Podschun R, Ullmann U: Klebsiella spp. as nosocomial pathogens: epidemiology, taxonomy, typing methods, and pathogenicity factors. Clin Microbiol Rev. 1998, 11: 589-603.
CAS
PubMed Central
PubMed
Google Scholar
Podschun R, Pietsch S, Holler C, Ullmann U: Incidence of Klebsiella species in surface waters and their expression of virulence factors. Appl Environ Microbiol. 2001, 67: 3325-3327. 10.1128/AEM.67.7.3325-3327.2001.
Article
CAS
PubMed Central
PubMed
Google Scholar
Wu K-M, Li L-H, Yan J-J, Tsao N, Liao T-L, Tsai H-C, Fung C-P, Chen H-J, Liu Y-M, Wang J-T, Fang C-T, Chang S-C, Shu H-Y, Liu T-T, Chen Y-T, Shiau Y-R, Lauderdale T-L, Su I-J, Kirby R, Tsai S-F: Genome sequencing and comparative analysis of Klebsiella pneumoniae NTUH-K2044, a strain causing liver abscess and meningitis. J Bacteriol. 2009, 191: 4492-4501. 10.1128/JB.00315-09.
Article
CAS
PubMed Central
PubMed
Google Scholar
Fouts DE, Tyler HL, DeBoy RT, Daugherty S, Ren Q, Badger JH, Durkin AS, Huot H, Shrivastava S, Kothari S, Dodson RJ, Mohamoud Y, Khouri H, Roesch LFW, Krogfelt KA, Struve C, Triplett EW, Methé BA: Complete genome sequence of the N2-fixing broad host range endophyte Klebsiella pneumoniae 342 and virulence predictions verified in mice. PLoS Genet. 2008, 4: e1000141-10.1371/journal.pgen.1000141.
Article
PubMed Central
PubMed
Google Scholar
Ogawa W, Li D-W, Yu P, Begum A, Mizushima T, Kuroda T, Tsuchiya T: Multidrug resistance in Klebsiella pneumoniae MGH78578 and cloning of genes responsible for the resistance. Biological and Pharmaceutical Bulletin. 2005, 28: 1505-1508. 10.1248/bpb.28.1505.
Article
CAS
PubMed
Google Scholar
Liu P, Li P, Jiang X, Bi D, Xie Y, Tai C, Deng Z, Rajakumar K, Ou H-Y: Complete genome sequence of Klebsiella pneumoniae subsp. pneumoniae HS11286, a multidrug-resistant strain isolated from human sputum. J Bacteriol. 2012, 194: 1841-1842. 10.1128/JB.00043-12.
Article
CAS
PubMed Central
PubMed
Google Scholar
Shin SH, Kim S, Kim JY, Lee S, Um Y, Oh M-K, Kim Y-R, Lee J, Yang K-S: Complete genome sequence of the 2,3-butanediol-producing Klebsiella pneumoniae strain KCTC 2242. J Bacteriol. 2012, 194: 2736-2737. 10.1128/JB.00027-12.
Article
CAS
PubMed Central
PubMed
Google Scholar
Lin A-C, Liao T-L, Lin Y-C, Lai Y-C, Lu M-C, Chen Y-T: Complete genome sequence of Klebsiella pneumoniae 1084, a hypermucoviscosity-negative K1 clinical strain. J Bacteriol. 2012, 194: 6316-10.1128/JB.01548-12.
Article
CAS
PubMed Central
PubMed
Google Scholar
Livermore DM, Woodford N: The β-lactamase threat in Enterobacteriaceae, Pseudomonas and Acinetobacter. Trends Microbiol. 2006, 14: 413-420. 10.1016/j.tim.2006.07.008.
Article
CAS
PubMed
Google Scholar
Seki LM, Pereira PS, Seki LM, Pereira PS, de Souza Mda P, Conceição MS, Marques EA, Porto CO, Colnago EML, Alves CFM, Gomes D, Carvalho-Assef APD, Samuelsen Ø, Asensi MD: Molecular epidemiology of KPC-2- producing Klebsiella pneumoniae isolates in Brazil: the predominance of sequence type 437. Diagn Microbiol Infect Dis. 2011, 70: 274-277. 10.1016/j.diagmicrobio.2011.01.006.
