TABLE 3.
Prevalences of marker alleles
| Presence/allele (accession no. or strain) | Code no. | Prevalences for isolates by type: |
|||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Total |
Human, Germany |
Human, Trinidad and Tobago |
Veterinary, Germany |
Human, invasive infection |
Human, localized infection |
Human, carriage |
|||||||||
| No. | % | No. | % | No. | % | No. | % | No. | % | No. | % | No. | % | ||
| bac negative | B-0 | 384 | 85,7 | 327 | 85.2 | 34 | 100.0 | 16 | 76.2 | 100 | 87.0 | 42 | 87.5 | 219 | 85.9 |
| bac positive | B-1 | 64 | 14.3 | 57 | 14.8 | 0 | 0.0 | 5 | 23.8 | 15 | 13.0 | 6 | 12.5 | 36 | 14.1 |
| alp negative | A-0 | 3 | 0.7 | 2 | 0.5 | 0 | 0.0 | 1 | 4.8 | 1 | 0.9 | 1 | 2.1 | 0 | 0.0 |
| alp-2 | A-2 | 25 | 5.6 | 23 | 6.0 | 0 | 0.0 | 1 | 4.8 | 4 | 3.5 | 9 | 18.8 | 10 | 3.9 |
| alp-3 | A-3 | 67 | 15.0 | 61 | 15.9 | 2 | 5.9 | 3 | 14.3 | 19 | 16.5 | 9 | 18.8 | 35 | 13.7 |
| alp-4 | A-4 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 |
| alp-5 | A-5 | 86 | 19.2 | 70 | 18.2 | 3 | 8.8 | 11 | 52.4 | 20 | 17.4 | 8 | 16.7 | 45 | 17.6 |
| alp-bca | A-B | 89 | 19.9 | 66 | 17.2 | 16 | 47.1 | 5 | 23.8 | 18 | 15.7 | 6 | 12.5 | 58 | 22.7 |
| alp-R2 | A-R2 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 |
| alp-rib (R4) | A-R4 | 177 | 39.5 | 161 | 41.9 | 13 | 38.2 | 0 | 0.0 | 53 | 46.1 | 15 | 31.3 | 106 | 41.6 |
| alp atypical/unidentified | A-X | 1 | 0.2 | 1 | 0.3 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 | 1 | 0.4 |
| pil1 negative | P1-0 | 120 | 26.8 | 83 | 21.6 | 24 | 70.6 | 10 | 47.6 | 24 | 20.9 | 9 | 18.8 | 74 | 29.0 |
| pil1A/C | P1–2 | 4 | 0.9 | 2 | 0.5 | 0 | 0.0 | 2 | 9.5 | 0 | 0.0 | 0 | 0.0 | 2 | 0.8 |
| pil1A/B/C | P1–3 | 320 | 71.4 | 296 | 77.1 | 10 | 29.4 | 8 | 38.1 | 89 | 77.4 | 39 | 81.3 | 178 | 69.8 |
| pil1 atypical/unidentified | P1-X | 4 | 0.9 | 3 | 0.8 | 0 | 0.0 | 1 | 4.8 | 2 | 1.7 | 0 | 0.0 | 1 | 0.4 |
| pepS8 negative | E-0 | 118 | 26.3 | 95 | 24.7 | 17 | 50.0 | 3 | 14.3 | 29 | 25.2 | 16 | 33.3 | 67 | 26.3 |
| pepS8 positive | E-1 | 330 | 73.7 | 289 | 75.3 | 17 | 50.0 | 18 | 85.7 | 86 | 74.8 | 32 | 66.7 | 188 | 73.7 |
| fbsB (AM050623) | F-3 | 12 | 2.7 | 5 | 1.3 | 0 | 0.0 | 7 | 33.3 | 0 | 0.0 | 1 | 2.1 | 4 | 1.6 |
