Table 1.

ExPEC/APEC genes used for virulence and phylogenetic typing

Category	Gene(s)	Comment	Reference
	fimH	D-mannose-specific adhesin, type 1 fimbriae	[7]
	fimAvMT78	Fim A variant MT78 of type 1 fimbriae	[7]
	pap	Pilus associated with pyelonephritis (P fimbriae)
	papC	Pilus assembly; central region of pap operon	[21]
	papG: papG I papG II papG III	Gal(α 1–4) Gal-specific pilus tip adhesin molecule rare Pyelonephritis-associated Cystitis-associated	[24]
Adhesins	sfa/focDE	Central region of sfa (S fimbriae) and foc (F1C fimbriae) operons	[21]
	sfaS	Pilus tip adhesin, S fimbriae (sialic acid-specific)	[7]
	focG	Pilus tip molecule, F1C fimbriae (sialic acid-specific)	[7]
	afa/draBC	Dr antigen-specific adhesin operons (AFA, Dr, F1845)	[21]
	bmaE	Blood group M-specific adhesin	[13]
	nfaE	Nonfimbrial adhesin I assembly and transport	[13]
	gafD	N-acetyl-D-glucosamine-specific (G, F17c) fimbriae adhesin	[13]
	cnf1	Cytotoxic necrotizing factor 1	[7]
	cdtB	Cytolethal distending toxin	[7]
Toxins	sat	Secreted autotransporter toxin	[25]
	hlyA	α- hemolysin	[26]
	fyuA	Yersinia siderophore receptor (ferric yersiniabactin uptake)	[13]
Siderophores	iutA*	Ferric aerobactin receptor (iron uptake: transport)	[7]
	iroN*	Novel catecholate siderophore receptor	[27]
	neuC	K1 antigen	[7]
	cvaC*	ColV; on plasmids with traT, iss, and antibiotic resistance	[13]
Protectin	iss*	Increased serum survival (outer membrane protein)	[27]
	traT*	Surface exclusion, serum survival (outer membrane protein)	[13]
	ibeA	Invasion of brain endothelium IbeA	[7]
	malX (PAI)	Pathogenicity-associated island marker	[13]
Miscelaneous	usp	Uropathogenic-specific protein (bacteriocin)	[28]
	fliCh7	H7 fliC flagellin	[29]
	tsh*	Tsh (temperature-sensitive hemagglutinin) serine protease	[7]
Phylogenetic typing	chuA	Haem transport gene	[30]
	yjaA	Gene of unknown fuction from the E. coli K-12 genome	[30]
	TSPE4.C2	Anonymous DNA fragment	[30]

*APEC plasmid-associated genes