Article
CAS
PubMed
Google Scholar
Pereira PS, de Araujo CFM, Seki LM, Zahner V, Carvalho-Assef APD, Asensi MD: Update of the molecular epidemiology of KPC-2-producing Klebsiella pneumoniae in Brazil: spread of clonal complex 11 (ST11, ST437 and ST340). J Antimicrob Chemother. 2013, 68: 312-316. 10.1093/jac/dks396.
Article
CAS
PubMed
Google Scholar
Ramos PI, Picão RC, Vespero EC, Pelisson M, Zuleta LFG, Almeida LGP, Gerber AL, Vasconcelos ATR, Gales AC, Nicolás MF: Pyrosequencing-based analysis reveals a novel capsular gene cluster in a KPC-producing Klebsiella pneumoniae clinical isolate identified in Brazil. BMC Microbiol. 2012, 12: 173-10.1186/1471-2180-12-173.
Article
CAS
PubMed Central
PubMed
Google Scholar
Darling AE, Mau B, Blattner FR, Perna NT: Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 2004, 14: 1394-1403. 10.1101/gr.2289704.
Article
CAS
PubMed Central
PubMed
Google Scholar
Hacker J, Carniel E: Ecological fitness, genomic islands and bacterial pathogenicity. A Darwinian view of the evolution of microbes. EMBO Rep. 2001, 2: 376-381. 10.1093/embo-reports/kve097.
Article
CAS
PubMed Central
PubMed
Google Scholar
Kittichotirat W, Bumgarner R, Chen C: Markedly different genome arrangements between serotype a strains and serotypes b or c strains of Aggregatibacter actinomycetemcomitans. BMC Genomics. 2010, 11: 489-10.1186/1471-2164-11-489.
Article
PubMed Central
PubMed
Google Scholar
Ochman H, Lawrence JG, Groisman EA: Lateral gene transfer and the nature of bacterial innovation. Nature. 2000, 405: 299-304. 10.1038/35012500.
Article
CAS
PubMed
Google Scholar
Pieper DH, Santos VAP M d, Golyshin PN: Genomic and mechanistic insights into the biodegradation of organic pollutants. Curr Opin Biotechnol. 2004, 15: 215-224. 10.1016/j.copbio.2004.03.008.
Article
CAS
PubMed
Google Scholar
Casjens SR, Gilcrease EB, Huang WM, Bunny KL, Pedulla ML, Ford ME, Houtz JM, Hatfull GF, Hendrix RW: The pKO2 linear plasmid prophage of Klebsiella oxytoca. J Bacteriol. 2004, 186: 1818-1832. 10.1128/JB.186.6.1818-1832.2004.
Article
CAS
PubMed Central
PubMed
Google Scholar
Bönemann G, Pietrosiuk A, Mogk A: Tubules and donuts: a type VI secretion story. Mol Microbiol. 2010, 76: 815-821. 10.1111/j.1365-2958.2010.07171.x.
Article
PubMed
Google Scholar
Mougous JD, Cuff ME, Raunser S, Shen A, Zhou M, Gifford CA, Goodman AL, Joachimiak G, Ordoñez CL, Lory S, Walz T, Joachimiak A, Mekalanos JJ: A virulence locus of Pseudomonas aeruginosa encodes a protein secretion apparatus. Science. 2006, 312: 1526-1530. 10.1126/science.1128393.
Article
CAS
PubMed Central
PubMed
Google Scholar
Cascales E, Cambillau C: Structural biology of type VI secretion systems. Phil Trans Roy Soc Lond. 2012, 367: 1102-1111. 10.1098/rstb.2011.0209.
