title: Multiple adaptive routes of Salmonella enterica Typhimurium to biocide and antibiotic exposure.
abstract: Biocides and antibiotics are used to eradicate or prevent the growth of microbial species on surfaces (occasionally on catheters), or infected sites, either in combination or sequentially, raising concerns about the development of co-resistance to both antimicrobial types. The effect of such compounds on Salmonella enterica, a major food-borne and zoonotic pathogen, has been analysed in different studies, but only few works evaluated its biological cost, and the overall effects at the genomic and transcriptomic levels associated with diverse phenotypes resulting from biocide exposure, which was the aim of this work.
  
  
  
  Exposure to triclosan, clorhexidine, benzalkonium, (but not to hypochlorite) resulted in mutants with different phenotypes to a wide range of antimicrobials even unrelated to the selective agent. Most biocide-resistant mutants showed increased susceptibility to compounds acting on the cell wall (β-lactams) or the cell membranes (poly-L-lysine, polymyxin B, colistin or toxic anions). Mutations (SNPs) were found in three intergenic regions and nine genes, which have a role in energy production, amino acids, carbohydrates or lipids metabolism, some of them involved in membrane transport and pathogenicity. Comparative transcriptomics of biocide-resistant mutants showed over-expression of genes encoding efflux pumps (sugE), ribosomal and transcription-related proteins, cold-shock response (cpeE) and enzymes of microaerobic metabolism including those of the phosphotransferase system. Mainly ribosomal, metabolic and pathogenicity-related genes had affected expression in both in vitro-selected biocide mutants and field Salmonella isolates with reduced biocide susceptibility.
  
  
  
  Multiple pathways can be involved in the adaptation of Salmonella to biocides, mainly related with global stress, or involving metabolic and membrane alterations, and eventually causing "collateral sensitivity" to other antimicrobials. These changes might impact the bacterial-environment interaction, imposing significant bacterial fitness costs which may reduce the chances of fixation and spread of biocide resistant mutants.
authors.affiliation: Servicio de Microbiología, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain. taniacuri@gmail.com.|CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain. taniacuri@gmail.com.
authors.forename: Tânia
authors.initials: T
authors.lastname: Curiao
authors.affiliation: Department of Agrifood Production and Environmental Sciences, University of Florence, Firenze, Italy.
authors.forename: Emmanuela
authors.initials: E
authors.lastname: Marchi
authors.affiliation: Neuroinfection Laboratory, Institute for Infectious Diseases, Bern, Switzerland.
authors.forename: Denis
authors.initials: D
authors.lastname: Grandgirard
authors.affiliation: Servicio de Microbiología, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain.|CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain.
authors.forename: Ricardo
authors.initials: R
authors.lastname: León-Sampedro
authors.affiliation: Department of Agrifood Production and Environmental Sciences, University of Florence, Firenze, Italy.
authors.forename: Carlo
authors.initials: C
authors.lastname: Viti
authors.affiliation: Neuroinfection Laboratory, Institute for Infectious Diseases, Bern, Switzerland.
authors.forename: Stephen L
authors.initials: SL
authors.lastname: Leib
authors.affiliation: Servicio de Microbiología, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain.|CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain.|Unidad de Resistencia a Antibióticos y Virulencia bacteriana asociada al Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain.
authors.forename: Fernando
authors.initials: F
authors.lastname: Baquero
authors.affiliation: University of Leicester, Leicester, UK.
authors.forename: Marco R
authors.initials: MR
authors.lastname: Oggioni
authors.affiliation: Unidad de Resistencia a Antibióticos y Virulencia bacteriana asociada al Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain.|Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología (CSIC), Darwin 3, Cantoblanco, Madrid, 28049, Spain.
authors.forename: José Luis
authors.initials: JL
authors.lastname: Martinez
authors.affiliation: Servicio de Microbiología, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain. teresacoque@gmail.com.|CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain. teresacoque@gmail.com.|Unidad de Resistencia a Antibióticos y Virulencia bacteriana asociada al Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain. teresacoque@gmail.com.
authors.forename: Teresa M
authors.initials: TM
authors.lastname: Coque
mesh_terms: D000220:Adaptation, Biological; D000900:Anti-Bacterial Agents / Q000494:pharmacology*; D016000:Cluster Analysis; D004202:Disinfectants / Q000494:pharmacology*; D024881:Drug Resistance, Bacterial; D020869:Gene Expression Profiling; D005798:Genes, Bacterial; D056084:Genetic Fitness; D016680:Genome, Bacterial; D059014:High-Throughput Nucleotide Sequencing; D008826:Microbial Sensitivity Tests; D009154:Mutation; D012486:Salmonella typhimurium / Q000187:drug effects* / Q000502:physiology*
chemical_list: D000900:Anti-Bacterial Agents; D004202:Disinfectants
keywords: Antimicrobial susceptibility; Biocide resistance; Collateral sensitivity; Transcriptomics; WGS