TY - JOUR AU - van der Poll, T. AU - Opal, S. M. PY - 2009 DA - 2009// TI - Pathogenesis, treatment, and prevention of pneumococcal pneumonia JO - Lancet. Elsevier Ltd VL - 374 ID - van der Poll2009 ER - TY - JOUR AU - Alonso, D. E. AU - Verheul, A. F. AU - Verhoef, J. AU - Snippe, H. PY - 1995 DA - 1995// TI - Streptococcus Pneumoniae: virulence factors, pathogenesis, and vaccines JO - Microbiol Rev VL - 59 ID - Alonso1995 ER - TY - STD TI - Henriques-Normark B, Tuomanen EI. The pneumococcus: Epidemiology, microbiology, and pathogenesis. Cold Spring Harb Perspect Med. 2013;3:a010215. ID - ref3 ER - TY - STD TI - Organization WH. Report of a meeting on priorities for pneumococcal and Haemophilus influenzae type b ( Hib ) vaccine development and introduction. Who. 2001;9–12. Available from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2907394/. UR - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2907394/ ID - ref4 ER - TY - JOUR AU - O’Brien, K. L. AU - Wolfson, L. J. AU - Watt, J. P. AU - Henkle, E. AU - Deloria-Knoll, M. AU - McCall, N. PY - 2009 DA - 2009// TI - Burden of disease caused by Streptococcus Pneumoniae in children younger than 5 years: global estimates JO - Lancet. Elsevier Ltd VL - 374 ID - O’Brien2009 ER - TY - JOUR AU - Bogaert, D. AU - De Groot, R. AU - Hermans, P. W. M. PY - 2004 DA - 2004// TI - Streptococcus Pneumoniae colonisation: the key to pneumococcal disease JO - Lancet Infect Dis VL - 4 UR - https://doi.org/10.1016/S1473-3099(04)00938-7 DO - 10.1016/S1473-3099(04)00938-7 ID - Bogaert2004 ER - TY - JOUR AU - Obaro, S. AU - Adegbola, R. PY - 2002 DA - 2002// TI - The pneumococcus: carriage, disease and conjugate vaccines JO - J Med Microbiol VL - 51 UR - https://doi.org/10.1099/0022-1317-51-2-98 DO - 10.1099/0022-1317-51-2-98 ID - Obaro2002 ER - TY - JOUR AU - Bravo, L. C. PY - 2009 DA - 2009// TI - Overview of the disease burden of invasive pneumococcal disease in Asia JO - Vaccine VL - 27 UR - https://doi.org/10.1016/j.vaccine.2009.04.046 DO - 10.1016/j.vaccine.2009.04.046 ID - Bravo2009 ER - TY - JOUR AU - Lin, T. -. Y. AU - Shah, N. K. AU - Brooks, D. AU - Garcia, C. S. PY - 2010 DA - 2010// TI - Summary of invasive pneumococcal disease burden among children in the Asia-Pacific region JO - Vaccine. Elsevier Ltd VL - 28 ID - Lin2010 ER - TY - JOUR AU - Jones, R. N. AU - Jacobs, M. R. AU - Sader, H. S. PY - 2010 DA - 2010// TI - Evolving trends in Streptococcus Pneumoniae resistance: implications for therapy of community-acquired bacterial pneumonia JO - Int J Antimicrob Agents VL - 36 UR - https://doi.org/10.1016/j.ijantimicag.2010.04.013 DO - 10.1016/j.ijantimicag.2010.04.013 ID - Jones2010 ER - TY - JOUR AU - Muhammad, R. D. AU - Oza-Frank, R. AU - Zell, E. AU - Link-Gelles, R. AU - Narayan, K. M. V. AU - Schaffner, W. PY - 2013 DA - 2013// TI - Epidemiology of invasive pneumococcal disease among high-risk adults since the introduction of pneumococcal conjugate vaccine for children JO - Clin Infect Dis VL - 56 UR - https://doi.org/10.1093/cid/cis971 DO - 10.1093/cid/cis971 ID - Muhammad2013 ER - TY - JOUR AU - Kadioglu, A. AU - Weiser, J. N. AU - Paton, J. C. AU - Andrew, P. W. PY - 2008 DA - 2008// TI - The role of Streptococcus Pneumoniae virulence factors in host respiratory colonization and disease JO - Nat Rev Microbiol VL - 6 UR - https://doi.org/10.1038/nrmicro1871 DO - 10.1038/nrmicro1871 ID - Kadioglu2008 ER - TY - JOUR AU - McCool, T. L. PY - 2002 DA - 2002// TI - The immune response to pneumococcal proteins during experimental human carriage JO - J Exp Med VL - 195 UR - https://doi.org/10.1084/jem.20011576 DO - 10.1084/jem.20011576 ID - McCool2002 ER - TY - JOUR AU - Jacobs, M. R. PY - 2004 DA - 2004// TI - Streptococcus Pneumoniae: epidemiology and patterns of resistance JO - Am J Med Suppl VL - 117 UR - https://doi.org/10.1016/j.amjmed.2004.07.003 DO - 10.1016/j.amjmed.2004.07.003 ID - Jacobs2004 ER - TY - JOUR AU - Zapun, A. AU - Contreras-Martel, C. AU - Vernet, T. PY - 2008 DA - 2008// TI - Penicillin-binding proteins and β-lactam resistance JO - FEMS Microbiol Rev VL - 32 UR - https://doi.org/10.1111/j.1574-6976.2007.00095.x DO - 10.1111/j.1574-6976.2007.00095.x ID - Zapun2008 ER - TY - JOUR AU - Grebe, T. AU - Hakenbeck, R. PY - 1996 DA - 1996// TI - Penicillin-binding proteins 2b and 2x of Streptococcus Pneumoniae are primary resistance determinants for different classes of beta-lactam antibiotics JO - Antimicrob Agents Chemother VL - 40 ID - Grebe1996 ER - TY - JOUR AU - Poole, K. PY - 2004 DA - 2004// TI - Resistance to beta-lactam antibiotics JO - Cell Mol Life Sci VL - 61 UR - https://doi.org/10.1007/s00018-004-4060-9 DO - 10.1007/s00018-004-4060-9 ID - Poole2004 ER - TY - JOUR AU - Cornick, J. E. AU - Bentley, S. D. PY - 2012 DA - 2012// TI - Streptococcus Pneumoniae: the evolution of antimicrobial resistance to beta-lactams, fluoroquinolones and macrolides JO - Microbes Infect. Elsevier Masson SAS VL - 14 UR - https://doi.org/10.1016/j.micinf.2012.01.012 DO - 10.1016/j.micinf.2012.01.012 ID - Cornick2012 ER - TY - JOUR AU - Charpentier, E. AU - Tuomanen, E. PY - 2000 DA - 2000// TI - Mechanisms of antibiotic resistance and tolerance in Streptococcus Pneumoniae JO - Microbes Infect VL - 2 UR - https://doi.org/10.1016/S1286-4579(00)01345-9 DO - 10.1016/S1286-4579(00)01345-9 ID - Charpentier2000 ER - TY - JOUR AU - Jones, R. N. AU - Sader, H. S. AU - Mendes, R. E. AU - Flamm, R. K. PY - 2013 DA - 2013// TI - Update on antimicrobial susceptibility trends among Streptococcus Pneumoniae in the United States: report of ceftaroline activity from the SENTRY antimicrobial surveillance program (1998-2011) JO - Diagn Microbiol Infect Dis. Elsevier Inc VL - 75 UR - https://doi.org/10.1016/j.diagmicrobio.2012.08.024 DO - 10.1016/j.diagmicrobio.2012.08.024 ID - Jones2013 ER - TY - JOUR AU - Ventola, C. L. PY - 2015 DA - 2015// TI - The antibiotic resistance crisis: part 1: causes and threats. P T a peer-reviewed J JO - Formul Manag VL - 40 ID - Ventola2015 ER - TY - JOUR AU - Hackel, M. AU - Lascols, C. AU - Bouchillon, S. AU - Hilton, B. AU - Morgenstern, D. AU - Purdy, J. PY - 2013 DA - 2013// TI - Serotype prevalence