Improved biosecurity through the engineering of microbial ecosystems

Funding: 2015: $89,967
2016: $183,967
2017: $170,375
2018: $76,375

Project Member(s): Djordjevic, S., Darling, A.

Funding or Partner Organisation: Australian Research Council (ARC Linkage Projects)
NSW Department of Primary Industries

Start year: 2016

Summary: Microorganisms including commensals and pathogens can live in complex communities in a range of environments including animal hosts. It is now known that these communities (known as microbiomes) can exert a profound effect on animal health. This project seeks (i) to understand where antimicrobial resistance genes reside in pig gut microbiotia and how they move between members of this complex microbial community and (ii) provide information on how probiotics may be utilised to reduce the dependence on antibiotics. The datasets will provide science-based foundation for surveillance and response programs for key biosecurity threats and assist with the development of predictive models for changes in the distribution of drug resistant bacteria.

Publications:

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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DeMaere, MZ & Darling, AE 2019, 'bin3C: exploiting Hi-C sequencing data to accurately resolve metagenome-assembled genomes', Genome Biology, vol. 20, no. 1, pp. 46-46.
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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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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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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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Gaio, D, Anantanawat, K, To, J, Liu, M, Monahan, L & Darling, AE 2019, 'Hackflex: low cost Illumina Nextera Flex sequencing library construction', Cold Spring Harbor Laboratory.
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DeMaere, MZ & Darling, AE 2018, 'bin3C : Exploiting Hi-C sequencing data to accurately resolve metagenome-assembled genomes (MAGs)', Genome Biology, vol. 20.
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DeMaere, MZ & Darling, AE 2018, 'Sim3C: simulation of Hi-C and Meta3C proximity ligation sequencing technologies', GigaScience, vol. 7, no. 2, pp. 1-12.
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O'Rourke, MB, Djordjevic, SP & Padula, MP 2018, 'The quest for improved reproducibility in MALDI mass spectrometry', Mass Spectrometry Reviews, vol. 37, no. 2, pp. 217-228.
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Liu, MY, Worden, P, Monahan, LG, DeMaere, MZ, Burke, CM, Djordjevic, SP, Charles, IG & Darling, AE 2017, 'Evaluation of ddRADseq for reduced representation metagenome sequencing', PeerJ, vol. 5, no. 9, pp. e3837-e3837.
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Quince, C, Delmont, TO, Raguideau, S, Alneberg, J, Darling, AE, Collins, G & Eren, AM 2017, 'DESMAN: a new tool for de novo extraction of strains from metagenomes', Genome Biology, vol. 18, no. 1.
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Sczyrba, A, Hofmann, P, Belmann, P, Koslicki, D, Janssen, S, Dröge, J, Gregor, I, Majda, S, Fiedler, J, Dahms, E, Bremges, A, Fritz, A, Garrido-Oter, R, Jørgensen, TS, Shapiro, N, Blood, PD, Gurevich, A, Bai, Y, Turaev, D, DeMaere, MZ, Chikhi, R, Nagarajan, N, Quince, C, Meyer, F, Balvočiūtė, M, Hansen, LH, Sørensen, SJ, Chia, BKH, Denis, B, Froula, JL, Wang, Z, Egan, R, Don Kang, D, Cook, JJ, Deltel, C, Beckstette, M, Lemaitre, C, Peterlongo, P, Rizk, G, Lavenier, D, Wu, Y-W, Singer, SW, Jain, C, Strous, M, Klingenberg, H, Meinicke, P, Barton, MD, Lingner, T, Lin, H-H, Liao, Y-C, Silva, GGZ, Cuevas, DA, Edwards, RA, Saha, S, Piro, VC, Renard, BY, Pop, M, Klenk, H-P, Göker, M, Kyrpides, NC, Woyke, T, Vorholt, JA, Schulze-Lefert, P, Rubin, EM, Darling, AE, Rattei, T & McHardy, AC 2017, 'Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software', Nature Methods, vol. 14, no. 11, pp. 1063-1071.
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Keywords: pigs, microbiome, antibiotic resistance, probiotics

FOR Codes: Microbial Ecology, Veterinary Microbiology (excl. Virology), Food Safety, Pigs, Veterinary sciences