Publications - Genomics and Evolution
Ahlstrom, C. et al. (2015) Limitations of variable number of tandem repeat typing identified through whole genome sequencing of Mycobacterium avium subsp. paratuberculosis on a national and herd level. BMC Genomics, 16(1), 161. (doi:10.1186/s12864-015-1387-6) (PMID:25765045) (PMCID:PMC4356054)
Biek, R., Pybus, O. G., Lloyd-Smith, J. O., and Didelot, X. (2015)Measurably evolving pathogens in the genomic era. Trends in Ecology and Evolution, (doi:10.1016/j.tree.2015.03.009) (PMID:25887947)(Early Online Publication)
Biek, R., O'Hare, A., Wright, D., Mallon, T., McCormick, C., Orton, R.J., McDowell, S., Trewby, H., Skuce, R.A., and Kao, R.R. (2012) Whole genome sequencing reveals local transmission patterns of Mycobacterium bovis in sympatric cattle and badger populations. PLoS Pathogens, 8(11), e1003008. (doi:10.1371/journal.ppat.1003008) (PMID:258879470
Bessell, P.R., Rotariu, O., Innocent, G.T., Smith-Palmer, A., Strachan, N.J.C., Forbes, K.J., Cowden, J.M., Reid, S.W.J., and Matthews, L. (2012) Using sequence data to identify alternative routes and risk of infection: a case-study of campylobacter in Scotland. BMC Infectious Diseases, 12(80), (doi:10.1186/1471-2334-12-80)
Fookes, M. et al. (2011) Salmonella bongori provides insights into the evolution of the Salmonellae. PLoS Pathogens, 7(8), e1002191. (doi:10.1371/journal.ppat.1002191
Gilchrist, T.L., Smith, D.G.E., Fitzpatrick, J.L., Zadoks, R.N., and Fontaine, M.C. (2013) Comparative molecular analysis of ovine and bovine Streptococcus uberis isolates. Journal of Dairy Science, 96(2), pp. 962-970. (doi:10.3168/jds.2012-5705)
Goldstone, R. J., Popat, R., Schuberth, H.-J., Sandra, O., Sheldon, I. M., and Smith, D. G. (2014) Genomic characterisation of an endometrial pathogenic Escherichia coli strain reveals the acquisition of genetic elements associated with extra-intestinal pathogenicity. BMC Genomics, 15(1), p. 1075. (doi:10.1186/1471-2164-15-1075)
Guinane, C.M., Penades, J.R., and Fitzgerald, J.R. (2011) The role of horizontal gene transfer in Staphylococcus aureus host adaptation. Virulence, 2(3), pp. 241-243. (doi:10.4161/viru.2.3.16193)
Holt KE, Wertheim H, Zadoks RN, Baker S, Whitehouse CA, Dance D, Jenney A, Connor TR, Hsu LY, Severin J, Brisse S, Cao H, Wilksch J, Gorrie C, Schultz MB, Edwards DJ, Nguyen KV, Nguyen TV, Dao TT, Mensink M, Minh VL, Nhu NT, Schultsz C, Kuntaman K, Newton PN, Moore CE, Strugnell RA, Thomson NR. Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health. Proc Natl Acad Sci U S A. 2015 Jun 22. pii: 201501049. [Epub ahead of print] PubMed PMID: 26100894;
Kao, R. R., Haydon, D. T., Lycett, S. J., and Murcia, P. R. (2014)Supersize me: how whole-genome sequencing and big data are transforming epidemiology. Trends in Microbiology, 22(5), pp. 282-291. (doi:10.1016/j.tim.2014.02.011)
Lee, I., and Davies, R.L. (2011) Evidence for a common gene pool and frequent recombinational exchange of the tbpBA operon in Mannheimia haemolytica, Mannheimia glucosida and Bibersteinia trehalosi. Microbiology, 157(1), pp. 123-135.(doi:10.1099/mic.0.041236-0)
Miao He, et.al. (2013).Emergence and global spread of epidemic healthcare-associated Clostridium difficile. Nature Genetics 45:109-13.
Millins, C., Magierecka, A., Gilbert, L., Edoff, A., Brereton, A., Kilbride, E., Denwood, M., Birtles, R., and Biek, R. (2015) An invasive mammal (grey squirrel, Sciurus carolinensis) commonly hosts diverse and atypical genotypes of the zoonotic pathogen Borrelia burgdorferi sensu lato. Applied and Environmental Microbiology, 81(13), pp. 4236-4245. (doi:10.1128/AEM.00109-15) (PMID:25888168)
Philbey AW, Mather HA, Gibbons JF, Thompson H, Taylor DJ, Coia JE. Serovars, bacteriophage types and antimicrobial sensitivities associated with salmonellosis in dogs in the UK (1954-2012). Vet Rec. 2014 Jan 25;174(4):94.
Quiles-Puchalt, N., Martínez-Rubio, R., Ram, G., Lasa, Í., and Penades, J. R. (2014) Unravelling bacteriophage ϕ11 requirements for packaging and transfer of mobile genetic elements in Staphylococcus aureus. Molecular Microbiology, 91(3), pp. 423-437. (doi:10.1111/mmi.12445)
Sait, M., Aitchison, K., Wheelhouse, N., Wilson, K., Lainson, F. A., Longbottom, D., and Smith, D. G.E. (2013) Genome sequence of Lawsonia intracellularis strain N343, isolated from a sow with hemorrhagic proliferative enteropathy. Genome Announcements, 1(1), e00027-13. (doi:10.1128/genomeA.00027-13)
Springman, A. C., Lacher, D. W., Waymire, E. A., Wengert, S. L., Singh, P., Zadoks, R. N., Davies, H. D., and Manning, S. D. (2014) Pilus distribution among lineages of group b streptococcus: an evolutionary and clinical perspective. BMC Microbiology, 14(1), p. 159. (doi:10.1186/1471-2180-14-159)
Stipetic, L. H., Hamilton, G., Dalby, M. J., Davies, R. L., Meek, R.M. D., Ramage, G., Smith, D. G.E., and Burgess, K. E.V. (2015) Draft genome sequence of isolate staphylococcus aureus LHSKBclinical, isolated from an infected hip. Genome Announcements, 3(2), e00336-15. (doi:10.1128/genomeA.00336-15) (PMID:25931597)(PMCID:PMC4417693)
Sullivan, C. B., Diggle, M. A., Davies, R. L., and Clarke, S. C. (2015) Clonal analysis of meningococci during a 26 year period prior to the introduction of meningococcal serogroup C vaccines. PLoS ONE, 10(a), e115741. (doi:10.1371/journal.pone.0115741) (PMID:25615448) (PMCID:PMC4304704)
Theethakaew, C., Feil, E.J., Castillo-Ramirez, S., Aanensen, D.M., Suthienkul, O., Neil, D.M., and Davies, R.L. (2013) Genetic relationships of vibrio parahaemolyticus isolates from clinical, human carrier, and environmental sources in Thailand, determined by multilocus sequence analysis. Applied and Environmental Microbiology, 79(7), pp. 2358-2370. (doi:10.1128/AEM.03067-12)