Article
CAS
Google Scholar
Bingle LE, Bailey CM, Pallen MJ: Type VI secretion: a beginner’s guide. Curr Opin Microbiol. 2008, 11: 3-8. 10.1016/j.mib.2008.01.006.
Article
CAS
PubMed
Google Scholar
Suarez G, Sierra JC, Kirtley ML, Chopra AK: Role of Hcp, a type 6 secretion system effector, of Aeromonas hydrophila in modulating activation of host immune cells. Microbiology. 2010, 156 (Pt 12): 3678-3688.
Article
CAS
PubMed Central
PubMed
Google Scholar
Lin T, Lee C-Z, Hsieh P-F, Tsai S, Wang J: Characterization of integrative and conjugative element ICEKp1-associated genomic heterogeneity in a Klebsiella pneumoniae strain isolated from a primary liver abscess. J Bacteriol. 2008, 190: 515-526. 10.1128/JB.01219-07.
Article
CAS
PubMed Central
PubMed
Google Scholar
Ogawa W, Onishi M, Ni R, Tsuchiya T, Kuroda T: Functional study of the novel multidrug efflux pump KexD from Klebsiella pneumoniae. Gene. 2012, 498: 177-182. 10.1016/j.gene.2012.02.008.
Article
CAS
PubMed
Google Scholar
Deng WL, Chang HY, Peng HL, Pengi H: Acetoin catabolic system of Klebsiella pneumoniae CG43: sequence, expression, and organization of the aco operon. J Bacteriol. 1994, 176: 3527-3535.
CAS
PubMed Central
PubMed
Google Scholar
Brilli M, Liò P, Lacroix V, Sagot M-F: Short and long-term genome stability analysis of prokaryotic genomes. BMC Genomics. 2013, 14: 309-10.1186/1471-2164-14-309.
Article
CAS
PubMed Central
PubMed
Google Scholar
Imazu K, Tanaka S, Kuroda A, Anbe Y, Kato J, Ohtake H: Enhanced utilization of phosphonate and phosphite by Klebsiella aerogenes. Appl Environ Microbiol. 1998, 64: 3754-3758.
CAS
PubMed Central
PubMed
Google Scholar
Wang W, Xi H, Bi Q, Hu Y, Zhang Y, Ni M: Cloning, expression and characterization of d-aminoacylase from Achromobacter xylosoxidans subsp. denitrificans ATCC 15173. Microbiol Res. 2013, 168: 360-366. 10.1016/j.micres.2013.01.002.
Article
CAS
PubMed
Google Scholar
Wiame E, Duquenne A, Delpierre G, Van Schaftingen E: Identification of enzymes acting on a-glycated amino acids in Bacillus subtilis. FEBS Lett. 2004, 577: 469-472. 10.1016/j.febslet.2004.10.049.
Article
CAS
PubMed
Google Scholar
Friedman EA: Advanced glycosylated end products and hyperglycemia in the pathogenesis of diabetic complications. Diabetes Care. 1999, 22: B65-B71. 10.2337/diacare.22.1.65.
Article
PubMed
Google Scholar
Schaible UE, Kaufmann SHE: Iron and microbial infection. Nat Rev. 2004, 2: 946-953.
CAS
Google Scholar
Hsieh P-F, Lin T-L, Lee C-Z, Tsai S-F, Wang J-T: Serum-induced iron-acquisition systems and TonB contribute to virulence in Klebsiella pneumoniae causing primary pyogenic liver abscess. J Infect Dis. 2008, 197: 1717-1727. 10.1086/588383.
Article
CAS
PubMed
Google Scholar
Russo TA, Shon AS, Beanan JM, Olson R, MacDonald U, Pomakov AO, Visitacion MP: Hypervirulent K. pneumoniae secretes more and more active iron-acquisition molecules than “Classical” K. pneumoniae thereby enhancing its Virulence. PLoS ONE. 2011, 6: e26734-10.1371/journal.pone.0026734.
