. 52, no. 3, pp. 430-435.
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Raymond, BBA, Jenkins, C, Turnbull, L, Whitchurch, CB & Djordjevic, SP 2018, 'Extracellular DNA release from the genome-reduced pathogen Mycoplasma hyopneumoniae is essential for biofilm formation on abiotic surfaces', Scientific Reports, vol. 8, no. 1, pp. 10373-10373.
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Raymond, BBA, Madhkoor, R, Schleicher, I, Uphoff, CC, Turnbull, L, Whitchurch, CB, Rohde, M, Padula, MP & Djordjevic, SP 2018, 'Extracellular Actin Is a Receptor for Mycoplasma hyopneumoniae', Frontiers in Cellular and Infection Microbiology, vol. 8, no. FEB.
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Raymond, BBA, Turnbull, L, Jenkins, C, Madhkoor, R, Schleicher, I, Uphoff, CC, Whitchurch, CB, Rohde, M & Djordjevic, SP 2018, 'Mycoplasma hyopneumoniae resides intracellularly within porcine epithelial cells', Scientific Reports, vol. 8, no. 1.
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Smalla, K, Cook, K, Djordjevic, SP, Klümper, U & Gillings, M 2018, 'Environmental dimensions of antibiotic resistance: assessment of basic science gaps', FEMS Microbiology Ecology, vol. 94, no. 12, pp. 1-6.
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Fourment, M & Darling, AE 2018, 'Local and relaxed clocks, the best of both worlds', PeerJ, PeerJ.
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Reid, CJ, Wyrsch, ER, Roy Chowdhury, P, Zingali, T, Liu, M, Darling, AE, Chapman, TA & Djordjevic, SP 2017, 'Porcine commensal Escherichia coli: a reservoir for class 1 integrons associated with IS26', Microbial Genomics, vol. 3, no. 12, pp. 1-13.
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Melvold, JA, Wyrsch, ER, McKinnon, J, Roy Chowdhury, P, Charles, IG & Djordjevic, SP 2017, 'Identification of a novel qnrA allele, qnrA8, in environmental Shewanella algae', Oxford University Press (OUP), pp. 2949-2952.
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Chowdhury, PR, DeMaere, M, Chapman, T, Worden, P, Charles, IG, Darling, AE & Djordjevic, SP 2016, 'Comparative genomic analysis of toxin-negative strains of Clostridium difficile from humans and animals with symptoms of gastrointestinal disease', BMC MICROBIOLOGY, vol. 16, no. 1.
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Fourment, Darling, AE & Matsen, E 1970, 'Phylogenetic inference with streaming data using sequential Monte Carlo', Sydney Bioinformatics Research Symposium, Sydney.
Djordjevic, SP, Jarocki, VM, Seemann, T, Cummins, ML, Watt, AE, Drigo, B, Wyrsch, ER, Reid, CJ, Donner, E & Howden, BP, 'Genomic surveillance for antimicrobial resistance - a One Health perspective', NATURE REVIEWS GENETICS.
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FOR Codes: Microbiology, Health, Animal Production and Animal Primary Products
