research articles
Ramsay JP, Parahitiyawa N, Mowlaboccus S, Mullally CA, Yee NWT, Shoby P, Colombi E, Tan HL, Pearson JC, Coombs GW. Genomic characterization of a unique Panton-Valentine leucocidin-positive community-associated methicillin-resistant Staphylococcus aureus lineage increasingly impacting on Australian indigenous communities. Microb Genom. 2023 Dec;9(12):001172. doi: 10.1099/mgen.0.001172.
William J Jowsey, Calum R P Morris, Drew A Hall, John T Sullivan, Robert D Fagerlund, Karina Y Eto, Paul D Solomon, Joel P Mackay, Charles S Bond, Joshua P Ramsay, Clive W Ronson. (2023) DUF2285 is a novel helix-turn-helix domain variant that orchestrates both activation and antiactivation of conjugative element transfer in proteobacteria. Nucleic Acids Research 10.1093/nar/gkad457.
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Colombi, E., Hill, Y., Lines, R., Sullivan, J. T., Kohlmeier, M. G., Christophersen, C. T., Ronson, C. W., Terpolilli, J. J. & Ramsay, J. P. (2023)
Population genomics of Australian indigenous Mesorhizobium reveals diverse nonsymbiotic genospecies capable of nitrogen-fixing symbioses following horizontal gene transfer. Microbial Genomics 9: mgen000918.
Verdonk, C. J., Marshall, A., Ramsay, J. P. & Bond, C. S. (2022) Crystallographic and X-ray scattering study of RdfS, a recombination directionality factor from an integrative and conjugative element. Acta Crystallographica Section D: Structural Biology 78, 1210-1220.
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Joshua P. Ramsay, Tahlia R. Bastholm, Callum J. Verdonk, Dinah D. Tambalo, John T. Sullivan, Liam K. Harold, Beatrice A. Panganiban, Elena Colombi, Benjamin J. Perry, William Jowsey, Calum Morris, Michael F. Hynes, Charles S. Bond, Andrew D.S. Cameron, Christopher K. Yost and Clive W. Ronson (2021) An epigenetic switch activates bacterial quorum sensing and horizontal transfer of an integrative and conjugative element Nucleic Acids Res. doi: 10.1093/nar/gkab1217
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Elena Colombi, Benjamin J. Perry, John T. Sullivan, Amanuel A. Bekuma, Jason J. Terpolilli, Clive W. Ronson, and Joshua P. Ramsay (2021) Comparative analysis of integrative and conjugative mobile genetic elements in the genus Mesorhizobium Microbial Genomics doi: 10.1099/mgen.0.000657
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Yui Eto K, Kwong SM, LaBreck PT, Crow JE, Traore DAK, Parahitiyawa N, Fairhurst HM, Merrell DS, Firth N, Bond CS, Ramsay JP.
Evolving origin-of-transfer sequences on staphylococcal conjugative and mobilizable plasmids-who's mimicking whom?
