After genomics, what proteomics tools could help us understand the antimicrobial resistance of Escherichia coli?

Journal of Proteomics

Volumn 75, Issue 10, 2012, Pages 2773-2789

  Radhouani, Hajer ^a,b   Pinto, Luís ^a,b   Poeta, Patrícia ^a,b   Igrejas, Gilberto ^a  

^a UNIVERSITY OF TRÁS OS MONTES AND ALTO DOURO   (Portugal)

^b UNIVERSITY OF TRÁS OS MONTES AND ALTO DOURO   (Portugal)

Author keywords

Antimicrobial resistance; Clinical isolates; Escherichia coli; Genomics; Proteomics

Indexed keywords

AMOXICILLIN; ANTIINFECTIVE AGENT; AZTREONAM; BACTERIAL DNA; BETA LACTAMASE AMPC; CEFTRIAXONE; CHLORAMPHENICOL; CILASTATIN PLUS IMIPENEM; CIPROFLOXACIN; DODECYL SULFATE SODIUM; DOXYCYCLINE; ERYTHROMYCIN; FUSIDIC ACID; LEVOFLOXACIN; MEROPENEM; PIPERACILLIN PLUS TAZOBACTAM; POLYMYXIN; RIFAMPICIN; SPIRAMYCIN; SULFAMETHOXAZOLE; SULTAMICILLIN; TETRACYCLINE; TRIMETHOPRIM;

AMINO ACID SEQUENCE; ANTIBIOTIC RESISTANCE; BACTERIAL GENOME; BACTERIAL GROWTH; BACTERIAL STRAIN; BIOINFORMATICS; DIARRHEA; DNA MICROARRAY; ENVIRONMENTAL STRESS; ESCHERICHIA COLI; ESCHERICHIA COLI PNEUMONIA; GAS CHROMATOGRAPHY; GENE SEQUENCE; HUMAN; INTRON; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; MENINGITIS; OPEN READING FRAME; PATHOGENESIS; PERITONITIS; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN SYNTHESIS; PROTEOMICS; REVIEW; SALMONELLA ENTERICA; SEPTICEMIA; TWO DIMENSIONAL GEL ELECTROPHORESIS; URINARY TRACT INFECTION;

ANTI-BACTERIAL AGENTS; BIOLOGICAL MARKERS; COMPREHENSION; DRUG RESISTANCE, MICROBIAL; ESCHERICHIA COLI; ESCHERICHIA COLI INFECTIONS; GENOMICS; HUMANS; MICROBIAL SENSITIVITY TESTS; PROTEOMICS;

ESCHERICHIA COLI; NEGIBACTERIA; PROKARYOTA;

EID: 84861346975     PISSN: 18743919     EISSN: 18767737     Source Type: Journal    
DOI: 10.1016/j.jprot.2011.12.035     Document Type: Review

References (139)

