Solving the Antibiotic Crisis

ACS Infectious Diseases

Volumn 1, Issue 2, 2016, Pages 80-84

  Wright, Gerard D ^a  

^a MCMASTER UNIVERSITY   (Canada)

Author keywords

antibiotic resistance; drug discovery; evolution; mechanism; natural products; reservoir; systems biology

Indexed keywords

ANTIBIOTIC AGENT;

ANTIBACTERIAL ACTIVITY; ANTIBIOTIC RESISTANCE; CRISIS THEORY; DRUG MECHANISM; INTEGRATION; NONHUMAN; PRIORITY JOURNAL; REVIEW; SYSTEMS BIOLOGY;

EID: 84969206734     PISSN: None     EISSN: 23738227     Source Type: Journal    
DOI: 10.1021/id500052s     Document Type: Review

References (53)

1. WHO. Antimicrobial Resistance: Global Report on Surveillance 2014; Geneva, Switzerland, 2014.
2. Centres for Disease Control and Prevention. Antibiotic Resistance Threats in the United States; Atlanta, GA, USA, 2013; p 114.
3. President's Council of Adviors on Science and Technology. Report to the President on Combating Antibiotic Resitance; (2014.
4. O'Neil, J. Antimicrobial Resistance: Tackling a Crisis for the Health and Wealth of Nations; HM Government: London, UK, 2014.
5. Government of Canada. Antimicrobial Resistance and Use in Canada: A Federal Framework for Action; Ottawa, Canada, 2014.
6. http://www.statcan.gc.ca/tables-tableaux/sum-som/l01/cst01/health26-eng.htm.
7. Shlaes, D. M. and Spellberg, B. (2012) Overcoming the challenges to developing new antibiotics Curr. Opin. Pharmacol. 12 (5) 522-526 10.1016/j.coph.2012.06.010
8. Brown, E. D. (2013) Is the GAIN Act a turning point in new antibiotic discovery? Can. J. Microbiol. 59 (3) 153-156 10.1139/cjm-2013-0089
9. Alekshun, M. N. and Levy, S. B. (2006) Commensals upon us Biochem. Pharmacol. 71 (7) 893-900 10.1016/j.bcp.2005.12.040
10. D'Costa, V. M., McGrann, K. M., Hughes, D. W., and Wright, G. D. (2006) Sampling the antibiotic resistome Science 311 (5759) 374-377 10.1126/science.1120800
11. Dantas, G., Sommer, M. O., Oluwasegun, R. D., and Church, G. M. (2008) Bacteria subsisting on antibiotics Science 320 (5872) 100-103 10.1126/science.1155157
12. Martinez, J. L., Coque, T. M., and Baquero, F. (2014) What is a resistance gene? Ranking risk in resistomes Nat. Rev. Microbiol. 10.1038/nrmicro3399
13. Cox, G. and Wright, G. D. (2013) Intrinsic antibiotic resistance: mechanisms, origins, challenges and solutions Int. J. Med. Microbiol.: IJMM 303 (6-7) 287-292 10.1016/j.ijmm.2013.02.009
14. Forsberg, K. J., Reyes, A., Wang, B., Selleck, E. M., Sommer, M. O., and Dantas, G. (2012) The shared antibiotic resistome of soil bacteria and human pathogens Science 337 (6098) 1107-1111 10.1126/science.1220761
15. Allen, H. K., Donato, J., Wang, H. H., Cloud-Hansen, K. A., Davies, J., and Handelsman, J. (2010) Call of the wild: antibiotic resistance genes in natural environments Nat. Rev. Microbiol. 8 (4) 251-259 10.1038/nrmicro2312
16. Wright, G. D. (2007) The antibiotic resistome: the nexus of chemical and genetic diversity Nat. Rev. Microbiol. 5 (3) 175-186 10.1038/nrmicro1614
