Antibiotic resistance as a model for strain engineering

Computers and Chemical Engineering

Volumn 29, Issue 3, 2005, Pages 509-517

  Bonomo, Jeanne ^a   Gill, Ryan T ^a  

^a UNIVERSITY OF COLORADO   (United States)

Author keywords

Antibiotic resistance; Metabolic engineering; Systems biology

Indexed keywords

BACTERIA; BIOMEDICAL ENGINEERING; DNA; ENZYMES; GENES; METABOLISM;

ANTIBIOTIC RESISTANCE; ANTIBIOTIC RESISTANCE BACTERIA; METABOLIC ENGINEERING; STRAIN ENGINEERING;

ANTIBIOTICS;

AMINOGLYCOSIDE ANTIBIOTIC AGENT; ANTIBIOTIC AGENT; BETA LACTAM ANTIBIOTIC; CIPROFLOXACIN; ERYTHROMYCIN; GLYCOPEPTIDE; MACROLIDE; PENICILLIN G; QUINOLINE DERIVATIVE; STREPTOMYCIN; TETRACYCLINE; TETRACYCLINE DERIVATIVE; VANCOMYCIN;

ANTIBIOTIC AGENT; CHEMICAL ENGINEERING;

ANTIBIOTIC RESISTANCE; ARTICLE; BACTERIAL STRAIN; CELL WALL; COST BENEFIT ANALYSIS; DNA SYNTHESIS INHIBITION; DRUG DETOXIFICATION; ENZYME MODIFICATION; EVOLUTION; METABOLIC ENGINEERING; MULTIDRUG RESISTANCE; MUTATION; NONHUMAN; PHENOTYPE; PROTEIN SYNTHESIS INHIBITION;

EID: 15744363403     PISSN: 00981354     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.compchemeng.2004.08.028     Document Type: Article

References (88)

