Staphylococcus aureus from patients with chronic rhinosinusitis show minimal genetic association between polyp and non-polyp phenotypes
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Hastan D, Fokkens W, Bachert C, Newson R, Bislimovska J, Bockelbrink A, et al. Chronic rhinosinusitis in Europe–an underestimated disease. A GA2LEN study. Allergy. 2011;66:1216–23.
Smith, Kristine A, Richard R. Orlandi, and Luke Rudmik. Cost of adult chronic rhinosinusitis: a systematic review. Laryngoscope. 2015;125(7):1547–1556.
Fokkens W, Lund V, Mullol J. European position paper on rhinosinusitis and nasal polyps. Rhinol Suppl. 2007;2006:1–136.
Van Crombruggen K, Zhang N, Gevaert P, Tomassen P, Bachert C. Pathogenesis of chronic rhinosinusitis: inflammation. J Allergy Clin Immunol. 2011;128:728–32.
Tomassen P, Zele TV, Zhang N, Perez-Novo C, Bruaene NV, Gevaert P, et al. Pathophysiology of chronic rhinosinusitis. Proc Am Thorac Soc. 2011;8:115–20.
Lam K, Schleimer R, Kern RC. The etiology and pathogenesis of chronic rhinosinusitis: a review of current hypotheses. Curr Allergy Asthma Rep. 2015;15:1–10.
Kern RC, Conley DB, Walsh W, Chandra R, Kato A, Tripathi-Peters A, et al. Perspectives on the etiology of chronic rhinosinusitis: an immune barrier hypothesis. Am J Rhinol. 2008;22:549.
Boase S, Foreman A, Cleland E, Tan L, Melton-Kreft R, Pant H, et al. The microbiome of chronic rhinosinusitis: culture, molecular diagnostics and biofilm detection. BMC Infect Dis. 2013;13:210.
Seiberling KA, Conley DB, Tripathi A, Grammer LC, Shuh L, Haines GK, et al. Superantigens and chronic rhinosinusitis: detection of staphylococcal exotoxins in nasal polyps. Laryngoscope. 2005;115:1580–5.
Psaltis AJ, Weitzel EK, Ha KR, Wormald P-J. The effect of bacterial biofilms on post–sinus surgical outcomes. Am J Rhinol. 2008;22:1–6.
Tan NCW, Foreman A, Jardeleza C, Douglas R, Vreugde S, Wormald PJ, editors. Intracellular Staphylococcus aureus: the Trojan horse of recalcitrant chronic rhinosinusitis? International forum of allergy & rhinology; 2013: Wiley Online Library.
Van Zele T, Gevaert P, Watelet JB, Claeys G, Holtappels G, Claeys C, et al. Staphylococcus aureus colonization and IgE antibody formation to enterotoxins is increased in nasal polyposis. J Allergy Clin Immunol. 2004;114:981–3.
Drilling A, Coombs GW, Tan HL, Pearson JC, Boase S, Psaltis A, et al., editors. Cousins, siblings, or copies: the genomics of recurrent Staphylococcus aureus infections in chronic rhinosinusitis. International forum of allergy & rhinology; 2014: Wiley Online Library.
Chan CL, Wabnitz D, Bardy JJ, Bassiouni A, Wormald PJ, Vreugde S, et al. The microbiome of otitis media with effusion. Laryngoscope. 2016;126:2844–51.
Inouye M, Dashnow H, Raven L-A, Schultz MB, Pope BJ, Tomita T, et al. SRST2: rapid genomic surveillance for public health and hospital microbiology labs. Genome Med. 2014;6:1–16.
Brakstad OG, Aasbakk K, Maeland JA. Detection of Staphylococcus aureus by polymerase chain reaction amplification of the nuc gene. J Clin Microbiol. 1992;30:1654–60.
Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008;18:821–9.
Swain MT, Tsai IJ, Assefa SA, Newbold C, Berriman M, Otto TD. A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs. Nat Protoc. 2012;7:1260–84.
Boetzer M, Henkel CV, Jansen HJ, Butler D, Pirovano W. Scaffolding pre-assembled contigs using SSPACE. Bioinformatics. 2010;27:578–9.
