Research Publications

24H. Wyrsch E.R., Hoye B.J., Sanderson-Smith M., Gorman J., Maute K., Cummins M.L., Jarocki V.M., Marenda M.S., Dolejska M., Djordjevic S.P. (2024)

The faecal microbiome of the Australian silver gull contains phylogenetically diverse ExPEC, aEPEC and Escherichia coli carrying the transmissible locus of stress tolerance. Science of the Total Environment Science of the Total Environment, 919, 170815

24G. Chen Y., Nguyen D.T., Wheeler D., Herron G.A. (2024).

A novel mutation in mitochondrial cytochrome b conferring resistance to bifenazate in two-spotted spider mite Tetranychus urticae Koch (Acarina: Tetranychidae) Pest Management Science, 80(7)

24F. Djordjevic S.P., Jarocki V.M., Seemann T., Cummins M.L., Watt A.E., Drigo B., Wyrsch E.R., Reid C.J., Donner E., Howden B.P. (2024)

Genomic surveillance for antimicrobial resistance — a One Health perspective.  Nature Reviews Genetics, 25(2)

24E. Tobin L.A., Jarocki V.M., Kenyon J., Drigo B., Donner E., Djordjevic S.P., Hamidian M. (2024)

Genomic analysis of diverse environmental Acinetobacter isolates identifies plasmids, antibiotic resistance genes, and capsular polysaccharides shared with clinical strains. Applied and Environmental Microbiology

Applied and Environmental Microbiology, 90(2)

24D. Jarocki V.M., Cummins M.L., Donato C.M., Howden B.P., Djordjevic S.P. (2024)

A One Health approach for the genomic surveillance of AMR Microbiology Australia, 45(2)

24C. Hem S., Cummins M.L., Wyrsch E.R., Drigo B., Hoye B.J., Maute K., Sanderson-Smith M., Gorman J., Bogema D.R., Jenkins C., Deutscher A.T., Yam J., Hai F., Donner E., Jarocki V.M., Djordjevic S.P. (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, 909, 168608

24B. Chowdhury P.R., Alhamami T., Venter H., Veltman T., Carr M., Mollinger J., Trott D.J., Djordjevic S.P. (2024)

Identification and evolution of ICE-PmuST394: a novel integrative conjugative element in Pasteurella multocida ST394 Journal of Antimicrobial Chemotherapy, 79(4)

24A. Siboni N., King W.L., Williams N.L.R., Scanes E., Giardina M., Green T.J., Ostrowski M., O’Connor W., Dove M., Labbate M., Seymour J.R. (2024)

Increased abundance of potentially pathogenic Vibrio and a marine heatwave co-occur with a Pacific Oyster summer mortality event Aquaculture, 583, 740618

23F. Alhamami T., Roy Chowdhury P., Venter H., Veltman T., Truswell A., Abraham S., Sapula S.A., Carr M., Djordjevic S.P., Trott D.J. (2023)

Genomic profiling of Pasteurella multocida isolated from feedlot cases of bovine respiratory disease Veterinary Microbiology, 283, 109773

23E. Brito B.P., Frost M.J., Anantanawat K., Jaya F., Batterham T., Djordjevic S.P., Chang W.-S., Holmes E.C., Darling A.E., Kirkland P.D. (2023)

Expanding the range of the respiratory infectome in Australian feedlot cattle with and without respiratory disease using metatranscriptomics Microbiome, 11(1), 158

23D. Li D., Elankumaran P., Kudinha T., Kidsley A.K., Trott D.J., Jarocki V.M., Djordjevic S.P. (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, 9(7), 1068

23C. Chowdhury P.R., Hastak P., DeMaere M., Wyrsch E., Li D., Elankumaran P., Dolejska M., Browning G.F., Marenda M.S., Gottlieb T., Cheong E., Merlino J., Myers G.S.A., Djordjevic S.P. (2023)

Phylogenomic analysis of a global collection of Escherichia coli ST38: evidence of interspecies and environmental transmission? mSystems, 8(5)

