Phenotypic profiling of antibiotic response signatures in Escherichia coli using raman spectroscopy

Antimicrobial Agents and Chemotherapy

Volumn 58, Issue 3, 2014, Pages 1302-1314

  Athamneh, A I M ^a   Alajlouni, R A ^b   Wallace, R S ^a   Seleem, M N ^b   Sengera, R S ^a  

^a Virginia Polytechnic Institute and State University   (United States)

^b PURDUE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMOXICILLIN; AMPICILLIN; ANTIBIOTIC AGENT; CEFOTAXIME; CHLORAMPHENICOL; CIPROFLOXACIN; CLINDAMYCIN; GENTAMICIN; KANAMYCIN; NALIDIXIC ACID; RIFAMPICIN; RIFAPENTINE; RIFAXIMIN; STREPTOMYCIN; TETRACYCLINE; TRIMETHOPRIM;

ANTIBACTERIAL ACTIVITY; ARTICLE; BACTERIAL CELL WALL; BACTERIAL CELL WALL SYNTHESIS INHIBITION; BACTERIAL GROWTH; CHEMOMETRIC ANALYSIS; CONTROLLED STUDY; DNA SYNTHESIS INHIBITION; DRUG MECHANISM; DRUG RESPONSE; ESCHERICHIA COLI; MINIMUM INHIBITORY CONCENTRATION; NONHUMAN; PHENOTYPE; PHENOTYPIC VARIATION; PREDICTIVE VALUE; PRIORITY JOURNAL; PROTEIN SYNTHESIS INHIBITION; RAMAN SPECTROMETRY; RIBONUCLEIC ACID SYNTHESIS INHIBITION; RNA SYNTHESIS; VALIDATION PROCESS; WILD TYPE;

ANTI-BACTERIAL AGENTS; ESCHERICHIA COLI; MICROBIAL SENSITIVITY TESTS; PHENOTYPE; SPECTRUM ANALYSIS, RAMAN;

EID: 84896810554     PISSN: 00664804     EISSN: 10986596     Source Type: Journal    
DOI: 10.1128/AAC.02098-13     Document Type: Article

References (42)

