TABLE 4.
Distribution of putative lineage II conserved markers among E. coli O157:H7 strains from various lineages
| Class | Primer set | SSH(s)a | Predicted amplicon size (bp) | No. of indicated markers/total no. (%)
|
Sequence homology | |||
|---|---|---|---|---|---|---|---|---|
| Lineage I (LSPA-6 111111) | Lineage II (LSPA-6 222222) | Lineage II (LSPA-6 211111) | Other lineage II | |||||
| B | A10 | 2, 3 | 435 | 0/17 (0) | 17/17 (100) | 3/5 (60) | 4/5 (80) | E. coli UTI89 (7) (96% homology over 1,388 nt) genes with homology to bacteriophage HK97 gp56 and bacteriophage Nil2p gene dnaB homologue |
| A11 | 1, 2, 3 | 365 | 0/17 (0) | 17/17 (100) | 3/5 (60) | 4/5 (80) | Bacteriophage BP-4795 (8) (95% homology over 762 nt), encoding a hypothetical protein | |
| A13 | 1, 2, 3 | 204 | 0/17 (0) | 17/17 (100) | 0/5 (0) | 5/5 (100) | E. coli K-12 (5) ORFs b1155 to b1157 (81% homology over 1,260 nt), encoding hypothetical proteins and a putative tail fiber assembly protein within the cryptic prophage e14 | |
| B02 | 1, 2, 3 | 136 | 0/17 (0) | 13/17 (76.5) | 5/5 (100) | 3/5 (60) | Bacteriophage P2 (accession no. AF063097) genes J and I (94% homology over 1,019 nt), encoding baseplate assembly proteins | |
| A05 | 1, 2, 3 | 246 | E. coli Sakai (14) ORF ECs0284 (88% homology over 338 nt), encoding a DNA invertase, adjacent to 213 nt of DNA sequence, without significant homology to known DNA sequences adjacent to bacteriophage P2 (accession no. AF063097) FI tail sheath protein gene (95% homology over 546 nt) | |||||
| B03 | 1, 2, 3 | 746 | 0/17 (0) | 17/17 (100) | 0/5 (0) | 5/5 (100) | E. coli O109I P4-like bacteriophage ORFs ecO109Im and psu (23) (98% homology over 1,248 nt), encoding methyltransferase and Psu-like proteins | |
| B06 | 1, 2, 3 | 327 | 0/17 (0) | 17/17 (100) | 0/5 (0) | 5/5 (100) | S. boydii strain Sb227 (45) ORFs SBO4168 to SBO4170 (97% homologous over 1,352 nt) and SBO3220 (98% homology over 170 nt), encoding a putative bacteriophage protein and conserved hypothetical proteins | |
| A09 | 2, 3 | 572 | S. boydii strain Sb227 (45) ORFs SBO4164 and SBO4165 (95% homology over 1,366 nt), encoding a prophage P4 integrase and a putative DNA primase | |||||
| B08 | 2, 3 | 616 | 0/17 (0) | 17/17 (100) | 3/5 (60) | 5/5 (100) | Bacteriophage HK022 (19) (93% homology over 632 nt, with gaps), intergenic region between genes encoding an excisionase and an Ea22 protein | |
| B10 | 1, 2, 3 | 272 | 0/17 (0) | 17/17 (100) | 5/5 (100) | 5/5 (100) | S. boydii strain Sb227 (45) ORF SBO2131 (99% homology over 892 nt), encoding conserved hypothetical protein | |
| A02 | 1, 2 | 582 | S. boydii strain Sb227 (45) ORFs SBO2122 to SBO2125 (94% homology over 1,013 nt), encoding conserved hypothetical protein and prophage capsid proteins | |||||
| A03 | 2, 3 | 483 | S. boydii strain Sb227 (45) ORFs SBO2131 to SBO2132 (98% homology over 995 nt), encoding conserved hypothetical proteins | |||||
| A04 | 2, 3 | 438 | S. boydii strain Sb227 (45) ORFs SBO2126 to SBO2127 (97% homology over 684 nt), encoding a conserved hypothetical protein and a hypothetical bacteriophage protein | |||||