23B. Elankumuran P., Browning G.F., Marenda M.S., Kidsley A., Osman M., Haenni M., Johnson J.R., Trott D.J., Reid C.J., Djordjevic S.P. (2023)

Identification of genes influencing the evolution of Escherichia coli ST372 in dogs and humans Microbial Genomics, 9(2), 930

23A. Cummins M.L., Li D., Ahmad A., Bushell R., Noormohammadi A.H., Wijesurendra D.S., Stent A., Marenda M.S., Djordjevic S.P. (2023)

Whole Genome Sequencing of Avian Pathogenic Escherichia coli Causing Bacterial Chondronecrosis and Osteomyelitis in Australian Poultry Microorganisms, 11(6), 1513

22O. Wyrsch E.R., Dolejska M., Djordjevic S.P. (2022)

Genomic Analysis of an I1 Plasmid Hosting a sul3-Class 1 Integron and blaSHV-12 within an Unusual Escherichia coli ST297 from Urban Wildlife Microorganisms, 10(7), 1387

22N. Webster J., Kehoe M.A., Nogarotto E., Falconer L., Donovan N.J., Chapman T.A. (2022)

Using Genomics to Design a Pathovar-Specific Loop-Mediated Isothermal Amplification (LAMP) Assay, for the Improved Detection of Xanthomonas citri pv. citri Microorganisms, 10(6), 1153

22M. Hem S., Jarocki V.M., Baker D.J., Charles I.G., Drigo B., Aucote S., Donner E., Burnard D., Bauer M.J., Harris P.N.A., Wyrsch E.R., Djordjevic S.P. (2022)

Genomic analysis of Elizabethkingia species from aquatic environments: Evidence for potential clinical transmission Current Research in Microbial Sciences, 3, 100083

22I. Reid C.J., Cummins M.L., Börjesson S., Brouwer M.S.M., Hasman H., Hammerum A.M., Roer L., Hess S., Berendonk T., Nešporová K., Haenni M., Madec J.-Y., Bethe A., Michael G.B., Schink A.-K., Schwarz S., Dolejska M., Djordjevic S.P. (2022)

A role for ColV plasmids in the evolution of pathogenic Escherichia coli ST58 Nature Communications, 13(1), 683

22K. Wyrsch E.R., Bushell R.N., Marenda M.S., Browning G.F., Djordjevic S.P. (2022)

Global Phylogeny and F Virulence Plasmid Carriage in Pandemic Escherichia coli ST1193 Microbiology Spectrum, 10(6)

22J. Medvecky M., Papagiannitsis C.C., Wyrsch E.R., Bitar I., Cummins M.L., Djordjevic S.P., Dolejska M. (2022)

Interspecies Transmission of CMY-2-Producing Escherichia coli Sequence Type 963 Isolates between Humans and Gulls in Australia mSphere, 7(4)

22I. Hem S., Wyrsch E.R., Drigo B., Baker D.J., Charles I.G., Donner E., Jarocki V.M., Djordjevic S.P. (2022)

Genomic Analysis of Carbapenem-Resistant Comamonas in Water Matrices: Implications for Public Health and Wastewater Treatments Applied and Environmental Microbiology, 88(13)

22H. Chowdhury P.R., Alhamami T., Venter H., Veltman T., Carr M., Mollinger J., Trott D.J., Djordjevic S.P. (2022)

Complete Genome Sequence of Pasteurella multocida Sequence Type 394, Isolated from a Case of Bovine Respiratory Disease in Australia Microbiology Resource Announcements, 11(3), 00890-21

22G. Cummins M.L., Reid C.J., Djordjevic S.P. (2022)

F Plasmid Lineages in Escherichia coli ST95: Implications for Host Range, Antibiotic Resistance, and Zoonoses mSystems, 7(1), e01212

22F. Elankumaran P., Browning G.F., Marenda M.S., Reid C.J., Djordjevic S.P. (2022).