| fbsB (AM050624) | F-4 | 2 | 0.4 | 2 | 0.5 | 0 | 0.0 | 0 | 0.0 | 1 | 0.9 | 1 | 2.1 | 0 | 0.0 |
| fbsB (515) | F-5 | 187 | 41.7 | 155 | 40.4 | 26 | 76.5 | 2 | 9.5 | 61 | 53.0 | 22 | 45.8 | 98 | 38.4 |
| fbsB (AY326423) | F-6 | 7 | 1.6 | 7 | 1.8 | 0 | 0.0 | 0 | 0.0 | 1 | 0.9 | 0 | 0.0 | 6 | 2.4 |
| fbsB (A909) | F-9 | 240 | 53.6 | 215 | 56.0 | 8 | 23.5 | 12 | 57.1 | 52 | 45.2 | 24 | 50.0 | 147 | 57.6 |
| Capsule type: | |||||||||||||||
| Ia | C-1A | 107 | 23.9 | 80 | 20.8 | 17 | 50.0 | 7 | 33.3 | 25 | 21.7 | 14 | 29.2 | 58 | 22.7 |
| Ib | C-1B | 26 | 5.8 | 23 | 6.0 | 0 | 0.0 | 2 | 9.5 | 10 | 8.7 | 0 | 0.0 | 13 | 5.1 |
| II | C-2 | 64 | 14.3 | 57 | 14.8 | 4 | 11.8 | 2 | 9.5 | 11 | 9.6 | 4 | 8.3 | 46 | 18.0 |
| III | C-3 | 137 | 30.6 | 129 | 33.6 | 3 | 8.8 | 3 | 14.3 | 47 | 40.9 | 14 | 29.2 | 71 | 27.8 |
| IV | C-4 | 20 | 4.5 | 11 | 2.9 | 6 | 17.6 | 3 | 14.3 | 1 | 0.9 | 4 | 8.3 | 12 | 4.7 |
| V | C-5 | 88 | 19.6 | 79 | 20.6 | 3 | 8.8 | 4 | 19.0 | 21 | 18.3 | 11 | 22.9 | 50 | 19.6 |
| VI | C-6 | 1 | 0.2 | 1 | 0.3 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 | 1 | 0.4 |
| VII | C-7 | 1 | 0.2 | 1 | 0.3 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 | 1 | 0.4 |
| VIII | C-8 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 |
| IX | C-9 | 3 | 0.7 | 3 | 0.8 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 | 1 | 2.1 | 2 | 0.8 |
| No capsule/truncated cap locus | C-0 | 1 | 0.2 | 0 | 0.0 | 1 | 2.9 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 | 1 | 0.4 |
| hylB negative | H-0 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 |
| hylB (NEM316) | H-3 | 401 | 89.5 | 348 | 90.6 | 34 | 100.0 | 12 | 57.1 | 102 | 88.7 | 46 | 95.8 | 234 | 91.8 |
| hylB (A909) | H-9 | 47 | 10.5 | 36 | 9.4 | 0 | 0.0 | 9 | 42.9 | 13 | 11.3 | 2 | 4.2 | 21 | 8.2 |
| abiG/Q8DZ34 negative | Q-0 | 309 | 69.0 | 261 | 68.0 | 28 | 82.4 | 15 | 71.4 | 92 | 80.0 | 28 | 58.3 | 169 | 66.3 |
| abiG/Q8DZ34 (NEM316) | Q-3 | 36 | 8.0 | 34 | 8.9 | 0 | 0.0 | 1 | 4.8 | 4 | 3.5 | 10 | 20.8 | 20 | 7.8 |
| abiG/Q8DZ34 (H36B) | Q-6 | 101 | 22.5 | 87 | 22.7 | 6 | 17.6 | 5 | 23.8 | 17 | 14.8 | 10 | 20.8 | 66 | 25.9 |
| abiG/Q8DZ34 (unidentified) | Q-X | 2 | 0.4 | 2 | 0.5 | 0 | 0.0 | 0 | 0.0 | 2 | 1.7 | 0 | 0.0 | 0 | 0.0 |