1. Diniz C.G., Farias L.M., Carvalho M.A., Rocha E.R., Smith C.J. Differential gene expression in a Bacteroides fragilis metronidazole-resistant mutant. J Antimicrob Chemother 2004, 54:100-108.
2. Linares-Rodriguez J.F., Martinez-Menendez J.L. Antimicrobial resistance and bacterial virulence. Enferm Infecc Microbiol Clin 2005, 23:86-93.
3. Lorian V. Effect of low concentration of antibiotics. J Chemother 1993, 5:188-189.
4. Xu C., Lin X., Ren H., Zhang Y., Wang S., Peng X. Analysis of outer membrane proteome of Escherichia coli related to resistance to ampicillin and tetracycline. Proteomics 2006, 6:462-473.
5. Levy S.B., Marshall B. Antibacterial resistance worldwide: causes, challenges and responses. Nat Med 2004, 10:S122-S129.
6. Johnson J.R., Stell A.L., Delavari P., Murray A.C., Kuskowski M., Gaastra W. Phylogenetic and pathotypic similarities between Escherichia coli isolates from urinary tract infections in dogs and extraintestinal infections in humans. J Infect Dis 2001, 183:897-906.
7. Johnson J.R., Kuskowski M.A., Smith K., O'Bryan T.T., Tatini S. Antimicrobial-resistant and extraintestinal pathogenic Escherichia coli in retail foods. J Infect Dis 2005, 191:1040-1049.
8. Bonnedahl J., Drobni M., Gauthier-Clerc M., Hernandez J., Granholm S., Kayser Y., et al. Dissemination of Escherichia coli with CTX-M type ESBL between humans and yellow-legged gulls in the south of France. PLoS One 2009, 4:e5958.
9. Tracz D.M., Boyd D.A., Bryden L., Hizon R., Giercke S., Van Caeseele P., et al. Increase in ampC promoter strength due to mutations and deletion of the attenuator in a clinical isolate of cefoxitin-resistant Escherichia coli as determined by RT-PCR. J Antimicrob Chemother 2005, 55:768-772.
10. Ewers C., Grobbel M., Bethe A., Wieler L.H., Guenther S. Extended-spectrum beta-lactamases-producing gram-negative bacteria in companion animals: action is clearly warranted!. Berl Munch Tierarztl Wochenschr 2011, 124:94-101.
11. Paterson D.L., Bonomo R.A. Extended-spectrum beta-lactamases: a clinical update. Clin Microbiol Rev 2005, 18:657-686.
12. Hsueh P.R., Chen W.H., Luh K.T. Relationships between antimicrobial use and antimicrobial resistance in Gram-negative bacteria causing nosocomial infections from 1991-2003 at a university hospital in Taiwan. Int J Antimicrob Agents 2005, 26:463-472.
13. Canton R., Novais A., Valverde A., Machado E., Peixe L., Baquero F., et al. Prevalence and spread of extended-spectrum beta-lactamase-producing Enterobacteriaceae in Europe. Clin Microbiol Infect 2008, 14(Suppl 1):144-153.
14. Bradford P.A. Extended-spectrum beta-lactamases in the 21st century: characterization, epidemiology, and detection of this important resistance threat. Clin Microbiol Rev 2001, 14:933-951. table of contents.
15. Jungblut P.R., Holzhutter H.G., Apweiler R., Schluter H. The speciation of the proteome. Chem Cent J 2008, 2:16.
16. Andrade H.M., Murta S.M.F., Chapeaurouge A., Perales J., Nirde P., Romanha A.J. Proteomic analysis of Trypanosoma cruzi resistance to benznidazole. J Proteome Res 2008, 7:2357-2367.
17. Cash P., Argo E., Ford L., Lawrie L., McKenzie H. A proteomic analysis of erythromycin resistance in Streptococcus pneumoniae. Electrophoresis 1999, 20:2259-2268.
18. Coldham N.G., Woodward M.J. Characterization of the Salmonella typhimurium proteome by semi-automated two dimensional HPLC-mass spectrometry: detection of proteins implicated in multiple antibiotic resistance. J Proteome Res 2004, 3:595-603.