Close genetic linkage between human and companion animal extraintestinal pathogenic Escherichia coli ST127 Current Research in Microbial Sciences, 3, 100106

22E. Yam J., Bogema D.R., Micallef M.L., Djordjevic S.P., Jenkins C. (2022)

Complete Genomes of Theileria orientalis Chitose and Buffeli Genotypes Reveal within Species Translocations and Differences in ABC Transporter Content Pathogens, 11(7), 801

22D. Elankumaran P., Cummins M.L., Browning G.F., Marenda M.S., Reid C.J., Djordjevic S.P. (2022)

Genomic and Temporal Trends in Canine ExPEC Reflect Those of Human ExPEC Microbiology Spectrum, 10(3)

22C. Gaio D., DeMaere M.Z., Anantanawat K., Eamens G.J., Falconer L., Chapman T.A., Djordjevic S., Darling A.E. (2022)

Phylogenetic diversity analysis of shotgun metagenomic reads describes gut microbiome development and treatment effects in the post-weaned pig PLoS ONE, 17(45449), e0270372

22B. Dadd-Daigle P., Collins D., Kirkby K., Roser S., Lonergan P., Chowdhury P.R., Labbate M., Chapman T.A. (2022)

Characterisation of Verticillium dahliae by inter-simple sequence repeats identified a virulent subpopulation affecting Australian cotton Australasian Plant Pathology, 51(4)

22A. Worden P.J., Bogema D.R., Micallef M.L., Go J., Deutscher A.T., Labbate M., Green T.J., King W.L., Liu M., Seymour J.R., Jenkins C. (2022)

Phylogenomic diversity of Vibrio species and other Gammaproteobacteria isolated from Pacific oysters (Crassostrea gigas) during a summer mortality outbreak Microbial Genomics, 8(12), 883

21H. Tarabai H., Wyrsch E.R., Bitar I., Dolejska M., Djordjevic S.P. (2021)

Epidemic hi2 plasmids mobilising the carbapenemase resistance gene blaimp-4 in australian clinical samples identified in multiple sublineages of escherichia coli st216 colonising silver gulls Microorganisms, 9(s3), 567

21G. Li D., Wyrsch E.R., Elankumaran P., Dolejska M., Marenda M.S., Browning G.F., Bushell R.N., McKinnon J., Chowdhury P.R., Hitchick N., Miller N., Donner E., Drigo B., Baker D., Charles I.G., Kudinha T., Jarocki V.M., Djordjevic S.P.

Genomic comparisons of Escherichia coli ST131 from Australia Microbial Genomics, 7(12), 721

21F. Gaio D., Demaere M.Z., Anantanawat K., Chapman T.A., Djordjevic S.P., Darling A.E.

Post-weaning shifts in microbiome composition and metabolism revealed by over 25000 pig gut metagenome-assembled genomes Microbial Genomics, 7(8), 501

21E. Berry I.J., Widjaja M., Jarocki V.M., Steele J.R., Padula M.P., Djordjevic S.P.

Protein cleavage influences surface protein presentation in Mycoplasma pneumoniae Scientific Reports, 11(1), 6743

21D. Nguyen V.K., King W.L., Siboni N., Mahbub K.R., Rahman M.H., Jenkins C., Dove M., O’Connor W., Seymour J.R., Labbate M.

Dynamics of the Sydney rock oyster microbiota before and during a QX disease event Aquaculture, 541, 736821

21C. Jarocki V.M., Heß S., Anantanawat K., Berendonk T.U., Djordjevic S.P.

Multidrug-Resistant Lineage of Enterotoxigenic Escherichia coli ST182 With Serotype O169:H41 in Airline Waste Frontiers in Microbiology, 12, 731050

21B. Nesporova K., Wyrsch E.R., Valcek A., Bitar I., Chaw K., Harris P., Hrabak J., Literak I., Djordjevic S.P., Dolejska M.

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, 65(1), e01118-20

21A. Alhamami T., Chowdhury P.R., Gomes N., Carr M., Veltman T., Khazandi M., Mollinger J., Deutscher A.T., Turni C., Mahdi L., Venter H., Abraham S., Djordjevic S.P., Trott D.J.

