title: Impacts of experimentally induced and clinically acquired quinolone resistance on the membrane and intracellular subproteomes of Salmonella Typhimurium DT104B.
abstract: Antimicrobial resistance is a growing public health threat worldwide that is still far from a complete understanding. Salmonella Typhimurium DT104 multiresistant strains with additional quinolone resistance are highly adaptive and have been responsible for global outbreaks and high mortality. In order to give new insights about the resistance mechanisms involved, the developed work aimed to point out subproteome changes between a DT104B clinical strain (Se20) that acquired quinolone resistance after patient treatment and an in vitro induced clonally related highly-resistant mutant (Se6-M). The intracellular subproteomes were compared by a 2-DE/LC-MS/MS approach and a total of 50 unique proteins were identified (32 more abundant in Se20 and 18 more abundant in Se6-M). The membrane subproteomes were analysed by a shotgun LC-MS/MS approach, where 7 differentially abundant proteins were identified (5 more abundant in Se6-M and 2 more abundant in Se20). Several proteins known to be directly related to quinolone resistance mechanisms (AAC(6')-Ib-cr4, OmpC, OmpD, OmpX, etc.) and MipA, recently reported as novel antibiotic resistance-related protein, were identified. Other proteins (Fur, SodA, SucB, AtpD/AtpG, OmpC, GltI, CheM/CheB, etc.) reflecting the metabolic re-adjustments occurred in each strain in order to acquire quinolone resistance were also identified. Moreover, proteins involved in lipopolysaccharide biosynthesis (RfbF, RfbG, GmhA) and export (LptA) were detected, supporting the importance of exploring these proteins as targets for the development of new antimicrobial agents. In conclusion, this study provides new insights into the mechanisms involved in the acquisition of antibiotic resistance, which can be highly valuable for the development of improved therapeutic strategies.
  
  
  
  This comparative proteomic study revealed a large number of differentially regulated proteins involved in antibiotic resistance which can be of great value to drug discovery, research and development programmes.
authors.affiliation: Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal; Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal; Veterinary Science Department, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal; UCIBIO-REQUIMTE, Faculty of Science and Technology, Nova University of Lisbon, Lisbon, Portugal.
authors.forename: Susana
authors.initials: S
authors.lastname: Correia
authors.affiliation: UR454 Microbiology, Institut National de la Recherche Agronomique (INRA), Centre Auvergne-Rhône-Alpes, site de Theix, Saint-Genès Champanelle, France; Plate-Forme d'Exploration du Métabolisme composante protéomique, UR370 QuaPA, Institut National de la Recherche Agronomique (INRA), Centre Auvergne-Rhône-Alpes, site de Theix, Saint-Genès Champanelle, France.
authors.forename: Michel
authors.initials: M
authors.lastname: Hébraud
authors.affiliation: UR454 Microbiology, Institut National de la Recherche Agronomique (INRA), Centre Auvergne-Rhône-Alpes, site de Theix, Saint-Genès Champanelle, France.
authors.forename: Ingrid
authors.initials: I
authors.lastname: Chafsey
authors.affiliation: Plate-Forme d'Exploration du Métabolisme composante protéomique, UR370 QuaPA, Institut National de la Recherche Agronomique (INRA), Centre Auvergne-Rhône-Alpes, site de Theix, Saint-Genès Champanelle, France.
authors.forename: Christophe
authors.initials: C
authors.lastname: Chambon
authors.affiliation: Plate-Forme d'Exploration du Métabolisme composante protéomique, UR370 QuaPA, Institut National de la Recherche Agronomique (INRA), Centre Auvergne-Rhône-Alpes, site de Theix, Saint-Genès Champanelle, France.
authors.forename: Didier
authors.initials: D
authors.lastname: Viala
authors.affiliation: Área de Bioquímica y Biología Molecular, Universidad de La Rioja, Logroño, La Rioja, Spain; Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja, Logroño, La Rioja, Spain.
authors.forename: Carmen
authors.initials: C
authors.lastname: Torres
authors.affiliation: Área de Bioquímica y Biología Molecular, Universidad de La Rioja, Logroño, La Rioja, Spain.
authors.forename: María
authors.initials: M
authors.lastname: de Toro
authors.affiliation: UCIBIO-REQUIMTE, Faculty of Science and Technology, Nova University of Lisbon, Lisbon, Portugal; ProteoMass Scientific Society, Faculty of Sciences and Technology, Campus de Caparica, Caparica, Portugal.
authors.forename: José L
authors.initials: JL
authors.lastname: Capelo
authors.affiliation: Veterinary Science Department, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal; UCIBIO-REQUIMTE, Faculty of Science and Technology, Nova University of Lisbon, Lisbon, Portugal.
authors.forename: Patrícia
authors.initials: P
authors.lastname: Poeta
authors.affiliation: Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal; Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal; UCIBIO-REQUIMTE, Faculty of Science and Technology, Nova University of Lisbon, Lisbon, Portugal.
authors.forename: Gilberto
authors.initials: G
authors.lastname: Igrejas
mesh_terms: D001426:Bacterial Proteins / Q000032:analysis / Q000502:physiology; D004351:Drug Resistance; D008070:Lipopolysaccharides / Q000096:biosynthesis; D053858:Metabolic Networks and Pathways / Q000187:drug effects; D040901:Proteomics / Q000379:methods; D015363:Quinolones / Q000494:pharmacology*; D012486:Salmonella typhimurium / Q000187:drug effects* / Q000502:physiology; D053719:Tandem Mass Spectrometry
chemical_list: D001426:Bacterial Proteins; D008070:Lipopolysaccharides; D015363:Quinolones
keywords: 2-DE; Antimicrobial resistance; LC–MS/MS; Quinolone; Salmonella Typhimurium DT104B; Subcellular proteomes