Table 5.

Sequences of oligonucleotide primers used for typing of eae intimin gene

Gene	Primer	Oligonucleotide sequence (5'-3')c	Fragment size (bp)	Annealing temperature	Primer coordinates	Accession number	Reference
eaea	EAE-1 EAE-2	GGAACGGCAGAGGTTAATCTGCAG GGCGCTCATCATAGTCTTTC	775	55°C	1441–1460 2193–2215	AF022236	7
eae-α1	EAE-FB EAE-A	AAAACCGCGGAGATGACTTC CACTCTTCGCATCTTGAGCT	820	60°C	1909–1928 2709–2728	AF022236	8
eae-α2	IH2498aF IH2498aR	AGACCTTAGGTACATTAAGTAAGC TCCTGAGAAGAGGGTAATC	517	60°C	2099–2122 2597–2615	AF530555	8
eae-β1	B1A B1B	ACTTCGCCACTTAATGCCAGC TTGCAGCACCCCATGTTGAAT	730	66°C	1924–1944 2633–2653	AF453441	9
eae-ξR/β2Bb,e	B2A B2B	AAGGGGGGAACCCCTGTGTCA ATTTATTCGCAGCCCCCCACG	604	66°C	2056–2076 2639–2659	AF530556 AJ715407	9
eae-δ/κ/β2Oc	EAE-FB EAE-D	AAAACCGCGGAGATGACTTC CTTGATACACCCGATGGTAAC	833	60°C	1909–1928 2721–2741	U66102	8
eae-γ1	EAE-FB EAE-C1	AAAACCGCGGAGATGACTTC AGAACGCTGCTCACTAGATGTC	804	60°C	1909–1928 2691–2712	AF071034	8
eae-θ/γ2d	EAE-FB EAE-C2	AAAACCGCGGAGATGACTTC CTGATATTTTATCAGCTTCA	808	58°C	1909–1928 2697–2716	AF025311	8
eae-ε1	EAE-FB LP5	AAAACCGCGGAGATGACTTC AGCTCACTCGTAGATGACGGCAAGCG	722	66°C	1909–1928 2605–2630	AF116899	8
eae-νR/ε2e	EAE-E2F EAE-E2R	AATACAGAAGTTAAGGCAT ACGACCACTATTCATTTC	378	58°C	2230–2248 2590–2607	AF530554	9
eae-ζ	Z1 Z2	GGTAAGCCGTTATCTGCC ATAGCAAGTGGGGTGAAG	206	62°C	2062–2079 2250–2267	AF449417	8
eae-η	EAE-FB ETA-B	AAAACCGCGGAGATGACTTC TAAGCGACCACTATTCGTG	702	60°C	1899–1918 2582–2600	AJ308550	9
eae-ι1	EAE-FB IOTA-B	AAAACCGCGGAGATGACTTC GTCATATTTAACTTTTACACTA	651	55°C	1909–1928 2538–2559	AJ308551	9
eae-μR/ι2e	Iota2-F Iota2-R	CTGGTAAAGCGATAGTCAAAC GCGTTTTTGAAGAAACATTTTGC	936	58°C	1850–1870 2763–2785	AF530553	9
eae-λ	68.4F 68.4R	CGGTCAGCCTGTGAAGGGC ATAGATGCCTCTTCCGGTATT	466	64°C	2061–2079 2506–2526	AJ715409	8
eae-μBf	EAE-FB FV373R	AAAACCGCGGAGATGACTTC ACTCATCATAATAAGCTTTTTGG	665	60°C	1909–1928 2541–2563	AJ705049	9
eae-νBf	IH1229aF IH1229aR	CACAGCTTACAATTGATAACA CTCACTATAAGTCATACGACT	311	60°C	269–289 559–579	AJ705050	8
eae-ξBf	EAE-FB B49R	AAAACCGCGGAGATGACTTC ACCACCTTTAGCAGTCAATTTG	468	66°C	1909–1928 363–384	AF116899 AJ705051	8

^aUniversal oligonucleotide primer pair EAE1 and EAE-2 wih homology to the 5'conserved region of eae gene (detects all types of eae variants described at the moment). Primers used to detect the eae gene.

^bThe intimin β2 of Blanco et al. (8) is identical to intimin ξ described by Ramachandran et al. (14). In this study our β2 is referred as ξR/β2B.

^cThe intimin δ of Adu-Bobie et al. (4) is identical to intimin κ of Zhan et al. (6). The intimin δ of Adu-Bobie et al. (4) was also termed β2 by Oswald et al. (5). Thus, in the present study this intimin is referred as δ/κ/β2O.

^dThe intimin θ of Tarr and Whittam (13) is the same as intimin γ2 of Oswald et al. (5).

^eIntimins μ, ν, and ξ described by Ramachandran et al. (14) in ruminant E. coli strains. When Ramachandran et al. (14) submitted the nucleotide sequences of μ, ν, and ξ genes these intimin types were designated ι2, ε2 and β2, respectively.

^fIntimins μ, ν, and ξ described by Blanco et al. (8, unpublished results).