Sarovich D. Microbial genome assembler pipeline 2016. Available from: https://github.com/dsarov/MGAP---Microbial-Genome-Assembler-Pipeline .
Chapple SN, Sarovich DS, Holden MT, Peacock SJ, Buller N, Golledge C, et al. Whole-genome sequencing of a quarter-century melioidosis outbreak in temperate Australia uncovers a region of low-prevalence endemicity. In: Microbial Genomics; 2016.
Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014. https://doi.org/10.1093/bioinformatics/btu153 .
Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S, Holden MT, et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics. 2015;31:3691–3.
Chen L, Yang J, Yu J, Yao Z, Sun L, Shen Y, et al. VFDB: a reference database for bacterial virulence factors. Nucleic Acids Res. 2005;33:D325–D8.
Gupta SK, Padmanabhan BR, Diene SM, Lopez-Rojas R, Kempf M, Landraud L, et al. ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes. Antimicrob Agents Chemother. 2014;58:212–20.
Rice P, Longden I, Bleasby A. EMBOSS: the European molecular biology open software suite. Trends Genet. 2000;16:276–7.
Sahl JW, Caporaso JG, Rasko DA, Keim P. The large-scale blast score ratio (LS-BSR) pipeline: a method to rapidly compare genetic content between bacterial genomes. PeerJ. 2014;2:e332.
Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet. 2007;81:559–75.
Li H, Durbin R. Fast and accurate short read alignment with burrows–wheeler transform. Bioinformatics. 2009;25:1754–60.
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25:2078–9.
McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, et al. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20:1297–303.
Sarovich DS, Price EP. SPANDx: a genomics pipeline for comparative analysis of large haploid whole genome re-sequencing datasets. BMC Res Notes. 2014;7:618.
Swofford DL, Documentation B. Phylogenetic analysis using parsimony. Champaign: Illinois Natural History Survey; 1991.
Proft T. Bacterial Toxins: Genetics, Cellular Biology and Practical Applications: Horizon Scientific Press; 2013.
Fraser JD, Proft T. The bacterial superantigen and superantigen-like proteins. Immunol Rev. 2008;225:226–43.
Hardy J, Singleton A. Genomewide association studies and human disease. N Engl J Med. 2009;360:1759–68.
Mullighan CG, Goorha S, Radtke I, Miller CB, Coustan-Smith E, Dalton JD, et al. Genome-wide analysis of genetic alterations in acute lymphoblastic leukaemia. Nature. 2007;446:758–64.
Read TD, Massey RC. Characterizing the genetic basis of bacterial phenotypes using genome-wide association studies: a new direction for bacteriology. Genome Med. 2014;6:109.
Sheppard SK, Didelot X, Meric G, Torralbo A, Jolley KA, Kelly DJ, et al. Genome-wide association study identifies vitamin B5 biosynthesis as a host specificity factor in campylobacter. Proc Natl Acad Sci. 2013;110:11923–7.
Andersson P, et al. Chlamydia trachomatis from Australian Aboriginal people with trachoma are polyphyletic composed of multiple distinctive lineages. Nat Commun. 2016;7:10688.
Price EP, Sarovich DS, Smith EJ, MacHunter B, Harrington G, Theobald V, et al. Unprecedented melioidosis cases in northern Australia caused by an Asian Burkholderia pseudomallei strain identified by using large-scale comparative genomics. Appl Environ Microbiol. 2016;82:954–63.
Laabei M, Recker M, Rudkin JK, Aldeljawi M, Gulay Z, Sloan TJ, et al. Predicting the virulence of MRSA from its genome sequence. Genome Res. 2014;24:839–49.
Heymans F, Fischer A, Stow NW, Girard M, Vourexakis Z, Des Courtis A, et al. Screening for staphylococcal superantigen genes shows no correlation with the presence or the severity of chronic rhinosinusitis and nasal polyposis. PLoS One. 2010;5:e9525.
Thunberg U, Hugosson S, Monecke S, Ehricht R, Söderquist B. Molecular characteristics of Staphylococcus aureus associated with chronic rhinosinusitis. Apmis. 2015;123:37–44.