Article
CAS
PubMed Central
PubMed
Google Scholar
Garénaux A, Caza M, Dozois CM: The Ins and Outs of siderophore mediated iron uptake by extra-intestinal pathogenic Escherichia coli. Vet Microbiol. 2011, 153: 89-98. 10.1016/j.vetmic.2011.05.023.
Article
PubMed
Google Scholar
Wilson JW, Schurr MJ, LeBlanc CL, Ramamurthy R, Buchanan KL, Nickerson CA: Mechanisms of bacterial pathogenicity. Postgrad Med J. 2002, 78: 216-224. 10.1136/pmj.78.918.216.
Article
CAS
PubMed Central
PubMed
Google Scholar
Struve C, Bojer M, Krogfelt KA: Characterization of Klebsiella pneumoniae type 1 fimbriae by detection of phase variation during colonization and infection and impact on virulence. Infect Immun. 2008, 76: 4055-4065. 10.1128/IAI.00494-08.
Article
CAS
PubMed Central
PubMed
Google Scholar
Ong C-LY, Beatson SA, Totsika M, Forestier C, McEwan AG, Schembri MA: Molecular analysis of type 3 fimbrial genes from Escherichia coli. Klebsiella and Citrobacter species. BMC Microbiol. 2010, 10: 183-10.1186/1471-2180-10-183.
Article
PubMed Central
PubMed
Google Scholar
Wu C-C, Huang Y-J, Fung C-P, Peng H-L: Regulation of the Klebsiella pneumoniae Kpc fimbriae by the site-specific recombinase KpcI. Microbiology. 2010, 156: 1983-1992. 10.1099/mic.0.038158-0.
Article
CAS
PubMed
Google Scholar
Wizemann TM, Adamou JE, Langermann S: Adhesins as targets for vaccine development. Emerg Infect Dis. 1999, 5: 395-403. 10.3201/eid0503.990310.
Article
CAS
PubMed Central
PubMed
Google Scholar
Haeggman S, Löfdahl S, Paauw A, Verhoef J, Brisse S: Diversity and evolution of the class A chromosomal beta-lactamase gene in Klebsiella pneumoniae. Antimicrob Agents Chemother. 2004, 48: 2400-2408. 10.1128/AAC.48.7.2400-2408.2004.
Article
CAS
PubMed Central
PubMed
Google Scholar
Bradford PA: Extended-spectrum beta-lactamases in the 21st century: characterization, epidemiology, and detection of this important resistance threat. Clin Microbiol Rev. 2001, 14: 933-951. 10.1128/CMR.14.4.933-951.2001.
Article
CAS
PubMed Central
PubMed
Google Scholar
Poirel L, Naas T, Nordmann P: Diversity, epidemiology, and genetics of class D beta-lactamases. Antimicrob Agents Chemother. 2010, 54: 24-38. 10.1128/AAC.01512-08.
Article
CAS
PubMed Central
PubMed
Google Scholar
D’Andrea MM, Arena F, Pallecchi L, Rossolini GM: CTX-M-type β-lactamases: A successful story of antibiotic resistance. Int J Med Microbiol. 2013, 303: 305-317. 10.1016/j.ijmm.2013.02.008.
Article
PubMed
Google Scholar
Arduino SM, Roy PH, Jacoby GA, Orman BE, Pineiro SA, Centron D: blaCTX-M-2 Is Located in an Unusual Class 1 Integron (In35) Which Includes Orf513. Antimicrob Agents Chemother. 2002, 46: 2303-2306. 10.1128/AAC.46.7.2303-2306.2002.
Article
CAS
PubMed Central
PubMed
Google Scholar
Clímaco EC, Minarini LAR, Lúcia A: CTX-M-producing Klebsiella spp. in a Brazilian hospital: what has changed in 6 years?. Diagn Microbiol Infect Dis. 2010, 68: 186-189. 10.1016/j.diagmicrobio.2010.05.013.
Article
PubMed
Google Scholar
Poirel L, Le Thomas I, Naas T, Karim A, Nordmann P: Biochemical sequence analyses of GES-1, a novel class A extended-spectrum beta-lactamase, and the class 1 integron In52 from Klebsiella pneumoniae. Antimicrob Agents Chemother. 2000, 44: 622-632. 10.1128/AAC.44.3.622-632.2000.
