Ribosomal DNA-directed PCR for identification of Achromobacter (Alcaligenes) xylosoxidans recovered from sputum samples from cystic fibrosis patients

Abstract

The opportunistic human pathogen Achromobacter (Alcaligenes) xylosoxidans has been recovered with increasing frequency from respiratory tract culture of persons with cystic fibrosis (CF). However, confusion of this species with other closely related respiratory pathogens has limited studies to better elucidate its epidemiology, natural history, and pathogenic role in CF. Misidentification of A. xylosoxidans as Burkholderia cepacia complex is especially problematic and presents a challenge to effective infection control in CF. To address the problem of accurate identification of A. xylosoxidans, we developed a PCR assay based on a 16S ribosomal DNA sequence. In an analysis of 149 isolates that included 47 A. xylosoxidans and several related glucose-nonfermenting species recovered from CF sputum, the sensitivity and specificity of this PCR assay were determined to be 100 and 97%, respectively. The availability of this assay will enhance identification of A. xylosoxidans, thereby facilitating study of the pathogenic role of this species and improving infection control efforts in CF.

FIG. 1.

Phylogenetic tree (based on neighbor-joining method analysis of 16S rDNA sequences) of the genus Achromobacter and related species. Numbers in parentheses are GenBank accession numbers for 16S rDNA nucleotide sequences of strains included. Bar, 10% sequence dissimilarity.

FIG. 2.

PCR analysis of A. xylosoxidans and related species. Lanes: M, DNA marker; 1, A. xylosoxidans AU0665; 2, A. xylosoxidans AU1011; 3, A. xylosoxidans ATCC9220; 4, A. piechaudii LMG 1873^T; 5, A. ruhlandii LMG 1866^T; 6, A. denitrificans LMG 1231^T; 7, Alcaligenes faecalis LMG 1229^T; 8, Bordetella hinzii LMG 13501^T; 9, Bordetella pertussis LMG 14455^T; 10, Bordetella parapertussis LMG 14449^T; 11, Bordetella bronchiseptica LMG 1231^T; 12, Burkholderia cepacia genomovar III HI2147; 13, Pandoraea apista AU0003; 14, Pseudomonas aeruginosa AU0225.