19. Bore E., Hebraud M., Chafsey I., Chambon C., Skjaeret C., Moen B., et al. Adapted tolerance to benzalkonium chloride in Escherichia coli K-12 studied by transcriptome and proteome analyses. Microbiology 2007, 153:935-946.
20. Lis M., Bobek L.A. Proteomic and metabolic characterization of a Candida albicans mutant resistant to the antimicrobial peptide MUC7 12-mer. FEMS Immunol Med Microbiol 2008, 54:80-91.
21. McAtee C.P., Hoffman P.S., Berg D.E. Identification of differentially regulated proteins in metronidozole resistant Helicobacter pylori by proteome techniques. Proteomics 2001, 1:516-521.
22. Pieper R., Gatlin-Bunai C.L., Mongodin E.F., Parmar P.P., Huang S.T., Clark D.J., et al. Comparative proteomic analysis of Staphylococcus aureus strains with differences in resistance to the cell wall-targeting antibiotic vancomycin. Proteomics 2006, 6:4246-4258.
23. Werner M., Semsey S., Sneppen K., Krishna S. Dynamics of uptake and metabolism of small molecules in cellular response systems. PLoS One 2009, 4:e4923.
24. Rodriguez-Ortega M.J., Norais N., Bensi G., Liberatori S., Capo S., Mora M., et al. Characterization and identification of vaccine candidate proteins through analysis of the group A Streptococcus surface proteome. Nat Biotechnol 2006, 24:191-197.
25. Cirulli C., Marino G., Amoresano A. Membrane proteome in Escherichia coli probed by MS3 mass spectrometry: a preliminary report. Rapid Commun Mass Spectrom 2007, 21:2389-2397.
26. Perna N.T., Plunkett G., Burland V., Mau B., Glasner J.D., Rose D.J., et al. Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature 2001, 409:529-533.
27. Schaechter M., Grp V.F.H. Escherichia coli and Salmonella 2000: the view from here. Microbiol Mol Biol Rev 2001, 65:119-130.
28. Mori H. From the sequence to cell modeling: comprehensive functional genomics in Escherichia coli. J Biochem Mol Biol 2004, 37:83-92.
29. Dobrindt U., Chowdary M.G., Krumbholz G., Hacker J. Genome dynamics and its impact on evolution of Escherichia coli. Med Microbiol Immunol 2010, 199:145-154.
30. Yan J.X., Devenish A.T., Wait R., Stone T., Lewis S., Fowler S. Fluorescence two-dimensional difference gel electrophoresis and mass spectrometry based proteomic analysis of Escherichia coli. Proteomics 2002, 2:1682-1698.
31. Lawrence J.G. Gene transfer, speciation, and the evolution of bacterial genomes. Curr Opin Microbiol 1999, 2:519-523.
32. Han M.J., Lee S.Y. The Escherichia coli proteome: past, present, and future prospects. Microbiol Mol Biol Rev 2006, 70:362-439.
33. Blattner F.R., Plunkett G., Bloch C.A., Perna N.T., Burland V., Riley M., et al. The complete genome sequence of Escherichia coli K-12. Science 1997, 277:1453-1462.
34. Tonella L., Walsh B.J., Sanchez J.C., Ou K., Wilkins M.R., Tyler M., et al. '98 Escherichia coli SWISS-2DPAGE database update. Electrophoresis 1998, 19:1960-1971.
35. Tonella L., Hoogland C., Binz P.A., Appel R.D., Hochstrasser D.F., Sanchez J.C. New perspectives in the Escherichia coli proteome investigation. Proteomics 2001, 1:409-423.
36. Pasquali C., Frutiger S., Wilkins M.R., Hughes G.J., Appel R.D., Bairoch A., et al. Two-dimensional gel electrophoresis of Escherichia coli homogenates: the Escherichia coli SWISS-2DPAGE database. Electrophoresis 1996, 17:547-555.
37. Butland G., Peregrin-Alvarez J.M., Li J., Yang W., Yang X., Canadien V., et al. Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 2005, 433:531-537.