1. Kohanski MA, Dwyer DJ, Collins JJ. 2010. How antibiotics kill bacteria: from targets to networks. Nat. Rev. Microbiol. 8:423-435. http://dx.doi.org/10. 1038/nrmicro2333.
2. Futamura Y, Muroi M, Osada H. 2013. Target identification of small molecules based on chemical biology approaches. Mol. Biosyst. 9:897-914. http://dx.doi.org/10.1039/c2mb25468a.
3. Toledo-Arana A, Solano C. 2010. Deciphering the physiological blueprint of a bacterial cell. Bioessays 32:461-467. http://dx.doi.org/10.1002/bies. 201000020.
4. Silver LL. 2011. Challenges of antibacterial discovery. Clin. Microbiol. Rev. 24:71-109. http://dx.doi.org/10.1128/CMR.00030-10.
5. Brazas MD, Hancock REW. 2005. Using microarray gene signatures to elucidate mechanisms of antibiotic action and resistance. Drug Discov. Today 10:1245-1252. http://dx.doi.org/10.1016/S1359-6446(05)03566-X. (Pubitemid 41411435)
6. Rix U, Superti-Furga G. 2009. Target profiling of small molecules by chemical proteomics. Nat. Chem. Biol. 5:616-624. http://dx.doi.org/10.1038/ nchembio.216.
7. Hart CP. 2005. Finding the target after screening the phenotype. Drug Discov. Today 10:513-519. http://dx.doi.org/10.1016/S1359-6446(05)03415-X.
8. Wang H, Charles Gill J, Sang Lee H, Mann P, Zuck P, Timothy Meredith C, Murgolo N, She X, Kales S, Liang L, Liu J, Wu J, Santa Maria J, Su J, Pan J, Hailey J, McGuinness D, Christopher Tan M, Flattery A, Walker S, Black T, Roemer T. 2013. Discovery of wall teichoic acid inhibitors as potential anti-MRSA β-lactam combination agents. Chem. Biol. 20:272-284. http://dx.doi.org/10. 1016/j.chembiol.2012.11.013.
9. Amini S, Tavazoie S. 2011. Antibiotics and the post-genome revolution. Curr. Opin. Microbiol. 14:513-518. http://dx.doi.org/10.1016/j.mib.2011.07.017.
10. Freiberg C, Fischer HP, Brunner NA. 2005. Discovering the mechanism of action of novel antibacterial agents through transcriptional profiling of conditional mutants. Antimicrob. Agents Chemother. 49:749-759. http://dx.doi.org/10.1128/AAC.49.2.749-759.2005. (Pubitemid 40175689)
11. Lamb J, Crawford ED, Peck D, Modell JW, Blat IC, Wrobel MJ, Lerner J, Brunet J-P, Subramanian A, Ross KN, Reich M, Hieronymus H, Wei G, Armstrong SA, Haggarty SJ, Clemons PA, Wei R, Carr SA, Lander ES, Golub TR. 2006. The connectivity map: using gene-expression signatures to connect small molecules, genes, and disease. Science 313:1929-1935. http://dx.doi.org/10.1126/science. 1132939. (Pubitemid 44497995)
12. Bandow J, Hecker M. 2007. Proteomic profiling of cellular stresses in Bacillus subtilis reveals cellular networks and assists in elucidating antibiotic mechanisms of action. Progress Drug Res. 64:79-101. http://dx.doi.org/10.1007/978-3-7643-7567-6-4. (Pubitemid 351495006)
13. Böddeker N, Bahador G, Gibbs C, Mabery E, Wolf J, Xu L, Watson J. 2002. Characterization of a novel antibacterial agent that inhibits bacterial translation. RNA 8:1120-1128. http://dx.doi.org/10.1017/S1355838202024020. (Pubitemid 35024568)
14. Yu Y, Yi ZB, Liang YZ. 2007. Main antimicrobial components of Tinospora capillipes, and their mode of action against Staphylococcus aureus. FEBS Lett. 581:4179-4183. http://dx.doi.org/10.1016/j.febslet.2007.07.056. (Pubitemid 47301850)
15. Perlman ZE, Slack MD, Feng Y, Mitchison TJ, Wu LF, Altschuler SJ. 2004. Multidimensional drug profiling by automated microscopy. Science 306:1194-1198. http://dx.doi.org/10.1126/science.1100709. (Pubitemid 39489001)
16. Futamura Y, Kawatani M, Kazami S, Tanaka K, Muroi M, Shimizu T, Tomita K, Watanabe N, Osada H. 2012. Morphobase, an encyclopedic cell morphology database, and Its use for drug target identification. Chem. Biol. 19:1620-1630. http://dx.doi.org/10.1016/j.chembiol.2012.10.014.
17. Huang WE, Li M, Jarvis RM, Goodacre R, Banwart SA. 2010. Shining light on the microbial world: the application of Raman microspectroscopy. Adv. Appl. Microbiol. 70:153-186. http://dx.doi.org/10.1016/S0065-2164(10)70005-8.
18. Moritz TJ, Taylor DS, Polage CR, Krol DM, Lane SM, Chan JW. 2010. Effect of cefazolin treatment on the nonresonant Raman signatures of the metabolic state of individual Escherichia coli cells. Anal. Chem. 82:2703-2710. http://dx.doi.org/10.1021/ac902351a.
19. Notingher I. 2007. Raman spectroscopy cell-based biosensors. Sensors 7:1343-1358. http://dx.doi.org/10.3390/s7081343.
20. López-Díez EC, Goodacre R. 2004. Characterization of microorganisms usingUVresonance Raman spectroscopy and chemometrics. Anal. Chem. 76:585-591. http://dx.doi.org/10.1021/ac035110d. (Pubitemid 38166561)
21. Goodacre R, Timmins EM, Burton R, Kaderbhai N, Woodward AM, Kell DB, Rooney PJ. 1998. Rapid identification of urinary tract infection bacteria using hyperspectral whole-organism fingerprinting and artificial neural networks. Microbiology 144:1157-1170. http://dx.doi.org/10.1099/00221287-144-5-1157. (Pubitemid 28233819)
