TABLE 1.
Distribution of ETT2 island PCR fragments among E. coli strains
| Straina | Category | ETT2 LPCR pattern | Indel-specific PCR resultsb | Conclusions from deletion-spanning PCRsc |
|---|---|---|---|---|
| CFT073 | UPEC | ++−−−−−−−+ | CFT073-like | ETT2 absent |
| RS218 | NMEC | |||
| ECOR 23 | ECOR A | |||
| ECOR 51, 52, 54, 55, 56, 57, 59, 61, 62, 63, 64, 65, 66 | ECOR B2 | |||
| ECOR 4 | ECOR A | CFT073-like, with 2.4-kb insertion | ETT2 absent and something else inserted next to glyU or ∼25-kb deletion in ETT2 between 3F and 9R | |
| H10407 | ETEC | ++++++−−++ | B171-8-like | 8.7-kb deletion as in B171-8 sequence |
| EAEC25 | EAEC | |||
| ECOR 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 15, 18, 22, 24, 25 | ECOR A | |||
| ECOR 26, 27, 28, 29, 30, 32, 33, 34, 58, 67, 68 | ECOR B1 | |||
| ECOR 39 | ECOR D | |||
| ECOR 45 | ECOR B1 | |||
| ECOR 14 | ECOR A | B171-8-like, with 1-kb insertion | 8.7-kb deletion as in B171-8 sequence, with ∼1-kb insertion | |
| ECOR 13, 20, 21 | ECOR A | ++−−−−−−−+ | Negative | ∼23-kb deletion between 3F and 9R |
| ECOR 19 | ∼30-kb deletion between 2R and 10F | |||
| ECOR 53 | ECOR B2 | ∼30-kb deletion between 3F and 9R, i.e., ETT2 absent | ||
| ECOR 60 | ||||
| ECOR 69 | ECOR B1 | Unresolved deletion between 2R and 10F | ||
| ECOR 16 | ECOR A | ++−+−−−−−+ | Unresolved deletion between 2R and 4F, ∼18-kb deletion between 4R and 9R | |
| ECOR 17 | ECOR A | +++−−−−−−+ | 22-kb deletion between 4F and 9R | |
| ECOR 38 | ECOR D | ++−−−−−+++ | ∼21-kb deletion between 3F and 7R | |
| ECOR 35 | ECOR D | +++−++−−−− | No deletion between 3R and 5F, unresolved deletion after 6R | |
| ECOR 31 | ECOR E | ++−−−−++++ | ∼15-kb deletion between 2R and 7F | |
| K12 | Laboratory | ++++−−−−++ | 18-kb deletion as in K12 sequence | |
| ECOR 36 | ECOR D | +++−++−−+− | No deletion between 3R and 5F, 8-kb deletion between 7F and 8R, unresolved deletion after 9R | |
| ECOR 40 | ECOR D | +++−+−−+++ | No deletion between 3R and 5F, 6-kb deletion between 6F and 7R | |
| ECOR 41 | No deletion between 3R and 5F, 4-kb deletion between 6F and 7R | |||
| ECOR 70 | ECOR B1 | ++++++−−−+ | ∼5-kb deletion between 6R and 9R | |
| ECOR 72 | ECOR B1 | ++++++−−++ | ∼5-kb deletion between 7F and 8R | |
| ECOR 71 | ECOR B1 | ∼8-kb deletion between 6R and 9F | ||
| ECOR 42, 43 | ECOR E | |||
| ECOR 37 | ECOR E | +++++−++++ | ∼3-kb deletion between 6R and 7F | |
| ECOR 48 | ECOR D | +++−++++−+ | No deletion between 3R and 5F, no deletion between 8R and 10F, i.e., Sakai-like | |
| ECOR 44, 46, 47, 49, 50 | +++−++++++ | No deletion between 3R and 5F, i.e., Sakai-like | ||
| 0157 | EHEC | ++++++++++ | No deletions detected, i.e., Sakai-like | |
| 042 | EAEC | ++++++++++ | No deletions detected, i.e., Sakai-like |
a
Strains in bold possess the eip cluster.
b
An ∼200-bp PCR was used to detect a deletion point identical to that seen in B171-8, while an ∼600-bp PCR was used to detect a CFT078-like vacant ETT2 insertion point. Negative means that both indel-specific PCRs failed to give a product.
c
When the indel-specific PCRs failed to resolve a deletion, deletion-scanning long PCRs were performed with forward and reverse primers from the sets flanking the deletion. Deletion sizes were calculated by subtracting the deletion-scanning PCR product size from the expected product size from the Sakai strain. This approach cannot resolve deletions followed by insertions, e.g., of IS elements.