38. Lockhart D.J., Winzeler E.A. Genomics, gene expression and DNA arrays. Nature 2000, 405:827-836.
39. Nielsen H., Engelbrecht J., Brunak S., von Heijne G. Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng 1997, 10:1-6.
40. Pandey A., Mann M. Proteomics to study genes and genomes. Nature 2000, 405:837-846.
41. Yu C.S., Lin C.J., Hwang J.K. Predicting subcellular localization of proteins for Gram-negative bacteria by support vector machines based on n-peptide compositions. Protein Sci 2004, 13:1402-1406.
42. Serres M.H., Gopal S., Nahum L.A., Liang P., Gaasterland T., Riley M. A functional update of the Escherichia coli K-12 genome. Genome Biol 2001, 2. RESEARCH0035.
43. Bjellqvist B., Basse B., Olsen E., Celis J.E. Reference points for comparisons of two-dimensional maps of proteins from different human cell types defined in a pH scale where isoelectric points correlate with polypeptide compositions. Electrophoresis 1994, 15:529-539.
44. Bjellqvist B., Hughes G.J., Pasquali C., Paquet N., Ravier F., Sanchez J.C., et al. The focusing positions of polypeptides in immobilized pH gradients can be predicted from their amino acid sequences. Electrophoresis 1993, 14:1023-1031.
45. Wilkins M.R., Gasteiger E., Bairoch A., Sanchez J.-C., Williams K.L., Appel R.D., et al. Protein identification and analysis tools on the ExPASy Server. 2-D Proteome Analysis Protocols Totowa 1998, 531-552. Human Press, New Jersey. A.J. Link (Ed.).
46. Lopez-Campistrous A., Semchuk P., Burke L., Palmer-Stone T., Brokx S.J., Broderick G., et al. Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth. Mol Cell Proteomics 2005, 4:1205-1209.
47. Aebersold R., Mann M. Mass spectrometry-based proteomics. Nature 2003, 422:198-207.
48. Wasinger V.C., Cordwell S.J., Cerpa-Poljak A., Yan J.X., Gooley A.A., Wilkins M.R., et al. Progress with gene-product mapping of the Mollicutes: Mycoplasma genitalium. Electrophoresis 1995, 16:1090-1094.
49. Lasonder E., Ishihama Y., Andersen J.S., Vermunt A.M., Pain A., Sauerwein R.W., et al. Analysis of the Plasmodium falciparum proteome by high-accuracy mass spectrometry. Nature 2002, 419:537-542.
50. Florens L., Washburn M.P., Raine J.D., Anthony R.M., Grainger M., Haynes J.D., et al. A proteomic view of the Plasmodium falciparum life cycle. Nature 2002, 419:520-526.
51. Uetz P., Giot L., Cagney G., Mansfield T.A., Judson R.S., Knight J.R., et al. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 2000, 403:623-627.
52. Gavin A.C., Bosche M., Krause R., Grandi P., Marzioch M., Bauer A., et al. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 2002, 415:141-147.
53. Huh W.K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W., Weissman J.S., et al. Global analysis of protein localization in budding yeast. Nature 2003, 425:686-691.
54. Minshull J., Ness J.E., Gustafsson C., Govindarajan S. Predicting enzyme function from protein sequence. Curr Opin Chem Biol 2005, 9:202-209.
55. Goshe M.B., Smith R.D. Stable isotope-coded proteomic mass spectrometry. Curr Opin Biotechnol 2003, 14:101-109.
56. Tao W.A., Aebersold R. Advances in quantitative proteomics via stable isotope tagging and mass spectrometry. Curr Opin Biotechnol 2003, 14:110-118.
57. Neidhardt F.C., Bloch P.L., Pedersen S., Reeh S. Chemical measurement of steady-state levels of ten aminoacyl-transfer ribonucleic acid synthetases in Escherichia coli. J Bacteriol 1977, 129:378-387.
