title: Direct identification of Gram-positive bacteria and resistance determinants from blood cultures using a microarray-based nucleic acid assay: in-depth analysis of microarray data for undetermined results.
abstract: BACKGROUND
  The Verigene Gram-Positive Blood Culture (BC-GP) nucleic acid assay (Nanosphere, Inc., Northbrook, IL, USA) is a newly developed microarray-based test with which 12 Gram-positive bacterial genes and three resistance determinants can be detected using blood culture broths. We evaluated the performance of this assay and investigated the signal characteristics of the microarray images.
  
  
  METHODS
  At the evaluation stage, we tested 80 blood cultures that were positive for various bacteria (68 bacteria covered and 12 not covered by the BC-GP panel) collected from the blood of 36 patients and 44 spiked samples. In instances where the automated system failed and errors were called, we manually inspected microarray images, measured the signal intensities of target spots, and reclassified the results.
  
  
  RESULTS
  With the manual analysis of the microarray images of 14 samples for which error calls were reported, we could obtain correct identification results for 12 samples without the need for retesting, because strong signals in the target spots were clearly discriminable from background noise. With our interpretation strategy, we could obtain 97.1% sensitivity and 100% specificity for bacterial identification by using the BC-GP assay. The two unidentified bacteria were viridans group streptococci, which produced weaker target signals. During the application stage, among 25 consecutive samples positive for Gram-positive bacteria, we identified two specimens with error calls as Streptococcus spp. by using manual analysis.
  
  
  CONCLUSIONS
  With help of the manual review of the microarray images, the BC-GP assay could successfully identify species and resistance markers for many clinically important Gram-positive bacteria.
authors.forename: Seon Young
authors.initials: SY
authors.lastname: Kim
authors.forename: Yun Ji
authors.initials: YJ
authors.lastname: Hong
authors.forename: Sang Mee
authors.initials: SM
authors.lastname: Hwang
authors.forename: Taek Soo
authors.initials: TS
authors.lastname: Kim
authors.forename: Jae-Seok
authors.initials: JS
authors.lastname: Kim
authors.forename: Kyoung Un
authors.initials: KU
authors.lastname: Park
authors.forename: Junghan
authors.initials: J
authors.lastname: Song
authors.forename: Eui-Chong
authors.initials: EC
authors.lastname: Kim
mesh_terms: D000900:Anti-Bacterial Agents / Q000494:pharmacology; D016470:Bacteremia / Q000097:blood / Q000382:microbiology*; D046508:Culture Techniques / Q000379:methods*; D004269:DNA, Bacterial / Q000032:analysis*; D024881:Drug Resistance, Bacterial; D006094:Gram-Positive Bacteria / Q000187:drug effects / Q000302:isolation & purification*; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012329:RNA, Bacterial / Q000032:analysis*
chemical_list: D000900:Anti-Bacterial Agents; D004269:DNA, Bacterial; D012329:RNA, Bacterial