title: Application of gene sequencing directly to identify the pathogens in specimens.
abstract: BACKGROUND
  Accurate identification of bacterial isolates is an essential task in clinical microbiology. This study compared culturing to analyzing 16S rRNA gene sequences as methods to identify bacteria in clinical samples. We developed a key technique to directly identify bacteria in clinical samples via nucleic acid sequences, thus improving the ability to confirm pathogens.
  
  
  METHODS
  We obtained 225 samples from Beijing Tongren Hospital and examined them by conventional culture and 16S rDNA sequencing to identify pathogens. This study made use of a modified sample pre-treatment technique which came from our laboratory to extract DNA. 16S rDNA was amplified by PCR. The amplified product was sequenced on a CEQ8000 capillary sequencer. Sequences were uploaded to the GenBank BLAST database for comparison.
  
  
  RESULTS
  Among the positively cultivated bacterial strains, seven strains were identified differently by Vitek32 and by 16S rDNA sequencing. Twelve samples that were negative by standard culturing were determined to have pathogens by sequence analysis.
  
  
  CONCLUSIONS
  The use of 16S rRNA gene sequencing can improve clinical microbiology by providing better identification of unidentified bacteria or providing reference identification of unusual strains.
authors.affiliation: Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China. luxinxin2009@126.com
authors.forename: Xin-Xin
authors.initials: XX
authors.lastname: Lu
authors.forename: Liang
authors.initials: L
authors.lastname: Yuan
authors.forename: Xiao-Hua
authors.initials: XH
authors.lastname: Wan
authors.forename: Jia-Jing
authors.initials: JJ
authors.lastname: Geng
mesh_terms: D001419:Bacteria / Q000302:isolation & purification*; D004275:DNA, Ribosomal / Q000737:chemistry*; D006801:Humans; D016133:Polymerase Chain Reaction; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S