1. D.I. Andersson, and B.R. Levin The biological cost of antibiotic resistance Current Opinion in Microbiology 2 5 1999 489 493
2. M. Arthur, and C. Molinas Structural relationship between the vancomycin resistance protein Vanh and 2-hydroxycarboxylic acid dehydrogenases Gene 103 1 1991 133 134
3. P.C. Babbitt, and G.T. Mrachko Functionally diverse enzyme superfamily that abstracts the alpha-protons of carboxylic-acids Science 267 5201 1995 1159 1161
4. V. Badarinarayana, and P.W. Estep III Selection analyses of insertional mutants using subgenic-resolution arrays Nature Biotechnology 19 11 2001 1060 1065
5. J.E. Bailey Toward a science of metabolic engineering Science 252 1991 1668 1675
6. J.E. Bailey Mathematical modeling and analysis in biochemical engineering: Past accomplishments and future opportunities Biotechnology Progress 14 1 1998 8 20
7. J.E. Bailey Lessons from metabolic engineering for functional genomics and drug discovery Nature Biotechnology 17 7 1999 616 618
8. R. Benevis, and J. Davies Aminoglycoside antibiotic inactivating enzymes in actinomycetes similar to those present in clinical isolates of antibiotic resistant bacteria Proceedings of the National Academy of Sciences of the United States of America 70 8 1973 2276 2280
9. J. Bjorkman, and D. Hughes Virulence of antibiotic-resistant Salmonella typhimurium Proceedings of the National Academy of Sciences of the United States of America 95 7 1998 3949 3953
10. J. Bjorkman, and I. Nagaev Effects of environment on compensatory mutations to ameliorate costs of antibiotic resistance Science 287 5457 2000 1479 1482
11. M. Brzezinska, and R. Benveniste Gentamicin resistance in strains of Pseudomonas aeruginosa mediated by enzymatic N-acetylation of the deoxystreptamine moiety Biochemistry 11 1972 761 765
12. T.D.H. Bugg, and S. Dutkamalen Identification of vancomycin resistance protein Vana as a d-alanine-d-alanine ligase of altered substrate-specificity Biochemistry 30 8 1991 2017 2021
13. T.D.H. Bugg, and G.D. Wright Molecular-basis for vancomycin resistance in enterococcus-faecium Bm4147 - Biosynthesis of a depsipeptide peptidoglycan precursor by vancomycin resistance proteins Vanh and Vana 30 43 1991 10408 10415
14. K. Bush, and S.K. Tanaka Resistance caused by decreased penetration of beta-lactam antibiotics into Enterobacter cloacae Antimicrobial Agents and Chemotherapy 27 4 1985 555 560
15. K. Bush, and G.A. Jacoby A functional classification scheme for beta-lactamases and its correlation with molecular-structure Antimicrobial Agents and Chemotherapy 39 6 1995 1211 1233
16. CDC. (2000). National Antimicrobial Resistance Monitoring System for Enteric Bacteria; 2003.
17. Y. Cetinkaya, and P. Falk Vancomycin-resistant enterococci Clinical Microbiology Reviews 13 2000 686 707
18. H.F. Chambers Methicillin resistance in staphylococci: Molecular and biochemical basis and clinical implications Clinical Microbiology Reviews 10 4 1997 781
19. R.N. Charrel, and J.M. Pages Prevalence of outer membrane porin alteration in beta-lactam-antibiotic-resistant enterobacter aerogenes Antimicrobial Agents and Chemotherapy 40 12 1996 2854 2858
20. J. Davies, and G.D. Wright Bacterial resistance to aminoglycoside antibiotics Trends in Microbiology 5 6 1997 234 240
21. M. Domach, S. Leung, R. Cahn, G. Cocks, and M. Shuler Computer model for glucose-limited growth of a single cell of Escherichia coli B/r-A Biotechnology and Bioengineering 26 3 1984 203 216
22. J. Edwards, and B.O. Palsson The Escherichia coli MG1655 in silico metabolic genotype: Its definition characteristics and capabilities Proceedings of the National Academy of Sciences of the United States of America 97 10 2000 5528 5533
23. W.R. Farmer, and J.C. Liao Improving lycopene production in Escherichia coli by engineering metabolic control Nature Biotechnology 18 5 2000 533 537
24. S. Fodor, J. Leighton, C. Pirrung, L. Stryer, A. Lu, and D. Solas Light-directed spatially addressable parallel chemical synthesis Science 251 1991 767 773
25. D. Fourmy, and M.I. Recht Structure of the A site of Escherichia coli 16S ribosomal RNA complexed with an aminoglycoside antibiotic Science 274 5291 1996 1367 1371
26. D. Fourmy, and M.I. Recht Binding of neomycin-class aminoglycoside antibiotics to the A-site of 16 S rRNA Journal of Molecular Biology 277 2 1998 347 362
27. M. Galimand, and T. Lamber Characterization of the aac(6′)-Ib gene encoding an aminoglycoside 6′-N-acetyltransferease in Pseudomonas aeruginosa BM2656 37 1993 1456 1462
28. L. Gambino, and S. Gracheck Overexpression of the MarA positive regulator is sufficient to confer multiple antibiotic resistance in Escherichia coli Journal of Bacteriology 175 10 1993 2888 2894
29. R.T. Gill, and S. Wildt Genome-wide screening for trait conferring genes using DNA microarrays Proceedings of the National Academy of Sciences of the United States of America 99 10 2002 7033 7038
30. J. Goldman, and D. White Multiple antibiotic resistance (mar) locus protects Escherichia coli from rapid cell killing by fluroroquinolones Antimicrobial Agents and Chemotherapy 40 1996 1266 1269