Article
CAS
PubMed Central
PubMed
Google Scholar
Naas T, Cuzon G, Villegas M, Lartigue M-F, Quinn JP, Nordmann P: Genetic structures at the origin of acquisition of the beta-lactamase blaKPC gene. Antimicrob Agents Chemother. 2008, 52: 1257-1263. 10.1128/AAC.01451-07.
Article
CAS
PubMed Central
PubMed
Google Scholar
Naville M, Ghuillot-Gaudeffroy A, Marchais A, Gautheret D: ARNold: a web tool for the prediction of Rho-independent transcription terminators. RNA Biol. 2011, 8: 11-13. 10.4161/rna.8.1.13346.
Article
CAS
PubMed
Google Scholar
Fu Y, Guo L, Xu Y, Zhang W, Gu J, Xu J, Chen X, Zhao Y, Ma J, Liu X, Zhang F: Alteration of GyrA amino acid required for ciprofloxacin resistance in Klebsiella pneumoniae isolates in China. Antimicrob Agents Chemother. 2008, 52: 2980-2983. 10.1128/AAC.00151-08.
Article
CAS
PubMed Central
PubMed
Google Scholar
Deguchi T, Fukuoka A, Yasuda M, Nakano M, Ozeki S, Kanematsu E, Nishino Y, Ishihara S, Ban Y, Kawada Y: Alterations in the GyrA subunit of DNA gyrase and the ParC subunit of topoisomerase IV in quinolone-resistant clinical isolates of Klebsiella pneumoniae. Antimicrob Agents Chemother. 1997, 41: 699-701.
CAS
PubMed Central
PubMed
Google Scholar
Wachino J, Arakawa Y: Exogenously acquired 16S rRNA methyltransferases found in aminoglycoside-resistant pathogenic Gram-negative bacteria: an update. Drug Resist Updat. 2012, 15: 133-148. 10.1016/j.drup.2012.05.001.
Article
CAS
PubMed
Google Scholar
Bueno MFC, Francisco GR, O’Hara JA, de Oliveira Garcia D, Doi Y: Coproduction of 16S rRNA methyltransferase RmtD or RmtG with KPC-2 and CTX-M group extended-spectrum β-lactamases in Klebsiella pneumoniae. Antimicrob Agents Chemother. 2013, 57: 2397-2400. 10.1128/AAC.02108-12.
Article
CAS
PubMed Central
PubMed
Google Scholar
Veiga DFT, Vicente FFR, Nicolás MF, Vasconcelos ATR: Predicting transcriptional regulatory interactions with artificial neural networks applied to E. coli multidrug resistance efflux pumps. BMC Microbiol. 2008, 8: 101-114. 10.1186/1471-2180-8-101.
Article
PubMed Central
PubMed
Google Scholar
Bialek-Davenet S, Marcon E, Leflon-Guibout V, Lavigne J-P, Bert F, Moreau R, Nicolas-Chanoine M-H: In vitro selection of ramR and soxR mutants overexpressing efflux systems by fluoroquinolones as well as cefoxitin in Klebsiella pneumoniae. Antimicrob Agents Chemother. 2011, 55: 2795-2802. 10.1128/AAC.00156-11.
Article
CAS
PubMed Central
PubMed
Google Scholar
Perez F, Rudin SD, Marshal SH, Coakley P, Chen L, Kreiswirth BN, Rather PN, Hujer AM, Toltzis P, van Duin D, Paterson DL, Bonomo RA: OqxAB, a Quinolone and Olaquindox Efflux Pump, is Widely Distributed among Multidrug Resistant Klebsiella pneumoniae of Human Origin. Antimicrob Agents Chemother. 2013, 57: 4602-4603. 10.1128/AAC.00725-13.