58. Pedersen S., Bloch P.L., Reeh S., Neidhardt F.C. Patterns of protein synthesis in E. coli: a catalog of the amount of 140 individual proteins at different growth rates. Cell 1978, 14:179-190.
59. Wilkins M.R., Pasquali C., Appel R.D., Ou K., Golaz O., Sanchez J.C., et al. From proteins to proteomes: large scale protein identification by two-dimensional electrophoresis and amino acid analysis. Biotechnology (N Y) 1996, 14:61-65.
60. Lin J., Ficht T.A. Protein synthesis in Brucella abortus induced during macrophage infection. Infect Immun 1995, 63:1409-1414.
61. Fountoulakis M., Takacs B., Langen H. Two-dimensional map of basic proteins of Haemophilus influenzae. Electrophoresis 1998, 19:761-766.
62. Cash P. Proteomics in medical microbiology. Electrophoresis 2000, 21:1187-1201.
63. Osman K.M., Ali M.M., Radwan M.I., Kim H.K., Han J. Comparative proteomic analysis on Salmonella Gallinarum and Salmonella Enteritidis exploring proteins that may incorporate host adaptation in poultry. J Proteomics 2009, 72:815-821.
64. Josic D., Kovac S. Application of proteomics in biotechnology-microbial proteomics. Biotechnol J 2008, 3:496-509.
65. Reinhart K., Hartog C.S. Biomarkers as a guide for antimicrobial therapy. Int J Antimicrob Agents 2010, 36(Suppl 2):S17-S21.
66. Werner G., Coque T.M., Hammerum A.M., Hope R., Hryniewicz W., Johnson A., et al. Emergence and spread of vancomycin resistance among enterococci in Europe. Euro Surveill 2008, 13.
67. Lee P.S., Lee K.H. Escherichia coli - a model system that benefits from and contributes to the evolution of proteomics. Biotechnol Bioeng 2003, 84:801-814.
68. Witzmann F.A., Li J. Cutting-edge technology. II. Proteomics: core technologies and applications in physiology. Am J Physiol Gastrointest Liver Physiol 2002, 282:G735-G741.
69. Check E. Proteomics and cancer: running before we can walk?. Nature 2004, 429:496-497.
70. Görg A., Postel W., Gunther S. The current state of two-dimensional electrophoresis with immobilized pH gradients. Electrophoresis 1988, 9:531-546.
71. Klose J., Kobalz U. Two-dimensional electrophoresis of proteins: an updated protocol and implications for a functional analysis of the genome. Electrophoresis 1995, 16:1034-1059.
72. Renzone G., D'Ambrosio C., Arena S., Rullo R., Ledda L., Ferrara L., et al. Differential proteomic analysis in the study of prokaryotes stress resistance. Ann Ist Super Sanita 2005, 41:459-468.
73. Maurya Bharati D., Pawar Shweta V., Chate Priya B., Kayarkar Namita A., Durgude Suvarna G., Boraste A., et al. Proteomics: emerging analytical techniques. Int J Genet 2009, 1:17-24.
74. Issaq H., Veenstra T. Two-dimensional polyacrylamide gel electrophoresis (2D-PAGE): advances and perspectives. Biotechniques 2008, 44:697-698. 700.
75. Gauci V.J., Wright E.P., Coorssen J.R. Quantitative proteomics: assessing the spectrum of in-gel protein detection methods. J Chem Biol 2011, 4:3-29.
76. Yates J.R. Database searching using mass spectrometry data. Electrophoresis 1998, 19:893-900.
77. Jungblut P., Thiede B. Protein identification from 2-DE gels by MALDI mass spectrometry. Mass Spectrom Rev 1997, 16:145-162.
78. Engelmann S., Hecker M. A proteomics view of virulence factors of Staphylococcus aureus. Genome Dyn 2009, 6:187-197.
79. Gilmore J.M., Washburn M.P. Advances in shotgun proteomics and the analysis of membrane proteomes. J Proteomics 2010, 73:2078-2091.
