Multiomics Assessment of Gene Expression in a Clinical Strain of Escherichia Coli Carrying blactx-M-15, blaoxa-1 and blatem-1b ß-Lactamase Genes. Authors: Luís Pinto, Carmen Torres, Concha Gil, Júlio Nunes-Miranda, Hugo Santos, Vítor Borges, João Paulo Gomes, Catarina Silva, Luís Vieira, José Eduardo Pereira, Patrícia Poeta, Gilberto Igrejas

Extended-spectrum ß-lactamase producing (ESBL) Escherichia coli strain C999 was isolated from a patient in a Spanish hospital (Logroño). Previous genotyping indicated that this strain has an extensive antimicrobial resistance and virulence profile, closely related to that of the CTX-M-15-producing O25:H4-ST131 clone known to have caused several outbreaks in community and healthcare settings worldwide. In our work were obtained the whole-cell proteome, membrane, cytoplasmic, periplasmic and extracellular sub-proteomes of C999 by two-dimensional gel electrophoresis followed by fingerprint sequencing through matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. A total of 602 proteins were identified in the different cell fractions, several of which are related to stress response systems, cellular responses, and antibiotic and drug responses, consistent with the multiresistance phenotype. In parallel, whole genome sequencing and RNA sequencing was done to confirm which genes are present and expressed and to quantify transcript levels. The presence of proteins related to pathogenesis and virulence in E. coli C999 as well its similarity to the O25:H4-ST131 clone are evidence of the continued threat of antibiotic resistance in healthcare institutions. On a positive note, a multiomics approach can facilitate surveillance and more detailed characterization of virulent bacterial clones from hospital environments.