Article
CAS
PubMed Central
PubMed
Google Scholar
Hansen LH, Jensen LB, Sørensen HI, Sørensen SJ: Substrate specificity of the OqxAB multidrug resistance pump in Escherichia coli and selected enteric bacteria. J Antimicrob Chemother. 2007, 60: 145-147. 10.1093/jac/dkm167.
Article
CAS
PubMed
Google Scholar
Nishino K, Yamaguchi A: Analysis of a complete library of putative drug transporter genes in Escherichia coli. J Bacteriol. 2001, 183: 5803-5812. 10.1128/JB.183.20.5803-5812.2001.
Article
CAS
PubMed Central
PubMed
Google Scholar
Hernández-Allés S, Albertí S, Alvarez D, Doménech-Sánchez A, Martínez-Martínez L, Gil J, Tomás JM, Benedí VJ: Porin expression in clinical isolates of Klebsiella pneumoniae. Microbiology. 1999, 145: 673-679. 10.1099/13500872-145-3-673.
Article
PubMed
Google Scholar
Tsai Y-K, Fung C-P, Lin J-C, Chen J-H, Chang F-Y, Chen T-L, Siu LK: Klebsiella pneumoniae outer membrane porins OmpK35 and OmpK36 play roles in both antimicrobial resistance and virulence. Antimicrob Agents Chemother. 2011, 55: 1485-1493. 10.1128/AAC.01275-10.
Article
CAS
PubMed Central
PubMed
Google Scholar
Llobet E, Campos MA, Giménez P, Moranta D, Bengoechea JA: Analysis of the networks controlling the antimicrobial-peptide-dependent induction of Klebsiella pneumoniae virulence factors. Infect Immun. 2011, 79: 3718-3732. 10.1128/IAI.05226-11.
Article
CAS
PubMed Central
PubMed
Google Scholar
Martínez J, Martínez L, Rosenblueth M, Silva J, Martínez-Romero E: How are gene sequence analyses modifying bacterial taxonomy? The case of Klebsiella. Int Microbiol. 2004, 7: 261-268.
PubMed
Google Scholar
Clinical and Laboratory Standards Institute: M02-A11, Approved Standard, Performance Standards for Antimicrobial Disk Susceptibility Tests. 2012, Wayne, PA: CLSI
Google Scholar
Clinical and Laboratory Standards Institute: Performance Standards for Antimicrobial Susceptibility Testing. 23rd Informational Supplement. 2013, Wayne, PA: CLSI
Google Scholar
Wyeth Pharmaceuticals: Tygacil [package insert]. 2005, Philadelphia, PA: Wyeth Pharmaceuticals Inc
Google Scholar
European Committee on Antimicrobial Susceptibility Testing: Breakpoint Tables for Interpretation of MICs and Zone Diameters, Version 3.0. 2013, EUCAST: Basel, Switzerland
Google Scholar
Almeida LGP, Paixão R, Souza RC, Costa GC, Barrientos FJA, dos Santos MT, Almeida DF, Vasconcelos ATR: A System for Automated Bacterial (genome) Integrated Annotation–SABIA. Bioinformatics. 2004, 20: 2832-2833. 10.1093/bioinformatics/bth273.
Article
CAS
PubMed
Google Scholar
Diancourt L, Passet V, Verhoef J, Grimont PAD, Brisse S: Multilocus sequence typing of Klebsiella pneumoniae nosocomial isolates. J Clin Microbiol. 2005, 43: 4178-4182. 10.1128/JCM.43.8.4178-4182.2005.
Article
CAS
PubMed Central
PubMed
Google Scholar
Francisco AP, Vaz C, Monteiro PT, Melo-Cristino J, Ramirez M, Carriço JA: PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods. BMC Bioinformatics. 2012, 13: 87-10.1186/1471-2105-13-87.