80. Bjellqvist B., Ek K., Righetti P.G., Gianazza E., Gorg A., Westermeier R., et al. Isoelectric focusing in immobilized pH gradients: principle, methodology and some applications. J Biochem Biophys Methods 1982, 6:317-339.
81. Fujii K., Nakano T., Hike H., Usui F., Bando Y., Tojo H., et al. Fully automated online multi-dimensional protein profiling system for complex mixtures. J Chromatogr A 2004, 1057:107-113.
82. Neverova I., Van Eyk J.E. Role of chromatographic techniques in proteomic analysis. J Chromatogr B Analyt Technol Biomed Life Sci 2005, 815:51-63.
83. Siegel R.E. Emerging gram-negative antibiotic resistance: daunting challenges, declining sensitivities, and dire consequences. Respir Care 2008, 53:471-479.
84. Chait B.T. Mass spectrometry in the postgenomic era. Annu Rev Biochem 2011, 80:239-246.
85. Zhang J., Chiodini R., Badr A., Zhang G. The impact of next-generation sequencing on genomics. J Genet Genomics 2011, 38:95-109.
86. Jabbour R.E., Wade M.M., Deshpande S.V., Stanford M.F., Wick C.H., Zulich A.W., et al. Identification of Yersinia pestis and Escherichia coli strains by whole cell and outer membrane protein extracts with mass spectrometry-based proteomics. J Proteome Res 2010, 9:3647-3655.
87. Storz G, Hengge-Aronis R. Bacterial stress responses. ASM Press ed. Washington, DC. 2000.
88. VanBogelen R.A., Greis K.D., Blumenthal R.M., Tani T.H., Matthews R.G. Mapping regulatory networks in microbial cells. Trends Microbiol 1999, 7:320-328.
89. Brotz-Oesterhelt H., Bandow J.E., Labischinski H. Bacterial proteomics and its role in antibacterial drug discovery. Mass Spectrom Rev 2005, 24:549-565.
90. McDermott P.F., Walker R.D., White D.G. Antimicrobials: modes of action and mechanisms of resistance. Int J Toxicol 2003, 22:135-143.
91. Howard E.M., Zhang H., Roepe P.D. A novel transporter, Pfcrt, confers antimalarial drug resistance. J Membr Biol 2002, 190:1-8.
92. Zhang H.Z., Hackbarth C.J., Chansky K.M., Chambers H.F. A proteolytic transmembrane signaling pathway and resistance to beta-lactams in staphylococci. Science 2001, 291:1962-1965.
93. Savage P.B. Multidrug-resistant bacteria: overcoming antibiotic permeability barriers of gram-negative bacteria. Ann Med 2001, 33:167-171.
94. Bandow J.E., Brotz H., Leichert L.I., Labischinski H., Hecker M. Proteomic approach to understanding antibiotic action. Antimicrob Agents Chemother 2003, 47:948-955.
95. Uchiyama I., Higuchi T., Kawai M. MBGD update 2010: toward a comprehensive resource for exploring microbial genome diversity. Nucleic Acids Res 2010, 38:D361-D365.
96. VanBogelen R.A., Neidhardt F.C. Ribosomes as sensors of heat and cold shock in Escherichia coli. Proc Natl Acad Sci U S A 1990, 87:5589-5593.
97. Coldham N.G., Randall L.P., Piddock L.J., Woodward M.J. Effect of fluoroquinolone exposure on the proteome of Salmonella enterica serovar Typhimurium. J Antimicrob Chemother 2006, 58:1145-1153.
98. Pinto L., Poeta P., Radhouani H., Coelho A.C., Carvalho C., Rodrigues J., et al. Proteomic evaluation of Escherichia coli from human clinical strains. J Integr OMICS 2011, 1:42-48.
99. Vinue L., Lantero M., Saenz Y., Somalo S., de Diego I., Perez F., et al. Characterization of extended-spectrum beta-lactamases and integrons in Escherichia coli isolates in a Spanish hospital. J Med Microbiol 2008, 57:916-920.
100. Ariza R.R., Li Z., Ringstad N., Demple B. Activation of multiple antibiotic resistance and binding of stress-inducible promoters by Escherichia coli Rob protein. J Bacteriol 1995, 177:1655-1661.