17. Gaze, W. H., Krone, S. M., Larsson, D. G., Li, X. Z., Robinson, J. A., Simonet, P., Smalla, K., Timinouni, M., Topp, E., Wellington, E. M., Wright, G. D., and Zhu, Y. G. Influence of humans on evolution and mobilization of environmental antibiotic resistome. Emerg. Infect. Dis. 2013, 19 (7), DOI: 10.3201/eid1907.120871.
18. Cho, H., Uehara, T., and Bernhardt, T. G. (2014) β-Lactam antibiotics induce a lethal malfunctioning of the bacterial cell wall synthesis machinery Cell 159 (6) 1300-1311 10.1016/j.cell.2014.11.017
19. Keren, I., Wu, Y., Inocencio, J., Mulcahy, L. R., and Lewis, K. (2013) Killing by bactericidal antibiotics does not depend on reactive oxygen species Science 339 (6124) 1213-1216 10.1126/science.1232688
20. Dwyer, D. J., Belenky, P. A., Yang, J. H., MacDonald, I. C., Martell, J. D., Takahashi, N., Chan, C. T., Lobritz, M. A., Braff, D., Schwarz, E. G., Ye, J. D., Pati, M., Vercruysse, M., Ralifo, P. S., Allison, K. R., Khalil, A. S., Ting, A. Y., Walker, G. C., and Collins, J. J. (2014) Antibiotics induce redox-related physiological alterations as part of their lethality Proc. Natl. Acad. Sci. U.S.A. 111 (20) E2100-E2109 10.1073/pnas.1401876111
21. Kohanski, M. A., Dwyer, D. J., Hayete, B., Lawrence, C. A., and Collins, J. J. (2007) A common mechanism of cellular death induced by bactericidal antibiotics Cell 130 (5) 797-810 10.1016/j.cell.2007.06.049
22. Liu, Y. and Imlay, J. A. (2013) Cell death from antibiotics without the involvement of reactive oxygen species Science 339 (6124) 1210-1213 10.1126/science.1232751
23. Du, D., Wang, Z., James, N. R., Voss, J. E., Klimont, E., Ohene-Agyei, T., Venter, H., Chiu, W., and Luisi, B. F. (2014) Structure of the AcrAB-TolC multidrug efflux pump Nature 509 (7501) 512-515 10.1038/nature13205
24. Cox, G., Koteva, K., and Wright, G. D. An unusual class of anthracyclines potentiate Gram-positive antibiotics in intrinsically resistant Gram-negative bacteria. J. Antimicrob. Chemother. 2014, 69, DOI: 10.1093/jac/dku057.
25. Liu, A., Tran, L., Becket, E., Lee, K., Chinn, L., Park, E., Tran, K., and Miller, J. H. (2010) Antibiotic sensitivity profiles determined with an Escherichia coli gene knockout collection: generating an antibiotic bar code Antimicrob. Agents Chemother. 54 (4) 1393-1403 10.1128/AAC.00906-09
26. Tamae, C., Liu, A., Kim, K., Sitz, D., Hong, J., Becket, E., Bui, A., Solaimani, P., Tran, K. P., Yang, H., and Miller, J. H. (2008) Determination of antibiotic hypersensitivity among 4,000 single-gene-knockout mutants of Escherichia coli J. Bacteriol. 190 (17) 5981-5988 10.1128/JB.01982-07
27. Gillings, M. R. (2013) Evolutionary consequences of antibiotic use for the resistome, mobilome and microbial pangenome Front. Microbiol. 4, 4 10.3389/fmicb.2013.00004
28. Perry, J. A. and Wright, G. D. (2013) The antibiotic resistance "mobilome": searching for the link between environment and clinic Front. Microbiol. 4, 138 10.3389/fmicb.2013.00138
29. Baba, T., Ara, T., Hasegawa, M., Takai, Y., Okumura, Y., Baba, M., Datsenko, K. A., Tomita, M., Wanner, B. L., and Mori, H. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection Mol. Syst. Biol. 2 0008 10.1038/msb4100050
