title: Assessing genetic diversity in plasmids from Escherichia coli and Salmonella enterica using a mixed-plasmid microarray.
abstract: OBJECTIVE
  To compare genetic composition of plasmids using microarrays composed of randomly selected fragments of plasmid DNA.
  
  
  RESULTS
  Separate shotgun libraries were constructed from plasmid DNA pooled from Escherichia coli and Salmonella enterica. Cloned fragments were used as probes for microarrays. Plasmid targets were labelled, hybridized overnight, and bound targets were imaged after enzymatic signal amplification. Control hybridizations demonstrated significantly higher signal when probes and targets shared >95% sequence identity. Diagnostic sensitivity and specificity of the assay was 95 and 99%, respectively. Cluster analysis showed close matches for replicate experiments with a high correlation between replicates (r = 0.91) compared with the correlation for nonreplicates (r = 0.09). Analysis of hybridization data from 43 plasmids generated five distinct clusters, two for known serovar-specific plasmids, one for enterohemorrhagic E. coli plasmids, and two for plasmids harboring a recently disseminated antibiotic resistance gene (bla(CMY-2)).
  
  
  CONCLUSIONS
  Mixed-plasmid microarrays are suitable for comparing genetic content of wild-type plasmids and hybridization results from this study suggest several novel hypotheses about plasmid gene exchange between E. coli and S. enterica.
  
  
  CONCLUSIONS
  Mixed-plasmid microarrays permit rapid, low cost analysis and comparison of many plasmids. This ability is critical to understanding the source, fate, and transport of plasmids amongst commensal and pathogenic bacteria.
authors.affiliation: Department of Veterinary Microbiology and Pathology, Washington State University, WA 99164-7040, USA. drcall@wsu.edu
authors.forename: D R
authors.initials: DR
authors.lastname: Call
authors.forename: M-S
authors.initials: MS
authors.lastname: Kang
authors.forename: J
authors.initials: J
authors.lastname: Daniels
authors.forename: T E
authors.initials: TE
authors.lastname: Besser
mesh_terms: D044822:Biodiversity; D018550:Cephalosporin Resistance / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics*; D015723:Gene Library; D005798:Genes, Bacterial / Q000235:genetics; D009693:Nucleic Acid Hybridization / Q000379:methods; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D010957:Plasmids / Q000235:genetics*; D015203:Reproducibility of Results; D019779:Salmonella enterica / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods; D001618:beta-Lactamases / Q000235:genetics
chemical_list: D004269:DNA, Bacterial; C103022:beta-lactamase CMY-2; D001618:beta-Lactamases