101. Hunstad D.A., Justice S.S., Hung C.S., Lauer S.R., Hultgren S.J. Suppression of bladder epithelial cytokine responses by uropathogenic Escherichia coli. Infect Immun 2005, 73:3999-4006.
102. Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., et al. Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110. Mol Syst Biol 2006, 2. 2006 0007.
103. dos Santos K.V., Diniz C.G., Veloso Lde C., de Andrade H.M., Giusta Mda S., Pires Sda F., et al. Proteomic analysis of Escherichia coli with experimentally induced resistance to piperacillin/tazobactam. Res Microbiol 2010, 161:268-275.
104. Sulavik M.C., Houseweart C., Cramer C., Jiwani N., Murgolo N., Greene J., et al. Antibiotic susceptibility profiles of Escherichia coli strains lacking multidrug efflux pump genes. Antimicrob Agents Chemother 2001, 45:1126-1136.
105. Teng C.H., Xie Y., Shin S., Di Cello F., Paul-Satyaseela M., Cai M., et al. Effects of ompA deletion on expression of type 1 fimbriae in Escherichia coli K1 strain RS218 and on the association of E-coli with human brain microvascular endothelial cells. Infect Immun 2006, 74:5609-5616.
106. Venkitanarayanan K., Nair M.K.M. Role of bacterial OmpA and host cytoskeleton in the invasion of human intestinal epithelial cells by Enterobacter sakazakii. Pediatr Res 2007, 62:664-669.
107. Orme R., Douglas C.W.I., Rimmer S., Webb M. Proteomic analysis of Escherichia coli biofilms reveals the overexpression of the outer membrane protein OmpA. Proteomics 2006, 6:4269-4277.
108. Wooster D.G., Maruvada R., Blom A.M., Prasadarao N.V. Logarithmic phase Escherichia coli K1 efficiently avoids serum killing by promoting C4bp-mediated C3b and C4b degradation. Immunology 2006, 117:482-493.
109. Stoorvogel J., Vanbussel M.J.A.W.M., Vandeklundert J.A.M. Cloning of a beta-lactam resistance determinant of Enterobacter-Cloacae affecting outer-membrane proteins of Enterobacteriaceae. FEMS Microbiol Lett 1987, 48:277-281.
110. Marre R., Borner K., Schulz E. Different mechanisms of TEM-1 and Oxa-1 mediated resistance to piperacillin in E. coli. Zentralbl Bakteriol Mikrobiol Hyg A 1984, 258:287-295.
111. Justice S.S., Hunstad D.A., Cegelski L., Hultgren S.J. Morphological plasticity as a bacterial survival strategy. Nat Rev Microbiol 2008, 6:162-168.
112. Roncada P., Deriu F., Gaviraghi A., Martino P.A., Bonizzi L. Proteomic study of antibiotic resistance in Escherichia coli strains. Vet Res Commun 2009, 33(Suppl 1):157-160.
113. Lin X.M., Li H., Wang C., Peng X.X. Proteomic analysis of nalidixic acid resistance in Escherichia coli: identification and functional characterization of OM proteins. J Proteome Res 2008, 7:2399-2405.
114. Zhang D.F., Jiang B., Xiang Z.M., Wang S.Y. Functional characterisation of altered outer membrane proteins for tetracycline resistance in Escherichia coli. Int J Antimicrob Agents 2008, 32:315-319.
115. Li H., Wang B.C., Xu W.J., Lin X.M., Peng X.X. Identification and network of outer membrane proteins regulating streptomysin resistance in Escherichia coli. J Proteome Res 2008, 7:4040-4049.
116. Li H., Lin X.M., Wang S.Y., Peng X.X. Identification and antibody-therapeutic targeting of chloramphenicol-resistant outer membrane proteins in Escherichia coli. J Proteome Res 2007, 6:3628-3636.