Nucleic Acids Res. 2021 May 3:gkab303. https://doi.org/10.1093/nar/gkab303
Vaitekenas A, Tai AS, Ramsay JP, Stick SM, Kicic A, (2021) Pseudomonas aeruginosa resistance to Bacteriophages and it's prevention by strategic therapeutic cocktail formulation. Antibiotics doi: 10.3390/antibiotics10020145
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Hill Y, Colombi E, Bonello E, Haskett T, Ramsay J, O'Hara G, Terpolilli J, (2021) Evolution of Diverse Effective N2-Fixing Microsymbionts of Cicer arietinum following Horizontal Transfer of the Mesorhizobium ciceri CC1192 Symbiosis Integrative and Conjugative Element. Applied and Environmental Microbiology doi: 10.1128/AEM.02558-20
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Perry BJ, Sullivan JT, Colombi E, Murphy RJT, Ramsay JP, Ronson CW, (2020) Symbiosis islands of Loteae-nodulating Mesorhizobium comprise three radiating lineages with concordant nod gene complements and nodulation host-range groupings. Microbial Genetics doi: 10.1099/mgen.0.000426
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Eto KY, Firth N, Davis AM, Kwong SM, Krysiak M, Lee YT, O'Brien FG, Grubb WB, Coombs GW, Bond CS, Ramsay JP. (2019) Evolution of a 72-kb cointegrant, conjugative multiresistance plasmid from early community-associated methicillin-resistant Staphylococcus aureus isolates. Antimicrobial Agents and Chemotherapy doi: 10.1128/AAC.01560-19
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Murphy RJT, Ramsay JP, Lee YT, Pang S, O'Dea MA, Pearson JC, Axon JE, Raby E, Abdulgader SM, Whitelaw A, Coombs GW. (2019) Multiple introductions of methicillin-resistant Staphylococcus aureus ST612 into Western Australia associated with both human and equine reservoirs. International Journal of Antimicrobial Agents doi: 10.1016/j.ijantimicag.2019.08.022
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Verdonk CJ, Sullivan JT, Williman KM, Nicholson L, Bastholm TR, Hynes MF, Ronson CW, Bond CS, Ramsay JP. (2019) Delineation of the integrase-attachment and origin-of-transfer regions of the symbiosis island ICEMlSymR7A. Plasmid doi: 10.1016/j.plasmid.2019.102416
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Dorji D, Graham RM, Singh AK, Ramsay JP, Price P, Lee S. (2019) Immunogenicity and protective potential of Bordetella pertussis biofilm and its associated antigens in a murine model. Cellular Immunology https://doi.org/10.1016/j.cellimm.2019.01.006
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Firth N, Jensen SO, Kwong SM, Skurray RA, Ramsay JP. (2018). Staphylococcal Plasmids, Transposable and Integrative Elements. Microbiology Spectrum doi:10.1128/microbiolspec.GPP3-0030-2018
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Permala RR, Glady-Croue J, Watkin ELJ, Ramsay JP, Croue JP. (2018). Complete Genome Sequence of Stenotrophomonas maltophilia AB550, an Environmental Solar Radiation- and Multidrug-Resistant Strain Isolated in Western Australia. Microbiology Resource Announcements doi:10.1128/MRA.00914-18
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Murphy RJT, Lee YT, Pang S, Bastholm TR, Crow JE, Davis AM, Coombs GW, O'Dea MA, Abraham S, Ramsay JP. (2018). Complete Genome Sequence of a Staphylococcus aureus Sequence Type 612 Isolate from an Australian Horse. Microbiology Resource Announcements doi:10.1128/MRA.00869-18
