Correlation between the genomic o454-nlpD region polymorphisms, virulence gene equipment and phylogenetic group of extraintestinal Escherichia coli (ExPEC) enables pathotyping irrespective of host, disease and source of isolation

Table 1 Oligonucleotide primers used for the amplification of the intergenic and adjacent o454-nlpD genomic region of E. coli

Primer name		Genetic region^a	Predicted amplicon size (bp) in reference strains^b				Forward/reverse primer sequences (5?-3?)
For	Rev		MG1655	CFT073	E2348/69	EDL933
F1	R1	fhlA-mutS	1.208	1.673	1.208	1.208	AGAGTTCCGTAGCGATCTC/CTGCTGCATCATGGGCGTAT
F1	R2	fhlA-nlpD	11.840	14.357	15.192	8.679	AGAGTTCCGTAGCGATCTC/ CATAACGACACAATGCTGGTCC
F2	R1	ygbA-mutS	361	360	359	361	TTCACGAGAGATACGCTTGC/CTGCTGCATCATGGGCGTAT
F3	R3	mutS-o388	2.881	2.881	2.881	-	AAAGCATTTCGCCGAACGCCGC/CATCGGCGATAACGCCAAT
F3	R4	mutS-yclC	-	-	7.365	1.318	AAAGCATTTCGCCGAACGCCGC/GACAACCGTGGTCACTACA
F4	R3	f265-o388	1.146	1.146	1.146	-	ACGCTCTACGGGTATCAACT/CATCGGCGATAACGCCAAT
F5	R2	o454-nlpD	1.318	3.685	4.546	-	AAGCCCTTGCCAACATGCTAC/CATAACGACACAATGCTGGTCC
F5	R5	o454-o347	-	816	-	-	AAGCCCTTGCCAACATGCTAC/CGTCAGGTTGAAATGCTTGACT
F5	R4	o454-yclC	-	-	716	-	AAGCCCTTGCCAACATGCTAC/GACAACCGTGGTCACTACA
F6	R2	slyA-nlpD	-	-	1.394	1.393	TTGAGTGCAGAAGAGCAGG/CATAACGACACAATGCTGGTCC
F2	R1	c3292-mutS	-	1.120	1.119	-	TAACCGGAACAGTTAGCGC/CTGCTGCATCATGGGCGTAT

^aBiological functions of amplified genes: fhlA, formate hydgrogen lyase; mutS, mismatch repair protein; nlpD, outer membrane lipoprotein; ygbA, hypothetical protein; o388 (syn. ygbK), hypothetical protein; yclC (syn. kpdC), 4-hydroxybenzoate decarboxylase determinant; f265 (syn. ygbL), hypothetical transcriptional regulator; o454 (syn. b2740 and ygbN), putative zinc-dependent hydrolase; o347 (syn. c3302), limited level of similarity to enzymes implicated in antibiotic hydrolysis and synthesis; slyA (syn. kpdR), 4-hydroxybenzoate decarboxylase determinant, in Salmonella transcriptional regulator, required for survival within macrophages the induction of hemolytic and pore-forming proteins; c3292, putative molybdenum-pterin-binding protein. ^bBased on whole genome sequences deposited to GenBank under accession numbers U00096 (MG1655), NC_004431 (CFT073), FM180568 (E2348/69), and NC_0022655 (EDL933).

ISSN: 1757-4749