TABLE 4.
E. coli ST-lineage-specific regions identified by genome comparison
| Region by ST, strain (GenBank accession no.) | Positions |
Size (bp) | Presence (% [no./total no.]) in ST: |
PNIa | No. of genes | Function(s) | ||||
|---|---|---|---|---|---|---|---|---|---|---|
| Start | End | 69 | 73 | 95 | 131 | |||||
| ST73, E. coli CFT073 (AE014075) | ||||||||||
| 1b | 2001254 | 2002243 | 989 | 100 (36/36) | 99.7–100 | 1 | Hypothetical | |||
| 2 | 5116943 | 5127677 | 10,734 | 80.5 (29/36) | 99.9–100 | 9 | Hypothetical | |||
| ST95, E. coli UTI89 (CP000243) | ||||||||||
| 3 | 1397376 | 1399596 | 2,220 | 100 (24/24) | 99.8–99.9 | 2 | Hypothetical | |||
| 4 | 2598930 | 2599265 | 335 | 100 (24/24) | 99.7–100 | 1 | Hypothetical | |||
| 5 | 2900299 | 2902003 | 1,704 | 83 (20/24) | 99.7–100 | 4 | Hypothetical | |||
| 6 | 2925552 | 2928212 | 2,660 | 75 (18/24) | 96.5–96.6 | 6 | Hypothetical and phage related | |||
| 7 | 2941113 | 2942983 | 1,870 | 83 (20/24) | 99.8–100 | 3 | Hypothetical | |||
| 8 | 3114339 | 3117642 | 3,303 | 100 (24/24) | 99.6–100 | 3 | Hypothetical | |||
| 9b | 3124006 | 3126499 | 2,493 | 100 (24/24) | 99.9–100 | 2 | Hypothetical | |||
| 10 | 3861904 | 3866248 | 4,344 | 100 (24/24) | 5 (1/22)c | 99.6–100 | 6 | Hypothetical, putative phosphotransferase, phosphoglycerate, dehydrogenase, and dihydrodipicolinate synthase | ||
| ST131, E. coli NA114 (CP002797) | ||||||||||
| 11 | 290463 | 291668 | 1,205 | 100 (22/22) | 97.8–100 | 1 | Hypothetical | |||
| 12 | 298525 | 299844 | 1,319 | 100 (22/22) | 100 | 2 | Phage related | |||
| 13 | 565237 | 566906 | 1,669 | 100 (22/22) | 99.6–100 | 2 | Putative oxidoreductase | |||
| 14 | 569537 | 576146 | 6,609 | 100 (22/22) | 99.5–100 | 6 | Hypothetical, putative transcriptional regulator, and transketolase | |||
| 15 | 1354460 | 1371763 | 17,303 | 100 (22/22) | 98.8–100 | 21 | Hypothetical, phage related, DNA repair, and transcriptional regulation | |||
| 16 | 1971120 | 1994937 | 23,817 | 86 (19/22) | 97.8–100 | 28 | Hypothetical and phage related | |||
| 17 | 2480863 | 2484064 | 3,201 | 82 (18/22) | 99.1–100 | 5 | Hypothetical and phage related | |||
| 18 | 2928397 | 2930371 | 1,974 | 100 (22/22) | 100 | 1 | Hypothetical | |||
| 19b | 4343837 | 4345117 | 1,280 | 100 (22/22) | 99.3–100 | 1 | Putative manganese transport | |||
| 20 | 4859427 | 4870212 | 10,785 | 86 (19/22) | 99.9–100 | 15 | Phage related and hypothetical | |||
| ST69, E. coli UMN026 (CU928163) | ||||||||||
| 21b | 3051269 | 3077864 | 26,595 | 100 (14/14) | 97.4–100 | 25 | Phage related | |||
| 22 | 1679641 | 1680431 | 790 | 100 (14/14) | 5 (1/22)c | 100 | 0 | Hypothetical | ||
a
PNI, percent nucleotide identity of ST-specific sequences in corresponding ST genomes determined against sequences from the published ST reference genomes.
b
Regions used in the PCR assay.
c
Indicates 91% and 94% nucleotide identities of ST95 region 8 and ST69 region 2 in the ST131 genomes, respectively.