68-2
63/110

6) Jolley KA, Bray JE, Maiden MCJ: Open-access bacte-rial population genomics: BIGSdb software, the PubMLST.org website and their applications. Well-come Open Research, 2018; 3: 124. doi:10.12688/wellco-meopenres.14826.1 7) Szabados F, Woloszyn J, Richter C, Kaase M, Gater-mann S. Identification of molecularly defined Staphylo︲coccus aureus strains using matrix-assisted laser desorption/ionization time of flight mass spectrometry and the Biotyper 2.0 database. Journal of Medical Microbiology, 2010; 59: 787-790. doi:10.1099/jmm.0. 016733-0 8) Chin CS, Alexander DH, Marks P, et al: Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nature Methods, 2013; 10: 563-569. doi:10.1038/nmeth.2474 9) Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM: DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. International Journal of Systematic and Evolutionary Microbiology, 2007; 57: 81-91. doi:10.1099/ijs.0.64483-010) Richter M, Rosselló-Móra R: Shifting the genomic gold standard for the prokaryotic species definition. Proceed-ings of the National Academy of Sciences of the United States of America, 2009; 106: 19126-19131. doi:10.1073/pnas.090641210611) Yoon SH, Ha SM, Lim J, Kwon S, Chun J: A large-scale evaluation of algorithms to calculate average nucleo-tide identity. Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology, 2017; 110: 1281-1286. doi:10.1007/s10482-017-0844-412) Brettin T, Davis JJ, Disz T, et al: RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and anno-tating batches of genomes. Scientific Reports, 2015; 5: 8365. doi:10.1038/srep0836513) Aziz RK, Bartels D, Best AA, et al: The RAST Server: rapid annotations using subsystems technology. BMC Genomics, 2008; 9: 75. doi:10.1186/1471-2164-9-7514) Clinical and Laboratory Standards Institute, Weinstein MP. Methods for Dilution Antimicrobial Susceptibility Tests for Bacteria That Grow Aerobically. 11th Edition.15) Joensen KG, Scheutz F, Lund O, et al: Real-time whole-genome sequencing for routine typing, surveil-lance, and outbreak detection of verotoxigenic Esche︲richia coli. Journal of Clinical Microbiology, 2014; 52: 1501-1510. doi:10.1128/JCM.03617-1316) Camacho C, Coulouris G, Avagyan V, et al: BLAST+: Architecture and applications. BMC Bioinformatics, 2009; 10: 421. doi:10.1186/1471-2105-10-42117) Clausen PTLC, Aarestrup FM, Lund O. Rapid and precise alignment of raw reads against redundant data-bases with KMA. BMC Bioinformatics, 2018; 19: 307. doi:10.1186/s12859-018-2336-618) Kaas RS, Leekitcharoenphon P, Aarestrup FM, Lund O: Solving the problem of comparing whole bacterial genomes across different sequencing platforms. PLoS One, 2014; 9: e104984. doi:10.1371/journal.pone.010498419) International Working Group on the Classification of Staphylococcal Cassette Chromosome Elements (IWG- SCC). Classification of staphylococcal cassette chromo-some mec (SCCmec): Guidelines for reporting novel SCCmec elements. Antimicrobial Agents and Chemo-therapy, 2009; 53: 4961-4967. doi:10.1128/AAC.00579-0920) Kondo Y, Ito T, Ma XX, et al: Combination of multiplex PCRs for staphylococcal cassette chromosome mec type assignment: rapid identification system for mec, ccr, and major differences in junkyard regions. Antimi-crobial Agents and Chemotherapy, 2007; 51: 264-274. doi:10.1128/AAC.00165-0621) Holden MTG, Lindsay JA, Corton C, et al: Genome sequence of a recently emerged, highly transmissible, multi-antibiotic- and antiseptic-resistant variant of methicillin-resistant Staphylococcus aureus, sequence type 239 (TW). Journal of Bacteriology, 2010; 192: 888-892. doi:10.1128/JB.01255-0922) Lakhundi S, Zhang K: Methicillin-resistant Staphylo︲coccus aureus: molecular characterization, evolution, and epidemiology. Clinical Microbiology Reviews, 2018; 31: e00020-18. doi:10.1128/CMR.00020-1823) Takeuchi F, Watanabe S, Baba T, et al: Whole-genome sequencing of Staphylococcus haemolyticus uncovers the extreme plasticity of its genome and the evolution of human-colonizing staphylococcal species. Journal of Bacteriology, 2005; 187: 7292-7308. doi:10.1128/JB.187. 21.7292-7308.200524) Baba T, Takeuchi F, Kuroda M, et al: Genome and virulence determinants of high virulence communi-ty-acquired MRSA. Lancet, 2002; 359: 1819-1827. doi: 10.1016/S0140-6736(02)08713-525) Sidhu MS, Heir E, Leegaard T, Wiger K, Holck A: Frequency of disinfectant resistance genes and genetic linkage with β-lactamase transposon Tn552 among clin-ical staphylococci. Antimicrobial Agents and Chemo-therapy, 2002; 46: 2797-2803. doi:10.1128/AAC.46.9.2797-2803.200226) Olsen JE, Christensen H, Aarestrup FM: Diversity and evolution of blaZ from Staphylococcus aureus and coag-ulase-negative staphylococci. Journal of Antimicrobial Chemotherapy, 2006; 57: 450-460. doi:10.1093/jac/dki49227) Kuroda M, Ohta T, Uchiyama I, et al: Whole genome sequencing of meticillin-resistant Staphylococcus aureus. Lancet, 2001; 357: 1225-1240. doi:10.1016/S0140-6736 (00)04403-228) Tettelin H, Masignani V, Cieslewicz MJ, et al: Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: Implications for the microbial “pan-genome.” Proceedings of the National Academy of Sciences of the United States of America, 2005; 102: 13950-13955. doi:10.1073/pnas.050675810229) Baba T, Bae T, Schneewind O, Takeuchi F, Hiramatsu K: Genome sequence of Staphylococcus aureus strain Newman and comparative analysis of staphylococcal genomes: polymorphism and evolution of two major pathogenicity islands. Journal of Bacteriology. 2008; 190: 300-310. doi:10.1128/JB.01000-0730) Lindsay JA, Ruzin A, Ross HF, Kurepina N, Novick RP: The gene for toxic shock toxin is carried by a family of mobile pathogenicity islands in Staphylococcus aureus. Molecular Microbiology, 1998; 29: 527-543. doi: 10.1046/j.1365-2958.1998.00947.x31) Fitzgerald JR, Monday SR, Foster TJ, et al: Character-ization of a putative pathogenicity island from bovine Staphylococcus aureus encoding multiple superanti-gens. Journal of Bacteriology, 2001; 183: 63-70. doi:10. 1128/JB.183.1.63-70.200132) Ito T, Katayama Y, Asada K, et al: Structural compar-ison of three types of staphylococcal cassette chromo-some mec integrated in the chromosome in methicillin- 155

元のページ  ../index.html#63

このブックを見る