Objectives:

To seek for novel genes involved in antimicrobial resistance in K. pneumoniae, we used DNA chip technology to compare the gene expression profile of two clonally related strains isolated from the same patient (CSUB10S, porin+ efflux–; CSUB10R, porin– efflux+).

Methods:

Total RNA from both strains was isolated, reverse transcribed, labelled with fluorescent nucleotides and hybridised to DNA microarrays displaying the complete genome of Escherichia coli. After hybridisation the microarrays were scanned and the intensity of the spots obtained for both samples were normalised and compared. Statistical analyses of five independent experiments identify those genes whose expression was significantly different between both strains. RT-PCR quantitation was used to verify the microarray data.

Results:

Nineteen genes were upregulated in the resistant isolate compared with the susceptible isolate. No changes related to the AcrAB-TolC system were found. ycjV gene, which encodes for a transporter, was 4-fold up-regulated suggesting that this protein might contribute to antimicrobial resistance. By contrast, 33 genes were down-regulated in the resistant isolate, including 11 unknown genes and genes involved in the permeability of the cell envelope like ompC.

Conclusions:

(1) E. coli DNA microarrays are suitable for K. pneumoniae gene expression profile analysis.

(2) The number of genes down-regulated in the resistant isolate is higher that the genes up-regulated when compared with the susceptible strain.

(3) ycjV is a candidate for a novel mechanism of antimicrobial resistance in K. pneumoniae.