title: Utility of 16S rDNA Sequencing for Identification of Rare Pathogenic Bacteria.
abstract: BACKGROUND
  Phenotypic identification systems are established methods for laboratory identification of bacteria causing human infections. Here, the utility of phenotypic identification systems was compared against 16S rDNA identification method on clinical isolates obtained during a 5-year study period, with special emphasis on isolates that gave unsatisfactory identification.
  
  
  METHODS
  One hundred and eighty-seven clinical bacteria isolates were tested with commercial phenotypic identification systems and 16S rDNA sequencing. Isolate identities determined using phenotypic identification systems and 16S rDNA sequencing were compared for similarity at genus and species level, with 16S rDNA sequencing as the reference method.
  
  
  RESULTS
  Phenotypic identification systems identified ~46% (86/187) of the isolates with identity similar to that identified using 16S rDNA sequencing. Approximately 39% (73/187) and ~15% (28/187) of the isolates showed different genus identity and could not be identified using the phenotypic identification systems, respectively. Both methods succeeded in determining the species identities of 55 isolates; however, only ~69% (38/55) of the isolates matched at species level. 16S rDNA sequencing could not determine the species of ~20% (37/187) of the isolates.
  
  
  CONCLUSIONS
  The 16S rDNA sequencing is a useful method over the phenotypic identification systems for the identification of rare and difficult to identify bacteria species. The 16S rDNA sequencing method, however, does have limitation for species-level identification of some bacteria highlighting the need for better bacterial pathogen identification tools.
authors.affiliation: Tropical Infectious Diseases Research & Education Centre (TIDREC), Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.
authors.forename: Shih Keng
authors.initials: SK
authors.lastname: Loong
authors.affiliation: Tropical Infectious Diseases Research & Education Centre (TIDREC), Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.
authors.forename: Chee Sieng
authors.initials: CS
authors.lastname: Khor
authors.affiliation: Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.
authors.forename: Faizatul Lela
authors.initials: FL
authors.lastname: Jafar
authors.affiliation: Tropical Infectious Diseases Research & Education Centre (TIDREC), Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia. sazaly@um.edu.my.|Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia. sazaly@um.edu.my.
authors.forename: Sazaly
authors.initials: S
authors.lastname: AbuBakar
mesh_terms: D000818:Animals; D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification / Q000472:pathogenicity; D015373:Bacterial Typing Techniques / Q000379:methods; D004269:DNA, Bacterial / Q000235:genetics*; D004275:DNA, Ribosomal / Q000235:genetics*; D006801:Humans; D012189:Retrospective Studies
chemical_list: D004269:DNA, Bacterial; D004275:DNA, Ribosomal
keywords: 16S rDNA; Malaysia; infectious disease; pathogenic bacteria