We examined if multilocus sequence typing (MLST), a method for genotyping and species identification of Burkholderia cepacia complex bacteria, could be applied directly to cystic fibrosis sputum. The redesigned nested-PCR MLST format was successfully used to accurately identify strains in 23 sputum samples, of which 8 were culture negative.Burkholderia cepacia complex (BCC) organisms have the capacity to spread within populations of patients with cystic fibrosis (CF) and to cause serious epidemic outbreaks (6, 16). Strict infection control measures are therefore in place in many CF centers to prevent person-to-person transmission of the organisms. Correct identification of BCC organisms in clinical specimens is an essential prerequisite for implementing a successful infection control system. The 17 bacterial species that form the BCC taxonomic cluster today (9, 12, 13) can only be accurately distinguished from each other by applying molecular genetic methods. Although several protocols have been developed to discriminate individual species (4, 8, 10), multilocus sequence typing (MLST) has proven to be the only method which has kept pace with the increasing complexity of BCC species. By sequence analysis of seven housekeeping genes, MLST enables unequivocal identification of all established BCC species and also has the advantage of being able to define novel BCC groups (1, 3, 7). In addition, it can serve as a highly standardized genotyping method that provides robust information on strain type, by defining a sequence type (ST).There is great potential in DNA-based identification methods, as they provide the possibility to detect minute quantities of BCC bacteria directly in clinical specimens. We previously described a diagnostic nested recA PCR with excellent sensitivity (5) that enabled the detection of BCC bacteria in sputum, weeks to months before patients became culture positive. Such direct PCR testing narrowed the diagnostic window between the time of the initial BCC infection and laboratory diagnosis and had a great impact on implementing infection control in advance of what was routine with conventional microbiology.Using direct PCR analysis, several instances of samples that were BCC positive by PCR, but not by culture, were identified. Follow-up of such cases was rather limited, as the recA PCR we used (5) did not allow strain identification, and with no culture to examine, conventional typing methods were ineffective. Yet obtaining the strain type information for such patients is vital in understanding the epidemiology behind their infection with BCC bacteria. All gel pattern-based genotyping systems such as pulsed-field gel electrophoresis require pure bacterial cultures that were not available in the reproducibly PCR-positive, but culture-negative patients. Although MLST is also a typing method primarily designed to work from pure bacterial cultures, in principle since it is based on DNA and PCR amplification, its applicability to samples where bacteria are present in a small, noncultivable amount ...