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Haskett TL, Terpolilli JJ, Ramachandran VK, Verdonk CJ, Poole PS, O'Hara GW, Ramsay JP. (2018). Sequential induction of three recombination directionality factors directs assembly of tripartite integrative and conjugative elements. PLoS Genetics https://doi.org/10.1371/journal.pgen.1007292
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Glady-Croue, J., Niu, X. Z., Ramsay, J. P., Watkin, E., Murphy, R. J. T., & Croue, J. P. (2018). Survival of antibiotic resistant bacteria following artificial solar radiation of secondary wastewater effluent. Science of the Total Environment, 626, 1005-1011. doi:10.1016/j.scitotenv.2018.01.101
Kwong, S. M., Ramsay, J. P., Jensen, S. O., & Firth, N. (2017). Replication of staphylococcal resistance plasmids. Frontiers In Microbiology, 8(NOV). doi:10.3389/fmicb.2017.02279
Khaleque, H. N., Corbett, M. K., Ramsay, J. P., Kaksonen, A. H., Boxall, N. J., & Watkin, E. L. J. (2017). Complete genome sequence of Acidihalobacter prosperus strain F5, an extremely acidophilic, iron- and sulfur-oxidizing halophile with potential industrial applicability in saline water bioleaching of chalcopyrite. Journal Of Biotechnology, 262, 56-59. doi:10.1016/j.jbiotec.2017.10.001
Brewer, R. J. M., Haskett, T. L., Ramsay, J. P., O'Hara, G. W., & Terpolilli, J. J. (2017). Complete Genome Sequence of Mesorhizobium ciceribv. biserrulae WSM1497, an Efficient Nitrogen-Fixing Microsymbiont of the Forage LegumeBiserrula pelecinus. Genome Announc, 5(35). doi:10.1128/genomeA.00902-17
Caparros-Martin, J. A., Lareu, R. R., Ramsay, J. P., Peplies, J., Reen, F. J., Headlam, H. A., . . . O'Gara, F. (2017). Statin therapy causes gut dysbiosis in mice through a PXR-dependent mechanism. MICROBIOME, 5, 15 pages. doi:10.1186/s40168-017-0312-4
Haskett, T. L., Ramsay, J. P., Bekuma, A. A., Sullivan, J. T., O'Hara, G. W., & Terpolilli, J. J. (2017). Evolutionary persistence of tripartite integrative and conjugative elements. Plasmid, 92, 30-36. doi:10.1016/j.plasmid.2017.06.001
Khaleque, H. N., Ramsay, J. P., Murphy, R. J. T., Kaksonen, A. H., Boxall, N. J., & Watkin, E. L. J. (2017). Draft genome sequence of Acidihalobacter ferrooxidans DSM 14175 (strain V8), a new ironand sulfur-oxidizing, halotolerant, acidophilic species. Genome Announcements, 5(21). doi:10.1128/genomeA.00413-17
Ramsay, J. P., & Firth, N. (2017). Diverse mobilization strategies facilitate transfer of non-conjugative mobile genetic elements. Current Opinion In Microbiology, 38, 1-9. doi:10.1016/j.mib.2017.03.003
Khaleque, H. N., Ramsay, J. P., Murphy, R. J. T., Kaksonen, A. H., Boxall, N. J., & Watkin, E. L. J. (2017). Draft genome sequence of the acidophilic, halotolerant, and iron/sulfur-oxidizing Acidihalobacter prosperus DSM 14174 (strain V6). Genome Announcements, 5(3). doi:10.1128/genomeA.01469-16
Haskett, T. L., Terpolilli, J. J., Bekuma, A., O'Hara, G. W., Sullivan, J. T., Wang, P., . . . Ramsay, J. P. (2016). Assembly and transfer of tripartite integrative and conjugative genetic elements. Proceedings of the National Academy of Sciences of the United States of America, 113(43), 12268-12273. doi:10.1073/pnas.1613358113
Ramsay, J. P. (2016). Replicating methicillin resistance? Nature Structural and Molecular Biology, 23(10), 874-875. doi:10.1038/nsmb.3303
Ulluwishewa, D., Wang, L., Pereira, C., Flynn, S., Cain, E., Stick, S., . . . O'Gara, F. (2016). Dissecting the regulation of bile-induced biofilm formation in Staphylococcus aureus. MICROBIOLOGY-SGM, 162, 1398-1406. doi:10.1099/mic.0.000317
