title: Analysis of sequence variation among smeDEF multi drug efflux pump genes and flanking DNA from defined 16S rRNA subgroups of clinical Stenotrophomonas maltophilia isolates.
abstract: OBJECTIVE
  To determine the level of variation in the smeDEF efflux pump and smeT transcriptional regulator genes among three defined 16S rRNA sequence subgroups of clinical Stenotrophomonas maltophilia isolates.
  
  
  METHODS
  smeDEF sequencing used a PCR genome walking approach. Determination of the sequence surrounding smeDEF used a flanking primer PCR method and specific primers anchored in smeD or smeF together with random primers.
  
  
  RESULTS
  smeDEF is chromosomal and located in the same position in the chromosome in all three subgroups of isolates. Flanking smeD is a gene, smeT, encoding a putative transcriptional repressor for smeDEF. Variation at these loci among the isolates is considerably lower (up to 10%) than at intrinsic beta-lactamase loci (up to 30%) in the same isolates, implying greater functional constraint. The smeD-smeT intergenic region contains a highly conserved section, which maps with previously predicted promoter/operator regions, and a hypervariable untranslated region, which can be used to subgroup clinical isolates.
  
  
  CONCLUSIONS
  These data provide further evidence that it is possible to group clinical isolates of the inherently variable species, S. maltophilia, based on genotypic properties. Isolate D457, in which most work concerning smeDEF expression has been performed, does not fall into S. maltophilia subgroup A, which is the most typical.
authors.affiliation: Bristol Centre for Antimicrobial Research and Evaluation, Department of Pathology & Microbiology, University of Bristol, School of Medical Sciences, University Walk, Bristol, BS8 1TD, UK.
authors.forename: Virginia C
authors.initials: VC
authors.lastname: Gould
authors.forename: Aki
authors.initials: A
authors.lastname: Okazaki
authors.forename: Robin A
authors.initials: RA
authors.lastname: Howe
authors.forename: Matthew B
authors.initials: MB
authors.lastname: Avison
mesh_terms: D001483:Base Sequence; D001693:Biological Transport, Active; D017931:DNA Primers; D004269:DNA, Bacterial / Q000235:genetics*; D024901:Drug Resistance, Multiple, Bacterial / Q000235:genetics*; D016905:Gram-Negative Bacterial Infections / Q000382:microbiology*; D006801:Humans; D026901:Membrane Transport Proteins / Q000235:genetics*; D008969:Molecular Sequence Data; D012329:RNA, Bacterial / Q000096:biosynthesis* / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000096:biosynthesis* / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction; D020615:Stenotrophomonas maltophilia / Q000187:drug effects* / Q000235:genetics*; D001618:beta-Lactamases / Q000235:genetics
chemical_list: D017931:DNA Primers; D004269:DNA, Bacterial; D026901:Membrane Transport Proteins; D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S; D001618:beta-Lactamases