and antibiotic resistance in Streptococcus Pneumoniae clinical isolates among global populations JO - Vaccine. Elsevier Ltd VL - 31 ID - Hackel2013 ER - TY - JOUR AU - Cui, L. AU - Neoh, H. AU - Shoji, M. AU - Hiramatsu, K. PY - 2009 DA - 2009// TI - Contribution of vraSR and graSR point mutations to vancomycin resistance in vancomycin-intermediate Staphylococcus Aureus JO - Antimicrob Agents Chemother VL - 53 UR - https://doi.org/10.1128/AAC.01173-08 DO - 10.1128/AAC.01173-08 ID - Cui2009 ER - TY - JOUR AU - Köser, C. U. AU - Ellington, M. J. AU - Peacock, S. J. PY - 2014 DA - 2014// TI - Whole-genome sequencing to control antimicrobial resistance JO - Trends Genet VL - 30 UR - https://doi.org/10.1016/j.tig.2014.07.003 DO - 10.1016/j.tig.2014.07.003 ID - Köser2014 ER - TY - JOUR AU - Palmer, A. C. AU - Kishony, R. PY - 2013 DA - 2013// TI - Understanding, predicting and manipulating the genotypic evolution of antibiotic resistance JO - Nat Rev Genet VL - 14 UR - https://doi.org/10.1038/nrg3351 DO - 10.1038/nrg3351 ID - Palmer2013 ER - TY - JOUR AU - Feng, J. AU - Lupien, A. AU - Gingras, H. AU - Wasserscheid, J. AU - Dewar, K. AU - Légaré, D. PY - 2009 DA - 2009// TI - Genome sequencing of linezolid-resistant Streptococcus Pneumoniae mutants reveals novel mechanisms of resistance JO - Genome Res VL - 19 UR - https://doi.org/10.1101/gr.089342.108 DO - 10.1101/gr.089342.108 ID - Feng2009 ER - TY - JOUR AU - Pai, R. AU - Gertz, R. E. AU - Beall, B. PY - 2006 DA - 2006// TI - Sequential multiplex PCR approach for determining capsular serotypes of Streptococcus Pneumoniae isolates JO - J Clin Microbiol VL - 44 UR - https://doi.org/10.1128/JCM.44.1.124-131.2006 DO - 10.1128/JCM.44.1.124-131.2006 ID - Pai2006 ER - TY - STD TI - Schmieder R, Edwards R. Quality control and preprocessing of metagenomic datasets. Bioinformatics. 2011;27(6):863-64. ID - ref28 ER - TY - JOUR AU - Bankevich, A. AU - Nurk, S. AU - Antipov, D. AU - A a, G. AU - Dvorkin, M. AU - Kulikov, A. S. PY - 2012 DA - 2012// TI - SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing JO - J Comput Biol VL - 19 UR - https://doi.org/10.1089/cmb.2012.0021 DO - 10.1089/cmb.2012.0021 ID - Bankevich2012 ER - TY - JOUR AU - Mikheenko, A. AU - Saveliev, V. AU - Gurevich, A. PY - 2016 DA - 2016// TI - MetaQUAST: evaluation of metagenome assemblies JO - Bioinformatics. Oxford University Press VL - 32 ID - Mikheenko2016 ER - TY - JOUR AU - Li, H. AU - Coghlan, A. AU - Ruan, J. AU - Coin, L. J. AU - Hériché, J. -. K. AU - Osmotherly, L. PY - 2006 DA - 2006// TI - TreeFam: a curated database of phylogenetic trees of animal gene families JO - Nucleic Acids Res VL - 34 UR - https://doi.org/10.1093/nar/gkj118 DO - 10.1093/nar/gkj118 ID - Li2006 ER - TY - JOUR AU - Gardner, S. N. AU - Slezak, T. AU - Hall, B. G. PY - 2015 DA - 2015// TI - kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genome JO - Bioinformatics VL - 31 UR - https://doi.org/10.1093/bioinformatics/btv271 DO - 10.1093/bioinformatics/btv271 ID - Gardner2015 ER - TY - JOUR AU - Tettelin, H. AU - Nelson, K. E. AU - Paulsen, I. T. AU - J a, E. AU - Read, T. D. AU - Peterson, S. PY - 2001 DA - 2001// TI - Complete genome sequence of a virulent isolate of Streptococcus Pneumoniae JO - Science VL - 293 UR - https://doi.org/10.1126/science.1061217 DO - 10.1126/science.1061217 ID - Tettelin2001 ER - TY - JOUR AU - Langmead, B. AU - Salzberg, S. PY - 2012 DA - 2012// TI - Fast gapped-read alignment with bowtie 2 JO - Nat Methods VL - 9 UR - https://doi.org/10.1038/nmeth.1923 DO - 10.1038/nmeth.1923 ID - Langmead2012 ER - TY - JOUR AU - Chen, L. AU - Xiong, Z. AU - Sun, L. AU - Yang, J. AU - Jin, Q. PY - 2012 DA - 2012// TI - VFDB 2012 update: toward the genetic diversity and molecular evolution of bacterial virulence factors JO - Nucleic Acids Res VL - 40 UR - https://doi.org/10.1093/nar/gkr989 DO - 10.1093/nar/gkr989 ID - Chen2012 ER - TY - JOUR AU - Song, X. -. M. AU - Connor, W. AU - Jalal, S. AU - Hokamp, K. AU - A a, P. PY - 2008 DA - 2008// TI - Microarray analysis of Streptococcus Pneumoniae gene expression changes to human lung epithelial cells JO - Can J Microbiol VL - 54 UR - https://doi.org/10.1139/W07-133 DO - 10.1139/W07-133 ID - Song2008 ER - TY - JOUR AU - Chen, L. AU - Yang, J. AU - Yu, J. AU - Yao, Z. AU - Sun, L. AU - Shen, Y. PY - 2005 DA - 2005// TI - VFDB: a reference database for bacterial virulence factors JO - Nucleic Acids Res VL - 33 UR - https://doi.org/10.1093/nar/gki008 DO - 10.1093/nar/gki008 ID - Chen2005 ER - TY - JOUR AU - Orihuela, C. J. AU - Radin, J. N. AU - Sublett, J. E. AU - Gao, G. AU - Kaushal, D. AU - Tuomanen, E. I. PY - 2004 DA - 2004// TI - Microarray analysis of pneumococcal gene expression during invasive disease JO - Infect Immun VL - 72 UR - https://doi.org/10.1128/IAI.72.10.5582-5596.2004 DO - 10.1128/IAI.72.10.5582-5596.2004 ID - Orihuela2004 ER - TY - JOUR AU - Rogers, P. D. AU - Liu, T. T. AU - Barker, K. S. AU - Hilliard, G. M. AU - English, B. K. AU - Thornton, J. PY - 2007 DA - 2007// TI - Gene expression profiling of the response of Streptococcus Pneumoniae to penicillin JO - J Antimicrob Chemother VL - 59 UR - https://doi.org/10.1093/jac/dkl560 DO - 10.1093/jac/dkl560 ID - Rogers2007 ER - TY - STD TI - Jansen G, Mahrt N, Tueffers L, Barbosa C, Harjes M, Adolph G, et al. Association between clinical antibiotic resistance and susceptibility of Pseudomonas in the cystic fibrosis lung. Evol Med Public Heal. 2016;eow016. Available from: http://www.ncbi.nlm.nih.gov/pubmed/27193199 UR - http://www.ncbi.nlm.nih.gov/pubmed/27193199 ID - ref40 ER - TY - JOUR AU - Morona, J. K. AU - Paton, J. C. AU - Miller, D. C. AU - Morona, R. PY - 2000 DA - 2000// TI - Tyrosine phosphorylation of CpsD negatively regulates capsular polysaccharide biosynthesis in streptococcus pneumoniae JO - Mol Microbiol VL - 35 UR - https://doi.org/10.1046/j.1365-2958.2000.01808.x DO - 10.1046/j.1365-2958.2000.01808.x ID - Morona2000 ER - TY - JOUR AU - Bender, M. H. AU - Cartee, R. T. AU - Yother, J. PY - 2003 DA - 2003// TI - Positive correlation between tyrosine phosphorylation of CpsD and capsular polysaccharide production in Streptococcus Pneumoniae