Ramsay, J. P., Kwon, S. M., Murphy, J. T., Yui Eto, K., Price, K. J., Nguyen, Q. T., . . . Firth, N. (2016). An updated view of plasmid conjugation and mobilisation in Staphylococcus. Mobile Genetic Elements, 6(4), 1. doi:10.1080/2159256X.2016.1208317
Tashiro, Y., Monson, R. E., Ramsay, J. P., & Salmond, G. P. C. (2016). Molecular genetic and physical analysis of gas vesicles in buoyant enterobacteria. Environmental Microbiology, 18(4), 1264-1276. doi:10.1111/1462-2920.13203
Pollet, R. M., Ingle, J. D., Hymes, J. P., Eakes, T. C., Eto, K. Y., Kwong, S. M., . . . Redinbo, M. R. (2016). Processing of Non-Conjugative Resistance Plasmids by Conjugation Nicking Enzyme of Staphylococci. J Bacteriol, Online, 888-897. doi:10.1128/JB.00832-15
Haskett, T., Wang, P., Ramsay, J., O'Hara, G., Reeve, W., Howieson, J., & Terpolilli, J. (2016). Complete genome sequence of Mesorhizobium ciceri strain CC1192, an efficient nitrogen-fixing microsymbiont of Cicer arietinum. Genome Announcements, 4(3), 1-2. doi:10.1128/genomeA.00516-16
Haskett, T., Wang, P., Ramsay, J., O'Hara, G., Reeve, W., Howieson, J., & Terpolilli, J. (2016). Complete genome sequence of Mesorhizobium ciceri bv. biserrulae strain WSM1284, an efficient nitrogen-fixing microsymbiont of the pasture legume Biserrula pelecinus. Genome Announcements, 4(3), 1-2. doi:10.1128/genomeA.00514-16
Ramsay, J. P., & Ronson, C. W. (2015). Silencing quorum sensing and ICE mobility through antiactivation and ribosomal frameshifting. Mob Genet Elements, 5(6), 103-108. doi:10.1080/2159256X.2015.1107177
O'Brien, F. G., Eto, K. Y., Murphy, R. J. T., Fairhurst, H. M., Coombs, G. W., Grubb, W. B., & Ramsay, J. P. (2015). Origin-of-transfer sequences facilitate mobilisation of non-conjugative antimicrobial-resistance plasmids in Staphylococcus aureus. Nucleic Acids Research, 43(16), 7971-7983. doi:10.1093/nar/gkv755
Ramsay, J. P., & Ronson, C. W. (2015). Genetic Regulation of Symbiosis Island Transfer in Mesorhizobium loti. In F. J. de Bruijn (Ed.), Biological Nitrogen Fixation, 2 Volume Set (pp. 219-224). Hoboken, New Jersey, USA: John Wiley & Sons.
O'Brien, F. G., Ramsay, J. P., Monecke, S., Coombs, G. W., Robinson., Htet, Z., . . . Grubb, W. B. (2015). Staphylococcus aureus plasmids without mobilization genes are mobilized by a novel conjugative plasmid from community isolates. Journal of Antimicrobial Chemotherapy, 70(3), 649-652. doi:10.1093/jac/dku454
Ramsay, J. P., Tester, L. G. L., Major, A. S., Sullivan, J. T., Edgar, C. D., Kleffmann, T., . . . Ronson, C. W. (2015). Ribosomal frameshifting and dual-target antiactivation restrict quorum-sensing-activated transfer of a mobile genetic element. Proceedings of the National Academy of Sciences of the United States of America, 112(13), 4104-4109. doi:10.1073/pnas.1501574112
Monson, R., Smith, D. S., Matilla, M. A., Roberts, K., Richardson, E., Drew, A., . . . Salmond, G. P. C. (2015). A plasmid-transposon hybrid mutagenesis system effective in a broad range of enterobacteria. Frontiers in Microbiology, 6, 1-13.
Tan, H., West, J. A., Ramsay, J. P., Monson, R. E., Griffin, J. L., Toth, I. K., & Salmond, G. P. C. (2014). Comprehensive overexpression analysis of cyclic-di-GMP signalling proteins in the phytopathogen Pectobacterium atrosepticum reveals diverse effects on motility and virulence phenotypes. Microbiology, 160, 1427-1439.
Ramsay, J. P. (2013). High-throughput β-galactosidase and β-glucuronidase Assays Using Fluorogenic Substrates. Bio-protocol, 3(14), 7 pages.
