Fifty-five epidemiologically linked Aspergillus fumigatus isolates obtained from six nosocomial outbreaks of invasive aspergillosis were subtyped by sequencing the polymorphic region of the gene encoding a putative cell surface protein, Afu3g08990 (denoted as CSP). Comparative sequence analysis showed that genetic diversity was generated in the coding region of this gene by both tandem repeats and point mutations. Each unique sequence in an outbreak cluster was assigned an arbitrary number or CSP sequence type. The CSP typing method was able to identify "clonal" and genotypically distinct A. fumigatus isolates, and the results of this method were concordant with those of another discriminatory genotyping technique, the Afut1 restriction fragment length polymorphism typing method. The novel single-locus sequence typing (CSP typing) strategy appears to be a simple, rapid, discriminatory tool that can be readily shared across laboratories. In addition, we found that A. fumigatus isolates substructured into multiple clades; interestingly, one clade consisted of isolates predominantly representing invasive clinical isolates recovered from cardiac transplant patients from two different outbreak situations. We also found that the A. fumigatus isolate Af293, whose genome has been sequenced, possesses a CSP gene structure that is substantially different from those of the other A. fumigatus strains studied here, highlighting the need for further taxonomic study.Conidia of Aspergillus fumigatus become airborne easily, and subsequent inhalation of these infectious particles is believed to be the route of transmission for invasive aspergillosis. Accordingly, several nosocomial outbreaks of invasive aspergillosis have been reported with strong evidence suggesting that such infections are acquired from the environment of the hospital (10,31,35,43). The Centers for Disease Control and Prevention (CDC) recommends that in the setting of a nosocomial aspergillosis outbreak and in the presence of continuing evidence of Aspergillus infection in the hospital population, an environmental assessment should be undertaken to determine and eliminate the source of infection (51). In such nosocomial outbreak investigations, Aspergillus strain typing methods can indicate the source and/or route of infection by determining whether epidemiologically related isolates are also genetically related. Once the source is identified, corrective measures can then be undertaken to eliminate the implicated source to contain the infection. Several molecular methods have been evaluated for A. fumigatus strain typing, and these methods include randomly amplified polymorphic DNA typing (1), sequence-specific DNA primer analysis (32), polymorphic microsatellite markers (6,7,12), and analysis of hybridization profiles with a dispersed, repetitive DNA probe Afut1 (Afut1 restriction fragment length polymorphism [Afut1 RFLP]) (11,36). Although a combination of typing methods appears to have more utility in strain typing, polymorphic microsatellite markers, and Af...