JO - J Bacteriol VL - 185 UR - https://doi.org/10.1128/JB.185.20.6057-6066.2003 DO - 10.1128/JB.185.20.6057-6066.2003 ID - Bender2003 ER - TY - JOUR AU - Morona, J. AU - Morona, R. AU - Miller, D. PY - 2003 DA - 2003// TI - Mutational analysis of the carboxy-terminal (YGX) 4 repeat domain of CpsD, an autophosphorylating tyrosine kinase required for capsule biosynthesis in JO - J Bacteriol VL - 185 UR - https://doi.org/10.1128/JB.185.10.3009-3019.2003 DO - 10.1128/JB.185.10.3009-3019.2003 ID - Morona2003 ER - TY - JOUR AU - Morona, J. K. AU - Morona, R. AU - Paton, J. C. PY - 2006 DA - 2006// TI - Attachment of capsular polysaccharide to the cell wall of Streptococcus Pneumoniae type 2 is required for invasive disease JO - Proc Natl Acad Sci U S A VL - 103 UR - https://doi.org/10.1073/pnas.0602148103 DO - 10.1073/pnas.0602148103 ID - Morona2006 ER - TY - JOUR AU - Chewapreecha, C. AU - Marttinen, P. AU - Croucher, N. J. AU - Salter, S. J. AU - Harris, S. R. AU - Mather, A. E. PY - 2014 DA - 2014// TI - Comprehensive identification of single nucleotide polymorphisms associated with Beta-lactam resistance within pneumococcal mosaic genes JO - PLoS Genet VL - 10 UR - https://doi.org/10.1371/journal.pgen.1004547 DO - 10.1371/journal.pgen.1004547 ID - Chewapreecha2014 ER - TY - JOUR AU - Fani, F. AU - Leprohon, P. AU - Légaré, D. AU - Ouellette, M. PY - 2011 DA - 2011// TI - Whole genome sequencing of penicillin-resistant Streptococcus Pneumoniae reveals mutations in penicillin-binding proteins and in a putative iron permease JO - Genome Biol BioMed Central Ltd VL - 12 UR - https://doi.org/10.1186/gb-2011-12-11-r115 DO - 10.1186/gb-2011-12-11-r115 ID - Fani2011 ER - TY - JOUR AU - Fani, F. AU - Brotherton, M. -. C. AU - Leprohon, P. AU - Ouellette, M. PY - 2013 DA - 2013// TI - Genomic analysis and reconstruction of cefotaxime resistance in Streptococcus Pneumoniae JO - J Antimicrob Chemother VL - 68 UR - https://doi.org/10.1093/jac/dkt113 DO - 10.1093/jac/dkt113 ID - Fani2013 ER - TY - JOUR AU - Grebe, T. AU - Paik, J. AU - Hakenbeck, R. PY - 1997 DA - 1997// TI - A novel resistance mechanism against??-lactams in Streptococcus Pneumoniae involves CpoA, a putative glycosyltransferase JO - J Bacteriol VL - 179 UR - https://doi.org/10.1128/jb.179.10.3342-3349.1997 DO - 10.1128/jb.179.10.3342-3349.1997 ID - Grebe1997 ER - TY - JOUR AU - Hakenbeck, R. AU - Grebe, T. AU - Zähner, D. AU - Stock, J. B. PY - 1999 DA - 1999// TI - Beta-lactam resistance in Streptococcus Pneumoniae: penicillin-binding proteins and non-penicillin-binding proteins. Mol JO - Microbiol VL - 33 ID - Hakenbeck1999 ER - TY - STD TI - Sánchez D, Gomila M, Bennasar A, Lalucat J, García-Valdes E. Genome analysis of environmental and clinical P. Aeruginosa isolates from sequence type-1146. PLoS One 2014;9. ID - ref50 ER - TY - JOUR AU - Alikhan, N. -. F. AU - Petty, N. K. AU - Ben Zakour, N. L. AU - Beatson, S. a. PY - 2011 DA - 2011// TI - BLAST ring image generator (BRIG): simple prokaryote genome comparisons JO - BMC Genomics BioMed Central Ltd VL - 12 ID - Alikhan2011 ER -