PCR-based subtractive genome hybridization produced clones harboring inserts present in Brazilian purpuric fever (BPF) prototype strain F3031 but absent in noninvasive Haemophilus influenzae biogroup aegyptius isolate F1947. Some of these inserts have no matches in the GenBank database, while others are similar to genes encoding either known or hypothetical proteins. One insert represents a 2.3-kb locus with similarity to a Thermotoga maritima hypothetical protein, while another is part of a 7.6-kb locus that contains predicted genes encoding hypothetical, phage-related, and carotovoricin Er-like proteins. The presence of DNA related to these loci is variable among BPF isolates and nontypeable H. influenzae strains, while neither of them was detected in strains of types a to f. The data indicate that BPF-causing strain F3031 harbors unique chromosomal regions, most of which appear to be acquired from unrelated microbial sources.Haemophilus influenzae biogroup aegyptius was identified in the mid 1980s as the etiological agent of Brazilian purpuric fever (BPF), a frequently fatal invasive pediatric disease (6). Originally, a clone was isolated from patients with BPF in Sao Paulo State, Brazil (7). However, after outbreaks in other regions of Brazil (12, 34) and in Australia (19, 37) and a case of a child from Connecticut with an infection consistent with BPF (35), it is clear that a single H. influenzae biogroup aegyptius strain or clone is not the sole agent responsible for BPF. These observations led to the hypothesis that BPF-causing strains harbor DNA that is absent in noninvasive isolates, which may encode the factors that transformed a benign microorganism into an aggressive pathogen. This hypothesis was tested by using a genomewide approach based on PCR-based subtractive genome hybridization.Generation of a subtracted genomic library. We first addressed an important concern: both strains contain a 24-MDa plasmid (7). The significance of this is that differences in plasmid content between the F3031 and F1947 strains could result in misleading subtractive hybridization results. Restriction and Southern blot analyses (25) showed that the plasmids from F3031 and F1947 have similar AccI restriction profiles and cross hybridize, although they have some differences in their RsaI patterns (Fig. 1A and B). Nevertheless, the plasmid contents of these two strains are similar and should not affect the subtractive hybridization process.A library enriched in DNA unique to F3031 was made with the Clontech PCR-Select bacterial genome subtractive kit by using F3031 and F1947 total DNAs. After confirming that such a library was obtained, a secondary PCR with nested primers was conducted and the amplicons were cloned with a TA system (Invitrogen) and Escherichia coli DH5␣ or TOP10FЈ (Table 1) competent cells. Colony hybridization (25) with 32 Plabeled, RsaI-digested F1947 and F3031 genomic DNA showed that approximately 27% of the clones contained DNA unique to F3031, a value comparable to that described by the kit manufacture...