TABLE 1.
Differentially prevalent operons by geographical site
| Operon | Gene(s) | Predicted function | No. (%) of Gambian LIC isolates | No. (%) of Sheffield HIC isolates | No. (%) of all LIC isolatesa | No. (%) of all HIC isolatesb |
|---|---|---|---|---|---|---|
| Streptococcin A-FF22 lantibiotic | scnK, scnR | Response histidine kinase, regulator | 38 (36) | 0 (0) | ||
| scnA1 | Lantibiotic | 38 (36) | 0 (0) | 222 (28) | 59 (1) | |
| scnA2 | Lantibiotic | 19 (18) | 0 (0) | |||
| scnA3 | Lantibiotic | 38 (36) | 0 (0) | |||
| scnM | Modifying enzyme | 38 (36) | 0 (0) | |||
| scnT | Transport and leader peptide cleaver | 38 (36) | 0 (0) | |||
| scnF, scnE, scnG | Immunity operon | 38 (36) | 0 (0) | |||
| Glucuronic acid (GCA) utilization | uidA | Beta-glucuronidase | 51 (48) | 15 (11) | 332 (42) | 581 (12) |
| uxaC, uxuB, uxuA, kdgK, kdgA | GCA utilization pathway | 51 (48) | 15 (11) | |||
| yagG | Sugar transporter | 51 (48) | 15 (11) | |||
| fadR | Regulator | 51 (48) | 15 (11) | |||
| hypothetical gene | Hydrolase | 51 (48) | 15 (11) | |||
| CRISPR | cas3, cas5c, cas8c, cas7, cas4, cas1, cas2 | Type 1C | 54 (50) | 74 (52) | 315 (40) | 3,471 (72) |
| cas9, cas1, cas2, csn2 | Type 2A | 41 (38) | 104 (73) | 310 (39) | 3,687 (76) |
a
All LIC isolates: Gambia, Kenya, and Fiji (n = 781) isolates.
b
All HIC isolates: Sheffield, BSAC (England/Wales), PHE (United Kingdom), and ABCs (United States) isolates (n = 4,820). Only the scnA and uidA genes were used to determine the presence or absence of these loci in all the LIC or all the HIC isolate genomes.