Table 1.
Bacterial isolates and genomic data used in this study
| Species | No. strains (no. with genome data) |
|---|---|
| Haemophilus influenzae, incl. NTHi and biogroup aegyptius a | 338 (201) |
| Haemophilus haemoglobinophilus | 1 (1) |
| Haemophilus haemolyticus b | 107 (32) |
| Haemophilus parahaemolyticus | 2 (1) |
| Haemophilus parainfluenzae | 5 (4) |
| Haemophilus paraphrohaemolyticus | 1 (1) |
| Haemophilus sp. (novel “fuzzy” species) | 17 (13) |
| Achromobacter sp. | 1 |
| Aggregatibacter (formerly Haemophilus) aphrophilus | 1 |
| Alcaligenes sp. | 1 |
| Alloiococcus otitidis | 1 |
| Bacillus sp. | 1 |
| Bacteroides fragilis | 1 |
| Burkholderia cenocepacia | 1 |
| Burkholderia cepacia | 1 |
| Burkholderia diffusa | 1 |
| Burkholderia multivorans | 1 |
| Burkholderia pseudomallei | 1 |
| Burkholderia pyrrocinia | 1 |
| Burkholderia thailandensis | 1 |
| Burkholderia vietnamiensis | 1 |
| Burkholderia spp. | 2 |
| Chromobacterium violaceum | 1 |
| Chryseobacterium sp. | 1 |
| Comamonas sp. | 1 |
| Cupriavidus spp. | 2 |
| Delftia sp. | 1 |
| Escherichia coli | 1 |
| Klebsiella pneumoniae | 1 |
| Moraxella catarrhalis | 1 |
| Neisseria meningitidis | 1 |
| Pandoraea sp. | 1 |
| Pigmentiphaga sp. | 1 |
| Proteus mirabilis | 1 |
| Pseudomonas aeruginosa | 2 |
| Ralstonia mannitolilytica | 1 |
| Staphylococcus aureus | 2 |
| Staphylococcus epidermidis | 1 |
| Stenotrophomonas sp. | 1 |
| Streptococcus mitis | 1 |
| Streptococcus pneumoniae | 1 |
| Streptococcus pyogenes | 2 |
| TOTAL | 511 (253) |
aSpecies determined according to a positive fucP assay result and/or by whole-genome sequencing
bSpecies determined by a negative fucP result, a positive H. haemolyticus hpd HRM result [27], and/or by whole-genome sequencing