Table 1 Genetic loci identified by IS3 profiling
Band ref no. | Band size | Criteria for selection | Sequence showing > 90% similarity at the nucleotide level (Genbank Accession #) | Subsequent evaluation of locus |
|---|---|---|---|---|
650 | 1.7 kb | Present in several (13/22) EAEC, absent in K12 | E. coli 2-acylglycerophosphoethanolamine acyltransferase/acyl-acyl carrier protein synthetase gene (gi|290402) | Gene is present in the K-12 genome |
651 | 1.2 kb | Present in ST31 and ST394 EAEC strains. Absent in all others. | orfz2240 (unknown function) from "O-island #62" of E. coli O157:H7 EDL933 genome (gi|12515207|gb|AE005358.1) | Present in ST31, ST38 and ST394-complex EAEC strains and EHEC O157. absent in other EAEC |
652 | 0.35 kb | Present in K12 and EDL933, absent in Shigella and 16/22 EAEC. No phylogenetic association. | E. coli racC and recE genes, complete cds and 5' end (gi|147534|gb|M24905.1|ECORECEA) | Present in EAEC |
708 | 0.65 kb | Absent in ST10 EAEC, present in most other strains | E. coli 23 S rRNA gene, strain K12 DSM 30083T (gi|12053855|emb|AJ278710.1) | 23 S rRNA, no diagnostic potential |
711 | 0.5 kb | Present in 8/22 EAEC strains, and Shigella, absent in other strains | E. coli aggR gene for fimbrial adhesin activator (gi|471301|emb|Z32523.1|ECAGGRG) | Previously described plasmid-borne EAEC gene [17] |
712 | 1.3 Kb | Absent in most EAEC (19/22), Present in K12 | E. coli glycine decarboxylase (gi|NC 000913|U00096) | Gene is present in EAEC strains |