Pulsed-field gel electrophoresis was used to determine genetic diversities of multiple nontypeable Haemophilus influenzae isolates from throat and ear specimens of eight children with otitis media. From five children, all ear and throat isolates were identical. The bacterial populations in these specimens showed less diversity than populations in throat isolates of healthy children.Nontypeable Haemophilus influenzae (NTHi) are gram-negative coccobacilli that naturally colonize the pharynges of humans, with carriage rates between 20 and 80% (1,6,8). In addition to colonizing asymptomatically, H. influenzae causes upper and lower respiratory tract infections, such as sinusitis, otitis media (OM), and bronchitis.OM is a common infection of the middle-ear space, experienced by 50 to 85% of children by 3 years of age (3,17). In children, between 30 and 52% of episodes have been attributed to infection with NTHi (4). Previous studies (9,11,13,19) examining single NTHi colonies from each specimen have shown that middle-ear isolates are both genotypically and phenotypically similar to throat isolates obtained from children with OM. Recent studies from our laboratory examining multiple NTHi colonies from each specimen suggest that throat isolates of healthy children attending day care are genetically very diverse; pulsed-field gel electrophoresis (PFGE) analysis found that between 37 and 43% of children were colonized by more than one strain of NTHi (5,16) and that the PFGE patterns of strains varied dramatically from week to week (16).The present study was designed to examine the genetic diversity of colonization and disease-causing NTHi isolates. Simultaneous pharyngeal and middle-ear specimens were collected from six children in Bardstown, KY, and from two children in Pittsburgh, PA, with acute OM; children P6, K8, and K21 had isolates obtained from both ears. A minimum of 5 and no more than 10 H. influenzae isolates were obtained from each specimen. All isolates were suspended in ϳ1 ml of sterile skim milk and stored at Ϫ80°C.Putative H. influenzae isolates were confirmed by growth on brain heart infusion agar (Difco, Detroit, MI) supplemented with X factor (hemin), V factor (NAD), or both (Sigma-Aldrich, St. Louis, MO); by porphyrin testing; and by an isolate's failure to hemolyze horse erythrocytes as determined using the methods of Kilian (12). In addition, each isolate was tested by colony blot analysis with the monoclonal antibody 7F3 for the presence of this epitope of P6 surface antigen (14) and by DNA dot blot hybridization for the immunoglobulin A1 protease gene to distinguish suspected H. influenzae isolates from nonhemolytic Haemophilus haemolyticus (7, 12). All isolates in this study bound to the 7F3 antibody and hybridized with the iga probe, indicating that they are H. influenzae.To examine genetic diversity, all study isolates were characterized by PFGE as previously described (15, 16). The PFGE patterns were first analyzed visually using the criteria of Tenover et al. (18) to determine band differenc...