First emergence of resistance to macrolides and tetracycline identified in mannheimia haemolytica and pasteurella multocida isolates from beef feedlots in Australia Microorganisms, 9(6), 1322

20P. Nguyen V.K., King W.L., Siboni N., Mahbub K.R., Dove M., O’Connor W., Seymour J.R., Labbate M

The Sydney rock oyster microbiota is influenced by location, season and genetics Aquaculture, 527, 735472

20O. McKinnon J., Roy Chowdhury P., Djordjevic S.P.

Molecular Analysis of an IncF ColV-Like Plasmid Lineage That Carries a Complex Resistance Locus with a Trackable Genetic Signature Microbial Drug Resistance, 26(7)

20N. Hastak P., Cummins M.L., Gottlieb T., Cheong E., Merlino J., Myers G.S.A., Djordjevic S.P., Chowdhury P.R. (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, 6(5), 371

20M. Hastak P., Fourment M., Darling A.E., Gottlieb T., Cheong E., Merlino J., Myers G.S.A., Djordjevic S.P., Chowdhury P.R. (2020)

Escherichia coli ST8196 is a novel, locally evolved, and extensively drug resistant pathogenic lineage within the ST131 clonal complex Emerging Microbes and Infections

20I. Massella E., Reid C.J., Cummins M.L., Anantanawat K., Zingali T., Serraino A., Piva S., Giacometti F., Djordjevic S.P. (2020)

Snapshot study of whole genome sequences of escherichia coli from healthy companion animals, livestock, wildlife, humans and food in italy Antibiotics, 9(11), 782

20K. Cummins M.L., Sanderson-Smith M., Newton P., Carlile N., Phalen D.N., Maute K., Monahan L.G., Hoye B.J., Djordjevic S.P. (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, 5(6)

20J. Bogema D.R., McKinnon J., Liu M., Hitchick N., Miller N., Venturini C., Iredell J., Darling A.E., Chowdury P.R., Djordjevic S.P. (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, 6(1), 255

20I. King W.L., Siboni N., Kahlke T., Dove M., O’Connor W., Mahbub K.R., Jenkins C., Seymour J.R., Labbate M. (2020)

Regional and oyster microenvironmental scale heterogeneity in the Pacific oyster bacterial community FEMS Microbiology Ecology, 96(5), fiaa054

20H. Zingali T., Chapman T.A., Webster J., Chowdhury P.R., Djordjevic S.P. (2020)

Genomic characterisation of a multiple drug resistant inchi2 st4 plasmid in Escherichia coli ST744 in Australia Microorganisms, 8(6), 896

20G. Zingali T., Reid C.J., Chapman T.A., Gaio D., Liu M., Darling A.E., Djordjevic S.P. (2020)

Whole genome sequencing analysis of porcine faecal commensal escherichia coli carrying class 1 integrons from sows and their offspring Microorganisms, 8(6), 843

20F. Cummins M.L., Hamidian M., Djordjevic S.P. (2020)

Salmonella genomic island 1 is broadly disseminated within gammaproteobacteriaceae Microorganisms, 8(2), 161

20E. Reid C.J., Blau K., Jechalke S., Smalla K., Djordjevic S.P. (2020)

Whole Genome Sequencing of Escherichia coli From Store-Bought Produce Frontiers in Microbiology, 10, 3050

20D. Jarocki V.M., Reid C.J., Chapman T.A., Djordjevic S.P. (2020)

Escherichia coli ST302: Genomic Analysis of Virulence Potential and Antimicrobial Resistance Mediated by Mobile Genetic Elements Frontiers in Microbiology, 10, 3098

20C. Wyrsch E.R., Chowdhury P.R., Wallis L., Cummins M.L., Zingali T., Brandis K.J., Djordjevic S.P. (2020)

Whole-genome sequence analysis of environmental Escherichia coli from the faeces of straw-necked ibis (Threskiornis spinicollis) nesting on inland wetlands Microbial Genomics, 6(6), 385

20B. Li D., Reid C.J., Kudinha T., Jarocki V.M., Djordjevic S.P. (2020)

