Abstract
To elucidate the mechanisms of antibiotic resistance, integrating phenotypic and genotypic features in resistant strains is important. Here, we describe the expression profiling of antibiotic-resistant Escherichia coli strains obtained by laboratory evolution, and a method for extracting a small number of genes whose expression changes can contribute to the acquisition of resistance.
Key words
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Lenski RE (1998) Bacterial evolution and the cost of antibiotic resistance. Int Microbiol 1(4):265–270
Lazar V, Nagy I, Spohn R, Csorgo B, Gyorkei A, Nyerges A, Horvath B, Voros A, Busa-Fekete R, Hrtyan M, Bogos B, Mehi O, Fekete G, Szappanos B, Kegl B, Papp B, Pal C (2014) Genome-wide analysis captures the determinants of the antibiotic cross-resistance interaction network. Nat Commun 5:4352. doi:10.1038/ncomms5352
Toprak E, Veres A, Michel JB, Chait R, Hartl DL, Kishony R (2012) Evolutionary paths to antibiotic resistance under dynamically sustained drug selection. Nat Genet 44(1):101–105. doi:10.1038/ng.1034
Suzuki S, Horinouchi T, Furusawa C (2014) Prediction of antibiotic resistance by gene expression profiles. Nat Commun 5:5792. doi:10.1038/ncomms6792
Ochman H, Lawrence JG, Groisman EA (2000) Lateral gene transfer and the nature of bacterial innovation. Nature 405(6784):299–304. doi:10.1038/35012500
Lee HH, Molla MN, Cantor CR, Collins JJ (2010) Bacterial charity work leads to population-wide resistance. Nature 467(7311):82–85. doi:10.1038/nature09354
Lazar V, Pal Singh G, Spohn R, Nagy I, Horvath B, Hrtyan M, Busa-Fekete R, Bogos B, Mehi O, Csorgo B, Posfai G, Fekete G, Szappanos B, Kegl B, Papp B, Pal C (2013) Bacterial evolution of antibiotic hypersensitivity. Mol Syst Biol 9:700. doi:10.1038/msb.2013.57
Imamovic L, Sommer MO (2013) Use of collateral sensitivity networks to design drug cycling protocols that avoid resistance development. Sci Transl Med 5(204):204ra132. doi:10.1126/scitranslmed.3006609
Posfai G, Plunkett G 3rd, Feher T, Frisch D, Keil GM, Umenhoffer K, Kolisnychenko V, Stahl B, Sharma SS, de Arruda M, Burland V, Harcum SW, Blattner FR (2006) Emergent properties of reduced-genome Escherichia coli. Science 312(5776):1044–1046. doi:10.1126/science.1126439
Bolstad BM, Irizarry RA, Åstrand M, Speed TP (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19(2):185–193
Matveeva OV, Shabalina SA, Nemtsov VA, Tsodikov AD, Gesteland RF, Atkins JF (2003) Thermodynamic calculations and statistical correlations for oligo-probes design. Nucleic Acids Res 31(14):4211–4217
Ono N, Suzuki S, Furusawa C, Agata T, Kashiwagi A, Shimizu H, Yomo T (2008) An improved physico-chemical model of hybridization on high-density oligonucleotide microarrays. Bioinformatics 24(10):1278–1285. doi:10.1093/bioinformatics/btn109
Markham NR, Zuker M (2005) DINAMelt web server for nucleic acid melting prediction. Nucleic Acids Res 33(Web Server Issue):W577–W581. doi:10.1093/nar/gki591
Suzuki S, Horinouchi T, Furusawa C (2015) Phenotypic changes associated with the fitness cost in antibiotic resistant Escherichia coli strains. Mol Biosyst. doi:10.1039/c5mb00590f
Acknowledgment
This work was supported in part by a Grant-in-Aid for Scientific Research (S) [15H05746], a Grant-in-Aid for Scientific Research (B) [26290071,15H04733], and a Grant-in-Aid for Challenging Exploratory Research [26650138] from JSPS.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2017 Springer Science+Business Media New York
About this protocol
Cite this protocol
Suzuki, S., Horinouchi, T., Furusawa, C. (2017). Expression Profiling of Antibiotic-Resistant Bacteria Obtained by Laboratory Evolution. In: Sass, P. (eds) Antibiotics. Methods in Molecular Biology, vol 1520. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6634-9_16
Download citation
DOI: https://doi.org/10.1007/978-1-4939-6634-9_16
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-6632-5
Online ISBN: 978-1-4939-6634-9
eBook Packages: Springer Protocols