title: Identification of coagulase-negative staphylococci isolated from continuous ambulatory peritoneal dialysis fluid using 16S ribosomal RNA, tuf, and SodA gene sequencing.
abstract: BACKGROUND
  Coagulase-negative staphylococcus (CoNS) is the most common pathogen in continuous ambulatory peritoneal dialysis (CAPD)-associated peritonitis. There is no well-organized, standardized database for CoNS, and few studies have used gene sequencing in reporting species distribution in CAPD peritonitis. In the present study, we used 3 housekeeping genes to evaluate the prevalence of CoNS isolated from CAPD peritonitis episodes and to estimate the accuracy of, and the characteristic differences between, these genes for species identification.
  
  
  METHODS
  All 51 non-duplicated CoNS isolates obtained from CAPD peritonitis between April 2006 and May 2008 were used. The strains were identified by polymerase chain reaction and by direct sequencing using the 16S ribosomal RNA (rRNA), tuf, and sodA genes. We determined species distribution, and using selected databases, we analyzed the characteristics and diagnostic utility of the individual genes for species identification.
  
  
  RESULTS
  In GenBank (National Institutes of Health, Bethesda, MD, USA), we found 49 type or reference strains for CoNS 16S rRNA, 17 for tuf, and 46 for sodA, and we used those data for sequence-similarity comparisons with CAPD isolates. Among our 51 strains, S. epidermidis (66.7%) was the most common, followed by S. haemolyticus (11.8%), S. warneri (7.8%), S. caprae (5.9%), S. capitis (3.9%), and S. pasteuri (2.0%). For 1 strain, different species results were obtained with each gene. The identification rates with 16S rRNA, sodA, and tuf gene sequencing were 84.0%, 96.0%, and 92.2% respectively. The discrimination capability of 16S rRNA gene was lower in a few individual species, and for the sodA gene, the percentage similarity to sequences from reference strains was also lower. The tuf gene had excellent identification capacity, but relatively few type strains are available in public databases. The 16S rRNA gene did not discriminate between S. caprae and S. capitis. The sodA gene showed a similarity rate that was lower than that for sequences of the 16S rRNA gene. The tuf type strain sequences for S. caprae and S. pasteuri are not available in public databases.
  
  
  CONCLUSIONS
  The sodA, tuf, and 16S rRNA genes were very useful for CoNS identification. Each has its own characteristics of similarity, discriminative power, and inclusion in databases.
authors: Laboratory Medicine, Inje University College of Medicine, Busan, Republic of Korea.
authors: Jeong Hwan
authors: JH
authors: Shin
authors: Si Hyun
authors: SH
authors: Kim
authors: Haeng Soon
authors: HS
authors: Jeong
authors: Seung Hwan
authors: SH
authors: Oh
authors: Hye Ran
authors: HR
authors: Kim
authors: Jeong Nyeo
authors: JN
authors: Lee
authors: Young Chul
authors: YC
authors: Yoon
authors: Yang Wook
authors: YW
authors: Kim
authors: Yeong Hoon
authors: YH
authors: Kim
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics*; D015314:Dialysis Solutions; D006801:Humans; D010444:Peptide Elongation Factor Tu / Q000235:genetics*; D010531:Peritoneal Dialysis, Continuous Ambulatory; D010538:Peritonitis / Q000382:microbiology*; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D015203:Reproducibility of Results; D017421:Sequence Analysis; D013210:Staphylococcus / Q000235:genetics* / Q000302:isolation & purification*; D013482:Superoxide Dismutase / Q000235:genetics*
chemical_list: D001426:Bacterial Proteins; D015314:Dialysis Solutions; D012336:RNA, Ribosomal, 16S; C095500:SodA protein, Bacteria; D013482:Superoxide Dismutase; D010444:Peptide Elongation Factor Tu