Adherent-invasive Escherichia coli (AIEC) in pediatric Crohn’s disease patients: phenotypic and genetic pathogenic features

Maria Pia Conte; Catia Longhi; Massimiliano Marazzato; Antonietta Lucia Conte; Marta Aleandri; Maria Stefania Lepanto; Carlo Zagaglia; Mauro Nicoletti; Marina Aloi; Valentina Totino; Anna Teresa Palamara; Serena Schippa

doi:10.1186/1756-0500-7-748

Table 1 Primers used for PCR analysis of known virulence genes of extra-intestinal pathogenic E. coli

From: Adherent-invasive Escherichia coli (AIEC) in pediatric Crohn’s disease patients: phenotypic and genetic pathogenic features

Virulence traits	Genes	Primer sequence (5′à 3′)	Expected amplicon size (bp)	References
P fimbriae	papA	ATGGCAGTGGTGTCTTTTGGTG	720	[33]
	papA	CGTCCCACCATACGTGCTCTTC	720	[33]
	papEF	GCAACAGCAACGCTGGTTGCATCAT	336	[33]
	papEF	AGAGAGAGCCACTCTTATACGGACA	336	[33]
P pili-associated G-adhesins	papC	GACGGCTGTACTGCAGGGTGTGGCG	328	[33]
P pili-associated G-adhesins	papC	ATATCCTTTCTGCAGGGATGCAATA	328	[33]
Pyelonephritis-associated pili	papG allele II e III	CTGTAATTACGGAAGTGATTTCTG	1070	[33]
	papG allele II e III	ACTATCCGGCTCCGGATAAACCAT	1070	[33]
	papG allele II	GGGATGAGCGGGCCTTTGAT	190	[33]
	papG allele II	CGGGCCCCCAAGTAACTCG	190	[33]
	papG allele III	GGCCTGCAATGGATTTACCTGG	258	[33]
	papG allele III	CCACCAAATGACCATGCCAGAC	258	[33]
S and F1C fimbriae	sfa//focDE	CTCCGGAGAACTGGGTGCATCTTAC	410	[33]
S and F1C fimbriae	sfa//focDE	CGGAGGAGTAATTACAAACCTGGCA	410	[33]
F1C fimbriae	focG	CAGCACAGGCAGTGGATACGA	360	[33]
F1C fimbriae	focG	GAATGTCGCCTGCCCATTGCT	360	[33]
Dr-binding adhesin	afa/draBC	GGCAGAGGGCCGGCAACAGGC	559	[33]
Dr-binding adhesin	afa/draBC	CCCGTAACGCGCCAGCATCTC	559	[33]
G fimbriae	gafD	TGTTGGACCGTCTCAGGGCTC	952	[33]
G fimbriae	gafD	CTCCCGGAACTCGCTGTTACT	952	[33]
Nonfimbrial adhesin type 1	nfaE	GCTTACTGATTCTGGGATGGA	559	[33]
Nonfimbrial adhesin type 1	nfaE	CGGTGGCCGAGTCATATGCCA	559	[33]
Mannose-specific adhesion gene. Type1 fimbriae.	fimH	TGCAGAACGGATAAGCCGTGG	508	[33]
Mannose-specific adhesion gene. Type1 fimbriae.	fimH	GCAGTCACCTGCCCTCCGGTA	508	[33]
Haemolysin A	hlyA	AACAAGGATAAGCACTGTTCTGGCT	1177	[33]
Haemolysin A	hlyA	ACCATATAAGCGGTCATTCCCGTCA	1177	[33]
Cytotoxic necrotizing factor 1	cnf1	GTGATAATATATCACATTATTC	498	[33]
Cytotoxic necrotizing factor 1	cnf1	GAATTCGTCTCGTTGAGCTTCACTG	498	[33]
Yersiniabactin siderophore receptor	fyuA	TGATTAACCCCGCGACGGGAA	880	[33]
Yersiniabactin siderophore receptor	fyuA	CGCAGTAGGCACGATGTTGTA	880	[33]
Aerobactin siderophore receptor	iutA	GGCTGGACATCATGGGAACTGG	300	[33]
Aerobactin siderophore receptor	iutA	CGTCGGGAACGGGTAGAATCG	300	[33]
Capsule synthesis primers	kpsMT II	GCGCATTTGCTGATACTGTTG	272	[33]
	kpsMT II	CATCCAGACGATAAGCATGAGCA	272	[33]
	kpsMT III	TCCTCTTGCTACTATTCCCCCT	392	[33]
	kpsMT III	AGGCGTATCCATCCCTCCTAAC	392	[33]
	kpsMT1 (K1)	TAGCAAACGTTCTATTGGTGC	153	[33]
	kpsMT1 (K1)	CATCCAGACGATAAGCATGAGCA	153	[33]
	kpsMT 5 (K5)	CAGTATCAGCAATCGTTCTGTA	159	[33]
	kpsMT 5 (K5)	CATCCAGACGATAAGCATGAGCA	159	[33]
Invasion of brain endothelium gene (associate with neonatal meningitis)	IbeA	AGGCAGGTGTGCGCCGCGTAC	170	[33]
	IbeA	TGGTGCTCCGGCAAACCATGC	170	[33]
Encodes colicin V	cvaC	CACACACAAACGGGAGCTGTT	680	[33]
Encodes colicin V	cvaC	CTTCCCGCAGCATAGTTCCAT	680	[33]
Serum resistance gene	traT	GGTGTGGTGCGATGAGCACAG	290	[33]
Serum resistance gene	traT	CACGGTTCAGCCATCCCTGAG	290	[33]
Pathogenicity islands described in a virulent uropathogen.	PAI	GGACATCCTGTTACAGCGCGCA	930	[33]
	PAI	TCGCCACCAATCACAGCCGAAC	930	[33]
Transcriptional Activator gene of aggregative adhesion fimbriae	aggR	GTATACACAAAAGAAGGAAGC	254	[34]
	aggR	ACAGAATCGTCAGCATCAGC	254	[34]
CVD432 gene probe sequence of the plasmid of aggregative adhesion	pAA (CVD432)	CTGGCCAAAGACTGTATCAT	630	[34]
	pAA (CVD432)	CAATGTATAGAAATCCGCTGTT	630	[34]

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