Genomic analysis of trimethoprim-resistant extraintestinal pathogenic Escherichia coli and recurrent urinary tract infections Microbial Genomics, 6(12), 475

20A. Wyrsch E.R., Chowdhury P.R., Jarocki V.M., Brandis K.J., Djordjevic S.P. (2020)

Duplication and diversification of a unique chromosomal virulence island hosting the subtilase cytotoxin in escherichia coli st58 Microbial Genomics, 6(6), 387

19R. King W.L., Jenkins C., Go J., Siboni N., Seymour J.R., Labbate M. (2019)

Characterisation of the Pacific Oyster Microbiome During a Summer Mortality Event Microbial Ecology, 77(2)

19Q. Wyrsch E.R., Hawkey J., Judd L.M., Haites R., Holt K.E., Djordjevic S.P., Billman-Jacobe H. (2019)

Z/i1 hybrid virulence plasmids carrying antimicrobial resistance genes in s. Typhimurium from australian food animal production Microorganisms, 7(9), 299

19P. Wyrsch E.R., Reid C.J., DeMaere M.Z., Liu M.Y., Chapman T.A., Roy Chowdhury P., Djordjevic S.P. (2019)

Complete Sequences of Multiple-Drug Resistant IncHI2 ST3 Plasmids in Escherichia coli of Porcine Origin in Australia Frontiers in Sustainable Food Systems, 3, 18

19O. Cummins M.L., Reid C.J., Chowdhury P.R., Bushell R.N., Esbert N., Tivendale K.A., Noormohammadi A.H., Islam S., Marenda M.S., Browning G.F., Markham P.F., Djordjevic S.P. (2019)

Whole genome sequence analysis of Australian avian pathogenic Escherichia coli that carry the class 1 integrase gene Microbial Genomics, 5(2), 250

19N. Fourment M., Darling A.E. (2019)

Evaluating probabilistic programming and fast variational Bayesian inference in phylogenetics PeerJ, 2019(12), e8272

19M. Reid C.J., De Maere M.Z., Djordjevic S.P. (2019)

Australian porcine clonal complex 10 (CC10) Escherichia coli belong to multiple sublineages of a highly diverse global CC10 phylogeny Microbial Genomics, 5(3)

19L. Monahan L.G., Demaere M.Z., Cummins M.L., Djordjevic S.P., Roy Chowdhury P., Darling A.E. (2019)

High contiguity genome sequence of a multidrug-resistant hospital isolate of Enterobacter hormaechei Gut Pathogens, 11(1), 3

19K. Demaere M.Z., Darling A.E. (2019).

Bin3C: Exploiting Hi-C sequencing data to accurately resolve metagenome-assembled genomes Genome Biology, 20(1), 46

19J. Maciuca I.E., Cummins M.L., Cozma A.P., Rimbu C.M., Guguianu E., Panzaru C., Licker M., Szekely E., Flonta M., Djordjevic S.P., Timofte D. (2019)

Genetic Features of mcr-1 Mediated Colistin Resistance in CMY-2-Producing Escherichia coli From Romanian Poultry Frontiers in Microbiology, 10, 2267

19I. Roy Chowdhury P., Fourment M., DeMaere M.Z., Monahan L., Merlino J., Gottlieb T., Darling A.E., Djordjevic S.P. (2019)

Identification of a novel lineage of plasmids within phylogenetically diverse subclades of IncHI2-ST1 plasmids Plasmid, 102

19H. Jarocki V.M., Steele J.R., Widjaja M., Tacchi J.L., Padula M.P., Djordjevic S.P. (2019).

