title: A PCR-based intergenic spacer region-capillary gel electrophoresis typing method for identification and subtyping of Nocardia species.
abstract: While 16S rRNA sequence-based identification of Nocardia species has become the gold standard, it is not without its limitations. We evaluated a novel approach encompassing the amplification of the Nocardia 16S-23S rRNA intergenic spacer (IGS) region followed by fragment analysis by capillary gel electrophoresis (CGE) of the amplified product for species identification of Nocardia. One hundred forty-five Nocardia isolates (19 species) and four non-Nocardia aerobic actinomycetes were studied. Reproducibility testing was performed in a subset (21%) of isolates. Ninety-five different electropherograms were identified, with heterogeneity within species being a general observation. Among common Nocardia species (e.g., Nocardia cyriacigeorgica, N. nova, N. farcinica), 2 or 3 dominant electropherogram subgroups were typical. While only a minority (8/19; 42%) of the different Nocardia species contained isolates displaying unique fragment sizes that were predictive of a particular species, virtually all isolates (142/145; 98%) could be assigned to the correct species using IGS-CGE typing based on the number and size of amplified fragments. The median number of fragments for each isolate was 2 (range, 1 to 5) with only a minority (17%) having a single fragment detected. The majority (93%) of amplified fragments were between 408 and 461 bp. The technique was also non-operator dependent, highly reproducible, and quicker and less expensive than 16S sequencing. In summary, PCR-based IGS-CGE typing is relatively simple, accurate, reproducible, and cost-effective and offers a potential alternative to 16S rRNA sequencing for identifying and subtyping Nocardia isolates.
authors.affiliation: Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, Westmead Hospital, NSW, Australia. mcwehrhahn@hotmail.com
authors.forename: M C
authors.initials: MC
authors.lastname: Wehrhahn
authors.forename: M
authors.initials: M
authors.lastname: Xiao
authors.forename: F
authors.initials: F
authors.lastname: Kong
authors.forename: Y-C
authors.initials: YC
authors.lastname: Xu
authors.forename: S C-A
authors.initials: SC
authors.lastname: Chen
mesh_terms: D003362:Cost-Benefit Analysis; D021903:DNA, Ribosomal Spacer / Q000235:genetics*; D019075:Electrophoresis, Capillary / Q000191:economics / Q000379:methods*; D006801:Humans; D058889:Molecular Typing / Q000191:economics / Q000379:methods*; D009615:Nocardia / Q000145:classification* / Q000235:genetics*; D016133:Polymerase Chain Reaction / Q000191:economics / Q000379:methods*; D015203:Reproducibility of Results
chemical_list: D021903:DNA, Ribosomal Spacer