30. Kitagawa, M., Ara, T., Arifuzzaman, M., Ioka-Nakamichi, T., Inamoto, E., Toyonaga, H., and Mori, H. (2005) Complete set of ORF clones of Escherichia coli ASKA library (a complete set of E. coli K-12 ORF archive): unique resources for biological research DNA Res. 12 (5) 291-299 10.1093/dnares/dsi012
31. Boucher, H. W., Talbot, G. H., Bradley, J. S., Edwards, J. E., Gilbert, D., Rice, L. B., Scheld, M., Spellberg, B., and Bartlett, J. (2009) Bad bugs, no drugs: no ESKAPE! An update from the Infectious Diseases Society of America Clin. Infect. Dis. 48 (1) 1-12 10.1086/595011
32. Lewenza, S., Falsafi, R. K., Winsor, G., Gooderham, W. J., McPhee, J. B., Brinkman, F. S., and Hancock, R. E. (2005) Construction of a mini-Tn5-luxCDABE mutant library in Pseudomonas aeruginosa PAO1: a tool for identifying differentially regulated genes Genome Res. 15 (4) 583-589 10.1101/gr.3513905
33. Fernandez, L., Alvarez-Ortega, C., Wiegand, I., Olivares, J., Kocincova, D., Lam, J. S., Martinez, J. L., and Hancock, R. E. (2013) Characterization of the polymyxin B resistome of Pseudomonas aeruginosa Antimicrob. Agents Chemother. 57 (1) 110-119 10.1128/AAC.01583-12
34. Alvarez-Ortega, C., Wiegand, I., Olivares, J., Hancock, R. E., and Martinez, J. L. (2011) The intrinsic resistome of Pseudomonas aeruginosa to β-lactams Virulence 2 (2) 144-146 10.4161/viru.2.2.15014
35. McArthur, A. G., Waglechner, N., Nizam, F., Yan, A., Azad, M. A., Baylay, A. J., Bhullar, K., Canova, M. J., De Pascale, G., Ejim, L., Kalan, L., King, A. M., Koteva, K., Morar, M., Mulvey, M. R., O'Brien, J. S., Pawlowski, A. C., Piddock, L. J., Spanogiannopoulos, P., Sutherland, A. D., Tang, I., Taylor, P. L., Thaker, M., Wang, W., Yan, M., Yu, T., and Wright, G. D. (2013) The comprehensive antibiotic resistance database Antimicrob. Agents Chemother. 57 (7) 3348-3357 10.1128/AAC.00419-13
36. Kalan, L. and Wright, G. D. (2011) Antibiotic adjuvants: multicomponent anti-infective strategies Expert Rev. Mol. Med. 13 e5 10.1017/S1462399410001766
37. Shlaes, D. M. (2013) New β-lactam-β-lactamase inhibitor combinations in clinical development Ann. N.Y. Acad. Sci. 1277, 105-114 10.1111/nyas.12010
38. Ejim, L., Farha, M. A., Falconer, S. B., Wildenhain, J., Coombes, B. K., Tyers, M., Brown, E. D., and Wright, G. D. (2011) Combinations of antibiotics and nonantibiotic drugs enhance antimicrobial efficacy Nat. Chem. Biol. 7 (6) 348-350 10.1038/nchembio.559
39. Farha, M. A. and Brown, E. D. (2010) Chemical probes of Escherichia coli uncovered through chemical-chemical interaction profiling with compounds of known biological activity Chem. Biol. 17 (8) 852-862 10.1016/j.chembiol.2010.06.008
40. Lewis, K. (2013) Platforms for antibiotic discovery Nat. Rev. Drug Discov. 12 (5) 371-387 10.1038/nrd3975
41. Payne, D. J., Gwynn, M. N., Holmes, D. J., and Pompliano, D. L. (2007) Drugs for bad bugs: confronting the challenges of antibacterial discovery Nat. Rev. Drug Discov. 6 (1) 29-40 10.1038/nrd2201