| pil2 negative | P2-0 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 |
| pil2a (18RS21) | P2-A1 | 104 | 23.2 | 96 | 25.0 | 5 | 14.7 | 1 | 4.8 | 19 | 16.5 | 9 | 18.8 | 73 | 28.6 |
| pil2a (NEM316) | P2-A3 | 115 | 25.7 | 105 | 27.3 | 2 | 5.9 | 6 | 28.6 | 32 | 27.8 | 13 | 27.1 | 62 | 24.3 |
| pil2a (ABC020013424) | P2-A4 | 7 | 1.6 | 7 | 1.8 | 0 | 0.0 | 0 | 0.0 | 1 | 0.9 | 3 | 6.3 | 3 | 1.2 |
| pil2a (515) | P2-A5 | 88 | 19.6 | 67 | 17.4 | 17 | 50.0 | 2 | 9.5 | 24 | 20.9 | 7 | 14.6 | 53 | 20.8 |
| pil2a (H36B) | P2-A6 | 1 | 0.2 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 |
| pil2a (ABC020016680) | P2-A8 | 18 | 4.0 | 17 | 4.4 | 0 | 0.0 | 1 | 4.8 | 2 | 1.7 | 8 | 16.7 | 7 | 2.7 |
| pil2a (ABC020005369) | P2-A9 | 11 | 2.5 | 10 | 2.6 | 0 | 0.0 | 1 | 4.8 | 2 | 1.7 | 1 | 2.1 | 7 | 2.7 |
| pil2a (unidentified) | P2-AX | 6 | 1.3 | 5 | 1.3 | 1 | 2.9 | 0 | 0.0 | 2 | 1.7 | 0 | 0.0 | 4 | 1.6 |
| pil2b (COH1) | P2-B1 | 79 | 17.6 | 69 | 18.0 | 9 | 26.5 | 0 | 0.0 | 33 | 28.7 | 7 | 14.6 | 38 | 14.9 |
| pil2b (527.25) | P2-B5 | 8 | 1.8 | 2 | 0.5 | 0 | 0.0 | 6 | 28.6 | 0 | 0.0 | 0 | 0.0 | 2 | 0.8 |
| pil2b (A909) | P2-B9 | 9 | 2.0 | 5 | 1.3 | 0 | 0.0 | 3 | 14.3 | 0 | 0.0 | 0 | 0.0 | 5 | 2.0 |
| pil2b (unidentified) | P2-BX | 2 | 0.4 | 1 | 0.3 | 0 | 0.0 | 1 | 4.8 | 0 | 0.0 | 0 | 0.0 | 1 | 0.4 |
| nss/srr/rogB2 negative | N-0 | 6 | 1.3 | 4 | 1.0 | 2 | 5.9 | 0 | 0.0 | 1 | 0.9 | 0 | 0.0 | 5 | 2.0 |
| nss/srr (COH1) | N-1 | 80 | 17.9 | 70 | 18.2 | 9 | 26.5 | 0 | 0.0 | 33 | 28.7 | 7 | 14.6 | 39 | 15.3 |
| nss/srr/rogB2 (NEM316) | N-3 | 268 | 59.8 | 234 | 60.9 | 21 | 61.8 | 7 | 33.3 | 62 | 53.9 | 29 | 60.4 | 164 | 64.3 |
| nss/srr/rogB2 (A909) | N-9 | 94 | 21.0 | 76 | 19.8 | 2 | 5.9 | 14 | 66.7 | 19 | 16.5 | 12 | 25.0 | 47 | 18.4 |
| rgf negative | R-0 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 |
| rgf (COH1) | R-1 | 75 | 16.7 | 70 | 18.2 | 2 | 5.9 | 2 | 9.5 | 33 | 28.7 | 7 | 14.6 | 32 | 12.5 |
| rgf (515) | R-5 | 233 | 52.0 | 188 | 49.0 | 30 | 88.2 | 10 | 47.6 | 48 | 41.7 | 24 | 50.0 | 146 | 57.3 |
| rgf (A909) | R-9 | 138 | 30.8 | 124 | 32.3 | 2 | 5.9 | 9 | 42.9 | 34 | 29.6 | 17 | 35.4 | 75 | 29.4 |
| rgf atypical/unidentified | R-X | 2 | 0.4 | 2 | 0.5 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 | 0 | 0.0 | 2 | 0.8 |