title: The impact of primer sets on detection of the gene encoding biofilm-associated protein (Bap) in Acinetobacter baumannii: in silico and in vitro analysis.
abstract: The Acinetobacter baumannii virulence protein Bap is encoded by a large gene and contains both variable sequence and repetitive modules. To date, four primer sets targeting different regions of bap have been designed, but no study has evaluated all these primers simultaneously for detection of bap. Here, we assessed the effect of primer sets Bap I-IV, on detection of bap both in silico and in vitro. Using the primer set Bap II, all 143 tested strains yielded an amplicon corresponding to the bap gene. This primer set showed the highest sensitivity (100, 95% CI: 97·9-100%) compared to the other primer sets. This study demonstrates that primer set Bap II performs with optimal efficiency for detection of the bap gene among different strains.
  
  
  CONCLUSIONS
  This study investigated the effect of nucleotide variation on PCR detection of the bap gene in various Acinetobacter baumannii strains. Since bap is the target gene for many detection assays, this variation can affect the detection efficiency. Here we present a primer set Bap II with optimal detection efficiency amongst 143 different strains, as shown by in silico and in vitro evidence.
authors.affiliation: Division of Microbiology, Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
authors.forename: M
authors.initials: M
authors.lastname: Kodori
authors.affiliation: Division of Microbiology, Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.|Food Microbiology Research Center, Tehran University of Medical Sciences, Tehran, Iran.
authors.forename: M
authors.initials: M
authors.lastname: Douraghi
authors.affiliation: Department of Epidemiology and Biostatistics, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
authors.forename: M
authors.initials: M
authors.lastname: Yaseri
authors.affiliation: Department of Microbiology, Reference Health Laboratories, Ministry of Health, Tehran, Iran.
authors.forename: M
authors.initials: M
authors.lastname: Rahbar
mesh_terms: D000151:Acinetobacter Infections / Q000382:microbiology*; D040981:Acinetobacter baumannii / Q000235:genetics* / Q000502:physiology; D001426:Bacterial Proteins / Q000235:genetics; D018441:Biofilms; D017931:DNA Primers / Q000235:genetics*; D006801:Humans; D007492:Iran; D016133:Polymerase Chain Reaction; D012680:Sensitivity and Specificity; D037521:Virulence Factors / Q000235:genetics*
chemical_list: D001426:Bacterial Proteins; D017931:DNA Primers; D037521:Virulence Factors
keywords: 
  Acinetobacter baumannii
  ; biofilm-associated protein (bap) gene; nucleotide variation; primer sets; repetitive sequence