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Res"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"13950","DOI":"10.1073\/pnas.0506758102","article-title":"Genome analysis of multiple pathogenic isolates of <italic>Streptococcus agalactiae<\/italic>: implications for the microbial \u201cpan-genome\u201d","volume":"102","author":"H Tettelin","year":"2005","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1093\/molbev\/msh018","article-title":"Neighbor-net: an agglomerative method for the construction of phylogenetic networks","volume":"21","author":"D Bryant","year":"2004","journal-title":"Mol Biol Evol"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"595","DOI":"10.1186\/1471-2105-11-595","article-title":"BIGSdb: Scalable analysis of bacterial genome variation at the population level","volume":"11","author":"KA Jolley","year":"2010","journal-title":"BMC 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Meyer","year":"2009","journal-title":"Annu Rev Genet"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"1394","DOI":"10.1096\/fj.12-223305","article-title":"Inhibition of bacterial thioredoxin reductase: an antibiotic mechanism targeting bacteria lacking glutathione","volume":"27","author":"J Lu","year":"2013","journal-title":"FASEB J"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"36912","DOI":"10.1074\/jbc.M507725200","article-title":"GTP cyclohydrolase II structure and mechanism","volume":"280","author":"J Ren","year":"2005","journal-title":"J Biol Chem"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1016\/0923-2508(91)90042-9","article-title":"Three genes preceding <italic>pyrE<\/italic> on the <italic>Escherichia coli<\/italic> chromosome are essential for survival and normal cell morphology in stationary culture and at high temperature","volume":"142","author":"P Poulsen","year":"1991","journal-title":"Res Microbiol"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"e18441","DOI":"10.1371\/journal.pone.0018441","article-title":"Virulence evolution of the human pathogen <italic>Neisseria meningitidis<\/italic> by recombination in the core and accessory genome","volume":"6","author":"B Joseph","year":"2011","journal-title":"PLoS One"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"1611","DOI":"10.1093\/gbe\/evt116","article-title":"Homologous recombination drives both sequence diversity and gene content variation in <italic>Neisseria meningitidis<\/italic>","volume":"5","author":"Y Kong","year":"2013","journal-title":"Genome Biol Evol"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"656","DOI":"10.1038\/ng.2625","article-title":"Population genomics of post-vaccine changes in pneumococcal epidemiology","volume":"45","author":"NJ Croucher","year":"2013","journal-title":"Nat 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Cirlan","year":"2005","journal-title":"Infect Genet Evol"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1086\/511034","article-title":"An outbreak in an intensive care unit of a strain of methicillin-resistant <italic>Staphylococcus aureus<\/italic> sequence type 239 associated with an increased rate of vascular access device-related bacteremia","volume":"44","author":"JD Edgeworth","year":"2007","journal-title":"Clin Infect Dis"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"130","DOI":"10.1016\/S1473-3099(12)70268-2","article-title":"Whole-genome sequencing for analysis of an outbreak of meticillin-resistant <italic>Staphylococcus aureus<\/italic>: a descriptive study","volume":"13","author":"SR Harris","year":"2013","journal-title":"Lancet Infect Dis"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"821","DOI":"10.1101\/gr.074492.107","article-title":"Velvet: algorithms for de novo short read assembly using de Bruijn graphs","volume":"18","author":"DR Zerbino","year":"2008","journal-title":"Genome Res"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"1005","DOI":"10.1099\/mic.0.055459-0","article-title":"Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain","volume":"158","author":"KA Jolley","year":"2012","journal-title":"Microbiology"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"500","DOI":"10.1186\/1471-2164-14-500","article-title":"Evidence of antimicrobial resistance-conferring genetic elements among pneumococci isolated prior to 1974","volume":"14","author":"KL Wyres","year":"2013","journal-title":"BMC Genomics"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"430","DOI":"10.1126\/science.1198545","article-title":"Rapid pneumococcal evolution in response to clinical interventions","volume":"331","author":"NJ Croucher","year":"2011","journal-title":"Science"},{"key":"ref32","unstructured":"Borrow R, Maiden M, Parkhill J, Green J, Kaczmarski E, <etal>et al<\/etal>.. (2011) Meningitis Research Foundation (MRF) Meningococcus Genome Library database. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.meningitis.org\/research\/genome\" xlink:type=\"simple\">http:\/\/www.meningitis.org\/research\/genome<\/ext-link>. Accessed 1 March 2014."},{"key":"ref33","unstructured":"Jolley K, Maiden M. (2010) PubMLST. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/pubmlst.org\" xlink:type=\"simple\">http:\/\/pubmlst.org<\/ext-link>. Accessed 1 March 2014."},{"key":"ref34","unstructured":"Jolley K, Maiden M. (2012) rMLST. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/pubmlst.org\/rmlst\/\" xlink:type=\"simple\">http:\/\/pubmlst.org\/rmlst\/<\/ext-link>. Accessed 1 March 2014."},{"key":"ref35","unstructured":"Chan MS, Aanensen D. (2000) MLST. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.mlst.net\" xlink:type=\"simple\">http:\/\/www.mlst.net<\/ext-link>. Accessed 1 March 2014."},{"key":"ref36","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1186\/1471-2105-10-152","article-title":"Global optimal eBURST analysis of multilocus typing data using a graphic matroid approach","volume":"10","author":"AP Francisco","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"2947","DOI":"10.1093\/bioinformatics\/btm404","article-title":"Clustal W and Clustal X version 2.0","volume":"23","author":"MA Larkin","year":"2007","journal-title":"Bioinformatics"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"254","DOI":"10.1093\/molbev\/msj030","article-title":"Application of phylogenetic networks in evolutionary studies","volume":"23","author":"DH Huson","year":"2006","journal-title":"Mol Biol Evol"},{"key":"ref39","unstructured":"Casella G, Berger RL. (1990) Statistical inference, vol. 70: Duxbury Press Belmont, CA."},{"key":"ref40","doi-asserted-by":"crossref","unstructured":"Jaynes ET. (2003) Probability theory: the logic of science: Cambridge University Press.","DOI":"10.1017\/CBO9780511790423"},{"key":"ref41","doi-asserted-by":"crossref","unstructured":"Jukes THaC, CR. (1969) Evolution of Protein Molecules. New York: Academic Press.","DOI":"10.1016\/B978-1-4832-3211-9.50009-7"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"1639","DOI":"10.1101\/gr.092759.109","article-title":"Circos: an information aesthetic for comparative genomics","volume":"19","author":"M Krzywinski","year":"2009","journal-title":"Genome Res"},{"key":"ref43","doi-asserted-by":"crossref","unstructured":"Silverman BW. (1986) Density estimation for statistics and data analysis, vol. 26: CRC press.","DOI":"10.1007\/978-1-4899-3324-9"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"D284","DOI":"10.1093\/nar\/gkr1060","article-title":"eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges","volume":"40","author":"S Powell","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"ref45","unstructured":"Gentleman R, Ihaka R. (1997) The R Project for Statistical Computing. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.r-project.org\/index.html\" xlink:type=\"simple\">http:\/\/www.r-project.org\/index.html<\/ext-link>. 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