TABLE 2.
Phylogenetic groups differ in distribution of genetic islands
| Locus or biotypea | No. of strains positive/no. examined (% positive), P valueb
|
||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| All strains | Clade 1 | Clade 2 | Clade 3 | Clade 6 | Clade 8 | Clade 9 | Clade 10 | Clade 11 | Clade 12 | Clade 13 | eBURST group 2 | No group | |
| hmw | 121/206 (58.7) | 8/8 (100) | 0/8, 0.0054 | 2/3 (66.7) | 1/5 (83.3) | 7/7 (100) | 10/13 (76.9) | 2/4 (50) | 0/22, 4.8 × 10−9 | 2/9 (22.2) | 22/35 (62.9) | 51/57 (89.5), 9.6 × 10−8 | 16/34 (47.0) |
| LPS biosynthetic locus (infA/ksgA) | |||||||||||||
| lic2BCc | 104/201 (51.7) | 0/7 | 6/8 (75) | 3/3 (100) | 5/5 (100) | 7/7 (100) | 5/13 (38.5) | 1/4 (25) | 0/21 | 1/9 (11.1) | 31/35 (88.6), 1.2 × 10−6 | 23/55 (41.8) | 22/34 (64.7) |
| losAB | 35/201 (17.4) | 7/7 (100), 2.2 × 10−5 | 0/8 | 0/3 | 0/5 | 0/7 | 7/13 (53.8), 0.016 | 0/4 | 0/21 | 0/9 | 2/35 (5.7) | 12/55 (21.8) | 7/34 (20.6) |
| No insert | 62/201 (30.8) | 0/7 | 2/8 (25) | 0/3 | 0/5 | 0/7 | 1/13 (7.7) | 3/4 (75) | 21/21 (100), 8 × 10−12 | 8/9 (88.9), 0.032 | 2/35 (5.7) | 20/55 (36.4) | 5/34 (14.7) |
| Biotype | |||||||||||||
| I | 30/208 (14.4) | 0/7 | 7/12 (62.5), 0.0025 | 1/2 (50) | 3/4 (75), 0.079 | 0/7 | 1/11 (9.1) | 2/4 (50) | 0/15 | 0/10 | 8/37 (21.6) | 2/49 (4.1) | 6/41 (14.6) |
| II | 92/208 (44.2) | 0/7 | 2/12 (16.7) | 0/2 (50) | 1/4 (25) | 7/7 (100), 0.023 | 0/11 | 2/4 (50) | 0/15 | 10/10 (100), 0.0016 | 4/37 (10.8) | 44/49 (89.6), 3.8 × 10−13 | 22/41 (53.6) |
| III | 61/208 (29.3) | 7/7 (100), 0.0011 | 2/12 (16.7) | 1/2 (50) | 0/4 | 0/7 | 8/11 (72.7), 0.022 | 0/4 | 0/15 | 0/10 | 21/37 (56.8), 0.0009 | 3/49 (6.1) | 10/41 (14.4) |
| IV | 6/208 (2.9) | 0/7 | 1/12 (8.3) | 0/2 | 0/4 | 0/7 | 2/11 (18.2) | 0/4 | 0/15 | 0/10 | 2/37 (5.4) | 0/49 | 1/41 (2.4) |
| V | 19/208 (9.1) | 0/7 | 0/12 | 0/2 | 0/4 | 0/7 | 15/15 (100), 1.1 × 10−18 | 0/10 | 2/37 (5.4) | 0/49 | 2/41 (4.9) | ||
The hmw and LPS biosynthetic loci were evaluated by PCR as described in the text,and biotypes were determined biochemically. Included are data for 52 strains described previously (11). The LPS biosynthetic locus is the locus flanked by infA and ksgA, containing lic2BC, losAB, or no genes. Biotype data include data reported to the MLST database by others (n = 45) as well as biotypes determined by ourselves (n = 163). Biotypes: I, positive for indole production, urease, and ornithine decarboxylase reactions; II, negative for ornithine decarboxylase only; III, positive for urease only; IV, negative for indole only; V, negative for urease only (30). No biotype VI, VII, or VIII strains were identified.
Clade 4 strains were not examined in the laboratory in this study. All clade 4 NTHI strains are H. influenzae biogroup aegyptius and are biotype III (31). Clades 5 and 7 are also omitted from this table, as they do not contain any NTHI strains. No group, NTHI strains with ST that are not in any of the 13 clades and not in eBURST group 2. For each of the eight phylogenetic groups for which five or more strains were studied, the frequency of the genotype (or biotype) among strains in each group was compared to the frequency in the remaining population using the Fisher exact test (two tailed). The resulting P value was multiplied by eight to apply the Bonferroni adjustment for multiple hypotheses on a set of data (42). P values of <0.10 are reported.
Strains listed as containing lic2BC include five strains that contain lic2C only. One of these is in eBURST group 2 (ST258); the others are not in any of the phylogenetic groups (two strains in ST2 and one each in ST162 and ST316).