Ronson, C., Hynes, M., Ramsay, J., & Sullivan, J. (2013). Symbiosis Islands. In Brenner's Encyclopedia of Genetics (2 ed., pp. 598-600). 32 Jamestown Road, London NW1 7BY, UK: Elsevier. Retrieved from http://www.sciencedirect.com/science/article/pii/B9780123749840014972
Wilf, N. M., Reid, A. J., Ramsay, J. P., Williamson, N. R., Croucher, N. J., Gatto, L., . . . Salmond, G. P. C. (2013). RNA-seq reveals the RNA binding proteins, Hfq and RsmA, play various roles in virulence, antibiotic production and genomic flux in Serratia sp. ATCC 39006. BMC Genomics, 14(822). doi:10.1186/1471-2164-14-822
Fineran, P. C., Iglesias Cans, M. C., Ramsay, J. P., Wilf, N. M., Cossyleon, D., McNeil, M. B., . . . Salmond, G. P. C. (2013). Draft Genome Sequence of Serratia sp. Strain ATCC 39006, a Model Bacterium for Analysis of the Biosynthesis and Regulation of Prodigiosin, a Carbapenem, and Gas Vesicles. Genome Announcements, 1(6). Retrieved from http://genomea.asm.org/content/1/6/e01039-13.full?sid=aab4003c-b6b6-45dc-9f4e-9d3faf1f9677
Ramsay, J. P., Major, A. S., Komarovsky, V. M., Sullivan, J. T., Dy, R. L., Hynes, M. F., . . . Ronson, C. W. (2013). A widely conserved molecular switch controls quorum sensing and symbiosis island transfer in Mesorhizobium loti through expression of a novel antiactivator. Molecular Microbiology, 87(1), 1-13. doi:10.1111/mmi.12079
Ramsay, J. P., & Salmond, G. P. C. (2012). Quorum sensing-controlled buoyancy through gas vesicles: Intracellular bacterial microcompartments for environmental adaptation. Communicative and Integrative Biology, 5, 96-98. doi:10.4161/cib.18532
Wilf, N. M., Williamson, N. R., Ramsay, J. P., Poulter, S., Bandyra, K. J., & Salmond, G. P. C. (2011). The RNA chaperone, Hfq, controls two luxR-type regulators and plays a key role in pathogenesis and production of antibiotics in Serratia sp. ATCC 39006. Environmental Microbiology, 13(10), 2649-2666. doi:10.1111/j.1462-2920.2011.02532.x
Ramsay, J. P., Williamson, N. R., Spring, D. R., & Salmond, G. P. C. (2011). A quorum-sensing molecule acts as a morphogen controlling gas vesicle organelle biogenesis and adaptive flotation in an enterobacterium. Proceedings Of The National Academy Of Sciences Of The United States Of America, 108(36), 14932-14937. doi:10.1073/pnas.1109169108
Ramsay, J. P., Sullivan, J. T., Jambari, N., Ortori, C. A., Heeb, S., Williams, P., . . . Ronson, C. W. (2009). A LuxRI-family regulatory system controls excision and transfer of the Mesorhizobium loti strain R7A symbiosis island by activating expression of two conserved hypothetical genes. Molecular Microbiology, 73(6), 1141-1155. doi:10.1111/j.1365-2958.2009.06843.x
Ramsay, J. P., Sullivan, J. T., Stuart, G. S., Lamont, I. L., & Ronson, C. W. (2006). Excision and transfer of the Mesorhizobium loti R7A symbiosis island requires an integrase IntS, a novel recombination directionality factor RdfS, and a putative relaxase RlxS. Molecular Microbiology, 62(3), 723-734. doi:10.1111/j.1365-2958.2006.05396.x
Glaser, R. L., Ramsay, J. P., & Morison, I. M. (2006). The imprinted gene and parent-of-origin effect database now includes parental origin of de novo mutations. Nucleic acids research., 34(Database issue).
Morison, I. M., Ramsay, J. P., & Spencer, H. G. (2005). A census of mammalian imprinting. Trends in Genetics, 21(8), 457-465. doi:10.1016/j.tig.2005.06.008