42. Costanzo, M., Baryshnikova, A., Bellay, J., Kim, Y., Spear, E. D., Sevier, C. S., Ding, H., Koh, J. L., Toufighi, K., Mostafavi, S., Prinz, J., St. Onge, R. P., VanderSluis, B., Makhnevych, T., Vizeacoumar, F. J., Alizadeh, S., Bahr, S., Brost, R. L., Chen, Y., Cokol, M., Deshpande, R., Li, Z., Lin, Z. Y., Liang, W., Marback, M., Paw, J., San Luis, B. J., Shuteriqi, E., Tong, A. H., van Dyk, N., Wallace, I. M., Whitney, J. A., Weirauch, M. T., Zhong, G., Zhu, H., Houry, W. A., Brudno, M., Ragibizadeh, S., Papp, B., Pal, C., Roth, F. P., Giaever, G., Nislow, C., Troyanskaya, O. G., Bussey, H., Bader, G. D., Gingras, A. C., Morris, Q. D., Kim, P. M., Kaiser, C. A., Myers, C. L., Andrews, B. J., and Boone, C. (2010) The genetic landscape of a cell Science 327 (5964) 425-431 10.1126/science.1180823
43. East, S. P. and Silver, L. L. (2013) Multitarget ligands in antibacterial research: progress and opportunities Expert Opin. Drug Discov. 8 (2) 143-156 10.1517/17460441.2013.743991
44. Farha, M. A., Leung, A., Sewell, E. W., D'Elia, M. A., Allison, S. E., Ejim, L., Pereira, P. M., Pinho, M. G., Wright, G. D., and Brown, E. D. (2013) Inhibition of WTA synthesis blocks the cooperative action of PBPs and sensitizes MRSA to β-lactams ACS Chem. Biol. 8 (1) 226-233 10.1021/cb300413m
45. Eaton, S. R. and Mazuski, J. E. (2013) Overview of severe Clostridium difficile infection Crit. Care Clin. 29 (4) 827-839 10.1016/j.ccc.2013.06.004
46. Lipinski, C. A., Lombardo, F., Dominy, B. W., and Feeney, P. J. (1997) Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings Adv. Drug Delivery Revi. 23, 3-25 10.1016/S0169-409X(96)00423-1
47. Berdy, J. (2005) Bioactive microbial metabolites J. Antibiot. 58 (1) 1-26 10.1038/ja.2005.1
48. Ito, T. and Masubuchi, M. (2014) Dereplication of microbial extracts and related analytical technologies J. Antibiot. 67 (5) 353-360 10.1038/ja.2014.12
49. Dubos, R. J. (1939) Studies on a bactericidal agent extracted from a soil Bacillus: I. Preparation of the agent. Its activity in vitro J. Exp. Med. 70 (1) 1-10 10.1084/jem.70.1.1
50. Schatz, A., Bugle, E., and Waksman, S. A. (1944) Streptomycin, a substance exhibiting antibiotic actiity against Gram-positive and Gram-negative bacteria Exp. Biol. Med. 55, 66-69 10.3181/00379727-55-14461
51. Ling, L., Schneider, T., Peoples, A. J., Spoering, A. L., Engels, I., Conlon, B. P., Mueller, A., Schäberle, T. F., Hughes, D. E., Espstein, S., Jones, M., Lazarides, L., Steadman, V. A., Cohen, D. R., Felix, C. R., Fetterman, K. A., Millett, W. P., Nitti, A. G., Zullo, A. M., Chen, C., and Lewis, K. (2015) A new antibiotic kills pathogens without detectable resistance Nature 10.1038/nature14098
52. Zakeri, B. and Lu, T. K. (2013) Synthetic biology of antimicrobial discovery ACS Synth. Biol. 2 (7) 358-372 10.1021/sb300101g
53. Blin, K., Medema, M. H., Kazempour, D., Fischbach, M. A., Breitling, R., Takano, E., and Weber, T. (2013) antiSMASH 2.0-a versatile platform for genome mining of secondary metabolite producers Nucleic Acids Res. 41 (Web Server issue) W204-W212 10.1093/nar/gkt449