Formylated N-terminal methionine is absent from the Mycoplasma hyopneumoniae proteome: Implications for translation initiation International Journal of Medical Microbiology, 309(5)

19G. Reid C.J., McKinnon J., Djordjevic S.P. (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, 5(9), 295

19F. Harvey K.L., Jarocki V.M., Charles I.G., Djordjevic S.P. (2019)

The diverse functional roles of elongation factor tu (Ef-tu) in microbial pathogenesis Frontiers in Microbiology, 10(OCT), 2351

19E. King W.L., Siboni N., Kahlke T., Green T.J., Labbate M., Seymour J.R. (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, 10, 2907

19D. Venturini C., Zingali T., Wyrsch E.R., Bowring B., Iredell J., Partridge S.R., Djordjevic S.P. (2019)

Diversity of P1 phage-like elements in multidrug resistant Escherichia coli Scientific Reports, 9(1), 18861

19C. Chowdhury P.R., McKinnon J., Liu M., Djordjevic S.P. (2019)

Multidrug resistant uropathogenic Escherichia coli ST405 with a novel, composite IS26 transposon in a unique chromosomal location Frontiers in Microbiology, 10(JAN), 3212

19B. King W.L., Jenkins C., Seymour J.R., Labbate M. (2019)

Oyster disease in a changing environment: Decrypting the link between pathogen, microbiome and environment Marine Environmental Research, 143

19A. Espinoza-Vergara G., Noorian P., Silva-Valenzuela C.A., Raymond B.B.A., Allen C., Hoque M.M., Sun S., Johnson M.S., Pernice M., Kjelleberg S., Djordjevic S.P., Labbate M., Camilli A., McDougald D. (2019)

Vibrio cholerae residing in food vacuoles expelled by protozoa are more infectious in vivo Nature Microbiology, 4(12)

18D. Raymond B.B.A., Jenkins C., Turnbull L., Whitchurch C.B., Djordjevic S.P. (2018)

Extracellular DNA release from the genome-reduced pathogen Mycoplasma hyopneumoniae is essential for biofilm formation on abiotic surfaces Scientific Reports, 8(1), 10373

18C. Raymond B.B.A., Turnbull L., Jenkins C., Madhkoor R., Schleicher I., Uphoff C.C., Whitchurch C.B., Rohde M., Djordjevic S.P. (2018)

Mycoplasma hyopneumoniae resides intracellularly within porcine epithelial cells Scientific Reports, 8(1), 17697

18B. McKinnon J., Roy Chowdhury P., Djordjevic S.P. (2018)

Genomic analysis of multidrug-resistant Escherichia coli ST58 causing urosepsis International Journal of Antimicrobial Agents, 52(3)

18A. DeMaere M.Z., Darling A.E. (2018)

Sim3C: Simulation of Hi-C and Meta3C proximity ligation sequencing technologies GigaScience, 7(2)

17E. Reid C.J., Wyrsch E.R., Chowdhury P.R., Zingali T., Liu M., Darling A.E., Chapman T.A., Djordjevic S.P. (2017)

Porcine commensal escherichia coli: A reservoir for class 1 integrons associated with IS26 Microbial Genomics, 3(12)

17D. Berry I.J., Jarocki V.M., Tacchi J.L., Raymond B.B.A., Widjaja M., Padula M.P., Djordjevic S.P. (2017)

N-terminomics identifies widespread endoproteolysis and novel methionine excision in a genome-reduced bacterial pathogen Scientific Reports, 7(1), 11063

17C. Chowdhury P.R., Scott M.J., Djordjevic S.P. (2017)

Genomic islands 1 and 2 carry multiple antibiotic resistance genes in Pseudomonas aeruginosa ST235, ST253, ST111 and ST175 and are globally dispersed Journal of Antimicrobial Chemotherapy, 72(2)

17B. Liu M.Y., Worden P., Monahan L.G., DeMaere M.Z., Burke C.M., Djordjevic S.P., Charles I.G., Darling A.E. (2017)

Evaluation of ddRADseq for reduced representation metagenome sequencing PeerJ, 2017(9), e3837

17A. Widjaja M., Harvey K.L., Hagemann L., Berry I.J., Jarocki V.M., Raymond B.B.A., Tacchi J.L., Gründel A., Steele J.R., Padula M.P., Charles I.G., Dumke R., Djordjevic S.P. (2017)

Elongation factor Tu is a multifunctional and processed moonlighting protein Scientific Reports, 7(1), 11227