Identification of Pandoraea species by 16S ribosomal DNA-based PCR assays

Abstract

The recently described genus Pandoraea contains five named species (Pandoraea apista, Pandoraea pulmonicola, Pandoraea pnomenusa, Pandoraea sputorum, and Pandoraea norimbergensis) and four unnamed genomospecies. Pandoraea spp. have mainly been recovered from the respiratory tracts of cystic fibrosis (CF) patients. Accurate genus- and species-level identification by routine clinical microbiology methods is difficult, and differentiation from Burkholderia cepacia complex organisms may be especially problematic. This can have important consequences for the management of CF patients. On the basis of 16S ribosomal DNA sequences, PCR assays for the identification of Pandoraea spp. were developed. A first PCR assay was developed for the identification of Pandoraea isolates to the genus level. PCR assays for the identification of P. apista and P. pulmonicola as a group, P. pnomenusa, P. sputorum, and P. norimbergensis were also developed. All five assays were evaluated with a panel of 123 bacterial isolates that included 69 Pandoraea sp. strains, 24 B. cepacia complex strains, 6 Burkholderia gladioli strains, 9 Ralstonia sp. strains, 5 Alcaligenes xylosoxidans strains, 5 Stenotrophomonas maltophilia strains, and 5 Pseudomonas aeruginosa strains. The use of these PCR assays facilitates the identification of Pandoraea spp. and avoids the misidentification of a Pandoraea sp. as a B. cepacia complex isolate.

FIG. 1

PCR analysis of Pandoraea sp. type strains and other isolates with primer pairs panF-panR (A), appuF-panR (B), spuF-spuR (C), pnoF-pnoR (D), and norF-norR (E). Lanes: M, 100-bp DNA ladder (Gibco BRL); 1, P. apista LMG 16407^T; 2, P. norimbergensis LMG 18379^T; 3, P. pulmonicola LMG 18106^T; 4, P. pnomenusa LMG 18087^T; 5, P. sputorum LMG 18819^T; 6, B. cepacia genomovar I LMG 1222^T; 7, B. cepacia genomovar III HI2711; 8, B. gladioli AU1750; 9, R. gilardii LMG 5886^T; 10, R. paucula LMG 3244^T; 11, P. aeruginosa AU0225; 12, S. maltophilia AU0026; 13, A. xylosoxidans AU2116.