Article
PubMed Central
PubMed
Google Scholar
Vallenet D, Engelen S, Mornico D, Cruveiller S, Fleury L, Lajus A, Rouy Z, Roche D, Salvignol G, Scarpelli C, Médigue C: MicroScope: a platform for microbial genome annotation and comparative genomics. Database. 2009, 2009: bap021-
Article
PubMed Central
PubMed
Google Scholar
Vallenet D, Belda E, Calteau A, Cruveiller S, Engelen S, Lajus A, Le Fèvre F, Longin C, Mornico D, Roche D, Rouy Z, Salvignol G, Scarpelli C, Thil Smith AA, Weiman M, Médigue C: MicroScope–an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data. Nucleic Acids Res. 2013, 41 (Database issue): D636-D647.
Article
CAS
PubMed Central
PubMed
Google Scholar
Vernikos GS, Parkhill J: Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands. Bioinformatics. 2006, 22: 2196-2203. 10.1093/bioinformatics/btl369.
Article
CAS
PubMed
Google Scholar
Waack S, Keller O, Asper R, Brodag T, Damm C, Fricke WF, Surovcik K, Meinicke P, Merkl R: Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models. BMC Bioinformatics. 2006, 7: 142-10.1186/1471-2105-7-142.
Article
PubMed Central
PubMed
Google Scholar
Sullivan MJ, Petty NK, Beatson SA: Easyfig: a genome comparison visualizer. Bioinformatics. 2011, 27: 1009-1010. 10.1093/bioinformatics/btr039.
Article
CAS
PubMed Central
PubMed
Google Scholar
Alikhan N-F, Petty NK, Ben Zakour NL, Beatson SA: BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons. BMC Genomics. 2011, 12: 402-10.1186/1471-2164-12-402.
Article
CAS
PubMed Central
PubMed
Google Scholar
Janssen PJ, Van Houdt R, Moors H, Monsieurs P, Morin N, Michaux A, Benotmane MA, Leys N, Vallaeys T, Lapidus A, Monchy S, Médigue C, Taghavi S, McCorkle S, Dunn J, van der Lelie D, Mergeay M: The complete genome sequence of Cupriavidus metallidurans strain CH34, a master survivalist in harsh and anthropogenic environments. PLoS ONE. 2010, 5: e10433-10.1371/journal.pone.0010433.
Article
PubMed Central
PubMed
Google Scholar
Chen H, Boutros PC: VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R. BMC Bioinformatics. 2011, 12: 35-10.1186/1471-2105-12-35.
Article
PubMed Central
PubMed
Google Scholar
Darling AE, Mau B, Perna NT: progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS ONE. 2010, 5: e11147-10.1371/journal.pone.0011147.
Article
PubMed Central
PubMed
Google Scholar
Zhou Y, Liang Y, Lynch KH, Dennis JJ, Wishart DS: PHAST: a fast phage search tool. Nucleic Acids Res. 2011, 39 (Web Server issue): W347-W352.
Article
CAS
PubMed Central
PubMed
Google Scholar
Quispe Saji del R G, Costa MOC, Netto DS, Lima NCB, Klein CC, Vasconcelos ATR, Nicolás MF: AtlasT4SS: a curated database for type IV secretion systems. BMC Microbiol. 2012, 12: 172-10.1186/1471-2180-12-172.
Article
Google Scholar
Liu B, Pop M: ARDB–Antibiotic Resistance Genes Database. Nucleic Acids Res. 2009, 37 (Database issue): D443-D447.
Article
CAS
PubMed Central
PubMed
Google Scholar
Siguier P, Perochon J, Lestrade L, Mahillon J, Chandler M: ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res. 2006, 34 (Database issue): D32-D36.
Article
CAS
PubMed Central
PubMed
Google Scholar
Lima NCB: MsC thesis. Computational Approach for Detection and Analysis of Single-Nucleotide Polymorphisms (SNPs) in Bacterial Genomes. 2011, Petrópolis, Brazil: National Laboratory for Scientific Computing
Google Scholar
Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL: Versatile and open software for comparing large genomes. Genome Biol. 2004, 5: R12-10.1186/gb-2004-5-2-r12.
Article
PubMed Central
PubMed
Google Scholar