31. E. Groisman The pleiotropic two-component regulatory system PhoP-PhoQ Journal of Bacteriology 183 2001 1835 1842
32. H. Hachler, and P. Santanam Sequence and characterization of a novel chromosomal aminoglycoside phophotransferase gene, aph(3′)-IIb, in Pseudomonas aeruginosa Antimicrobial Agents and Chemotherapy 40 1996 1254 1256
33. I. Ho, and C. Chan Aminoglycoside resistance in M. kansasii, M. avium-M. intracellulare, and M. fortuitum: Are amionglycoside-modifying enzymes responsible? Antimicrobial Agents and Chemotherapy 44 2000 39 42
34. Kauffman, S. (1994). The origins of order. Oxford: Oxford University Press.
35. M.A.G. Koffas, and G.Y. Jung Engineering metabolism and product formation in Cory neb acterium glutamicum by coordinated gene overexpression Metabolic Engineering 5 1 2003 32 41
36. R. Leclercq, and E. Derlot Plasmid-mediated resistance to vancomycin and teicoplanin in enterococcus-faecium New England Journal of Medicine 319 3 1988 157 161
37. B.R. Levin, and V. Perrot Compensatory mutations, antibiotic resistance and the population genetics of adaptive evolution in bacteria Genetics 154 3 2000 985 997
38. D. Livermore β-Lactamases in laboratory and clinical resistance Clinical Microbiology Reviews 8 1995 557 584
39. O. Lomovskaya, and M.S. Warren Identification and characterization of inhibitors of multidrug resistance efflux pumps in Pseudomonas aeruginosa: Novel agents for combination therapy Antimicrobial Agents and Chemotherapy 45 1 2001 105 116
40. E. Macfarlane, and A. Kwasnicka Role of Pseudomonas aeruginosa PhoP-PhoQ in resistance to antimicrobial cationic peptides and aminoglycosides Microbiology 126 2000 2543 2554
41. S. Maisnier-Patin, and O.G. Berg Compensatory adaptation to the deleterious effect of antibiotic resistance in Salmonella typhimurium Molecular Microbiology 46 2 2002 355 366
42. W. Mao, and M. Warren MexXY-OprM efflux pump is required for antagonism of aminoglycosides by divalent cations in Pseudomonas aeruginosa Antimicrobial Agents and Chemotherapy 45 2001 2001 2007
43. N. Masuda, and E. Sakagawa Outer membrane proteins responsible for multiple drug resistance in Pseudomonas aeruginosa Antimicrobial Agents and Chemotherapy 39 1995 645 649
44. Y. Matsubashi, and M. Yagisawa Aminoglycoside 3′- phosphotransferases I and II in Pseudomonas aeruginosa Journal of Antibiotics 28 1975 442 447
45. K.S. McKeegan, and M.I. Borges-Walmsley Microbial and viral drug resistance mechanisms Trends in Microbiology 10 10 2002 S8 S14
46. L. McMurry, and M. Oethinger Overrexpression of marA, soxS, and acrAB produces resistance to triclosan in laboratory and clinical strains of Escherichia coli FEMS Microbiology Letters 166 1998 305 309
47. R. Menard, and C. Molinas Overproduction of 3′-aminoglycoside phosphotransferase type I confers resistance to tobramycin in E. coli Antimicrobial Agents and Chemotherapy 37 1993 78 83
48. NIH. (2000). Fact sheet on antimicrobial resistance. National Institute of Allergy and Infectious Diseases; 2003.
49. H. Nikaido Prevention of drug access to bacterial targets - Permeability barriers and active efflux Science 264 5157 1994 382 388
50. M. Ochs, and M. McCusker Negative regulation of the Pseudomonas aeruginosa outer membrane porin OprD selective for imipenem and basic amino acids Antimicrobial Agents and Chemotherapy 43 1999 1085 1090
51. M. Oethigner, and I. Podglajen Overexpression of the marA or soxS regulatory gene in clinical topoisomerase mutants of Escherichia coli Antimicrobial Agents and Chemotherapy 42 1998 2089 2094
52. J. Ohnishi, and S. Mitsuhashi A novel methodology employing Corynebacterium glutamicum genome information to generate a new l-lysine-producing mutant Applied Microbiology and Biotechnology 58 2 2002 217 223
53. J. Ohnishi, and M. Hayashi Efficient 40 degrees C fermentation of l-lysine by a new Corynebacterium glutamicum mutant developed by genome breeding Applied Microbiology and Biotechnology 62 1 2003 69 75
54. M.C. Orencia, and J.S. Yoon Predicting the emergence of antibiotic resistance by directed evolution and structural analysis Nature Structural Biology 8 3 2001 238 242
55. H. Pai, and J. Kim Carbapenem resistance mechanisms in Pseudomonas aeruginosa clinical isolates Antimicrobial Agents and Chemotherapy 45 2001 480 484
56. S.M. Park, and C. ShawReid Elucidation of anaplerotic pathways in Corynebacterium glutamicum via C-13-NMR spectroscopy and GC-MS Applied Microbiology and Biotechnology 47 4 1997 430 440
57. S.M. Park, and A.J. Sinskey Metabolic and physiological studies of Corynebacterium glutamicum mutants Biotechnology and Bioengineering 55 6 1997 864 879
58. S. Petersen, and A.A. de Graaf In vivo quantification of parallel and bidirectional fluxes in the anaplerosis of Corynebacterium glutamicum Journal of Biological Chemistry 275 46 2000 35932 35941
