Identification by subtractive hybridization of a novel insertion element specific for two widespread Burkholderia cepacia genomovar III strains

Abstract

Species of the Burkholderia cepacia complex cause chronic and life-threatening infections in persons with cystic fibrosis. Epidemic strains infect multiple patients, reside primarily in genomovar III, and have an apparent enhanced capacity for human infection and/or interpatient transmission. By using subtractive hybridization, a novel insertion element, designated IS1363, was identified in epidemic strain PHDC, known to infect many cystic fibrosis patients in the mid-Atlantic region of the United States. IS1363 was also found in most isolates of the ET12 lineage, responsible for infecting large numbers of patients in Ontario, Canada, and the United Kingdom. Southern blot analysis demonstrated that whereas multiple copies of IS1363 were present in strain PHDC, only one copy was present in ET12 isolates. IS1363 was used to probe a collection of 943 B. cepacia complex isolates, representing all nine genomovars, recovered from 761 cystic fibrosis patients or the natural environment. IS1363 was not found in other genomovar III strains and, with the exception of B. ambifaria, was absent from other B. cepacia complex species. Genotyping analyses of all IS1363-positive isolates demonstrated that strain PHDC was more widely distributed in the United States than previously appreciated; 212 cystic fibrosis patients in 24 states were identified as being infected with PHDC.

FIG. 1.

Schematic map and partial nucleotide sequence of IS1363. Sequences of perfect terminal inverted repeats (TIR) and additional inverted repeats (IR1 and IR2) are underlined with arrowheads. The putative ribosome-binding site (RB) is in bold. Potential −35 promoter regions in the terminal inverted repeats (oriented outward from the IS element) are indicated with overlining.

FIG. 2.

Distribution of strain PHDC. Shaded U.S. states are those in which at least one cystic fibrosis patient infected with strain PHDC receives care. PHDC-infected patients also received care in Alaska and the District of Columbia (not depicted).