117. Lorian V., Gemmel G.C. Effect of low antibiotic concentrations on bacteria: effects on ultrastructure, virulence, and susceptibility toi immunodefenses. Antibiotics in laboratory medicine 2005, 493-555. Lippincott Williams & Wilkins, Philadelphia. V. Lorian (Ed.).
118. Servin A.L. Pathogenesis of Afa/Dr diffusely adhering Escherichia coli. Clin Microbiol Rev 2005, 18:264-292.
119. Dudley E.G., Thomson N.R., Parkhill J., Morin N.P., Nataro J.P. Proteomic and microarray characterization of the AggR regulon identifies a pheU pathogenicity island in enteroaggregative Escherichia coli. Mol Microbiol 2006, 61:1267-1282.
120. Alteri C.J., Smith S.N., Mobley H.L. Fitness of Escherichia coli during urinary tract infection requires gluconeogenesis and the TCA cycle. PLoS Pathog 2009, 5:e1000448.
121. Alekshun M.N., Levy S.B. Molecular mechanisms of antibacterial multidrug resistance. Cell 2007, 128:1037-1050.
122. Gale E.F., Cundliffe E., Reynolds P.E., Richmond M.H., Waring M.J. The molecular basis of antibiotic action 1981, John Wiley & Sons Ltd, Chichester, United Kingdom. 2nd edition.
123. Walsh C. Washington, DC: Amer Society for Microbiology; 1 edition; 2003.
124. Davies J. Inactivation of antibiotics and the dissemination of resistance genes. Science 1994, 264:375-382.
125. Prescott JF, Baggot JD, Walker RD. Antimicrobial therapy in veterinary epidemiology. In: Iowa State University Press A, editor.2000.
126. Rubens C.E., McNeill W.F., Farrar W.E. Evolution of multiple-antibiotic-resistance plasmids mediated by transposable plasmid deoxyribonucleic acid sequences. J Bacteriol 1979, 140:713-719.
127. Hachler H., Cohen S.P., Levy S.B. marA, a regulated locus which controls expression of chromosomal multiple antibiotic resistance in Escherichia coli. J Bacteriol 1991, 173:5532-5538.
128. Martinez J.L., Baquero F. Mutation frequencies and antibiotic resistance. Antimicrob Agents Chemother 2000, 44:1771-1777.
129. Gniadkowski M. Evolution of extended-spectrum beta-lactamases by mutation. Clin Microbiol Infect 2008, 14(Suppl 1):11-32.
130. Philippon A., Arlet G., Jacoby G.A. Plasmid-determined AmpC-type beta-lactamases. Antimicrob Agents Chemother 2002, 46:1-11.
131. Brazas M.D., Hancock R.E. Using microarray gene signatures to elucidate mechanisms of antibiotic action and resistance. Drug Discov Today 2005, 10:1245-1252.
132. Brazas M.D., Hancock R.E. Ciprofloxacin induction of a susceptibility determinant in Pseudomonas aeruginosa. Antimicrob Agents Chemother 2005, 49:3222-3227.
133. Ochman H., Jones I.B. Evolutionary dynamics of full genome content in Escherichia coli. EMBO J 2000, 19:6637-6643.
134. Garza-Ramos U., Silva-Sanchez J., Martinez-Romero E. Genetics and genomics for the study of bacterial resistance. Salud Publica Mex 2009, 51(Suppl 3):S439-S446.
135. Ackermann B.L., Hale J.E., Duffin K.L. The role of mass spectrometry in biomarker discovery and measurement. Curr Drug Metab 2006, 7:525-539.
136. Veenstra T.D. Global and targeted quantitative proteomics for biomarker discovery. J Chromatogr B Analyt Technol Biomed Life Sci 2007, 847:3-11.
137. Boja E.S., Rodriguez H. The path to clinical proteomics research: integration of proteomics, genomics, clinical laboratory and regulatory science. Korean J Lab Med 2011, 31:61-71.
138. Lin J.C. Protein microarrays for cancer diagnostics and therapy. Med Princ Pract 2010, 19:247-254.
139. Chiou S.H., Wu C.Y. Clinical proteomics: current status, challenges, and future perspectives. Kaohsiung J Med Sci 2011, 27:1-14.