59. P.G. Peters-Wendisch, and C. Kreutzer Pyruvate carboxylase from Corynebacterium glutamicum: Characterization, expression and inactivation of the pyc gene Microbiology-Uk 144 1998 915 927
60. L. Poirel, and T. Lambert Characterization of class 1 integrons from Pseudomonas aeruginosa that contain the blavim2 carbapenem-hydrolyzing β-lactamase gene and of two novel aminoglycoside resistence gene casettes Antimicrobial Agents and Chemotherapy 45 2001 546 552
61. T. Prammananan, and P. Sander RecA-mediated gene conversion and aminoglycoside resistance in strains heterozygous for rRNA Antimicrobial Agents and Chemotherapy 43 1999 447 453
62. C.H. Rammelkamp, and T. Maxon Resistance of Staphylococcus aureus to the action of penicillin Proceedings of the Royal Society of Experimental and Biological Medicine 51 1942 386 389
63. P.E. Reynolds, and F. Depardieu Glycopeptide resistance mediated by enterococcal transposon Tn1546 requires production of Vanx for hydrolysis of d-alanyl-d-alanine Molecular Microbiology 13 6 1994 1065 1070
64. P. Sander, and B. Springer Fitness cost of chromosomal drug resistance-conferring mutations Antimicrobial Agents and Chemotherapy 46 5 2002 1204 1211
65. M. Schena, D. Shalon, R.W. Davis, and P.O. Brown Quantitative monitoring of gene expression patterns with a complementary DNA microarray Science 270 1995 467 470
66. S.J. Schrag, and V. Perrot Reducing antibiotic resistance Nature 381 6578 1996 120 121
67. S.J. Schrag, and V. Perrot Adaptation to the fitness costs of antibiotic resistance in Escherichia coli Proceedings of the Royal Society of London Series B: Biological Sciences 264 1386 1997 1287 1291
68. R. Schroeder, and C. Waldsich Modulation of RNA function by aminoglycoside antibiotics EMBO Journal 19 1 2000 1 9
69. L. Schwocho, and C. Schaffner Cloning and characterization of a 3-N-aminoglycoside acetyltransf erase gene, aac(3)-Ib, from Pseudomonas aeruginosa Antimicrobial Agents and Chemotherapy 39 17 1995 1790 1796
70. K. Shaw, and P. Rather Molecular genetics of aminoglycoside resistance genes and familial relationships of the aminoglycoside modifying enzymes Microbiology Reviews 57 1993 138 163
71. Shnayerson, M., & Plotkin, M. (2002). The killers within: The deadly rise of drug-resistant bacteria. Boston, MA: Little, Brown, and Company.
72. S. Silver Bacterial resistance to toxic metal ions - A review Gene 179 1 1996 9 19
73. B.G. Spratt Antibiotic resistance: Counting the cost Current Biology 6 10 1996 1219 1221
74. R. Srikumar, and T. Kon Expression of Pseudomonas aeruginosa multidrug efflux pumps MexA-MexB-OprM and MexC-MexD-OprJ in a multidrug-sensitive Escherichia coli strain Antimicrobial Agents and Chemotherapy 42 1998 65 71
75. R. Srivastava, and M.S. Peterson Stochastic kinetic analysis of the Escherichia coli stress circuit using sigma(32)-targeted antisense Biotechnology and Bioengineering 75 1 2001 120 129
76. W.P.C. Stemmer Rapid evolution of a protein in vitro by DNA shuffling Nature 370 6488 1994 389 391
77. Stephanopoulos, G., & Gill, R. T. (2000). After a decade of progress, an expanded role for metabolic engineering. New York: NY; Springer. Advances in Biochemical Engineering, 73, 1-8.
78. A.H.C. Uttley, and C.H. Collins Vancomycin-resistant enterococci Lancet 1 8575-8576 1988 57 58
79. R. van Boxtel, and J. van de Klundert Expression of the Pseudomonas aeruginoas gentamicin resistance gene aaC3 in Escherichia coli Antimicrobial Agents and Chemotherapy 42 1998 3173 3178
80. A. Wagner, and D.A. Fell The small world inside large metabolic networks Proceedings of the Royal Society of London Series B: Biological Sciences 268 1478 2001 1803 1810
81. C.T. Walsh, and S.L. Fisher Bacterial resistance to vancomycin: Five genes and one missing hydrogen bond tell the story Chemistry and Biology 3 1 1996 21 28
82. D.J. Watts, and S.H. Strogatz Collective dynamics of 'small-world' networks Nature 393 6684 1998 440 442
83. C. Weikert, and U. Sauer Use of a glycerol-limited, long-term chemostat for isolation of Escherichia coli mutants with improved physiological properties Microbiology-Uk 143 1997 1567 1574
84. C. Weikert, and F. Canonaco Co-overexpression of RspAB improves recombinant protein production in Escherichia coli Metabolic Engineering 2 4 2000 293 299
85. S. Westbrock-Wadman, and D. Sherman Characterization of a Pseudomonas aeruginosa efflux pump contributing to aminoglycoside impermeability Antimicrobial Agents and Chemotherapy 43 1999 2975 2983
86. S. Wright The roles of mutation, inbreeding, cross-breeding, and selection in evolution Proceedings of the Sixth International Congress on Genetics 1 1932 356 366
87. Z. Wu, and G.D. Wright Overexpression, purification, and characterization of Vanx, a d-, d-dipeptidase which is essential for vancomycin resistance in enterococcus-faecium-Bm4147 Biochemistry 34 8 1995 2455 2463
88. M. Young, and M. Bains Role of Pseudomonas aeruginosa outer membrane protein OprH in polymyxin and gentamicin resistance: Isolation of an OprH deficient mutant by gene replacement techniques Antimicrobial Agents and Chemotherapy 36 1992 2566 2568