| B16 | 1, 2, 3 | 830 | 0/17 (0) | 17/17 (100) | 0/5 (0) | 5/5 (100) | S. flexneri bacteriophage V (16) ORFs int, xis, orf28, orf29, orf30, and orf31 (97% homologous over 2,453 nt), encoding an integrase, an excisionase, and hypothetical proteins | |
| B01 | 1, 2, 3 | 316 | S. flexneri bacteriophage V (16) ORFs orf39, orf40, and dam (96% homology over 823 nt), encoding a replication protein, a hypothetical protein, and a DNA adenine methylase | |||||
| B07 | 1,3 | 97 | S. flexneri bacteriophage V (16) ORF5 and ORF6 (98% homology over 803 nt), encoding a capsid protein and a hypothetical protein | |||||
| C | A14 | 2, 3 | 474 | 0/17 (0) | 17/17 (100) | 4/5 (80) | 5/5 (100) | 599 nt of DNA sequence without significant homology to known DNA sequences adjacent to E. coli Sakai (14) ORFs ECs1599 and ECs1600 (90 to 91% homologous over 367 nt), encoding hypothetical proteins |
| A15 | 1, 2, 3 | 1,068 | 0/17 (0) | 17/17 (100) | 4/5 (80) | 4/5 (80) | 247 nt of DNA sequence without significant homology to known DNA sequences adjacent to E. coli Sakai (14) ORFs ECs1557 and ECs1558 (96% homology over 1,968 nt), encoding a putative antirepressor protein and a putative tail assembly protein | |
| D | A06c | 2 | 1,212 | 1/17 (5.9) | 17/17 (100) | 5/5 (100) | 5/5 (100) | E. coli Sakai (14) intergenic region between ORFs ECs1159 and ECs1160 (98% homology over 365 nt), encoding a hypothetical protein and a putative integrase, adjacent to ECs1252 (95% homologous over 929 nt with a single 82-nt gap), encoding a putative transport protein |
| A07 | 1, 3 | 226 | 0/17 (0) | 15/17 (88.2) | 5/5 (100) | 4/5 (80) | E. coli Sakai (14) ORF ECs1928 (97% homology over 148 nt), encoding a hypothetical protein, adjacent to ECs1997 (99% homology over 269 nt), encoding a putative filament protein | |
| B15 | 3 | 558 | 0/17 (0) | 17/17 (100) | 1/5 (20) | 5/5 (100) | E. coli Sakai (14) ORF ECs1688 (100% homology over 378 nt), encoding a murein transglycosylase, adjacent to ORFs ECs1705 and ECs1706 (99% homologous over 672 nt), encoding a putative dihydroxyacetone kinase and a hypothetical protein | |
| E | A01 | 1 | 432 | 0/17 (0) | 12/17 (70.6) | 0/5 (0) | 2/5 (40) | E. coli strain EC93 contact-dependent inhibition (cdiB) gene (3) (98% homologous over 523 nt) |
| B05 | 1 | 512 | 0/17 (0) | 1/17 (5.9) | 0/5 (0) | 0/5 (0) | ColE6-CT14 colicin plasmid (1) colicin E6 gene (99% homologous over 1,605 nt) | |
| B12 | 2, 3 | 258 | 0/17 (0) | 17/17 (100) | 0/5 (0) | 5/5 (100) | E. coli UTI89 (7) ORFs (91% homologous over 710 nt), encoding a regulatory protein and a hypothetical protein | |
| B18 | 1 | 290 | 5/17 (29.4) | 8/17 (47.1) | 0/5 (0) | 2/5 (40) | pColD-157 plasmid (15) colicin D-157 activity protein (99% homology over 921 nt) | |
| F | A12 | 1, 2, 3 | 446 | 0/17 (0) | 16/17 (94.1) | 4/5 (80) | 4/5 (80) | 643 nt of DNA sequence without significant homology to known DNA sequences |
| B13 | 1, 2 | 507 | 0/17 (0) | 14/17 (82.4) | 4/5 (80) | 5/5 (100) | DNA sequence without significant homology to known DNA sequences | |
a
Sequence found in the following SSH experiments: 1, E. coli FRIK 920-E. coli Sakai; 2, E. coli FRIK 1999-E. coli Sakai; 3, E. coli FRIK 2001-E. coli 93-001.