22. Maquelin K, Kirschner C, Choo-Smith LP, van den Braak N, Endtz HP, Naumann D, Puppels GJ. 2002. Identification of medically relevant microorganisms by vibrational spectroscopy. J. Microbiol. Methods 51:255-271. http://dx.doi.org/10.1016/S0167-7012(02)00127-6. (Pubitemid 35245847)
23. Athamneh AIM, Senger RS. 2012. Peptide-guided surface-enhanced Raman scattering probes for localized cell composition analysis. Appl. Environ. Microbiol. 78:7805-7808. http://dx.doi.org/10.1128/AEM.02000-12.
24. Hall EK, Singer GA, Polzl M, Hammerle I, Schwarz C, Daims H, Maixner F, Battin TJ. 2011. Looking inside the box: using Raman microspectroscopy to deconstruct microbial biomass stoichiometry one cell at a time. ISME J. 5:196-208. http://dx.doi.org/10.1038/ismej.2010.115.
25. Schuster KC, Urlaub E, Gapes JR. 2000. Single-cell analysis of bacteria by Raman microscopy: spectral information on the chemical composition of cells and on the heterogeneity in a culture. J. Microbiol. Methods 42:29-38. http://dx.doi.org/10.1016/S0167-7012(00)00169-X.
26. Walter A, Reinicke M, Bocklitz T, Schumacher W, Rösch P, Kothe E, Popp J. 2011. Raman spectroscopic detection of physiology changes in plasmid-bearing Escherichia coli with and without antibiotic treatment. Anal. Bioanal. Chem. 400:2763-2773. http://dx.doi.org/10.1007/s00216-011-4819-4.
27. Neugebauer U, Schmid U, Baumann K, Holzgrabe U, Schmitt M, Popp J. 2007. Towards an understanding of the mode of action of fluoroquinolone drugs, poster. Abstr. Eur. Conf. Biomed. Optics, poster 6633-68.
28. Neugebauer U, Schmid U, Baumann K, Holzgrabe U, Ziebuhr W, Kozitskaya S, Kiefer W, Schmitt M, Popp J. 2006. Characterization of bacterial growth and the influence of antibiotics by means of UV resonance Raman spectroscopy. Biopolymers 82:306-311. http://dx.doi.org/10.1002/bip.20447. (Pubitemid 44000894)
29. López-Díez EC, Winder CL, Ashton L, Currie F, Goodacre R. 2005. Monitoring the mode of action of antibiotics using Raman spectroscopy: investigating subinhibitory effects of amikacin on Pseudomonas aeruginosa. Anal. Chem. 77:2901-2906. http://dx.doi.org/10.1021/ac048147m. (Pubitemid 40617339)
30. Moritz TJ, Polage CR, Taylor DS, Krol DM, Lane SM, Chan JW. 2010. Evaluation of Escherichia coli cell response to antibiotic treatment by use of Raman spectroscopy with laser tweezers. J. Clin. Microbiol. 48:4287-4290. http://dx.doi.org/10.1128/JCM.01565-10.
31. Efrima S, Zeiri L. 2009. Understanding SERS of bacteria. J. Raman Spectrosc. 40:277-288. http://dx.doi.org/10.1002/jrs.2121.
32. Bocklitz T, Walter A, Hartmann K, Rösch P, Popp J. 2011. How to pre-process Raman spectra for reliable and stable models? Anal. Chim. Acta 704:47-56. http://dx.doi.org/10.1016/j.aca.2011.06.043.
33. Fisher RA. 1936. The use of multiple measurements in taxonomic problems. Ann. Hum. Genet. 7:179-188. http://dx.doi.org/10.1111/j.1469-1809.1936.tb02137. x.
34. Ringner M. 2008. What is principal component analysis? Nat. Biotechnol. 26:303-304. http://dx.doi.org/10.1038/nbt0308-303. (Pubitemid 351355122)
35. Chapelle O, Vapnik V, Bousquet O, Mukherjee S. 2002. Choosing multiple parameters for support vector machines. Mach. Learn. 46:131-159. http://dx.doi.org/10.1023/A:1012450327387. (Pubitemid 34129966)
36. Sullivan R. 2012. Introduction to data mining for the life sciences. Humana Press, Totowa, NJ.
37. Novo DJ, Perlmutter NG, Hunt RH, Shapiro HM. 2000. Multiparameter flow cytometric analysis of antibiotic effects on membrane potential, membrane permeability, and bacterial counts of Staphylococcus aureus and Micrococcus luteus. Antimicrob. Agents Chemother. 44:827-834. http://dx.doi.org/10.1128/AAC. 44.4.827-834.2000. (Pubitemid 30165256)
38. Pato ML. 1977. Tetracycline inhibits propagation of deoxyribonucleic acid replication and alters membrane properties. Antimicrob. Agents Chemother. 11:318-323. http://dx.doi.org/10.1128/AAC.11.2.318. (Pubitemid 8042488)
39. Verma I, Rohilla A, Khuller GK. 1999. Alterations in macromolecular composition and cell wall integrity by ciprofloxacin in Mycobacterium smegmatis. Lett. Appl. Microbiol. 29:113-117. http://dx.doi.org/10.1046/j.1365-2672.1999. 00597.x. (Pubitemid 29423826)
40. Bryskier A. 1993. Fluoroquinolones: mechanisms of action and resistance. Int. J. Antimicrob. Agents 2:151-183. http://dx.doi.org/10.1016/0924-8579(93) 90052-7.
41. Schmid U, Rösch P, Krause M, Harz M, Popp J, Baumann K. 2009. Gaussian mixture discriminant analysis for the single-cell differentiation of bacteria using micro-Raman spectroscopy. Chemometr. Intell. Lab. Syst. 96:159-171. http://dx.doi.org/10.1016/j.chemolab.2010.07.008.
42. Notingher I, Jell G, Notingher PL, Bisson I, Tsigkou O, Polak JM, Stevens MM, Hench LL. 2005. Multivariate analysis of Raman spectra for in vitro non-invasive studies of living cells. J. Mol. Struct. 747:179-185. http://dx.doi.org/10.1016/j.molstruc.2004.12.046. (Pubitemid 40717371)